WorldWideScience

Sample records for high-resolution nucleosome mapping

  1. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.

    Science.gov (United States)

    Schep, Alicia N; Buenrostro, Jason D; Denny, Sarah K; Schwartz, Katja; Sherlock, Gavin; Greenleaf, William J

    2015-11-01

    Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around nucleosomes in Saccharomyces cerevisiae, and use this distinctive two-dimensional nucleosomal "fingerprint" as the basis for a new nucleosome-positioning algorithm called NucleoATAC. We show that NucleoATAC can identify the rotational and translational positions of nucleosomes with up to base-pair resolution and provide quantitative measures of nucleosome occupancy in S. cerevisiae, Schizosaccharomyces pombe, and human cells. We demonstrate the application of NucleoATAC to a number of outstanding problems in chromatin biology, including analysis of sequence features underlying nucleosome positioning, promoter chromatin architecture across species, identification of transient changes in nucleosome occupancy and positioning during a dynamic cellular response, and integrated analysis of nucleosome occupancy and transcription factor binding.

  2. Reading sequence-directed computational nucleosome maps.

    Science.gov (United States)

    Nibhani, Reshma; Trifonov, Edward N

    2015-01-01

    Recently developed latest version of the sequence-directed single-base resolution nucleosome mapping reveals existence of strong nucleosomes and chromatin columnar structures (columns). Broad application of this simple technique for further studies of chromatin and chromosome structure requires some basic understanding as to how it works and what information it affords. The paper provides such an introduction to the method. The oscillating maps of singular nucleosomes, of short and long oligonucleosome columns, are explained, as well as maps of chromatin on satellite DNA and occurrences of counter-phase (antiparallel) nucleosome neighbors.

  3. GRANULOMETRIC MAPS FROM HIGH RESOLUTION SATELLITE IMAGES

    Directory of Open Access Journals (Sweden)

    Catherine Mering

    2011-05-01

    Full Text Available A new method of land cover mapping from satellite images using granulometric analysis is presented here. Discontinuous landscapes such as steppian bushes of semi arid regions and recently growing urban settlements are especially concerned by this study. Spatial organisations of the land cover are quantified by means of the size distribution analysis of the land cover units extracted from high resolution remotely sensed images. A granulometric map is built by automatic classification of every pixel of the image according to the granulometric density inside a sliding neighbourhood. Granulometric mapping brings some advantages over traditional thematic mapping by remote sensing by focusing on fine spatial events and small changes in one peculiar category of the landscape.

  4. Venus gravity - A high-resolution map

    Science.gov (United States)

    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.

  5. nuMap:A Web Platform for Accurate Prediction of Nucleosome Positioning

    Institute of Scientific and Technical Information of China (English)

    Bader A Alharbi; Thamir H Alshammari; Nathan L Felton; Victor B Zhurkin; Feng Cui

    2014-01-01

    Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and param-eters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site.

  6. Nucleosome positioning in yeasts: methods, maps, and mechanisms.

    Science.gov (United States)

    Lieleg, Corinna; Krietenstein, Nils; Walker, Maria; Korber, Philipp

    2015-06-01

    Eukaryotic nuclear DNA is packaged into nucleosomes. During the past decade, genome-wide nucleosome mapping across species revealed the high degree of order in nucleosome positioning. There is a conserved stereotypical nucleosome organization around transcription start sites (TSSs) with a nucleosome-depleted region (NDR) upstream of the TSS and a TSS-aligned regular array of evenly spaced nucleosomes downstream over the gene body. As nucleosomes largely impede access to DNA and thereby provide an important level of genome regulation, it is of general interest to understand the mechanisms generating nucleosome positioning and especially the stereotypical NDR-array pattern. We focus here on the most advanced models, unicellular yeasts, and review the progress in mapping nucleosomes and which nucleosome positioning mechanisms are discussed. There are four mechanistic aspects: How are NDRs generated? How are individual nucleosomes positioned, especially those flanking the NDRs? How are nucleosomes evenly spaced leading to regular arrays? How are regular arrays aligned at TSSs? The main candidates for nucleosome positioning determinants are intrinsic DNA binding preferences of the histone octamer, specific DNA binding factors, nucleosome remodeling enzymes, transcription, and statistical positioning. We summarize the state of the art in an integrative model where nucleosomes are positioned by a combination of all these candidate determinants. We highlight the predominance of active mechanisms involving nucleosome remodeling enzymes which may be recruited by DNA binding factors and the transcription machinery. While this mechanistic framework emerged clearly during recent years, the involved factors and their mechanisms are still poorly understood and require future efforts combining in vivo and in vitro approaches.

  7. Inferring coarse-grain histone-DNA interaction potentials from high-resolution structures of the nucleosome

    Science.gov (United States)

    Meyer, Sam; Everaers, Ralf

    2015-02-01

    The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex.

  8. High Resolution Airborne Shallow Water Mapping

    Science.gov (United States)

    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

  9. Updating Maps Using High Resolution Satellite Imagery

    Science.gov (United States)

    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.

  10. High resolution fire risk mapping in Italy

    Science.gov (United States)

    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.

  11. Universal full-length nucleosome mapping sequence probe.

    Science.gov (United States)

    Tripathi, Vijay; Salih, Bilal; Trifonov, Edward N

    2015-01-01

    For the computational sequence-directed mapping of the nucleosomes, the knowledge of the nucleosome positioning motifs - 10-11 base long sequences - and respective matrices of bendability, is not sufficient, since there is no justified way to fuse these motifs in one continuous nucleosome DNA sequence. Discovery of the strong nucleosome (SN) DNA sequences, with visible sequence periodicity allows derivation of the full-length nucleosome DNA bendability pattern as matrix or consensus sequence. The SN sequences of three species (A. thaliana, C. elegans, and H. sapiens) are aligned (512 sequences for each species), and long (115 dinucleotides) matrices of bendability derived for the species. The matrices have strong common property - alternation of runs of purine-purine (RR) and pyrimidine-pyrimidine (YY) dinucleotides, with average period 10.4 bases. On this basis the universal [R,Y] consensus of the nucleosome DNA sequence is derived, with exactly defined positions of respective penta- and hexamers RRRRR, RRRRRR, YYYYY, and YYYYYY.

  12. High resolution, large dynamic range field map estimation

    Science.gov (United States)

    Dagher, Joseph; Reese, Timothy; Bilgin, Ali

    2013-01-01

    Purpose We present a theory and a corresponding method to compute high resolution field maps over a large dynamic range. Theory and Methods We derive a closed-form expression for the error in the field map value when computed from two echoes. We formulate an optimization problem to choose three echo times which result in a pair of maximally distinct error distributions. We use standard field mapping sequences at the prescribed echo times. We then design a corresponding estimation algorithm which takes advantage of the optimized echo times to disambiguate the field offset value. Results We validate our method using high resolution images of a phantom at 7T. The resulting field maps demonstrate robust mapping over both a large dynamic range, and in low SNR regions. We also present high resolution offset maps in vivo using both, GRE and MEGE sequences. Even though the proposed echo time spacings are larger than the well known phase aliasing cutoff, the resulting field maps exhibit a large dynamic range without the use of phase unwrapping or spatial regularization techniques. Conclusion We demonstrate a novel 3-echo field map estimation method which overcomes the traditional noise-dynamic range trade-off. PMID:23401245

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

    Science.gov (United States)

    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.

  14. 3D mapping from high resolution satellite images

    Science.gov (United States)

    Goulas, D.; Georgopoulos, A.; Sarakenos, A.; Paraschou, Ch.

    2013-08-01

    In recent years 3D information has become more easily available. Users' needs are constantly increasing, adapting to this reality and 3D maps are in more demand. 3D models of the terrain in CAD or other environments have already been common practice; however one is bound by the computer screen. This is why contemporary digital methods have been developed in order to produce portable and, hence, handier 3D maps of various forms. This paper deals with the implementation of the necessary procedures to produce holographic 3D maps and three dimensionally printed maps. The main objective is the production of three dimensional maps from high resolution aerial and/or satellite imagery with the use of holography and but also 3D printing methods. As study area the island of Antiparos was chosen, as there were readily available suitable data. These data were two stereo pairs of Geoeye-1 and a high resolution DTM of the island. Firstly the theoretical bases of holography and 3D printing are described, and the two methods are analyzed and there implementation is explained. In practice a x-axis parallax holographic map of the Antiparos Island is created and a full parallax (x-axis and y-axis) holographic map is created and printed, using the holographic method. Moreover a three dimensional printed map of the study area has been created using 3dp (3d printing) method. The results are evaluated for their usefulness and efficiency.

  15. Single-nucleosome mapping of histone modifications in S. cerevisiae.

    Directory of Open Access Journals (Sweden)

    Chih Long Liu

    2005-10-01

    Full Text Available Covalent modification of histone proteins plays a role in virtually every process on eukaryotic DNA, from transcription to DNA repair. Many different residues can be covalently modified, and it has been suggested that these modifications occur in a great number of independent, meaningful combinations. Published low-resolution microarray studies on the combinatorial complexity of histone modification patterns suffer from confounding effects caused by the averaging of modification levels over multiple nucleosomes. To overcome this problem, we used a high-resolution tiled microarray with single-nucleosome resolution to investigate the occurrence of combinations of 12 histone modifications on thousands of nucleosomes in actively growing S. cerevisiae. We found that histone modifications do not occur independently; there are roughly two groups of co-occurring modifications. One group of lysine acetylations shows a sharply defined domain of two hypo-acetylated nucleosomes, adjacent to the transcriptional start site, whose occurrence does not correlate with transcription levels. The other group consists of modifications occurring in gradients through the coding regions of genes in a pattern associated with transcription. We found no evidence for a deterministic code of many discrete states, but instead we saw blended, continuous patterns that distinguish nucleosomes at one location (e.g., promoter nucleosomes from those at another location (e.g., over the 3' ends of coding regions. These results are consistent with the idea of a simple, redundant histone code, in which multiple modifications share the same role.

  16. Clickstream data yields high-resolution maps of science

    Energy Technology Data Exchange (ETDEWEB)

    Bollen, Johan [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory; Hagberg, Aric [Los Alamos National Laboratory; Bettencourt, Luis [Los Alamos National Laboratory; Chute, Ryan [Los Alamos National Laboratory; Rodriguez, Marko A [Los Alamos National Laboratory; Balakireva, Lyudmila [Los Alamos National Laboratory

    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.

  17. High resolution map of light pollution over Poland

    Science.gov (United States)

    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.

  18. A chemical approach to mapping nucleosomes at base pair resolution in yeast.

    Science.gov (United States)

    Brogaard, Kristin R; Xi, Liqun; Wang, Ji-Ping; Widom, Jonathan

    2012-01-01

    Most eukaryotic DNA exists in DNA-protein complexes known as nucleosomes. The exact locations of nucleosomes along the genome play a critical role in chromosome functions and gene regulation. However, the current methods for nucleosome mapping do not provide the necessary accuracy to identify the precise nucleosome locations. Here we describe a new experimental approach that directly maps nucleosome center locations in vivo genome-wide at single base pair resolution.

  19. Inferring coarse-grain histone-DNA interaction potentials from high-resolution structures of the nucleosome

    CERN Document Server

    Meyer, Sam

    2014-01-01

    The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unkown despite a growing structural knowledge of the complex. Here, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We apply the procedure on a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at the sites of histone-DNA contact, the DNA base-pairs are locally shifted outwards, consistent with locally repulsive forces exerted by the histones. In a second step, we show that the various force profiles of the analyzed structures derive locally from a unique, sequence-independent, quadratic repulsive force field, while the sequence preferences are entirely due to the internal DNA mechanics. We thus obtain the first knowledge-derived nanosca...

  20. High-resolution gene mapping using admixture linkage disequilibrium

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    This note reports simulation study on the rate of decay in linkage dis equilibrium (LD) in mixed populations over multiple discrete generations and explores the usefulness of the LD analysis in high-resolution gene mapping. The results indicate that the smaller the recombination fraction and the fewer generati ons since admixtureevent, the higher power of the approach in gene mapping. The expected estimate of recombination fraction would give an estimate that is slig htly biased upwards, if relevant genes are in tight linkage. The estimated recom bination fraction is usually larger than the true value within 2-5 generations. From generations 10-20, the mean estimates are in good agreement with the true value. The method presented here enables estimation of means and corresponding confidence intervals of the recombination fraction at any number of generations.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Antoni Burguera

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  4. High resolution thermal infrared mapping of Martian channels

    Science.gov (United States)

    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.

  5. High-resolution mapping of protein sequence-function relationships.

    Science.gov (United States)

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

    2010-09-01

    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 had 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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

  10. High Resolution Ionospheric Mapping Using Spaceborne Synthetic Aperture Radars

    Science.gov (United States)

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

    2012-12-01

    Spaceborne Synthetic Aperture Radars (SARs) are imaging radar systems that utilize the Doppler history of signals acquired during satellite flyby to produce high resolution images of the Earth. With modern sensors, operating at frequencies between about 1 GHz (L-band) and 10 GHz (X-band), radar images with resolutions in the meter to sub-meter range can be produced. The presence of the ionosphere is significantly affecting the propagation properties of the microwave signals transmitted by these systems, causing distortions of signal polarization and phase. These distortions can lead to a wide range of imaging artifacts including image range shifts, interferometric phase biases, loss of image focus, change of image geometry, and Faraday rotation. While these artifacts are particularly pronounced at L-band, they are still observable in data acquired at C- or even X-band. In recent years, a wealth of methods for measuring and correcting ionospheric influence were developed. These methods are self-calibration procedures that measure ionosphere-induced distortions to infer the two-dimensional TEC maps that affected the data. These TEC maps are then removed from the data to produce high performance SAR images. Besides being effective in correcting SAR observations, these self-calibration methods are producing high quality TEC information with sub-TECU sensitivity and sub-kilometer spatial resolution. The intent of this paper is to utilize SAR-derived ionospheric information and make the case for SAR as a data source for ionospheric research. After a short summary of ionosphere-induced distortions, the concept of TEC estimation from SAR is introduced. Here, the current state-of-the-art of ionospheric TEC estimation is presented, including Faraday rotation-based, interferometric, correlation-based, and autofocus-based techniques. For every approach, performance numbers are given that quantify the achievable TEC estimation accuracy as a function of system parameters, scene

  11. Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection.

    Science.gov (United States)

    Oh, Jaewook; Sanders, Iryna F; Chen, Eric Z; Li, Hongzhe; Tobias, John W; Isett, R Benjamin; Penubarthi, Sindura; Sun, Hao; Baldwin, Don A; Fraser, Nigel W

    2015-01-01

    HSV is a large double stranded DNA virus, capable of causing a variety of diseases from the common cold sore to devastating encephalitis. Although DNA within the HSV virion does not contain any histone protein, within 1 h of infecting a cell and entering its nucleus the viral genome acquires some histone protein (nucleosomes). During lytic infection, partial micrococcal nuclease (MNase) digestion does not give the classic ladder band pattern, seen on digestion of cell DNA or latent viral DNA. However, complete digestion does give a mono-nucleosome band, strongly suggesting that there are some nucleosomes present on the viral genome during the lytic infection, but that they are not evenly positioned, with a 200 bp repeat pattern, like cell DNA. Where then are the nucleosomes positioned? Here we perform HSV-1 genome wide nucleosome mapping, at a time when viral replication is in full swing (6 hr PI), using a microarray consisting of 50mer oligonucleotides, covering the whole viral genome (152 kb). Arrays were probed with MNase-protected fragments of DNA from infected cells. Cells were not treated with crosslinking agents, thus we are only mapping tightly bound nucleosomes. The data show that nucleosome deposition is not random. The distribution of signal on the arrays suggest that nucleosomes are located at preferred positions on the genome, and that there are some positions that are not occupied (nucleosome free regions -NFR or Nucleosome depleted regions -NDR), or occupied at frequency below our limit of detection in the population of genomes. Occupancy of only a fraction of the possible sites may explain the lack of a typical MNase partial digestion band ladder pattern for HSV DNA during lytic infection. On average, DNA encoding Immediate Early (IE), Early (E) and Late (L) genes appear to have a similar density of nucleosomes.

  12. A map of nucleosome positions in yeast at base-pair resolution.

    Science.gov (United States)

    Brogaard, Kristin; Xi, Liqun; Wang, Ji-Ping; Widom, Jonathan

    2012-06-28

    The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function. However, existing methods for mapping nucleosomes do not provide the necessary single-base-pair accuracy to determine these positions. Here we develop and apply a new approach for direct mapping of nucleosome centres on the basis of chemical modification of engineered histones. The resulting map locates nucleosome positions genome-wide in unprecedented detail and accuracy. It shows new aspects of the in vivo nucleosome organization that are linked to transcription factor binding, RNA polymerase pausing and the higher-order structure of the chromatin fibre.

  13. Towards a Global High Resolution Peatland Map in 2020

    Science.gov (United States)

    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

  14. Towards a Global High Resolution Peatland Map in 2020

    Science.gov (United States)

    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

  15. Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning.

    Science.gov (United States)

    Moyle-Heyrman, Georgette; Zaichuk, Tetiana; Xi, Liqun; Zhang, Quanwei; Uhlenbeck, Olke C; Holmgren, Robert; Widom, Jonathan; Wang, Ji-Ping

    2013-12-10

    Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair resolution. The shorter linker length previously identified in S. pombe is due to a preponderance of nucleosomes separated by ∼4/5 bp, placing nucleosomes on opposite faces of the DNA. The periodic dinucleotide feature thought to position nucleosomes is equally strong in exons as in introns, demonstrating that nucleosome positioning information can be superimposed on coding information. Unlike the case in Saccharomyces cerevisiae, A/T-rich sequences are enriched in S. pombe nucleosomes, particularly at ±20 bp around the dyad. This difference in nucleosome binding preference gives rise to a major distinction downstream of the transcription start site, where nucleosome phasing is highly predictable by A/T frequency in S. pombe but not in S. cerevisiae, suggesting that the genomes and DNA binding preferences of nucleosomes have coevolved in different species. The poly (dA-dT) tracts affect but do not deplete nucleosomes in S. pombe, and they prefer special rotational positions within the nucleosome, with longer tracts enriched in the 10- to 30-bp region from the dyad. S. pombe does not have a well-defined nucleosome-depleted region immediately upstream of most transcription start sites; instead, the -1 nucleosome is positioned with the expected spacing relative to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. Although there is generally very good agreement between nucleosome maps generated by chemical cleavage and micrococcal nuclease digestion, the chemical map shows consistently higher nucleosome occupancy on DNA with high A/T content.

  16. Towards high resolution soil property maps for Austria

    Science.gov (United States)

    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

  17. High resolution skin colorimetry, strain mapping and mechanobiology.

    Science.gov (United States)

    Devillers, C; Piérard-Franchimont, C; Schreder, A; Docquier, V; Piérard, G E

    2010-08-01

    Skin colours are notoriously different between individuals. They are governed by ethnicities and phototypes, and further influenced by a variety of factors including photoexposures and sustained mechanical stress. Indeed, mechanobiology is a feature affecting the epidermal melanization. High-resolution epiluminescence colorimetry helps in deciphering the effects of forces generated by Langer's lines or relaxed skin tension lines on the melanocyte activity. The same procedure shows a prominent laddering pattern of melanization in striae distensae contrasting with the regular honeycomb pattern in the surrounding skin.

  18. Multi-Volume High Resolution RGB-D Mapping with Dynamic Volume Placement

    OpenAIRE

    Salvato, Michael; Finman, Ross; Leonard, John

    2015-01-01

    We present a novel RGB-D mapping system for generating 3D maps over spatially extended regions with higher resolution than current methods using multiple, dynamically placed mapping volumes. Our method takes in RGB-D frames and dynamically assigns multiple mapping volumes to the environment, exchanging mapping volumes between the CPU and GPU. Mapping volumes are added or removed as needed to allow for spatially extended, high resolution mapping. Our system is designed to maximize the resoluti...

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

    Science.gov (United States)

    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

  20. High-resolution Geophysical Mapping of Submarine Glacial Landforms

    Science.gov (United States)

    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.

  1. Estimated Depth Maps of the Northwestern Hawaiian Islands Derived from High Resolution IKONOS Satellite Imagery (Draft)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Estimated shallow-water, depth maps were produced using rule-based, semi-automated image analysis of high-resolution satellite imagery for nine locations in the...

  2. Estimated Depth Maps of the Northwestern Hawaiian Islands Derived from High Resolution IKONOS Satellite Imagery

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Estimated shallow-water, depth maps were produced using rule-based, semi-automated image analysis of high-resolution satellite imagery for nine locations in the...

  3. High resolution reflection seismic mapping of shallow coal seams

    CSIR Research Space (South Africa)

    Mngadi, SB

    2013-10-01

    Full Text Available in acoustic impedance at depths 10 m, 17 m and 21 m. We believe that we were able to map two undulating interfaces, at approximately 12 ms and 21 ms (Figure 4). CONCLUSIONS The shallow reflection seismic technique is a very useful technique...

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  7. A high resolution submillimeter map of OMC-1

    Science.gov (United States)

    Keene, J.; Hildebrand, R. H.; Whitcomb, S. E.

    1982-01-01

    The 400 micron emission from the central region of OMC-1 has been mapped with 35 resolution. This region contains two emission peaks with sizes of about 0.5 arcmin, separated by approximately 1.5 arcmin which probably represent distinct density condensations in the molecular cloud. Comparison of observations with earlier far-infrared observations shows the two condensations to have similar optical depths and dust masses. A bar of 400 micron emission is found about 15 arcsec SE of the ionization front near Theta 2 A Ori, indicating a sharp increase in dust density in the neutral matter outside the ionized region.

  8. A high resolution submillimeter map of OMC-1

    Science.gov (United States)

    Keene, J.; Hildebrand, R. H.; Whitcomb, S. E.

    1982-01-01

    The 400 micron emission from the central region of OMC-1 has been mapped with 35 resolution. This region contains two emission peaks with sizes of about 0.5 arcmin, separated by approximately 1.5 arcmin which probably represent distinct density condensations in the molecular cloud. Comparison of observations with earlier far-infrared observations shows the two condensations to have similar optical depths and dust masses. A bar of 400 micron emission is found about 15 arcsec SE of the ionization front near Theta 2 A Ori, indicating a sharp increase in dust density in the neutral matter outside the ionized region.

  9. High Resolution Molecular Gas Maps of M33

    CERN Document Server

    Rosolowsky, E; Matsushita, S; Willner, S

    2007-01-01

    New observations of CO (J=1->0) line emission from M33, using the 25 element BEARS focal plane array at the Nobeyama Radio Observatory 45-m telescope, in conjunction with existing maps from the BIMA interferometer and the FCRAO 14-m telescope, give the highest resolution (13'') and most sensitive (RMS ~ 60 mK) maps to date of the distribution of molecular gas in the central 5.5 kpc of the galaxy. A new catalog of giant molecular clouds (GMCs) has a completeness limit of 1.3 X 10^5 M_sun. The fraction of molecular gas found in GMCs is a strong function of radius in the galaxy, declining from 60% in the center to 20% at galactocentric radius R_gal ~ 4 kpc. Beyond that radius, GMCs are nearly absent, although molecular gas exists. Most (90%) of the emission from low mass clouds is found within 100 pc projected separation of a GMC. In an annulus 2.1< R_gal <4.1 kpc, GMC masses follow a power law distribution with index -2.1. Inside that radius, the mass distribution is truncated, and clouds more massive tha...

  10. MBARI Mapping AUV: A High-Resolution Deep-Ocean Seafloor Mapping Capability

    Science.gov (United States)

    Kirkwood, W. J.; Caress, D. W.; Thomas, H.; McEwen, R.; Henthorn, R.; Sibenac, M.; McGill, P.; Hamilton, A.; Shane, F.; Thompson, D.; Jensen, S.; Salamy, K.

    2005-12-01

    The Monterey Bay Aquarium Research Institute (MBARI) has developed an autonomous seafloor mapping capability for deep ocean science applications. The MBARI Mapping AUV is a 0.53 m (21 in) diameter, 5.1 m (16.7 ft) long, Dorado-class vehicle designed to carry four mapping sonars. The primary sensor is a 200 kHz multibeam sonar producing swath bathymetry and sidescan. In addition, the vehicle carries 100 kHz and 410 kHz chirp sidescan sonars, and a 2-16 kHz sweep chirp subbottom profiler. Navigation and attitude data are obtained from an inertial navigation system (INS) incorporating a ring laser gyro and a 300 kHz Doppler velocity log (DVL). The vehicle also includes acoustic modem, ultra-short baseline navigation, and long-baseline navigation systems. The Mapping AUV is powered by 6 kWhr of Li-polymer batteries, providing a mission duration of 12 hours at a typical speed of 1.5 m/s. All components of the vehicle are rated to 6000 m depth, allowing MBARI to conduct high-resolution mapping of the deep-ocean seafloor. The sonar package can also be mounted on ROV Ventana, allowing surveys at altitudes less than 10 m at topographically challenging sites. The vehicle was assembled and underwent initial tests during 2004. During 2005 we have commenced science survey operations while completing the integration and testing of the complete suite of sensors and systems. MBARI is now using this capability in both autonomous and ROV-mounted surveys to observe the changing morphology of dynamic systems such as submarine canyons and active slumps, to map deep-water benthic habitats at resolutions comparable to ROV and submersible observations, to provide basemaps for ROV dives, and to provide high resolution bathymetry and subbottom profiles in support of seafloor observatory installations.

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

    Science.gov (United States)

    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.

  12. A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin.

    Science.gov (United States)

    Svensson, J Peter; Shukla, Manu; Menendez-Benito, Victoria; Norman-Axelsson, Ulrika; Audergon, Pauline; Sinha, Indranil; Tanny, Jason C; Allshire, Robin C; Ekwall, Karl

    2015-06-01

    Nucleosome composition actively contributes to chromatin structure and accessibility. Cells have developed mechanisms to remove or recycle histones, generating a landscape of differentially aged nucleosomes. This study aimed to create a high-resolution, genome-wide map of nucleosome turnover in Schizosaccharomyces pombe. The recombination-induced tag exchange (RITE) method was used to study replication-independent nucleosome turnover through the appearance of new histone H3 and the disappearance or preservation of old histone H3. The genome-wide location of histones was determined by chromatin immunoprecipitation-exonuclease methodology (ChIP-exo). The findings were compared with diverse chromatin marks, including histone variant H2A.Z, post-translational histone modifications, and Pol II binding. Finally, genome-wide mapping of the methylation states of H4K20 was performed to determine the relationship between methylation (mono, di, and tri) of this residue and nucleosome turnover. Our analysis showed that histone recycling resulted in low nucleosome turnover in the coding regions of active genes, stably expressed at intermediate levels. High levels of transcription resulted in the incorporation of new histones primarily at the end of transcribed units. H4K20 was methylated in low-turnover nucleosomes in euchromatic regions, notably in the coding regions of long genes that were expressed at low levels. This transcription-dependent accumulation of histone methylation was dependent on the histone chaperone complex FACT. Our data showed that nucleosome turnover is highly dynamic in the genome and that several mechanisms are at play to either maintain or suppress stability. In particular, we found that FACT-associated transcription conserves histones by recycling them and is required for progressive H4K20 methylation.

  13. MBARI Mapping AUV: A High-Resolution Deep Ocean Seafloor Mapping Capability

    Science.gov (United States)

    Caress, D. W.; Kirkwood, W. J.; Thomas, H.; McEwen, R.; Henthorn, R.; McGill, P.; Thompson, D.; Sibenac, M.; Jensen, S.; Shane, F.; Hamilton, A.

    2005-05-01

    The Monterey Bay Aquarium Research Institute (MBARI) is developing an autonomous seafloor mapping capability for deep ocean science applications. The MBARI Mapping AUV is a 0.53 m (21 in) diameter, 5.1 m (16.7 ft) long, Dorado-class vehicle designed to carry four mapping sonars. The primary sensor is a 200 kHz multibeam sonar producing swath bathymetry and sidescan. In addition, the vehicle carries 100 kHz and 410 kHz chirp sidescan sonars, and a 2-16 kHz sweep chirp subbottom profiler. Navigation and attitude data are obtained from an inertial navigation system (INS) incorporating a ring laser gyro and a 300 kHz Doppler velocity log (DVL). The vehicle also includes acoustic modem, ultra-short baseline navigation, and long-baseline navigation systems. The Mapping AUV is powered by 6 kWhr of Li-polymer batteries, providing expected mission duration of 12 hours at a typical speed of 1.5 m/s. All components of the vehicle are rated to 6000 m depth, allowing MBARI to conduct high-resolution mapping of the deep-ocean seafloor. The sonar package is also be mountable on ROV Ventana, allowing surveys at altitudes less than 20 m at topographically challenging sites. The vehicle was assembled and extensively tested during 2004; this year we are commencing operations for MBARI science projects while continuing the process of testing and integrating the complete suite of sensors and systems. MBARI is beginning to use this capability to observe the changing morphology of dynamic systems such as submarine canyons and active slumps, to map deep-water benthic habitats at resolutions comparable to ROV and submersible observations, to provide basemaps for ROV dives, and to provide high resolution bathymetry and subbottom profiles as part of a variety of projects requiring knowledge of the seafloor. We will present initial results from surveys in and around Monterey Canyon, including high resolution repeat surveys of four sites along the canyon axis.

  14. Machine vision-based high-resolution weed mapping and patch-sprayer performance simulation

    NARCIS (Netherlands)

    Tang, L.; Tian, L.F.; Steward, B.L.

    1999-01-01

    An experimental machine vision-based patch-sprayer was developed. This sprayer was primarily designed to do real-time weed density estimation and variable herbicide application rate control. However, the sprayer also had the capability to do high-resolution weed mapping if proper mapping techniques

  15. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed Missael Vargas;

    2014-01-01

    data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery...... of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues...

  16. Functional roles of nucleosome stability and dynamics.

    Science.gov (United States)

    Chereji, Răzvan V; Morozov, Alexandre V

    2015-01-01

    Nucleosome is a histone-DNA complex known as the fundamental repeating unit of chromatin. Up to 90% of eukaryotic DNA is wrapped around consecutive octamers made of the core histones H2A, H2B, H3 and H4. Nucleosome positioning affects numerous cellular processes that require robust and timely access to genomic DNA, which is packaged into the tight confines of the cell nucleus. In living cells, nucleosome positions are determined by intrinsic histone-DNA sequence preferences, competition between histones and other DNA-binding proteins for genomic sequence, and ATP-dependent chromatin remodelers. We discuss the major energetic contributions to nucleosome formation and remodeling, focusing especially on partial DNA unwrapping off the histone octamer surface. DNA unwrapping enables efficient access to nucleosome-buried binding sites and mediates rapid nucleosome removal through concerted action of two or more DNA-binding factors. High-resolution, genome-scale maps of distances between neighboring nucleosomes have shown that DNA unwrapping and nucleosome crowding (mutual invasion of nucleosome territories) are much more common than previously thought. Ultimately, constraints imposed by nucleosome energetics on the rates of ATP-dependent and spontaneous chromatin remodeling determine nucleosome occupancy genome-wide, and shape pathways of cellular response to environmental stresses.

  17. High-resolution mapping of forest carbon stocks in the Colombian Amazon

    Directory of Open Access Journals (Sweden)

    G. P. Asner

    2012-07-01

    Full Text Available High-resolution mapping of tropical forest carbon stocks can assist forest management and improve implementation of large-scale carbon retention and enhancement programs. Previous high-resolution approaches have relied on field plot and/or light detection and ranging (LiDAR samples of aboveground carbon density, which are typically upscaled to larger geographic areas using stratification maps. Such efforts often rely on detailed vegetation maps to stratify the region for sampling, but existing tropical forest maps are often too coarse and field plots too sparse for high-resolution carbon assessments. We developed a top-down approach for high-resolution carbon mapping in a 16.5 million ha region (> 40% of the Colombian Amazon – a remote landscape seldom documented. We report on three advances for large-scale carbon mapping: (i employing a universal approach to airborne LiDAR-calibration with limited field data; (ii quantifying environmental controls over carbon densities; and (iii developing stratification- and regression-based approaches for scaling up to regions outside of LiDAR coverage. We found that carbon stocks are predicted by a combination of satellite-derived elevation, fractional canopy cover and terrain ruggedness, allowing upscaling of the LiDAR samples to the full 16.5 million ha region. LiDAR-derived carbon maps have 14% uncertainty at 1 ha resolution, and the regional map based on stratification has 28% uncertainty in any given hectare. High-resolution approaches with quantifiable pixel-scale uncertainties will provide the most confidence for monitoring changes in tropical forest carbon stocks. Improved confidence will allow resource managers and decision makers to more rapidly and effectively implement actions that better conserve and utilize forests in tropical regions.

  18. High-resolution Mapping of Forest Carbon Stocks in the Colombian Amazon

    Directory of Open Access Journals (Sweden)

    G. P. Asner

    2012-03-01

    Full Text Available High-resolution mapping of tropical forest carbon stocks can assist forest management and improve implementation of large-scale carbon retention and enhancement programs. Previous high-resolution approaches have relied on field plot and/or Light Detection and Ranging (LiDAR samples of aboveground carbon density, which are typically upscaled to larger geographic areas using stratification maps. Such efforts often rely on detailed vegetation maps to stratify the region for sampling, but existing tropical forest maps are often too coarse and field plots too sparse for high resolution carbon assessments. We developed a top-down approach for high-resolution carbon mapping in a 16.5 million ha region (>40 % of the Colombian Amazon – a remote landscape seldom documented. We report on three advances for large-scale carbon mapping: (i employing a universal approach to airborne LiDAR-calibration with limited field data; (ii quantifying environmental controls over carbon densities; and (iii developing stratification- and regression-based approaches for scaling up to regions outside of LiDAR coverage. We found that carbon stocks are predicted by a combination of satellite-derived elevation, fractional canopy cover and terrain ruggedness, allowing upscaling of the LiDAR samples to the full 16.5 million ha region. LiDAR-derived carbon mapping samples had 14.6 % uncertainty at 1 ha resolution, and regional maps based on stratification and regression approaches had 25.6 % and 29.6 % uncertainty, respectively, in any given hectare. High-resolution approaches with reported local-scale uncertainties will provide the most confidence for monitoring changes in tropical forest carbon stocks. Improved confidence will allow resource managers and decision-makers to more rapidly and effectively implement actions that better conserve and utilize forests in tropical regions.

  19. High resolution regional soil carbon mapping in Madagascar : towards easy to update maps

    Science.gov (United States)

    Grinand, Clovis; Dessay, Nadine; Razafimbelo, Tantely; Razakamanarivo, Herintsitoaina; Albrecht, Alain; Vaudry, Romuald; Tiberghien, Matthieu; Rasamoelina, Maminiaina; Bernoux, Martial

    2013-04-01

    The soil organic carbon plays an important role in climate change regulation through carbon emissions and sequestration due to land use changes, notably tropical deforestation. Monitoring soil carbon emissions from shifting-cultivation requires to evaluate the amount of carbon stored at plot scale with a sufficient level of accuracy to be able to detect changes. The objective of this work was to map soil carbon stocks (30 cm and 100 cm depths) for different land use at regional scale using high resolution satellite dataset. The Andohahela National Parc and its surroundings (South-Est Madagascar) - a region with the largest deforestation rate in the country - was selected as a pilot area for the development of the methodology. A three steps approach was set up: (i) carbon inventory using mid infra-red spectroscopy and stock calculation, (ii) spatial data processing and (iii) modeling and mapping. Soil spectroscopy was successfully used for measuring organic carbon in this region. The results show that Random Forest was the inference model that produced the best estimates on calibration and validation datasets. By using a simple and robust method, we estimated uncertainty levels of of 35% and 43% for 30-cm and 100-cm carbon maps respectively. The approach developed in this study was based on open data and open source software that can be easily replicated to other regions and for other time periods using updated satellite images.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  4. AFM Imaging of SWI/SNF action: mapping the nucleosome remodeling and sliding

    CERN Document Server

    Montel, Fabien; Saint-Jean, Philippe; Castelnovo, Martin; Moskalenko-Faivre, Cendrine

    2007-01-01

    We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA complexed length distribution and nucleosome position in various contexts. First, we show that differences in the nucleo-proteic structure observed between conventional H2A and H2A.Bbd variant nucleosomes induce quantitative changes in the in the length distribution of DNA complexed with histones. Then, the sliding action of remodeling complex SWI/SNF is characterized through the evolution of the nucleosome position and wrapped DNA length mapping. Using a linear energetic model for the distribution of DNA complexed length, we extract the net wrapping energy of DNA onto the histone octamer, and compare it to previous studies.

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

    Science.gov (United States)

    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

  6. GERLUMPH Data Release 1: High-resolution cosmological microlensing magnification maps and eResearch tools

    CERN Document Server

    Vernardos, Georgios; Bate, Nicholas F; Croton, Darren

    2014-01-01

    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 disc 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 12342 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...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  9. Rapid High Resolution Single Nucleotide Polymorphism–Comparative Genome Hybridization Mapping in Caenorhabditis elegans

    Science.gov (United States)

    Flibotte, Stephane; Edgley, Mark L.; Maydan, Jason; Taylor, Jon; Zapf, Rick; Waterston, Robert; Moerman, Donald G.

    2009-01-01

    We have developed a significantly improved and simplified method for high-resolution mapping of phenotypic traits in Caenorhabditis elegans using a combination of single nucleotide polymorphisms (SNPs) and oligo array comparative genome hybridization (array CGH). We designed a custom oligonucleotide array using a subset of confirmed SNPs between the canonical wild-type Bristol strain N2 and the Hawaiian isolate CB4856, populated with densely overlapping 50-mer probes corresponding to both N2 and CB4856 SNP sequences. Using this method a mutation can be mapped to a resolution of ∼200 kb in a single genetic cross. Six mutations representing each of the C. elegans chromosomes were detected unambiguously and at high resolution using genomic DNA from populations derived from as few as 100 homozygous mutant segregants of mutant N2/CB4856 heterozygotes. Our method completely dispenses with the PCR, restriction digest, and gel analysis of standard SNP mapping and should be easy to extend to any organism with interbreeding strains. This method will be particularly powerful when applied to difficult or hard-to-map low-penetrance phenotypes. It should also be possible to map polygenic traits using this method. PMID:18957702

  10. Towards high resolution mapping of 3-D mesoscale dynamics from observations

    Directory of Open Access Journals (Sweden)

    B. Buongiorno Nardelli

    2012-10-01

    Full Text Available The MyOcean R&D project MESCLA (MEsoSCaLe dynamical Analysis through combined model, satellite and in situ data was devoted to the high resolution 3-D retrieval of tracer and velocity fields in the oceans, based on the combination of in situ and satellite observations and quasi-geostrophic dynamical models. The retrieval techniques were also tested and compared with the output of a primitive equation model, with particular attention to the accuracy of the vertical velocity field as estimated through the Q vector formulation of the omega equation. The project focused on a test case, covering the region where the Gulf Stream separates from the US East Coast. This work demonstrated that innovative methods for the high resolution mapping of 3-D mesoscale dynamics from observations can be used to build the next generations of operational observation-based products.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Vernardos, G.; Fluke, C. J.; Croton, D. [Centre for Astrophysics and Supercomputing, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria, 3122 (Australia); Bate, N. F. [Sydney Institute for Astronomy, School of Physics, A28, University of Sydney, NSW, 2006 (Australia)

    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/.

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

    Science.gov (United States)

    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.

  18. Molecular potentials and wave function mapping by high-resolution electron spectroscopy and ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Kimberg, Victor, E-mail: victor.kimberg@pks.mpi.de [Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, 01187 Dresden (Germany); Miron, Catalin, E-mail: miron@synchrotron-soleil.fr [Synchrotron SOLEIL, l’Orme des Merisiers, Saint-Aubin, BP 48, FR-91192 Gif-sur-Yvette Cedex (France)

    2014-08-15

    Highlights: • Some studies related to the vibrational wave functions mapping phenomenon are reviewed. • The core-excited vibrational wave functions were mapped using dissociative and bound final states. • High-resolution experimental data is accompanied by ab initio calculations. • The mapping phenomenon allows one to extract constants of the molecular potentials. • The mapping techniques are general and can be applied for the study of many systems. - Abstract: The recent development of high brightness 3{sup rd} generation soft X-ray sources and high energy resolution electron spectrometers made it possible to accurately trace quantum phenomena associated to the vibrational dynamics in core-excited molecules. The present paper reviews the recent results on mapping of vibrational wave functions and molecular potentials based on electron spectroscopy. We discuss and compare the mapping phenomena in various systems, stressing the advantages of the resonant X-ray scattering for studying of the nuclear dynamics and spectroscopic constants of small molecules. The experimental results discussed in the paper are most often accompanied by state-of-the-art ab initio calculations allowing for a deeper understanding of the quantum effects. Besides its fundamental interest, the vibrational wave function mapping is shown to be useful for the analysis of core- and valence-excited molecular states based on the reflection principle.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Ren, Yi; Zhao, Hong; Kou, Qinghe; Jiang, Jiao; Guo, Shaogui; Zhang, Haiying; Hou, Wenju; Zou, Xiaohua; Sun, Honghe; Gong, Guoyi; Levi, Amnon; Xu, Yong

    2012-01-01

    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 the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F(8) population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  5. High-resolution elemental mapping of titanium oxide/aluminium oxide multilayer by spectrum-imaging.

    Science.gov (United States)

    Kurata, H; Kumagai, H; Ozasa, K

    2001-01-01

    A spectrum-imaging technique based on scanning transmission electron microscopy combined with an electron energy-loss spectroscopy has been applied for the multilayer of amorphous titanium oxide and aluminium oxide layers on silicon substrate. We demonstrate the high-resolution elemental mapping and discuss the advantage of this method compared to an energy-filtering transmission electron microscopy. The main advantage is the absence of chromatic broadening, which allows the use of a large collection angle to acquire spectrum-image data and a wide energy window to integrate the core-loss signals. This suggests that the spatial resolution of elemental maps is mainly determined by the size of the electron probe.

  6. A high resolution RH map of the bovine major histocompatibility complex

    Directory of Open Access Journals (Sweden)

    Womack James E

    2009-04-01

    Full Text Available Abstract Background The cattle MHC is termed the bovine leukocyte antigen (BoLA and, along with the MHCs of other ruminants, is unique in its genomic organization. Consequently, correct and reliable gene maps and sequence information are critical to the study of the BoLA region. The bovine genome sequencing project has produced two assemblies (Btau_3.1 and 4.0 that differ substantially from each other and from conventional gene maps in the BoLA region. To independently compare the accuracies of the different sequence assemblies, we have generated a high resolution map of BoLA using a 12,000rad radiation hybrid panel. Seventy-seven unique sequence tagged site (STS markers chosen at approximately 50 kb intervals from the Btau 2.0 assembly and spanning the IIa-III-I and IIb regions of the bovine MHC were mapped on a 12,000rad bovine radiation hybrid (RH panel to evaluate the different assemblies of the bovine genome sequence. Results Analysis of the data generated a high resolution RH map of BoLA that was significantly different from the Btau_3.1 assembly of the bovine genome but in good agreement with the Btau_4.0 assembly. Of the few discordancies between the RH map and Btau_4.0, most could be attributed to closely spaced markers that could not be precisely ordered in the RH panel. One probable incorrectly-assembled sequence and three missing sequences were noted in the Btau_4.0 assembly. The RH map of BoLA is also highly concordant with the sequence-based map of HLA (NCBI build 36 when reordered to account for the ancestral inversion in the ruminant MHC. Conclusion These results strongly suggest that studies using Btau_3.1 for analyses of the BoLA region should be reevaluated in light of the Btau_4.0 assembly and indicate that additional research is needed to produce a complete assembly of the BoLA genomic sequences.

  7. Operational High Resolution Land Cover Map Production at the Country Scale Using Satellite Image Time Series

    Directory of Open Access Journals (Sweden)

    Jordi Inglada

    2017-01-01

    Full Text Available A detailed and accurate knowledge of land cover is crucial for many scientific and operational applications, and as such, it has been identified as an Essential Climate Variable. This accurate knowledge needs frequent updates. This paper presents a methodology for the fully automatic production of land cover maps at country scale using high resolution optical image time series which is based on supervised classification and uses existing databases as reference data for training and validation. The originality of the approach resides in the use of all available image data, a simple pre-processing step leading to a homogeneous set of acquisition dates over the whole area and the use of a supervised classifier which is robust to errors in the reference data. The produced maps have a kappa coefficient of 0.86 with 17 land cover classes. The processing is efficient, allowing a fast delivery of the maps after the acquisition of the image data, does not need expensive field surveys for model calibration and validation, nor human operators for decision making, and uses open and freely available imagery. The land cover maps are provided with a confidence map which gives information at the pixel level about the expected quality of the result.

  8. Using High-Resolution Airborne LiDAR-Data for Landslide Mapping in the Eastern Alps

    Science.gov (United States)

    Kamp, N.

    2012-04-01

    Due to the increasing frequency of natural disasters like floods and landslides, the active remote sensing technique LiDAR (Light Detection and Ranging), has become a topic of great interest to the Federal State Government of Styria, Federal Republic of Austria. In a perennial project from 2008 to 2012 high-resolution 3D Airborne LiDAR Data of the Province of Styria, an area about 16.000km2 in south-eastern Austria were collected. These data were processed to create Digital Terrain Models (DTM) and Digital Surface Models (DSM) at 1m resolution with a vertical accuracy of 15 [cm] and a positional accuracy of 40 [cm]. High resolution DTMs can be used in different geo-related applications like geomorphological mapping or natural hazard mapping. DTMs show because of its high accuracy various natural and anthropogenic terrain features such as erosion scarps, alluvial fans, landslides, old creeks, topographic edges and karstforms, as well as walking paths and roads and in addition to that LiDAR data allows the detection and outlining of these different geomorphological and anthropogenic features with the help of ArcGIS 10 geoprocessing and analysing techniques, mathematical, statistical and image processing methods and the open source scripting language Python. As a result complex workflows and new geoprocessing tools can be implemented in an ArcGIS 10 workspace and are provided as easy to use toolbox contents. The landslide phenomena take in centre stage of the research work of the author. Thereby the main focus is targeted on sliding movements out of soils and bedrock. Factors like gravity take effect on slope stability directly and cause complex mass movements with a downslope directed, gliding movement of bed- and/or loose-rock as well as soil material. In this paper the author presents the result of her master thesis, an automatic ArcGIS 10 landslide mapping tool using high-resolution LiDAR data in the rock masses of the Eastern Alps (Province of Styria, Austria

  9. Prioritizing spatial accuracy in high-resolution fMRI data using multivariate feature weight mapping

    Directory of Open Access Journals (Sweden)

    Johannes eStelzer

    2014-04-01

    Full Text Available Although ultra-high-field fMRI at field strengths of 7T or above provides substantial gains in BOLD contrast-to-noise ratio, when very high-resolution fMRI is required such gains are inevitably reduced. The improvement in sensitivity provided by multivariate analysis techniques, as compared with univariate methods, then becomes especially welcome. Information mapping approaches are commonly used, such as the searchlight technique, which take into account the spatially distributed patterns of activation in order to predict stimulus conditions. However, the popular searchlight decoding technique, in particular, has been found to be prone to spatial inaccuracies. For instance, the spatial extent of informative areas is generally exaggerated, and their spatial configuration is distorted. We propose the combination of a nonparametric and permutation-based statistical framework with linear classifiers. We term this new combined method Feature Weight Mapping (FWM. The main goal of the proposed method is to map the specific contribution of each voxel to the classification decision while including a correction for the multiple comparisons problem. Next, we compare this new method to the searchlight approach using a simulation and ultra-high-field 7T experimental data. We found that the searchlight method led to spatial inaccuracies that are especially noticeable in high-resolution fMRI data. In contrast, FWM was more spatially precise, revealing both informative anatomical structures as well as the direction by which voxels contribute to the classification. By maximizing the spatial accuracy of ultra-high-field fMRI results, global multivariate methods provide a substantial improvement for characterizing structure-function relationships.

  10. A high-resolution CNV map across Brown Swiss cattle populations.

    Directory of Open Access Journals (Sweden)

    Raphaëlle Teresa Matilde Maria Prinsen

    2015-07-01

    Full Text Available Genomic studies and their use in selection programs are having a strong impact in dairy cattle selection (E. Liu et al., 2010. The first aim was to create a high resolution map of CNV regions (CNVRs in Brown Swiss cattle and the characterization of identified CNVs as markers for quantitative and population genetic studies. CNVs were called in a set of 164 sires with PennCNV and genoCN. PennCNV identified 2,377 CNVRs comprising 1,162 and 1,131 gain and loss events, respectively, and 84 regions of complex nature. GenoCN detected 41,519 CNVRs comprising 3,475 and 34,485 gain and loss events, respectively, and 3,559 regions of complex ones. Consensus calls between algorithms were summarized to CNVRs at the population level. GenoCN was also used to identify total allelic content in consensus CNVRs. Moreover, population haplotype frequencies were calculated. Linkage disequilibrium (LD was established between CNVs and SNPs in and around CNVRs. In this study the potential contribution of CNVs as genetic markers for genome wide association studies (GWAS has been assessed thanks to PIC and LD values. The next aim is to investigate genomic structural variation in cattle using dense SNP information in more than 1000 samples of the Italian and Swiss Brown Swiss breed genotyped on HD Bovine BeadChips. Today there is still no CNV map available across Brown Swiss populations belonging to different countries. This study therefore expands the catalogue of CNVRs in the bovine genome, delivers an international based high-resolution map of CNVRs specific to Brown Swiss dairy cattle and will lastly provide information for GEBV estimation with CNVs.

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

    Science.gov (United States)

    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.

  12. Evaluation of ALOS PALSAR Data for High-Resolution Mapping of Vegetated Wetlands in Alaska

    Directory of Open Access Journals (Sweden)

    Daniel Clewley

    2015-06-01

    Full Text Available As the largest natural source of methane, wetlands play an important role in the carbon cycle. High-resolution maps of wetland type and extent are required to quantify wetland responses to climate change. Mapping northern wetlands is particularly important because of a disproportionate increase in temperatures at higher latitudes. Synthetic aperture radar data from a spaceborne platform can be used to map wetland types and dynamics over large areas. Following from earlier work by Whitcomb et al. (2009 using Japanese Earth Resources Satellite (JERS-1 data, we applied the “random forests” classification algorithm to variables from L-band ALOS PALSAR data for 2007, topographic data (e.g., slope, elevation and locational information (latitude, longitude to derive a map of vegetated wetlands in Alaska, with a spatial resolution of 50 m. We used the National Wetlands Inventory and National Land Cover Database (for upland areas to select training and validation data and further validated classification results with an independent dataset that we created. A number of improvements were made to the method of Whitcomb et al. (2009: (1 more consistent training data in upland areas; (2 better distribution of training data across all classes by taking a stratified random sample of all available training pixels; and (3 a more efficient implementation, which allowed classification of the entire state as a single entity (rather than in separate tiles, which eliminated discontinuities at tile boundaries. The overall accuracy for discriminating wetland from upland was 95%, and the accuracy at the level of wetland classes was 85%. The total area of wetlands mapped was 0.59 million km2, or 36% of the total land area of the state of Alaska. The map will be made available to download from NASA’s wetland monitoring website.

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

    Science.gov (United States)

    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.

  14. High-resolution statistical mapping reveals gene territories in live yeast.

    Science.gov (United States)

    Berger, Axel B; Cabal, Ghislain G; Fabre, Emmanuelle; Duong, Tarn; Buc, Henri; Nehrbass, Ulf; Olivo-Marin, Jean-Christophe; Gadal, Olivier; Zimmer, Christophe

    2008-12-01

    The nonrandom positioning of genes inside eukaryotic cell nuclei is implicated in central nuclear functions. However, the spatial organization of the genome remains largely uncharted, owing to limited resolution of optical microscopy, paucity of nuclear landmarks and moderate cell sampling. We developed a computational imaging approach that creates high-resolution probabilistic maps of subnuclear domains occupied by individual loci in budding yeast through automated analysis of thousands of living cells. After validation, we applied the technique to genes involved in galactose metabolism and ribosome biogenesis. We found that genomic loci are confined to 'gene territories' much smaller than the nucleus, which can be remodeled during transcriptional activation, and that the nucleolus is an important landmark for gene positioning. The technique can be used to visualize and quantify territory positions relative to each other and to nuclear landmarks, and should advance studies of nuclear architecture and function.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  18. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals.

    Directory of Open Access Journals (Sweden)

    Yair Field

    2008-11-01

    Full Text Available The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence. However, less is known about the functional consequences of this encoding. Here, we address this question using a genome-wide map of approximately 380,000 yeast nucleosomes that we sequenced in their entirety. Utilizing the high resolution of our map, we refine our understanding of how nucleosome organizations are encoded by the DNA sequence and demonstrate that the genomic sequence is highly predictive of the in vivo nucleosome organization, even across new nucleosome-bound sequences that we isolated from fly and human. We find that Poly(dA:dT tracts are an important component of these nucleosome positioning signals and that their nucleosome-disfavoring action results in large nucleosome depletion over them and over their flanking regions and enhances the accessibility of transcription factors to their cognate sites. Our results suggest that the yeast genome may utilize these nucleosome positioning signals to regulate gene expression with different transcriptional noise and activation kinetics and DNA replication with different origin efficiency. These distinct functions may be achieved by encoding both relatively closed (nucleosome-covered chromatin organizations over some factor binding sites, where factors must compete with nucleosomes for DNA access, and relatively open (nucleosome-depleted organizations over other factor sites, where factors bind without competition.

  19. High resolution orientation mapping of secondary phases in ATI 718Plus® alloy

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    Krakow Robert

    2014-01-01

    Full Text Available The polycrystalline superalloy ATI 718Plus ® (hereafter 718Plus has been developed to replace the established alloy Inconel 718 by offering higher temperature capability for applications in gas turbines. The alloy exhibits two secondary phases in the austenitic matrix; it is strengthened by the γ′-phase with η-phase discontinuously precipitated at the grain boundaries. It can be utilized to control grain growth during forging. Generally, hexagonal η phase has been reported to possess a defined crystallographic orientation with the matrix. However, the material studied here exhibits blocky η-phase that has been precipitated and grown during thermo-mechanical processing. Therefore a measurable change in orientation relationship is expected. The standard technique for orientation mapping is electron back-scattered diffraction with spatial resolution of 100 nm. That is insufficient for studying η-phase in 718Plus. By applying high resolution orientation mapping in the transmission electron microscope (Philips CM 300 FEGTEM equipped with a Nanomegas ASTARTM system a resolution of 3 nm was achieved. The indexed diffraction data was analysed using the Matlab Toolbox Mtex. The analysis included grain reconstruction and exclusion of low confidence measurements. The data set allows generating phase boundary maps indicating interfaces characteristics. Quantitative assessment shows that only 19% of the γ-η-interfaces fulfil the orientation relationship.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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 (entrainment onset was quantified over successive waves in spatiotemporal detail. In the second demonstration, slow-wave velocity was accurately determined with HR field analysis, and paced propagation was found to be anisotropic (longitudinal 2.6 +/- 1.7 vs. circumferential 4.5 +/- 0.6 mm/s; P 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.

  3. The high resolution bathymetric map of the exhalative area of Panarea (Aeolian Islands, Italy

    Directory of Open Access Journals (Sweden)

    G. Bortoluzzi

    2005-06-01

    Full Text Available On November 3, 2002 a shallow submarine gas eruption occurred in an area of 2.3 km2 east of Panarea (Aeolian volcanic arc, Southern Thyrrenian Sea, Italy. The exhalative area, surrounded by the islets of Dattilo, Panarelli, Lisca Bianca, Bottaro and Lisca Nera, has been known since historical times for the hydrothermal activity related to the Panarea volcanic complex. Due to the exceptional characteristics of the phenomenon, different geological, geochemical, geophysical and studies were carried out in this still poorly known volcanic area. A particular effort was devoted to producing a high resolution bathymetric map that also aimed to estimate the amount and location of the active exhalative centers and their variations in space and time. Data were obtained by three RTK multibeam surveys performed between December 2002 and December 2003. Here we show and discuss the technical details of the bathymetric surveys, the bathymetric map at 0.5 m resolution, and the accurate location of the 606 main exhalative centres active during the 2002-2003 crisis. The bathymetric data and the maps show two prevailing principal NE-SW and NW-SE alignments that match the spatial distribution of the exhalation centres. The accurate positioning at submeter accuracy of the gas vents is useful in the monitoring activity and to study their temporal and spatial variability.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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 ...

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

    Science.gov (United States)

    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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Patterns of recombination activity on mouse chromosome 11 revealed by high resolution mapping.

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    Timothy Billings

    Full Text Available The success of high resolution genetic mapping of disease predisposition and quantitative trait loci in humans and experimental animals depends on the positions of key crossover events around the gene of interest. In mammals, the majority of recombination occurs at highly delimited 1-2 kb long sites known as recombination hotspots, whose locations and activities are distributed unevenly along the chromosomes and are tightly regulated in a sex specific manner. The factors determining the location of hotspots started to emerge with the finding of PRDM9 as a major hotspot regulator in mammals, however, additional factors modulating hotspot activity and sex specificity are yet to be defined. To address this limitation, we have collected and mapped the locations of 4829 crossover events occurring on mouse chromosome 11 in 5858 meioses of male and female reciprocal F1 hybrids of C57BL/6J and CAST/EiJ mice. This chromosome was chosen for its medium size and high gene density and provided a comparison with our previous analysis of recombination on the longest mouse chromosome 1. Crossovers were mapped to an average resolution of 127 kb, and thirteen hotspots were mapped to <8 kb. Most crossovers occurred in a small number of the most active hotspots. Females had higher recombination rate than males as a consequence of differences in crossover interference and regional variation of sex specific rates along the chromosome. Comparison with chromosome 1 showed that recombination events tend to be positioned in similar fashion along the centromere-telomere axis but independently of the local gene density. It appears that mammalian recombination is regulated on at least three levels, chromosome-wide, regional, and at individual hotspots, and these regulation levels are influenced by sex and genetic background but not by gene content.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  11. Combination of comprehensive geophysical measurements and conventional soil sampling for high resolution soil mapping

    Science.gov (United States)

    Werban, U.; Nuesch, A.; Vienken, T.; Dietrich, P.; Behrens, T.

    2010-12-01

    The focus of the FP7-EU project iSOIL “Interactions between soil related sciences - Linking geophysics, soil science and digital soil mapping” is to develop new and to improve existing strategies and innovative methods for generating accurate, high-resolution soil property maps. Thus we will develop, validate, and evaluate concepts and strategies for transferring measured physical parameter distributions into soil property, soil function and soil threat maps of different scales. The resulting soil property maps can be used for agriculture applications and soil degradation threats studies, e.g. erosion, compaction and soil organic matter decline. A fast and cost efficient way to detect physical parameters of soils at large areas is the application of mobile geophysical platforms. An advantage of these platforms is the flexibility since different kind of instruments can be mounted and combined. Following instruments are used on platforms within iSOIL project: EMI, GPR, gamma-spectrometry and magnetics. Since geophysical methods provide only physical parameters it is essential to combine them with conventional soil sampling methods for ground truthing. Physical parameters have to be converted into soil parameters via (site specific) transfer functions. One focus of the project was the development of measuring designs for the evaluation and combination of different geophysical methods. The application of a hierarchical approach is one way to combine different scales and parameters. The implementation of this approach will be presented and can be summarized as follows: - The first step is a survey of the total area with EMI and gamma-spectrometry. The distance between two lines is 10 - 20 meters. - By means of the geophysical data and a digital elevation model, representative soil sampling points are chosen, via a weighted conditioned latin hypercube sampling scheme (wLHS) based on conditioned latin hypercube sampling (cLHS). - All soil sampling points are probed

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

    Directory of Open Access Journals (Sweden)

    T. Xia

    2015-11-01

    Full Text Available 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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  15. Assessing Usefulness of High-Resolution Satellite Imagery (HRSI) for Re-Survey of Cadastral Maps

    Science.gov (United States)

    Rao, S. S.; Sharma, J. R.; Rajashekar, S. S.; Rao, D. S. P.; Arepalli, A.; Arora, V.; Kuldeep; Singh, R. P.; Kanaparthi, M.

    2014-11-01

    The Government of India has initiated "National Land Records Modernization Programme (NLRMP)" with emphasis to modernize management of land records, minimize scope of land/property disputes, enhance transparency in the land records maintenance system, and facilitate moving eventually towards guaranteed conclusive titles to immovable properties in the country. One of the major components of the programme is survey/re-survey and updating of all survey and settlement records including creation of original cadastral records wherever necessary. The use of ETS/GPS, Aerial or High Resolution Satellite Images (HRSI) and hybrid method of images are suggested for re-survey in the guidelines. The emerging new satellite technologies enabling earth observation at a spatial resolution of 1.0m or 0.5m or even 0.41m have brought revolutionary changes in the field of cadastral survey. The highresolution satellite imagery (HRSI) is showing its usefulness for cadastral surveys in terms of clear identification of parcel boundaries and other cultural features due to which traditional cadastre and land registration systems have been undergoing major changes worldwide. In the present research study, cadastral maps are derived from ETS/GPS, HRSI of 1.0m and 0.5m and used for comparison. The differences in areas, perimeter and position of parcels derived from HRSI are compared vis-a-vis ETS/GPS boundaries. An assessment has been made on the usefulness of HRSI for re-survey of cadastral maps vis-a-vis conventional ground survey.

  16. High-resolution linkage map for two honeybee chromosomes: the hotspot quest.

    Science.gov (United States)

    Mougel, Florence; Poursat, Marie-Anne; Beaume, Nicolas; Vautrin, Dominique; Solignac, Michel

    2014-02-01

    Meiotic recombination is a fundamental process ensuring proper disjunction of homologous chromosomes and allele shuffling in successive generations. In many species, this cellular mechanism occurs heterogeneously along chromosomes and mostly concentrates in tiny fragments called recombination hotspots. Specific DNA motifs have been shown to initiate recombination in these hotspots in mammals, fission yeast and drosophila. The aim of this study was to check whether recombination also occurs in a heterogeneous fashion in the highly recombinogenic honeybee genome and whether this heterogeneity can be connected with specific DNA motifs. We completed a previous picture drawn from a routine genetic map built with an average resolution of 93 kb. We focused on the two smallest honeybee chromosomes to increase the resolution and even zoomed at very high resolution (3.6 kb) on a fragment of 300 kb. Recombination rates measured in these fragments were placed in relation with occurrence of 30 previously described motifs through a Poisson regression model. A selection procedure suitable for correlated variables was applied to keep significant motifs. These fine and ultra-fine mappings show that recombination rate is significantly heterogeneous although poorly contrasted between high and low recombination rate, contrarily to most model species. We show that recombination rate is probably associated with the DNA methylation state. Moreover, three motifs (CGCA, GCCGC and CCAAT) are good candidates of signals promoting recombination. Their influence is however moderate, doubling at most the recombination rate. This discovery extends the way to recombination dissection in insects.

  17. Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination.

    Science.gov (United States)

    Camara, Pablo G; Rosenbloom, Daniel I S; Emmett, Kevin J; Levine, Arnold J; Rabadan, Raul

    2016-07-01

    Meiotic recombination is a fundamental evolutionary process driving diversity in eukaryotes. In mammals, recombination is known to occur preferentially at specific genomic regions. Using topological data analysis (TDA), a branch of applied topology that extracts global features from large data sets, we developed an efficient method for mapping recombination at fine scales. When compared to standard linkage-based methods, TDA can deal with a larger number of SNPs and genomes without incurring prohibitive computational costs. We applied TDA to 1,000 Genomes Project data and constructed high-resolution whole-genome recombination maps of seven human populations. Our analysis shows that recombination is generally under-represented within transcription start sites. However, the binding sites of specific transcription factors are enriched for sites of recombination. These include transcription factors that regulate the expression of meiosis- and gametogenesis-specific genes, cell cycle progression, and differentiation blockage. Additionally, our analysis identifies an enrichment for sites of recombination at repeat-derived loci matched by piwi-interacting RNAs.

  18. HIGH-RESOLUTION DEBRIS FLOW VOLUME MAPPING WITH UNMANNED AERIAL SYSTEMS (UAS AND PHOTOGRAMMETRIC TECHNIQUES

    Directory of Open Access Journals (Sweden)

    M. S. Adams

    2016-06-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  1. High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly

    Directory of Open Access Journals (Sweden)

    Womack James E

    2007-09-01

    Full Text Available Abstract Background High resolution radiation hybrid (RH maps can facilitate genome sequence assembly by correctly ordering genes and genetic markers along chromosomes. The objective of the present study was to generate high resolution RH maps of bovine chromosomes 19 (BTA19 and 29 (BTA29, and compare them with the current 7.1X bovine genome sequence assembly (bovine build 3.1. We have chosen BTA19 and 29 as candidate chromosomes for mapping, since many Quantitative Trait Loci (QTL for the traits of carcass merit and residual feed intake have been identified on these chromosomes. Results We have constructed high resolution maps of BTA19 and BTA29 consisting of 555 and 253 Single Nucleotide Polymorphism (SNP markers respectively using a 12,000 rad whole genome RH panel. With these markers, the RH map of BTA19 and BTA29 extended to 4591.4 cR and 2884.1 cR in length respectively. When aligned with the current bovine build 3.1, the order of markers on the RH map for BTA19 and 29 showed inconsistencies with respect to the genome assembly. Maps of both the chromosomes show that there is a significant internal rearrangement of the markers involving displacement, inversion and flips within the scaffolds with some scaffolds being misplaced in the genome assembly. We also constructed cattle-human comparative maps of these chromosomes which showed an overall agreement with the comparative maps published previously. However, minor discrepancies in the orientation of few homologous synteny blocks were observed. Conclusion The high resolution maps of BTA19 (average 1 locus/139 kb and BTA29 (average 1 locus/208 kb presented in this study suggest that by the incorporation of RH mapping information, the current bovine genome sequence assembly can be significantly improved. Furthermore, these maps can serve as a potential resource for fine mapping QTL and identification of causative mutations underlying QTL for economically important traits.

  2. Exploiting High Resolution Multi-Seasonal Textural Measures and Spectral Information for Reedbed Mapping

    Directory of Open Access Journals (Sweden)

    Alex Okiemute Onojeghuo

    2016-02-01

    Full Text Available Reedbeds across the UK are amongst the most important habitats for rare and endangered birds, wildlife and organisms. However, over the past century, this valued wetland habitat has experienced a drastic reduction in quality and spatial coverage due to pressures from human related activities. To this end, conservation organisations across the UK have been charged with the task of conserving and expanding this threatened habitat. With this backdrop, the study aimed to develop a methodology for accurate reedbed mapping through the combined use of multi-seasonal texture measures and spectral information contained in high resolution QuickBird satellite imagery. The key objectives were to determine the most effective single-date (autumn or summer and multi-seasonal QuickBird imagery suitable for reedbed mapping over the study area; to evaluate the effectiveness of combining multi-seasonal texture measures and spectral information for reedbed mapping using a variety of combinations; and to evaluate the most suitable classification technique for reedbed mapping from three selected classification techniques, namely maximum likelihood classifier, spectral angular mapper and artificial neural network. Using two selected grey-level co-occurrence textural measures (entropy and angular second moment, a series of experiments were conducted using varied combinations of single-date and multi-seasonal QuickBird imagery. Overall, the results indicate the multi-seasonal pansharpened multispectral bands (eight layers combined with all eight grey level co-occurrence matrix texture measures (entropy and angular second moment computed using windows 3 × 3 and 7 × 7 produced the optimal reedbed (76.5% and overall classification (78.1% accuracies using the maximum likelihood classifier technique. Using the optimal 16 layer multi-seasonal pansharpened multispectral and texture combined image dataset, a total reedbed area of 9.8 hectares was successfully mapped over the

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

    Science.gov (United States)

    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

  4. Comparative studies of genome-wide maps of nucleosomes between deletion mutants of elp3 and hos2 genes of Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Takashi Matsumoto

    Full Text Available In order to elucidate the influence of histone acetylation upon nucleosomal DNA length and nucleosome position, we compared nucleosome maps of the following three yeast strains; strain BY4741 (control, the elp3 (one of histone acetyltransferase genes deletion mutant, and the hos2 (one of histone deactylase genes deletion mutant of Saccharomyces cerevisiae. We sequenced mononucleosomal DNA fragments after treatment with micrococcal nuclease. After mapping the DNA fragments to the genome, we identified the nucleosome positions. We showed that the distributions of the nucleosomal DNA lengths of the control and the hos2 disruptant were similar. On the other hand, the distribution of the nucleosomal DNA lengths of the elp3 disruptant shifted toward shorter than that of the control. It strongly suggests that inhibition of Elp3-induced histone acetylation causes the nucleosomal DNA length reduction. Next, we compared the profiles of nucleosome mapping numbers in gene promoter regions between the control and the disruptant. We detected 24 genes with low conservation level of nucleosome positions in promoters between the control and the elp3 disruptant as well as between the control and the hos2 disruptant. It indicates that both Elp3-induced acetylation and Hos2-induced deacetylation influence the nucleosome positions in the promoters of those 24 genes. Interestingly, in 19 of the 24 genes, the profiles of nucleosome mapping numbers were similar between the two disruptants.

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

    Science.gov (United States)

    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.

  6. A High-Resolution Map of Emerald Ash Borer Invasion Risk for Southern Central Europe

    Directory of Open Access Journals (Sweden)

    Viktoria Valenta

    2015-08-01

    Full Text Available Ash species (Fraxinus spp. in Europe are threatened by the Emerald Ash Borer (Agrilus planipennis, EAB, an invasive wood boring beetle native to East Asia and currently spreading from European Russia westwards. Based on a high-resolution habitat distribution map (grid cell size: 25 × 25 m and data on distribution and abundance of Common Ash (Fraxinus excelsior, the most widespread and highly susceptive host species of EAB in Europe, we assess the spatial distribution of EAB invasion risks for southern Central Europe (Austria, Switzerland, Liechtenstein, southern Germany, South Tyrol. We found highest F. excelsior abundance and thus invasion risks in extensive lowland floodplain forests, medium risks in zonal lowland forests and low risks in upper montane and subalpine forests. Based on average velocities of spread in Russia (13–31 km/year and North America (2.5–80 km/year from flight and human-assisted transport, EAB is likely to cover the distance (1500 km between its current range edge in western Russia and the eastern border of the study region within few decades. However, secondary spread by infested wood products make earlier introductions likely. The high susceptibility and mortality of F. excelsior leave no doubt that this beetle will become a major forest pest once it reaches Central Europe. Therefore, developing and testing management approaches with the aim to halt or at least slow down the invasion of EAB in Europe have to be pursued with great urgency.

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

    Science.gov (United States)

    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.

  8. High-Resolution Mapping of Urban Surface Water Using ZY-3 Multi-Spectral Imagery

    Directory of Open Access Journals (Sweden)

    Fangfang Yao

    2015-09-01

    Full Text Available Accurate information of urban surface water is important for assessing the role it plays in urban ecosystem services under the content of urbanization and climate change. However, high-resolution monitoring of urban water bodies using remote sensing remains a challenge because of the limitation of previous water indices and the dark building shadow effect. To address this problem, we proposed an automated urban water extraction method (UWEM which combines a new water index, together with a building shadow detection method. Firstly, we trained the parameters of UWEM using ZY-3 imagery of Qingdao, China. Then we verified the algorithm using five other sub-scenes (Aksu, Fuzhou, Hanyang, Huangpo and Huainan ZY-3 imagery. The performance was compared with that of the Normalized Difference Water Index (NDWI. Results indicated that UWEM performed significantly better at the sub-scenes with kappa coefficients improved by 7.87%, 32.35%, 12.64%, 29.72%, 14.29%, respectively, and total omission and commission error reduced by 61.53%, 65.74%, 83.51%, 82.44%, and 74.40%, respectively. Furthermore, UWEM has more stable performances than NDWI’s in a range of thresholds near zero. It reduces the over- and under-estimation issues which often accompany previous water indices when mapping urban surface water under complex environmental conditions.

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

    Directory of Open Access Journals (Sweden)

    Lucia Carbone

    2006-12-01

    Full Text Available 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.

  10. Expressway deformation mapping using high-resolution TerraSAR-X images

    KAUST Repository

    Shi, Xuguo

    2014-01-27

    Monitoring deformation of linear infrastructures such as expressway and railway caused by natural processes or anthropogenic activities is a vital task to ensure the safety of human lives and properties. Interferometric Synthetic Aperture Radar (InSAR) has been widely recognized as an effective technology to carry out large-area surface deformation mapping. However, its application in linear infrastructure deformation monitoring has not been intensively studied till now. In this article, a modified Small BAseline Subset (SBAS) method is proposed to retrieve the deformation patterns of the expressway. In our method, only the point-like targets identified on the expressway were kept in our analysis, and two complementary subsets of interferograms were formed to better separate the signals of height error and deformation from inteferometric phase observations. We successfully applied this method with multitemporal high-resolution TerraSAR-X images to retrieve the spatialoral pattern of surface deformation along the Beian-Heihe expressway that is located in island-permafrost areas and threatened by geohazards. © 2014 Taylor & Francis.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  15. High-resolution physical map for chromosome 16q12.1-q13, the Blau syndrome locus

    Directory of Open Access Journals (Sweden)

    Bonavita Gina

    2002-08-01

    Full Text Available Abstract Background The Blau syndrome (MIM 186580, an autosomal dominant granulomatous disease, was previously mapped to chromosome 16p12-q21. However, inconsistent physical maps of the region and consequently an unknown order of microsatellite markers, hampered us from further refining the genetic locus for the Blau syndrome. To address this problem, we constructed our own high-resolution physical map for the Blau susceptibility region. Results We generated a high-resolution physical map that provides more than 90% coverage of a refined Blau susceptibility region. The map consists of four contigs of sequence tagged site-based bacterial artificial chromosomes with a total of 124 bacterial artificial chromosomes, and spans approximately 7.5 Mbp; however, three gaps still exist in this map with sizes of 425, 530 and 375 kbp, respectively, estimated from radiation hybrid mapping. Conclusions Our high-resolution map will assist genetic studies of loci in the interval from D16S3080, near D16S409, and D16S408 (16q12.1 to 16q13.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  18. High-Resolution, Semi-Automatic Fault Mapping Using Umanned Aerial Vehicles and Computer Vision: Mapping from an Armchair

    Science.gov (United States)

    Micklethwaite, S.; Vasuki, Y.; Turner, D.; Kovesi, P.; Holden, E.; Lucieer, A.

    2012-12-01

    Our ability to characterise fractures depends upon the accuracy and precision of field techniques, as well as the quantity of data that can be collected. Unmanned Aerial Vehicles (UAVs; otherwise known as "drones") and photogrammetry, provide exciting new opportunities for the accurate mapping of fracture networks, over large surface areas. We use a highly stable, 8 rotor, UAV platform (Oktokopter) with a digital SLR camera and the Structure-from-Motion computer vision technique, to generate point clouds, wireframes, digital elevation models and orthorectified photo mosaics. Furthermore, new image analysis methods such as phase congruency are applied to the data to semiautomatically map fault networks. A case study is provided of intersecting fault networks and associated damage, from Piccaninny Point in Tasmania, Australia. Outcrops >1 km in length can be surveyed in a single 5-10 minute flight, with pixel resolution ~1 cm. Centimetre scale precision can be achieved when selected ground control points are measured using a total station. These techniques have the potential to provide rapid, ultra-high resolution mapping of fracture networks, from many different lithologies; enabling us to more accurately assess the "fit" of observed data relative to model predictions, over a wide range of boundary conditions.igh resolution DEM of faulted outcrop (Piccaninny Point, Tasmania) generated using the Oktokopter UAV (inset) and photogrammetric techniques.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  1. High resolution physical map of porcine chromosome 7 QTL region and comparative mapping of this region among vertebrate genomes

    Directory of Open Access Journals (Sweden)

    Demeure Olivier

    2006-01-01

    Full Text Available Abstract Background On porcine chromosome 7, the region surrounding the Major Histocompatibility Complex (MHC contains several Quantitative Trait Loci (QTL influencing many traits including growth, back fat thickness and carcass composition. Previous studies highlighted that a fragment of ~3.7 Mb is located within the Swine Leucocyte Antigen (SLA complex. Internal rearrangements of this fragment were suggested, and partial contigs had been built, but further characterization of this region and identification of all human chromosomal fragments orthologous to this porcine fragment had to be carried out. Results A whole physical map of the region was constructed by integrating Radiation Hybrid (RH mapping, BAC fingerprinting data of the INRA BAC library and anchoring BAC end sequences on the human genome. 17 genes and 2 reference microsatellites were ordered on the high resolution IMNpRH212000rad Radiation Hybrid panel. A 1000:1 framework map covering 550 cR12000 was established and a complete contig of the region was developed. New micro rearrangements were highlighted between the porcine and human genomes. A bovine RH map was also developed in this region by mapping 16 genes. Comparison of the organization of this region in pig, cattle, human, mouse, dog and chicken genomes revealed that 1 the translocation of the fragment described previously is observed only on the bovine and porcine genomes and 2 the new internal micro rearrangements are specific of the porcine genome. Conclusion We estimate that the region contains several rearrangements and covers 5.2 Mb of the porcine genome. The study of this complete BAC contig showed that human chromosomal fragments homologs of this heavily rearranged QTL region are all located in the region of HSA6 that surrounds the centromere. This work allows us to define a list of all candidate genes that could explain these QTL effects.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Phillippa K Bricher

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  8. VERITAS: A Mission Concept for the High Resolution Topographic Mapping and Imaging of Venus

    Science.gov (United States)

    Hensley, S.; Smrekar, S. E.; Pollard, B.

    2012-12-01

    Magellan, a NASA mission to Venus in the early 1990's, mapped nearly the entire surface of Venus with an S-band (12 cm) synthetic aperture radar and microwave radiometer and made radar altimeter measurements of the topography. These measurements revolutionized our understanding of the geomorphology, geology and geophysical processes that have shaped the evolution of the surface of Venus. The Magellan spacecraft had an elliptical orbit with an apoapsis of approximately 8000 km and a periapsis of 257 km and an orbital inclination of 86°. In this way the radar was able to collect long strips of data approximately 10000 km in length running north to south with altitudes varying from 3000 km to 257 km. During the remainder of the orbit the collected data was down linked to earth. The SAR mode operated in burst mode fashion whereby it transmitted a small string of pulses up to a couple of hundred pulses in length followed by a quiescent period when the radar ceased transmission and allowed interleaved operation of the altimeter and radiometer modes. This mode of operation allowed for a significant reduction in downlinked SAR imaging data at the expense of azimuth (i.e. along-track) resolution. However, the lack of finer resolution imagery and topography of the surface than that obtained by the Magellan mission has hampered the definitive answer to key questions concerning the processes and evolution of the surface of Venus. The Venus Emissivity, Radio Science, InSAR Topography And Spectroscopy (VERITAS) Mission is a proposed mission to Venus designed to obtain high resolution imagery and topography of the surface using an X-band radar configured as a single pass radar interferometer coupled with a multispectral NIR emissivity mapping capability. VERITAS would map surface topography with a spatial resolution of 250 m and 5 m vertical accuracy and generate radar imagery with 30 m spatial resolution. These capabilities represent an order of magnitude or better improvement

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  14. On the synergy of SMOS and Terra/Aqua MODIS: high resolution soil moisture maps in near real-time

    OpenAIRE

    Piles Guillem, Maria; Vall-Llossera Ferran, Mercedes Magdalena; Camps Carmona, Adriano José; Sanchez, Nilda; Martinez Fernandez, Jose; Martinez, Justino; Gonzalez Gambau, Verónica; Riera, R.

    2013-01-01

    An innovative downscaling approach to obtain fine-scale soil moisture estimates from 40 km SMOS observations has been developed. It optimally blends SMOS multi-angular and full-polarimetric information with MODIS visible/data into high resolution soil moisture maps. The core of the algorithm is a model that linksmicrowave/optical sensitivity to soilmoisture and linearly relates the two instruments across spatial scales. This algorithm has been implemented at SMOS-BEC facilities and near real-...

  15. Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.

    Science.gov (United States)

    Hanghøj, Kristian; Seguin-Orlando, Andaine; Schubert, Mikkel; Madsen, Tobias; Pedersen, Jakob Skou; Willerslev, Eske; Orlando, Ludovic

    2016-12-01

    The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts.

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

    Science.gov (United States)

    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.

  17. Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters

    Science.gov (United States)

    Helbo, Alexandra Søgaard; Lay, Fides D.; Jones, Peter A.; Liang, Gangning; Grønbæk, Kirsten

    2017-02-01

    Chromatin is structurally involved in the transcriptional regulation of all genes. While the nucleosome positioning at RNA polymerase II (pol II) promoters has been extensively studied, less is known about the chromatin structure at pol III promoters in human cells. We use a high-resolution analysis to show substantial differences in chromatin structure of pol II and pol III promoters, and between subtypes of pol III genes. Notably, the nucleosome depleted region at the transcription start site of pol III genes extends past the termination sequences, resulting in nucleosome free gene bodies. The +1 nucleosome is located further downstream than at pol II genes and furthermore displays weak positioning. The variable position of the +1 location is seen not only within individual cell populations and between cell types, but also between different pol III promoter subtypes, suggesting that the +1 nucleosome may be involved in the transcriptional regulation of pol III genes. We find that expression and DNA methylation patterns correlate with distinct accessibility patterns, where DNA methylation associates with the silencing and inaccessibility at promoters. Taken together, this study provides the first high-resolution map of nucleosome positioning and occupancy at human pol III promoters at specific loci and genome wide.

  18. A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1.

    Science.gov (United States)

    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.

  19. High-resolution tree canopy mapping for New York City using LIDAR and object-based image analysis

    Science.gov (United States)

    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.

  20. Surface Temperature Mapping of the University of Northern Iowa Campus Using High Resolution Thermal Infrared Aerial Imageries.

    Science.gov (United States)

    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.

  1. Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX

    DEFF Research Database (Denmark)

    Hanghøj, Kristian Ebbesen; Seguin-Orlando, Andaine; Schubert, Mikkel

    2016-01-01

    present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH......, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained...... of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts....

  2. High-resolution mapping and transcriptional activity analysis of chicken centromere sequences on giant lampbrush chromosomes.

    Science.gov (United States)

    Krasikova, Alla; Fukagawa, Tatsuo; Zlotina, Anna

    2012-12-01

    Exploration into morphofunctional organisation of centromere DNA sequences is important for understanding the mechanisms of kinetochore specification and assembly. In-depth epigenetic analysis of DNA fragments associated with centromeric nucleosome proteins has demonstrated unique features of centromere organisation in chicken karyotype: there are both mature centromeres, which comprise chromosome-specific homogeneous arrays of tandem repeats, and recently evolved primitive centromeres, which consist of non-tandemly organised DNA sequences. In this work, we describe the arrangement and transcriptional activity of chicken centromere repeats for Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 and non-repetitive centromere sequences of chromosomes 5, 27, and Z using highly elongated lampbrush chromosomes, which are characteristic of the diplotene stage of oogenesis. The degree of chromatin packaging and fine spatial organisations of tandemly repetitive and non-tandemly repetitive centromeric sequences significantly differ at the lampbrush stage. Using DNA/RNA FISH, we have demonstrated that during the lampbrush stage, DNA sequences are transcribed within the centromere regions of chromosomes that lack centromere-specific tandem repeats. In contrast, chromosome-specific centromeric repeats Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 do not demonstrate any transcriptional activity during the lampbrush stage. In addition, we found that CNM repeat cluster localises adjacent to non-repetitive centromeric sequences in chicken microchromosome 27 indicating that centromere region in this chromosome is repeat-rich. Cross-species FISH allowed localisation of the sequences homologous to centromeric DNA of chicken chromosomes 5 and 27 in centromere regions of quail orthologous chromosomes.

  3. Comparative high-resolution mapping of the wax inhibitors Iw1 and Iw2 in hexaploid wheat.

    Directory of Open Access Journals (Sweden)

    Haibin Wu

    Full Text Available The wax (glaucousness on wheat leaves and stems is mainly controlled by two sets of genes: glaucousness loci (W1 and W2 and non-glaucousness loci (Iw1 and Iw2. The non-glaucousness (Iw loci act as inhibitors of the glaucousness loci (W. High-resolution comparative genetic linkage maps of the wax inhibitors Iw1 originating from Triticum dicoccoides, and Iw2 from Aegilops tauschii were developed by comparative genomics analyses of Brachypodium, sorghum and rice genomic sequences corresponding to the syntenic regions of the Iw loci in wheat. Eleven Iw1 and eight Iw2 linked EST markers were developed and mapped to linkage maps on the distal regions of chromosomes 2BS and 2DS, respectively. The Iw1 locus mapped within a 0.96 cM interval flanked by the BE498358 and CA499581 EST markers that are collinear with 122 kb, 202 kb, and 466 kb genomic regions in the Brachypodium 5S chromosome, the sorghum 6S chromosome and the rice 4S chromosome, respectively. The Iw2 locus was located in a 4.1 to 5.4-cM interval in chromosome 2DS that is flanked by the CJ886319 and CJ519831 EST markers, and this region is collinear with a 2.3 cM region spanning the Iw1 locus on chromosome 2BS. Both Iw1 and Iw2 co-segregated with the BF474014 and CJ876545 EST markers, indicating they are most likely orthologs on 2BS and 2DS. These high-resolution maps can serve as a framework for chromosome landing, physical mapping and map-based cloning of the wax inhibitors in wheat.

  4. Using GeoMapApp to access and interpret high-resolution bathymetric data collected with deep submergence vehicles

    Science.gov (United States)

    Ferrini, V.; Carbotte, S. M.; Ryan, W. B.; O'hara, S. H.; Bonczkowski, J.; Arko, R. A.

    2011-12-01

    Bathymetric data products generated with deep submergence technology can be of meter to sub-meter resolution, providing an unprecedented view of seafloor features. Data at this resolution provide near photo-quality information that can be used to not only quantify morphologic features and create geologic maps, but can also be used to develop and refine remote seafloor characterization techniques. Nesting these data within regional lower resolution data, and supplementing them with ground-truth photos and observations from seafloor samples is often the key to understanding the geologic features revealed in bathymetric data. Through the efforts of the Ridge 2000 Program and the Ridge 2000 Data Portal, many of these data have been acquired, assembled, spatially co-registered, and made directly accessible through a variety of programmatic interfaces. The Data Portal provides direct downloads of raw and processed data files with full attribution to contributing scientists and links to publications. In addition, GeoMapApp, a free Java-based visualization and analysis tool, provides quantitative access to several high-resolution bathymetry data sets within the context of important complementary data. The default basemap in GeoMapApp is the Global Multi-Resolution Topography (GMRT) Synthesis, which includes ship-based bathymetry data from over 500 research cruises as well as contributed regional grids, providing resolution of 100 m or better in many areas. GeoMapApp provides quantitative access to the GMRT, which can be used to understand the regional context of localized high-resolution bathymetry data. Other related data directly accessible through GeoMapApp include sidescan data, sample positions and descriptions, and bottom photos acquired with National Deep Submergence Facility assets and the WHOI TowCam System. Quantitative tools for interrogating and interpreting the data (e.g. profiling, changing sun-illumination and color scale) are provided within GeoMapApp to

  5. High-resolution mapping of European fishing pressure on the benthic habitats

    DEFF Research Database (Denmark)

    Eigaard, Ole Ritzau; Bastardie, Francois; Hintzen, Niels T.

    -scale maps of benthic fishing pressure covering the EU, Norwegian and Turkish waters. First individual logbook observations from 13 countries were assigned to 17 different functional gear groups (métiers) based on target species and gear type information. Secondly, relationships between gear width and vessel......Mapping and monitoring of pressure from fishery on the marine benthic environment is necessary to support an ecosystem approach to fisheries management (EAFM). In many cases this need is not reflected in official fisheries statistics and logbooks, where focus typically is on catch rather than......-resolution fishing pressure maps were overlaid with existing marine habitat maps to identify areas of potential ecosystem service conflicts...

  6. A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

    Directory of Open Access Journals (Sweden)

    Daniel Fulop

    2016-10-01

    Full Text Available 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.

  7. A split personality for nucleosomes.

    Science.gov (United States)

    McKay, Daniel J; Lieb, Jason D

    2014-12-04

    A high-resolution look at where histones touch DNA reveals a surprisingly intricate, dynamic, and modular nucleosome. Three advances in the study by Rhee et al. include unexpected interactions between the H3 tail and linker DNA, new evidence for existence of subnucleosomal particles, and asymmetric patterns of histone modification within a single nucleosome that correspond to the direction of transcription.

  8. Generation of Land Cover Maps Using High-Resolution Multispectral Aerial Cameras

    DEFF Research Database (Denmark)

    Höhle, Joachim

    2013-01-01

    . The classification had an overall accuracy of 79%. Suggestions for the improvements in the applied methodology are made. The potential of land cover maps lies in updating of topographic databases, quality control of maps, studies of town development, and other geo-spatial domain applications. The automatic...

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

    Science.gov (United States)

    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.

  10. High-resolution three-dimensional quantitative map of the macromolecular proton fraction distribution in the normal rat brain

    Directory of Open Access Journals (Sweden)

    Anna V. Naumova

    2017-02-01

    Full Text Available 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 µm3 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.

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

    Directory of Open Access Journals (Sweden)

    Xue-Feng Ma

    Full Text Available 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.

  12. A high-resolution radiation hybrid map of the human genome draft sequence.

    Science.gov (United States)

    Olivier, M; Aggarwal, A; Allen, J; Almendras, A A; Bajorek, E S; Beasley, E M; Brady, S D; Bushard, J M; Bustos, V I; Chu, A; Chung, T R; De Witte, A; Denys, M E; Dominguez, R; Fang, N Y; Foster, B D; Freudenberg, R W; Hadley, D; Hamilton, L R; Jeffrey, T J; Kelly, L; Lazzeroni, L; Levy, M R; Lewis, S C; Liu, X; Lopez, F J; Louie, B; Marquis, J P; Martinez, R A; Matsuura, M K; Misherghi, N S; Norton, J A; Olshen, A; Perkins, S M; Perou, A J; Piercy, C; Piercy, M; Qin, F; Reif, T; Sheppard, K; Shokoohi, V; Smick, G A; Sun, W L; Stewart, E A; Fernando, J; Tejeda; Tran, N M; Trejo, T; Vo, N T; Yan, S C; Zierten, D L; Zhao, S; Sachidanandam, R; Trask, B J; Myers, R M; Cox, D R

    2001-02-16

    We have constructed a physical map of the human genome by using a panel of 90 whole-genome radiation hybrids (the TNG panel) in conjunction with 40,322 sequence-tagged sites (STSs) derived from random genomic sequences as well as expressed sequences. Of 36,678 STSs on the TNG radiation hybrid map, only 3604 (9.8%) were absent from the unassembled draft sequence of the human genome. Of 20,030 STSs ordered on the TNG map as well as the assembled human genome draft sequence and the Celera assembled human genome sequence, 36% of the STSs had a discrepant order between the working draft sequence and the Celera sequence. The TNG map order was identical to one of the two sequence orders in 60% of these discrepant cases.

  13. Creating a high resolution social vulnerability map in support of national decision makers in South Africa

    CSIR Research Space (South Africa)

    Le Roux, Alice

    2015-08-01

    Full Text Available The core objective of this study was to create a social vulnerability map based on generally accepted variables that are indicative of drivers of social vulnerability, capturing the unique attributes of South African communities. The paper explains...

  14. Generation and Assessment of Urban Land Cover Maps Using High-Resolution Multispectral Aerial Images

    DEFF Research Database (Denmark)

    Höhle, Joachim; Höhle, Michael

    2013-01-01

    to a tree structured classifier, which automatically derives land cover maps in 2D or 3D. We investigate the thematic accuracy of the produced land cover map by a class-wise stratified design and provide a method for deriving necessary sample sizes. Corresponding survey adjusted accuracy measures...... and their associated confidence intervals are used to adequately reflect uncertainty in the assessment based on the chosen sample size. Proof of concept for the method is given for an urban area in Switzerland. Here, the produced land cover map with six classes (building, wall and carport, road and parking lot, hedge...... tree learning based on recursive partitioning is investigated. We conclude that the open source software “R” provides all the tools needed for performing statistical prudent classification and accuracy evaluations of urban land cover maps....

  15. High-resolution mapping of ice-marginal landforms in the Barnim region, northeast Germany

    Science.gov (United States)

    Hardt, Jacob; Hebenstreit, Robert; Lüthgens, Christopher; Böse, Margot

    2015-12-01

    Despite more than a 100-year-long research history, timing and position of the last glacial ice margins in the northeast German lowland are still up for debate. The Barnim region, a till plain in the northeast German young morainic landscape, is traversed by the contradictorily discussed Frankfurt ice marginal position. It is located in a key position to reassess the current state of research with help of a geographic information system (GIS) and field methods. A qualitative geomorphological analysis of a high resolution LiDAR digital elevation model (DEM) in the Barnim area uncovers a variety of landforms that were previously not described. The most prominent discovery is a set of about 10 lobe-shaped ridges in the middle Barnim area. Fieldwork and geophysical measurements were carried out to investigate the structure of the ridges. The ridges are 1000-1500 m in length and their widths vary from 10 to 15 km. They are raised some 6-10 m from their surroundings. The Frankfurt ice marginal position can only partially be traced in the DEM. Sedimentological and geophysical investigations indicate that the ridges are composed of glacial till that was deposited on glaciofluvial sediments. Their formation most probably took place during the ice retreat of the Brandenburg phase (W1B) and hence represents the W1F phase in the region.

  16. High resolution electron energy loss spectroscopy with two-dimensional energy and momentum mapping

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Xuetao; Cao, Yanwei; Zhang, Shuyuan; Jia, Xun; Guo, Qinlin; Yang, Fang [Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Zhu, Linfan [Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Zhang, Jiandi; Plummer, E. W. [Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70808 (United States); Guo, Jiandong, E-mail: jdguo@iphy.ac.cn [Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Collaborative Innovation Center of Quantum Matter, Beijing 100871 (China)

    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.

  17. High-Resolution Mapping of Dust via Extinction in the M31 Bulge

    CERN Document Server

    Dong, Hui; Wang, Q D; Lauer, Tod R; Olsen, Knut A G; Saha, Abhijit; Dalcanton, Julianne J; Groves, Brent A

    2016-01-01

    We map the dust distribution in the central 180" (~680 pc) region of the M31 bulge, based on HST/WFC3 and ACS observations in ten bands from near-ultraviolet (2700 A) to near-infrared (1.5 micron). This large wavelength coverage gives us great leverage to detect not only dense dusty clumps, but also diffuse dusty molecular gas. We fit a pixel-by-pixel spectral energy distributions to construct a high-dynamic-range extinction map with unparalleled angular resolution (~0.5" , i.e., ~2 pc) and sensitivity (the extinction uncertainty, \\delta A_V~0.05). In particular, the data allow to directly fit the fractions of starlight obscured by individual dusty clumps, and hence their radial distances in the bulge. Most of these clumps seem to be located in a thin plane, which is tilted with respect to the M31 disk and appears face-on. We convert the extinction map into a dust mass surface density map and compare it with that derived from the dust emission as observed by Herschel . The dust masses in these two maps are co...

  18. Mapping of odor-related neuronal activity in the olfactory bulb by high-resolution 2-deoxyglucose autoradiography

    Energy Technology Data Exchange (ETDEWEB)

    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.

  19. High Resolution Weak Lensing Mass-Mapping Combining Shear and Flexion

    CERN Document Server

    Lanusse, Francois; Leonard, Adrienne; Pires, Sandrine

    2016-01-01

    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. In order 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, 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. We test 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 ...

  20. Detailed Maps Depicting the Shallow-Water Benthic Habitats of the Northwestern Hawaiian Islands Derived from High Resolution IKONOS Satellite Imagery (Draft)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Detailed, shallow-water coral reef ecosystem maps were generated by rule-based, semi-automated image analysis of high-resolution satellite imagery for nine locations...

  1. Detailed Maps Depicting the Shallow-Water Benthic Habitats of the Northwestern Hawaiian Islands Derived from High Resolution IKONOS Satellite Imagery

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Detailed, shallow-water coral reef ecosystem maps were generated by rule-based, semi-automated image analysis of high-resolution satellite imagery for nine locations...

  2. A high-resolution interval map of the q21 region of the human X chromosome

    Energy Technology Data Exchange (ETDEWEB)

    Philippe, C.; Monaco, A.P. [ICRF Laboratories, Oxford (United Kingdom)] [and others; Arnould, C. [Laboratoire de Genetique Humaine, Vandoeuvre-les-Nancy (France)] [and others

    1995-06-10

    In a previous study, we have developed a panel of chromosomal rearrangements for the physical mapping of the q13-q21 region of the human X chromosome. Here, we report the physical localization of 36 additional polymorphic markers by polymerase chain reaction analysis. The high density of chromosomal breakpoints in Xq21 allows us to map 58 DNA loci in 22 intervals. As a result, this segment of the X chromosome is saturated with approximately three sequence tagged sites per megabase of DNA, which will facilitate the construction of a YAC contig of this region. 26 refs., 1 fig., 1 tab.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  5. Validating a high-resolution digital soil map for precision agriculture across multiple fields

    Science.gov (United States)

    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...

  6. Mapping tropical forest trees using high-resolution aerial digital photographs

    NARCIS (Netherlands)

    Garzon-Lopez, Carol X.; Bohlman, Stephanie A.; Olff, Han; Jansen, Patrick A.

    2013-01-01

    The spatial arrangement of tree species is a key aspect of community ecology. Because tree species in tropical forests occur at low densities, it is logistically challenging to measure distributions across large areas. In this study, we evaluated the potential use of canopy tree crown maps, derived

  7. High resolution genetic map of the adenomatous polyposis coli gene (APC) region

    Energy Technology Data Exchange (ETDEWEB)

    Olschwang, S.; Laurent-Puig, P.; Melot, T. [Institut Curie, Paris (France)

    1995-05-08

    Familial adenomatous polyposis coli (APC) is a dominantly inherited colorectal cancer susceptibility disease caused by mutation in a gene called APC located on chromosome 5q21. Presymptomatic diagnosis of this condition is recommended because it enables restriction of the efficient but demanding prevention program to those relatives that are genetically affected. The large size of the APC gene makes the direct search for the casual alteration difficult to implement in routine diagnostic laboratories. Because APC appears to be genetically homogeneous with alteration in a single locus causing the disease, cosegregation analysis may represent an alternative efficient method for presymptomatic diagnosis. However, the reliability of the risk estimation by linkage analysis in APC families is hampered by the lack of a short range genetic map of the APC locus. A combined approach including genotyping of 65 APC families, analysis of the CEPH database, and complementary typing of both APC and CEPH families has made it possible to derive the following genetic map: Centromere-[D5S82-D5S49]-0.02-D5S122-0.01-D5S136-0.01-D5S135-0.02-[APC-D5S346-MCC]-0.04-[D5S81-D5S64]-Telomere. This order, which differs from previously proposed genetic maps, is fully compatible with recent physical mapping data. These data should contribute to increase the reliability of the presymptomatic test for APC. 42 refs., 1 fig., 3 tabs.

  8. 4 Vesta in Color: High Resolution Mapping from Dawn Framing Camera Images

    Science.gov (United States)

    Reddy, V.; LeCorre, L.; Nathues, A.; Sierks, H.; Christensen, U.; Hoffmann, M.; Schroeder, S. E.; Vincent, J. B.; McSween, H. Y.; Denevi, B. W.; Li, J.-Y.; Pieters, C. M.; Gaffey, M.; Mittlefehldt, D.; Buratti, B.; Hicks, M.; McCord, T.; Combe, J.-P.; DeSantis, M. C.; Russell, C. T.; Raymond, C. A.; Marques, P. Gutierrez; Maue, T.; Hall, I.

    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.

  9. High-Resolution 3-D Mapping of Soil Texture in Denmark

    DEFF Research Database (Denmark)

    Adhikari, Kabindra; Bou Kheir, Rania; Greve, Mette Balslev

    2013-01-01

    calculated. For example, in the prediction of silt content at 0 to 5 cm depth, factors that registered a higher level of importance included the soil map scored (90%), landscape types (54%), and landuse (27%), while factors with lower scores were direct insolation (17%) and slope aspect (14%). Model...

  10. High-resolution three-dimensional mapping of semiconductor dopant potentials

    DEFF Research Database (Denmark)

    Twitchett, AC; Yates, TJV; Newcomb, SB;

    2007-01-01

    Semiconductor device structures are becoming increasingly three-dimensional at the nanometer scale. A key issue that must be addressed to enable future device development is the three-dimensional mapping of dopant distributions, ideally under "working conditions". Here we demonstrate how a combin...

  11. A high resolution radiation hybrid map of wheat chromosome 4A

    Science.gov (United States)

    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...

  12. High-resolution AUV mapping of the 2015 flows at Axial Seamount, Juan de Fuca Ridge

    Science.gov (United States)

    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

  13. Current techniques for high-resolution mapping of behavioral circuits in Drosophila.

    Science.gov (United States)

    Sivanantharajah, Lovesha; Zhang, Bing

    2015-09-01

    Understanding behavior requires unraveling the mysteries of neurons, glia, and their extensive connectivity. Drosophila has emerged as an excellent organism for studying the neural basis of behavior. This can be largely attributed to the extensive effort of the fly community to develop numerous sophisticated genetic tools for visualizing, mapping, and manipulating behavioral circuits. Here, we attempt to highlight some of the new reagents, techniques and approaches available for dissecting behavioral circuits in Drosophila. We focus on detailing intersectional strategies such as the Flippase-induced intersectional Gal80/Gal4 repression (FINGR), because of the tremendous potential they possess for mapping the minimal number of cells required for a particular behavior. The logic and strategies outlined in this review should have broad applications for other genetic model organisms.

  14. Spotlight-Mode Synthetic Aperture Radar Processing for High-Resolution Lunar Mapping

    Science.gov (United States)

    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.

  15. High Resolution Mapping of Soils and Landforms for the Desert Renewable Energy Conservation Plan (DRECP)

    Science.gov (United States)

    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 mapping, modeling, and evolution of subsurface geomorphology using ground-penetrating radar techniques

    Digital Repository Service at National Institute of Oceanography (India)

    Loveson, V.J.; Gujar, A.R.

    data over an area under study. The gap between sample locations are to be either simulated or manipulated through various statistical methods. Under such conditions, mapping of the area may not yield the reality of the subsurface features in between... continuous profiles along with 200 MHz antenna and measuring wheel. Some times for confirmation, 400 MHz antenna was also used. GPR system was initialized in the field so that the ground reality, related to geo-electrical conditions of the field...

  17. High Resolution Mapping of Interstellar Clouds by Near--IR Scattering

    CERN Document Server

    Padoan, P; Pelkonen, V M; Padoan, Paolo; Juvela, Mika; Pelkonen, Veli-Matti

    2006-01-01

    We discuss the possibility of mapping interstellar clouds at unprecedentedly high spatial resolution by means of near-IR imaging of their scattered light. We calculate the scattering of the interstellar radiation field by a cloud model obtained from the simulation of a supersonic turbulent flow. Synthetic maps of scattered light are computed in the J, H and K bands and are found to allow an accurate estimate of column density, in the range of visual extinction between 1 and 20 magnitudes. We provide a formalism to convert the intensity of scattered light at these near-IR bands into a total gas column density. We also show that this new method of mapping interstellar clouds is within the capability of existing near-IR facilities, which can achieve a spatial resolution of up to ~ 0.1 arcsec. This opens new perspectives in the study of interstellar dust and gas structure on very small scales. The validity of the method has been recently demonstrated by the extraordinary images of the Perseus region obtained by F...

  18. Mapping cardiac fiber orientations from high-resolution DTI to high-frequency 3D ultrasound

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Andrea E Gaughan

    Full Text Available 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.

  20. Time-Evolution and Thermal Mapping of Io's Loki Patera at High Resolution

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Yu Wang

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  4. High-Resolution AUV Mapping Reveals Structural Details of Submarine Inflated Lava Flows

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Michael D. Caggiano

    2016-10-01

    Full Text Available 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

  6. Nationwide high-resolution mapping of hazards in the Philippines (Plinius Medal Lecture)

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  9. A high-resolution map of the chromosomal region surrounding the nude gene

    Energy Technology Data Exchange (ETDEWEB)

    Blackburn, C.C.; Griffith, J.; Morahan, G. [Royal Melbourne Hospital, Victoria (Australia)

    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.

  10. A multi-plate velocity-map imaging design for high-resolution photoelectron spectroscopy

    Science.gov (United States)

    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.

  11. High-Resolution Mapping of Thermal History in Polymer Nanocomposites: Gold Nanorods as Microscale Temperature Sensors.

    Science.gov (United States)

    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.

  12. High-resolution myocardial perfusion mapping in small animals in vivo by spin-labeling gradient-echo imaging.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  14. Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.

    Directory of Open Access Journals (Sweden)

    Rajini R Haraksingh

    Full Text Available Accurate and efficient genome-wide detection of copy number variants (CNVs is essential for understanding human genomic variation, genome-wide CNV association type studies, cytogenetics research and diagnostics, and independent validation of CNVs identified from sequencing based technologies. Numerous, array-based platforms for CNV detection exist utilizing array Comparative Genome Hybridization (aCGH, Single Nucleotide Polymorphism (SNP genotyping or both. We have quantitatively assessed the abilities of twelve leading genome-wide CNV detection platforms to accurately detect Gold Standard sets of CNVs in the genome of HapMap CEU sample NA12878, and found significant differences in performance. The technologies analyzed were the NimbleGen 4.2 M, 2.1 M and 3×720 K Whole Genome and CNV focused arrays, the Agilent 1×1 M CGH and High Resolution and 2×400 K CNV and SNP+CGH arrays, the Illumina Human Omni1Quad array and the Affymetrix SNP 6.0 array. The Gold Standards used were a 1000 Genomes Project sequencing-based set of 3997 validated CNVs and an ultra high-resolution aCGH-based set of 756 validated CNVs. We found that sensitivity, total number, size range and breakpoint resolution of CNV calls were highest for CNV focused arrays. Our results are important for cost effective CNV detection and validation for both basic and clinical applications.

  15. Distinct laterality alterations distinguish mild cognitive impairment and Alzheimer's disease from healthy aging: statistical parametric mapping with high resolution MRI.

    Science.gov (United States)

    Long, Xiaojing; Zhang, Lijuan; Liao, Weiqi; Jiang, Chunxiang; Qiu, Bensheng

    2013-12-01

    Laterality of human brain varies under healthy aging and diseased conditions. The alterations in hemispheric asymmetry may embed distinct biomarkers linked to the disease dynamics. Statistical parametric mapping based on high-resolution magnetic resonance imaging (MRI) and image processing techniques have allowed automated characterization of morphological features across the entire brain. In this study, 149 subjects grouped in healthy young, healthy elderly, mild cognitive impairment (MCI), and Alzheimer's disease (AD) were investigated using multivariate analysis for regional cerebral laterality indexed by surface area, curvature index, cortical thickness, and subjacent white matter volume measured on high-resolution MR images. Asymmetry alteration of MCI and AD were characterized by marked region-specific reduction, while healthy elderly featured a distinct laterality shift in the limbic system in addition to regional asymmetry loss. Lack of the laterality shift in limbic system and early loss of asymmetry in entorhinal cortex may be biomarkers to identify preclinical AD among other dementia. Multivariate analysis of hemispheric asymmetry may provide information helpful for monitoring the disease progress and improving the management of MCI and AD.

  16. High-resolution global maps of 21st-century forest cover change.

    Science.gov (United States)

    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.

  17. A high-resolution land-use map; Nogales, Sonora, Mexico

    Science.gov (United States)

    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.

  18. High-resolution global maps of 21st-century forest cover change

    Science.gov (United States)

    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.

    2013-01-01

    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.

  19. A Flat Universe from High-Resolution Maps of the Cosmic MicrowaveBackground Radiation

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. High-resolution mapping and genetic characterization of the Lazy-2 gravitropic mutant of tomato

    Science.gov (United States)

    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.

  1. High-resolution mapping of linear antibody epitopes using ultrahigh-density peptide microarrays

    DEFF Research Database (Denmark)

    Buus, Søren; Rockberg, Johan; Forsström, Björn

    2012-01-01

    -resolution mapping of linear antibody epitopes, we have used ultrahigh-density peptide microarrays generating several hundred thousand different peptides per array. Using exhaustive length and substitution analysis, we have successfully examined the specificity of a panel of polyclonal antibodies raised against......Antibodies empower numerous important scientific, clinical, diagnostic, and industrial applications. Ideally, the epitope(s) targeted by an antibody should be identified and characterized, thereby establishing antibody reactivity, highlighting possible cross-reactivities, and perhaps even warning...... against unwanted (e.g. autoimmune) reactivities. Antibodies target proteins as either conformational or linear epitopes. The latter are typically probed with peptides, but the cost of peptide screening programs tends to prohibit comprehensive specificity analysis. To perform high-throughput, high...

  2. Object-Based Land-Cover Mapping with High Resolution Aerial Photography at a County Scale in Midwestern USA

    Directory of Open Access Journals (Sweden)

    Xiaoxiao Li

    2014-11-01

    Full Text Available There are growing demands for detailed and accurate land cover maps in land system research and planning. Macro-scale land cover maps normally cannot satisfy the studies that require detailed land cover maps at micro scales. In the meantime, applying conventional pixel-based classification methods in classifying high-resolution aerial imagery is ineffective to develop high accuracy land-cover maps, especially in spectrally heterogeneous and complicated urban areas. Here we present an object-based approach that identifies land-cover types from 1-meter resolution aerial orthophotography and a 5-foot DEM. Our study area is Tippecanoe County in the State of Indiana, USA, which covers about a 1300 km2 land area. We used a countywide aerial photo mosaic and normalized digital elevation model as input datasets in this study. We utilized simple algorithms to minimize computation time while maintaining relatively high accuracy in land cover mapping at a county scale. The aerial photograph was pre-processed using principal component transformation to reduce its spectral dimensionality. Vegetation and non-vegetation were separated via masks determined by the Normalized Difference Vegetation Index. A combination of segmentation algorithms with lower calculation intensity was used to generate image objects that fulfill the characteristics selection requirements. A hierarchical image object network was formed based on the segmentation results and used to assist the image object delineation at different spatial scales. Finally, expert knowledge regarding spectral, contextual, and geometrical aspects was employed in image object identification. The resultant land cover map developed with this object-based image analysis has more information classes and higher accuracy than that derived with pixel-based classification methods.

  3. Drawing a high-resolution functional map of adeno-associated virus capsid by massively parallel sequencing.

    Science.gov (United States)

    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.

  4. New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome

    Directory of Open Access Journals (Sweden)

    Deng Yangyang

    2010-01-01

    Full Text Available Abstract Background Recently, a number of high-resolution genome-wide maps of nucleosome locations in S. cerevisiae have been derived experimentally. However, nucleosome positions are determined in vivo by the combined effects of numerous factors. Consequently, nucleosomes are not simple static units, which may explain the discrepancies in reported nucleosome positions as measured by different experiments. In order to more accurately depict the genome-wide nucleosome distribution, we integrated multiple nucleosomal positioning datasets using a multi-angle analysis strategy. Results To evaluate the contribution of chromatin structure to transcription, we used the vast amount of available nucleosome analyzed data. Analysis of this data allowed for the comprehensive identification of the connections between promoter nucleosome positioning patterns and various transcription-dependent properties. Further, we characterised the function of nucleosome destabilisation in the context of transcription regulation. Our results indicate that genes with similar nucleosome occupancy patterns share general transcription attributes. We identified the local regulatory correlation (LRC regions for two distinct types of nucleosomes and we assessed their regulatory properties. We also estimated the nucleosome reproducibility and measurement accuracy for high-confidence transcripts. We found that by maintaining a distance of ~13 bp between the upstream border of the +1 nucleosome and the transcription start sites (TSSs, the stable +1 nucleosome may form a barrier against the accessibility of the TSS and shape an optimum chromatin conformation for gene regulation. An in-depth analysis of nucleosome positioning in normally growing and heat shock cells suggested that the extent and patterns of nucleosome sliding are associated with gene activation. Conclusions Our results, which combine different types of data, suggest that cross-platform information, including

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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 (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, the resulting fine resolution UTC map will be

  7. High-Resolution Air Pollution Mapping with Google Street View Cars: Exploiting Big Data.

    Science.gov (United States)

    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.

  8. 3-Dimentional Mapping Coastal Zone using High Resolution Satellite Stereo Imageries

    Science.gov (United States)

    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.

  9. High-resolution radiation mapping to investigate FDNPP derived contaminant migration.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  11. High-resolution mapping of the gene for cystinosis, using combined biochemical and linkage analysis.

    Science.gov (United States)

    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.

  12. Mapping of Agricultural Crops from Single High-Resolution Multispectral Images—Data-Driven Smoothing vs. Parcel-Based Smoothing

    Directory of Open Access Journals (Sweden)

    Asli Ozdarici-Ok

    2015-05-01

    Full Text Available Mapping agricultural crops is an important application of remote sensing. However, in many cases it is based either on hyperspectral imagery or on multitemporal coverage, both of which are difficult to scale up to large-scale deployment at high spatial resolution. In the present paper, we evaluate the possibility of crop classification based on single images from very high-resolution (VHR satellite sensors. The main objective of this work is to expose performance difference between state-of-the-art parcel-based smoothing and purely data-driven conditional random field (CRF smoothing, which is yet unknown. To fulfill this objective, we perform extensive tests with four different classification methods (Support Vector Machines, Random Forest, Gaussian Mixtures, and Maximum Likelihood to compute the pixel-wise data term; and we also test two different definitions of the pairwise smoothness term. We have performed a detailed evaluation on different multispectral VHR images (Ikonos, QuickBird, Kompsat-2. The main finding of this study is that pairwise CRF smoothing comes close to the state-of-the-art parcel-based method that requires parcel boundaries (average difference ≈ 2.5%. Our results indicate that a single multispectral (R, G, B, NIR image is enough to reach satisfactory classification accuracy for six crop classes (corn, pasture, rice, sugar beet, wheat, and tomato in Mediterranean climate. Overall, it appears that crop mapping using only one-shot VHR imagery taken at the right time may be a viable alternative, especially since high-resolution multitemporal or hyperspectral coverage as well as parcel boundaries are in practice often not available.

  13. Nucleosome switches.

    Science.gov (United States)

    Schwab, David J; Bruinsma, Robijn F; Rudnick, Joseph; Widom, Jonathan

    2008-06-06

    We present a statistical-mechanical model for the positioning of nucleosomes along genomic DNA molecules as a function of the strength of the binding potential and the chemical potential of the nucleosomes. We show that a significant section of the DNA is composed of two-level nucleosome switching regions where the nucleosome distribution undergoes a localized, first-order transition. The location of the nucleosome switches shows a strong correlation with the location of gene-regulation regions.

  14. OnEarth: An Open Source Solution for Efficiently Serving High-Resolution Mapped Image Products

    Science.gov (United States)

    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.

  15. Perspectives on heterococcolith geochemical proxies based on high-resolution X-ray fluorescence mapping.

    Science.gov (United States)

    Suchéras-Marx, B; Giraud, F; Simionovici, A; Daniel, I; Tucoulou, R

    2016-07-01

    Heterococcoliths are micron-scale calcite platelets produced by coccolithophores. They have been the most abundant and continuous fossil record over the last 215 million years (Myr), offering great potential for geochemical studies, although the heterococcolith fossil record remains underutilised in this domain. We have mapped heterococcoliths' composition using X-ray fluorescence (XRF) with a 100-nm resolution beam to decipher element distributions in heterococcoliths and to investigate the potential development of geochemical proxies for palaeoceanography. The study presents two Middle Jurassic Watznaueria britannica heterococcoliths from Cabo Mondego, Portugal. XRF analysis was performed with a 17 keV incident energy beam at the European Synchrotron Radiation Facility ID22NI beamline to study elements from Sr down to S. Ca, Sr and Mn are distributed following the heterococcolith crystalline arrangement. Cl, Br and S display an homogeneous distribution, whereas K, Fe, Cu, Zn and Rb are concentrated at the edges and in the central area of the heterococcoliths. Distributions of K, Fe, Ti, Fe, Cu, Zn, Rb and to a lesser extent V and Cr are highly influenced by clay contamination and peripheral diagenetic overgrowth. Mn is related to diagenetic Mn-rich CaCO3 overgrowth on top of or between heterococcoliths shields. Cl and Br are likely to be present in heterococcoliths inside interstitial nano-domains. We assume that the cytoplasm [Cl(-) ] and [Br(-) ] are mediated and constant during heterococcolithogenesis. Assuming a linear correlation between cytoplasm [Cl(-) ] and sea water [Cl(-) ], heterococcolith Cl may have potential as a salinity proxy. As S is incorporated into heterococcoliths by sulphated polysaccharides, our study suggests a role for such polysaccharides in heterococcolithogenesis for at least 170 Myr. The low Sr/Ca in the W. britannica specimens studied here may either highlight an unusual cellular physiology of Mesozoic coccolithophores or result

  16. Mars MOURA magnetometer demonstration for high-resolution mapping on terrestrial analogues

    Science.gov (United States)

    Díaz-Michelena, Marina; Kilian, Rolf; Sanz, Ruy; Rios, Francisco; Baeza, Oscar

    2016-05-01

    Satellite-based magnetic measurements of Mars indicate complex and very strong magnetic anomalies, which led to an intensive and long-lasting discussion about their possible origin. To make some progress in the investigation of the origin of these anomalies the MOURA vector magnetometer was developed for in situ measurements on Mars. In this work we propose the utilisation of such an instrument for future planetary on-ground surveys. The proof of its suitability is seen through testing it on various terrestrial analogues characterised by the distinct magnetic anomalies of their basement rocks: (1) a magnetite body of EL Laco (up to +110 000 nT) and its transition to surrounding andesites ( Pali Aike volcanic field, in southern Chile, was characterised by very strong magnetic anomalies along the crater rim (up to +12 000 nT), controlled by the amount of single domain magnetites in the ground mass of the basalts. Due to their strong remanent signature, palaeo-declinations of the lavas and reorientations of collapsed blocks could be constrained by the vector data. (3) The Monturaqui meteorite crater (350 m diameter), in northern Chile, shows significant variations of its anomalies (from -2000 to > +6000 nT) in restricted areas of several square metres along its crater rim related to unexposed iron-bearing fragments of the impactor while its granitic and ignimbritic target rocks exhibit only very weak anomalies. (4) An area with several amphibolitic dykes, which cross-cut a Cretaceous granitoid in the southernmost Andes, where a decimetre-scale mapping was performed. In this case, pyrrhotite is the only magnetic carrier. It was formed during hydrothermal processes within the dykes. Very low (+40 to +120 nT) positive magnetic anomalies clearly depict the amount of 1-4 vol % pyrrhotite in these dykes, which is important as a mineralogical indicator as well as to detect associated gold and copper enrichment.

  17. High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon.

    Science.gov (United States)

    Reddy, Umesh K; Nimmakayala, Padma; Levi, Amnon; Abburi, Venkata Lakshmi; Saminathan, Thangasamy; Tomason, Yan R; Vajja, Gopinath; Reddy, Rishi; Abburi, Lavanya; Wehner, Todd C; Ronin, Yefim; Karol, Abraham

    2014-09-15

    We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Collinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD), and selective sweep for wild, semi-wild, and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1563 SNPs obtained after LD pruning with minor allele frequency of 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild, and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima's D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication. Copyright © 2014 Reddy et al.

  18. High Resolution Near-Infrared Survey of the Pipe Nebula I: A Deep Infrared Extinction Map of Barnard 59

    CERN Document Server

    Román-Zúñiga, Carlos G; Alves, João F

    2009-01-01

    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, that 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$_3$ pointed observations towards the high column density center of the core appear to show that the core is still thermally dominated, with sub-sonic non-thermal motions. The stars in the cluster could be providing feedback to support the core against collapse, but the relat...

  19. Joint Processing of Uav Imagery and Terrestrial Mobile Mapping System Data for Very High Resolution City Modeling

    Science.gov (United States)

    Gruen, A.; Huang, X.; Qin, R.; Du, T.; Fang, W.; Boavida, J.; Oliveira, A.

    2013-08-01

    Both unmanned aerial vehicle (UAV) technology and Mobile Mapping Systems (MMS) are important techniques for surveying and mapping. In recent years, the UAV technology has seen tremendous interest, both in the mapping community and in many other fields of application. Carrying off-the shelf digital cameras, the UAV can collect high quality aerial optical images for city modeling using photogrammetric techniques. In addition, a MMS can acquire high density point clouds of ground objects along the roads. The UAV, if operated in an aerial mode, has difficulties in acquiring information of ground objects under the trees and along façades of buildings. On the contrary, the MMS collects accurate point clouds of objects from the ground, together with stereo images, but it suffers from system errors due to loss of GPS signals, and also lacks the information of the roofs. Therefore, both technologies are complementary. This paper focuses on the integration of UAV images, MMS point cloud data and terrestrial images to build very high resolution 3D city models. The work we will show is a practical modeling project of the National University of Singapore (NUS) campus, which includes buildings, some of them very high, roads and other man-made objects, dense tropical vegetation and DTM. This is an intermediate report. We present work in progress.

  20. Cold-seep habitat mapping: high-resolution spatial characterization of the Blake Ridge Diapir seep field

    Science.gov (United States)

    Wagner, Jamie K.S.; McEntee, Molly H.; Brothers, Laura L.; German, Christopher R.; Kaiser, Carl L.; Yoerger, Dana R.; Van Dover, Cindy Lee

    2013-01-01

    Relationships among seep community biomass, diversity, and physiographic controls such as underlying geology are not well understood. Previous efforts to constrain these relationships at the Blake Ridge Diapir were limited to observations from piloted deep-submergence vehicles. In August 2012, the autonomous underwater vehicle (AUV) Sentry collected geophysical and photographic data over a 0.131 km2 area at the Blake Ridge Diapir seeps. A nested survey approach was used that began with a regional or reconnaissance-style survey using sub-bottom mapping systems to locate and identify seeps and underlying conduits. This survey was followed by AUV-mounted sidescan sonar and multibeam echosounder systems mapping on a mesoscale to characterize the seabed physiography. At the most detailed survey level, digital photographic imaging was used to resolve sub-meter characteristics of the biology. Four pockmarks (25–70 m diameter) were documented, each supporting chemosynthetic communities. Concentric zonation of mussels and clams suggests the influence of chemical gradients on megafaunal distribution. Data collection and analytical techniques used here yield high-resolution habitat maps that can serve as baselines to constrain temporal evolution of seafloor seeps, and to inform ecological niche modeling and resource management.

  1. SAETTA: high resolution 3D mapping of the lightning activity around Corsica Island

    Science.gov (United States)

    Coquillat, Sylvain; Defer, Eric; Lambert, Dominique; Pinty, Jean-Pierre; Pont, Véronique; Prieur, Serge

    2017-04-01

    In the frame of the French atmospheric observatory CORSiCA (http://www.obs-mip.fr/corsica), a total lightning activity detection system called SAETTA (Suivi de l'Activité Electrique Tridimensionnelle Totale de l'Atmosphère) has been deployed in Corsica Island in order to strengthen the potential of observation of convective events causing heavy rainfall and flash floods in the West Mediterranean basin. SAETTA is a network of 12 LMA stations (Lightning Mapping Array) developed by New Mexico Tech (USA). The instrument allows observing lightning flashes in 3D and real time, at high temporal (80 µs) and spatial resolutions. It detects the radiations emitted by cloud discharges in the 60-66 MHz band, in a radius of about 350 km from the centre of the network, in passive mode and standalone (solar panel and batteries). Initially deployed in May 2014, SAETTA operated from July 13 to October 20 in 2014 and from April 19 to December 1st in 2015. It is now in permanent operation since 16 April 2016. Many high quality observations have been performed so far that provide an accurate location in space and time of the convective events. They also bring interesting dynamical and microphysical features of those events. For example the intensity of the convective surges, the transport of charged ice particles in the stratiform area of the thunderclouds can be deduced from SAETTA observations. Specific events have also been detected as well: bolts-from-the-blue, inter cloud discharges, high level discharges in convective but also in stratiform areas, inverted dipoles. The specific lightning patterns of 2015 illustrate the complex influence of the relief, probably via slope and valley winds over Corsica and via induced lee-side convergences over the sea. SAETTA is expected to operate for at least a decade over Corsica so it will participate to the calibration/validation of upcoming lightning detectors from space such as MTG-LI. It will also be a key instrument during the field

  2. Mapping Sub-Saharan African Agriculture in High-Resolution Satellite Imagery with Computer Vision & Machine Learning

    Science.gov (United States)

    Debats, Stephanie Renee

    Smallholder farms dominate in many parts of the world, including Sub-Saharan Africa. These systems are characterized by small, heterogeneous, and often indistinct field patterns, requiring a specialized methodology to map agricultural landcover. In this thesis, we developed a benchmark labeled data set of high-resolution satellite imagery of agricultural fields in South Africa. We presented a new approach to mapping agricultural fields, based on efficient extraction of a vast set of simple, highly correlated, and interdependent features, followed by a random forest classifier. The algorithm achieved similar high performance across agricultural types, including spectrally indistinct smallholder fields, and demonstrated the ability to generalize across large geographic areas. In sensitivity analyses, we determined multi-temporal images provided greater performance gains than the addition of multi-spectral bands. We also demonstrated how active learning can be incorporated in the algorithm to create smaller, more efficient training data sets, which reduced computational resources, minimized the need for humans to hand-label data, and boosted performance. We designed a patch-based uncertainty metric to drive the active learning framework, based on the regular grid of a crowdsourcing platform, and demonstrated how subject matter experts can be replaced with fleets of crowdsourcing workers. Our active learning algorithm achieved similar performance as an algorithm trained with randomly selected data, but with 62% less data samples. This thesis furthers the goal of providing accurate agricultural landcover maps, at a scale that is relevant for the dominant smallholder class. Accurate maps are crucial for monitoring and promoting agricultural production. Furthermore, improved agricultural landcover maps will aid a host of other applications, including landcover change assessments, cadastral surveys to strengthen smallholder land rights, and constraints for crop modeling

  3. Machine vision approach to auto-generation of high resolution, continental-scale geomorphometric map from DEM

    Science.gov (United States)

    Jasiewicz, J.; Stepinski, T. F.

    2012-04-01

    -generation of GM from this high resolution, continental size raster having 168000x104000 cells took 60 hours on a single processor computer. Future applications of such GM include coupling it with a search tool capable of querying the continental-scale GM in order to identify all instances of a given type of local landscape.

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

    Directory of Open Access Journals (Sweden)

    Guyon Richard

    2012-06-01

    Full Text Available Abstract 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

  5. High-resolution mapping of zym, a recessive gene for Zucchini yellow mosaic virus resistance in cucumber.

    Science.gov (United States)

    Amano, Masashi; Mochizuki, Akira; Kawagoe, Yumi; Iwahori, Keisuke; Niwa, Kaori; Svoboda, Jiri; Maeda, Takanori; Imura, Yoshiyuki

    2013-12-01

    Using a high-resolution mapping approach, we identified a candidate gene for ZYMV resistance in cucumber. Our findings should assist the development of high-versatility molecular markers for MAS for ZYMV resistance. Zucchini yellow mosaic virus (ZYMV) causes significant disease, which leads to fruit yield loss in cucurbit crops. Since ZYMV resistance is often inherited recessively in cucumber, marker-assisted selection (MAS) is a useful tool for the development of resistant cucumber cultivars. Using 128 families of an F2:3 population derived from a cross between susceptible 'CS-PMR1' and resistant 'A192-18' cucumber inbred lines, we confirmed that ZYMV resistance is conferred by a single recessive locus: zym (A192-18) . We constructed a cucumber genetic linkage map that included 125 simple sequence repeat (SSR) markers segregating into 7 linkage groups (chromosomes). The zym (A192-18) locus was mapped to chromosome 6, at genetic distances of 0.9 and 1.3 cM from two closely linked SSR markers. For high-resolution genetic mapping, we identified new molecular markers cosegregating with the zym (A192-18) locus; using cucumber genomic and molecular marker resources and screening an F2 population of 2,429 plants, we narrowed down the zym (A192-18) locus to a <50-kb genomic region flanked by two SSR markers, which included six candidate genes. Sequence analysis of the candidate genes' coding regions revealed that the vacuolar protein sorting-associated protein 4-like (VPS4-like) gene had two SNPs between the parental lines. Based on SNPs of the VPS-4-like gene, we developed zym (A192-18) -linked DNA markers and found that genotypes associated with these markers were correlated with the ZYMV resistance phenotype in 48 cucumber inbred lines. According to our data, the gene encoding VPS4-like protein is a candidate for the zym (A192-18) locus. These results may be valuable for MAS for ZYMV resistance in cucumber.

  6. Ecosystem services - from assessements of estimations to quantitative, validated, high-resolution, continental-scale mapping via airborne LIDAR

    Science.gov (United States)

    Zlinszky, András; Pfeifer, Norbert

    2016-04-01

    service potential" which is the ability of the local ecosystem to deliver various functions (water retention, carbon storage etc.), but can't quantify how much of these are actually used by humans or what the estimated monetary value is. Due to its ability to measure both terrain relief and vegetation structure in high resolution, airborne LIDAR supports direct quantification of the properties of an ecosystem that lead to it delivering a given service (such as biomass, water retention, micro-climate regulation or habitat diversity). In addition, its high resolution allows direct calibration with field measurements: routine harvesting-based ecological measurements, local biodiversity indicator surveys or microclimate recordings all take place at the human scale and can be directly linked to the local value of LIDAR-based indicators at meter resolution. Therefore, if some field measurements with standard ecological methods are performed on site, the accuracy of LIDAR-based ecosystem service indicators can be rigorously validated. With this conceptual and technical approach high resolution ecosystem service assessments can be made with well established credibility. These would consolidate the concept of ecosystem services and support both scientific research and evidence-based environmental policy at local and - as data coverage is continually increasing - continental scale.

  7. High-resolution area-wide sea-floor mapping: The paleo Elbe valley (S North Sea) revisited

    Science.gov (United States)

    Papenmeier, Svenja; Hass, H. Christian

    2014-05-01

    The North Sea Basin is shaped by multiple glacial advances and retreats that left complex sequences of glacio-fluvial and sub-glacial deposits, cut by sub-glacial tunnel valleys. Today, the submerged valley of the Elbe forms one of the most prominent structures of the southern North Sea. Flanked by huge moraine deposits of older glacials, the valley developed to its present form during the Weichselian sea-level lowstand (-130 m below present). Melt waters that discharged in north-westerly directions along the Scandinavian Ice Sheet fed the paleo Elbe at that time. During the Holocene the valley drowned in the rising sea. Here we present an area-wide high-resolution map of the seafloor and high-resolution shallow seismic data covering 1,600 km2 of the paleo Elbe valley (PEV) including its eastern levee. The data allow to shed new light on the PEV development including the historical process of sedimentary infill with the successive Holocene sea level rise in detail. Shallow seismic data with transect distances of 400 m and several cross sections allow 3-D visualization. The eastern flank of the valley is characterized by a relatively steep slope with one or more terraces. At its levee a significant sediment change is present on the modern sea floor, representing moraine and marine deposits. High resolution sidescan sonar data of this area show a much higher heterogeneity and complexity in sediment and habitat distribution as assumed before. Holocene marine sediments form a patchy and thin drape east of the valley floor. The western slip-off slope of the valley slope is much smoother than the eastern undercut slope. As yet, significant sedimentological changes at the present seafloor are not known for the western side of the PEV. Shallow seismic data show the base of the PEV. There are conspicuous internal seismic reflectors above the base, inclined in northeastern direction. They indicate a sedimentary infill of the valley from the southwest when the southern part

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

    Science.gov (United States)

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

    2010-05-01

    Keywords : land cover mapping, very high resolution, remote sensing processing techniques, object oriented approach, distributed hydrological model, peri-urban area Urbanization and other modifications of land use affect the hydrological cycle of suburban catchments. In order to quantify these impacts, the AVuPUR project (Assessing the Vulnerability of Peri-Urban Rivers) is currently developing a distributed hydrological model that includes anthropogenic features. The case study is the Yzeron catchment (150 km²), located close to Lyon city, France. This catchment experiences a growing of urbanization and a modification of traditional land use since the middle of the 20th century, resulting in an increase of flooding, water pollution and river banks erosion. This contribution discusses the potentials of automated data processing techniques on three different VHR images, in order to produce appropriate and detailed land cover data for the models. Of particular interest is the identification of impermeable surfaces (buildings, roads, and parking places) and permeable surfaces (forest areas, agricultural fields, gardens, trees…) within the catchment, because their infiltration capacity and their impact on runoff generation are different. Three aerial and spatial images were acquired: (1) BD Ortho IGN aerial images, 0.50 m resolution, visible bands, may 5th 2008; (2) QuickBird satellite image, 2.44 m resolution, visible and near-infrared bands, august 29th 2008; (3) Spot satellite image, 2.50 m resolution, visible and near-infrared bands, September 22nd 2008. From these images, we developed three image processing methods: (1) a pixel-based method associated to a segmentation using Matlab®, (2) a pixel-based method using ENVI®, (3) an object-based classification using Definiens®. We extracted six land cover types from the BD Ortho IGN (visible bands) and height classes from the satellite images (visible and near infrared bands). The three classified images are

  9. High-Resolution Multibeam, Sidescan, and Subbottom Surveys in and Around Monterey Canyon Using the MBARI Mapping AUV

    Science.gov (United States)

    Caress, D. W.; Thomas, H.; McEwen, R.; Henthorn, R.; Kirkwood, W. J.; Thompson, D.; Paull, C. K.; McGill, P.

    2005-12-01

    During 2004 and 2005, MBARI has conducted several high-resolution bathymetry, sidescan, and subbottom profiler surveys in and around Monterey Canyon, Monterey Bay, California. These surveys were conducted using the new MBARI Mapping Autonomous Underwater Vehicle (AUV). This torpedo-shaped, 6000 m deep rated vehicle is equipped with a 200 kHz multibeam sonar, 110 kHz and 410 kHz chirp sidescan sonar, and a 2-16 kHz sweep subbottom profiler. The sonar package can also be mounted on ROV Ventana, allowing near-bottom bathymetric surveys of sites where extreme topography (e.g. the Monterey Canyon axis) preclude safe autonomous operation. The Mapping AUV is being used to monitor sediment transport through Monterey Canyon by conducting repeated high-resolution bathymetric surveys in the upper canyon. Upper Monterey Canyon is known to have frequent sediment transport events. Four sites have been selected with canyon axis depths of 300 m, 520 m, 1000 m, and 1400 m, respectively. Each survey nominally covers a 600 m by 600 m area with a 35 m line spacing and a 20 m altitude. We are achieving sub-meter lateral resolution and a vertical precision of 0.3 m. The combined bathymetry and backscatter successfully image fine scale channel features, including bedforms, small scarps and plunge pools, and undercutting of the inner canyon walls. All four sites have been surveyed at least once, and we will revisit these sites three times annually for the foreseeable future. We have also collected in excess of 170 km of subbottom profiles around and across the upper canyon. The subbottom profiler successfully images sediment structure to subsurface depths of as much as 50 m. These profiles demonstrate that the upper canyon walls are draped with sediment rather than exposing an erosional surface. Another Mapping AUV survey target is Smooth Ridge, located immediately north of Monterey Canyon and west of Soquel canyon. The upper reaches of Smooth Ridge are connected to the shelf across a

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

    Science.gov (United States)

    Xia, Ting; Kustas, William P.; Anderson, Martha C.; Alfieri, Joseph G.; Gao, Feng; McKee, Lynn; Prueger, John H.; Geli, Hatim M. E.; Neale, Christopher M. U.; Sanchez, Luis; Mar Alsina, Maria; Wang, Zhongjing

    2016-04-01

    Thermal and multispectral remote sensing data from low-altitude aircraft can provide high spatial resolution necessary for sub-field (≤ 10 m) and plant canopy (≤ 1 m) scale evapotranspiration (ET) monitoring. In this study, high-resolution (sub-meter-scale) thermal infrared and multispectral shortwave data from aircraft are used to map ET over vineyards in central California with the two-source energy balance (TSEB) model and with a simple model having operational immediate capabilities called DATTUTDUT (Deriving Atmosphere Turbulent Transport Useful To Dummies Using Temperature). The latter 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 5 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 measurements of sensible (H) and latent heat (LE) flux 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 2 of the 5 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

  11. Evaluation of Surface Energy Balance models for mapping evapotranspiration using very high resolution airborne remote sensing data

    Science.gov (United States)

    Paul, George

    Agriculture is the largest (90%) consumer of all fresh water in the world. The consumptive use of water by vegetation represented by the process evapotranspiration (ET) has a vital role in the dynamics of water, carbon and energy fluxes of the biosphere. Consequently, mapping ET is essential for making water a sustainable resource and also for monitoring ecosystem response to water stress and changing climate. Over the past three decades, numerous thermal remote sensing based ET mapping algorithms were developed and these have brought a significant theoretical and technical advancement in the spatial modeling of ET. Though these algorithms provided a robust, economical, and efficient tool for ET estimations at field and regional scales, yet the uncertainties in flux estimations were large, making evaluation a difficult task. The main objective of this study was to evaluate and improve the performance of widely used remote sensing based energy balance models, namely: the Surface Energy Balance Algorithm for Land (SEBAL), Mapping Evapotranspiration at high Resolution and with Internalized Calibration (METRIC), and Surface Energy Balance System (SEBS). Data used in this study was collected as part of a multi-disciplinary and multi-institutional field campaign BEAREX (Bushland Evapotranspiration and Agricultural Remote Sensing Experiment) that was conducted during 2007 and 2008 summer cropping seasons at the USDA-ARS Conservation and Production Research Laboratory (CPRL) in Bushland, Texas. Seventeen high resolution remote sensing images taken from multispectral sensors onboard aircraft and field measurements of the agro-meteorological variables from the campaign were used for model evaluation and improvement. Overall relative error measured in terms of mean absolute percent difference (MAPD) for instantaneous ET (mm h -1) were 22.7%, 23.2%, and 12.6% for SEBAL, METRIC, and SEBS, respectively. SEBAL and METRIC performances for irrigated fields representing higher ET

  12. High-resolution Digital Mapping of Historical Lava Flows as a Test-bed for Lava Flow Models

    Science.gov (United States)

    Pyle, D. M.; Parks, M.; Nomikou, P.; Mather, T. A.; Simou, E.; Kalnins, L. M.; Paulatto, M.; Watts, A. B.

    2013-12-01

    Quantitative analysis of high-resolution lava flow morphology can improve our understanding of past effusive eruptions by providing insight into eruptive processes and the rheological properties of erupted magmas. We report the results of an ongoing investigation into the young dacite lava flows of the Kameni islands, Santorini volcano, Greece, which were emplaced during both subaerial and shallow submarine eruptions over the past 3000 years. Historical eruptions of the Kameni islands since 1866 have been very carefully documented in contemporaneous scientific reports. Eruptions since 1573 appear to be time-predictable, with a close relationship between eruption length, the size of extruded lava domes, and the time elapsed since the previous eruption. A new NERC - Airborne Survey and Research Facility LiDAR survey of the Kameni islands was completed in May 2012, using a Leica ALS50 Airborne Laser Scanner mounted on a Dornier 228 aircraft. The topographic surface was mapped at an average point density of 2.1 points per square metre, and covers the entire extent of the youngest subaerial lava flow fields on Santorini. A 2-m DEM derived from the 2012 LiDAR dataset was merged with a 5-m resolution bathymetric grid, based on multibeam surveys carried out by the Hellenic Centre for Marine Research, during cruises in 2001 and 2006, using a SEABEAM 2120 hull-mounted swath system. The resultant grid provides the first high resolution map of both subaerial and submarine historic lava flows emplaced in the centre of the Santorini caldera, and includes several previously unidentified submarine flows and cones. Attribute maps were used to delineate and identify discrete lava flows both onshore and offshore; and morphometric profiles were used to compute accurate volumetric estimates for each of the historic flows, and to determine bulk rheological properties of the lavas, assuming a Bingham rheology. This ongoing work will improve our analysis of the relationship between

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

    Science.gov (United States)

    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

  14. High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H.

    Science.gov (United States)

    Shahinnia, Fahimeh; Druka, Arnis; Franckowiak, Jerome; Morgante, Michele; Waugh, Robbie; Stein, Nils

    2012-02-01

    Spike density in barley is under the control of several major genes, as documented previously by genetic analysis of a number of morphological mutants. One such class of mutants affects the rachis internode length leading to dense or compact spikes and the underlying genes were designated dense spike (dsp). We previously delimited two introgressed genomic segments on chromosome 3H (21 SNP loci, 35.5 cM) and 7H (17 SNP loci, 20.34 cM) in BW265, a BC(7)F(3) nearly isogenic line (NIL) of cv. Bowman as potentially containing the dense spike mutant locus dsp.ar, by genotyping 1,536 single nucleotide polymorphism (SNP) markers in both BW265 and its recurrent parent. Here, the gene was allocated by high-resolution bi-parental mapping to a 0.37 cM interval between markers SC57808 (Hv_SPL14)-CAPSK06413 residing on the short and long arm at the genetic centromere of chromosome 7H, respectively. This region putatively contains more than 800 genes as deduced by comparison with the collinear regions of barley, rice, sorghum and Brachypodium, Classical map-based isolation of the gene dsp.ar thus will be complicated due to the infavorable relationship of genetic to physical distances at the target locus.

  15. Exploring the Potential of High Resolution Remote Sensing Data for Mapping Vegetation and the Age Groups of Oil Palm Plantation

    Science.gov (United States)

    Kamiran, N.; Sarker, M. L. R.

    2014-02-01

    The land use/land cover transformation in Malaysia is enormous due to palm oil plantation which has provided huge economical benefits but also created a huge concern for carbon emission and biodiversity. Accurate information about oil palm plantation and the age of plantation is important for a sustainable production, estimation of carbon storage capacity, biodiversity and the climate model. However, the problem is that this information cannot be extracted easily due to the spectral signature for forest and age group of palm oil plantations is similar. Therefore, a noble approach "multi-scale and multi-texture algorithms" was used for mapping vegetation and different age groups of palm oil plantation using a high resolution panchromatic image (WorldView-1) considering the fact that pan imagery has a potential for more detailed and accurate mapping with an effective image processing technique. Seven texture algorithms of second-order Grey Level Co-occurrence Matrix (GLCM) with different scales (from 3×3 to 39×39) were used for texture generation. All texture parameters were classified step by step using a robust classifier "Artificial Neural Network (ANN)". Results indicate that single spectral band was unable to provide good result (overall accuracy = 34.92%), while higher overall classification accuracies (73.48%, 84.76% and 93.18%) were obtained when textural information from multi-scale and multi-texture approach were used in the classification algorithm.

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

    Energy Technology Data Exchange (ETDEWEB)

    Weinhardt, L.; Fuchs, O.; Blum, M.; B& #228; r, 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.

  17. A multi-method approach for benthic habitat mapping of shallow coastal areas with high-resolution multibeam data

    Science.gov (United States)

    Micallef, Aaron; Le Bas, Timothy P.; Huvenne, Veerle A. I.; Blondel, Philippe; Hühnerbach, Veit; Deidun, Alan

    2012-05-01

    The coastal waters of the Maltese Islands, central Mediterranean Sea, sustain a diversity of marine habitats and support a wide range of human activities. The islands' shallow waters are characterised by a paucity of hydrographic and marine geo-environmental data, which is problematic in view of the requirements of the Maltese Islands to assess the state of their coastal waters by 2012 as part of the EU Marine Strategy Directive. Multibeam echosounder (MBES) systems are today recognised as one of the most effective tools to map the seafloor, although the quantitative characterisation of MBES data for seafloor and habitat mapping is still an underdeveloped field. The purpose of this study is to outline a semi-automated, Geographic Information System-based methodology to map the distribution of habitats in shallow coastal waters using high-resolution MBES data. What distinguishes our methodology from those proposed in previous studies is the combination of a suite of geomorphometric and textural analytical techniques to map specific types of seafloor morphologies and compositions; the selection of the techniques is based on identifying which geophysical parameter would be influenced by the seabed type under consideration. We tested our approach in a 28 km2 area of Maltese coastal waters. Three data sets were collected from this study area: (i) MBES bathymetry and backscatter data; (ii) Remotely Operated Vehicle imagery and (iii) photographs and sediment samples from dive surveys. The seabed was classified into five elementary morphological zones and features - flat and sloping zones, crests, depressions and breaks of slope - using morphometric derivatives, the Bathymetric Position Index and geomorphometric mapping. Segmentation of the study area into seagrass-covered and unvegetated seafloor was based on roughness estimation. Further subdivision of these classes into the four predominant types of composition - medium sand, maërl associated with sand and gravel

  18. Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.

    Directory of Open Access Journals (Sweden)

    Amy Sebeson

    Full Text Available The binding sequence for any transcription factor can be found millions of times within a genome, yet only a small fraction of these sequences encode functional transcription factor binding sites. One of the reasons for this dichotomy is that many other factors, such as nucleosomes, compete for binding. To study how the competition between nucleosomes and transcription factors helps determine a functional transcription factor site from a predicted transcription factor site, we compared experimentally-generated in vitro nucleosome occupancy with in vivo nucleosome occupancy and transcription factor binding in murine embryonic stem cells. Using a solution hybridization enrichment technique, we generated a high-resolution nucleosome map from targeted regions of the genome containing predicted sites and functional sites of Oct4/Sox2 regulation. We found that at Pax6 and Nes, which are bivalently poised in stem cells, functional Oct4 and Sox2 sites show high amounts of in vivo nucleosome displacement compared to in vitro. Oct4 and Sox2, which are active, show no significant displacement of in vivo nucleosomes at functional sites, similar to nonfunctional Oct4/Sox2 binding. This study highlights a complex interplay between Oct4 and Sox2 transcription factors and nucleosomes among different target genes, which may result in distinct patterns of stem cell gene regulation.

  19. Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.

    Science.gov (United States)

    Sebeson, Amy; Xi, Liqun; Zhang, Quanwei; Sigmund, Audrey; Wang, Ji-Ping; Widom, Jonathan; Wang, Xiaozhong

    2015-01-01

    The binding sequence for any transcription factor can be found millions of times within a genome, yet only a small fraction of these sequences encode functional transcription factor binding sites. One of the reasons for this dichotomy is that many other factors, such as nucleosomes, compete for binding. To study how the competition between nucleosomes and transcription factors helps determine a functional transcription factor site from a predicted transcription factor site, we compared experimentally-generated in vitro nucleosome occupancy with in vivo nucleosome occupancy and transcription factor binding in murine embryonic stem cells. Using a solution hybridization enrichment technique, we generated a high-resolution nucleosome map from targeted regions of the genome containing predicted sites and functional sites of Oct4/Sox2 regulation. We found that at Pax6 and Nes, which are bivalently poised in stem cells, functional Oct4 and Sox2 sites show high amounts of in vivo nucleosome displacement compared to in vitro. Oct4 and Sox2, which are active, show no significant displacement of in vivo nucleosomes at functional sites, similar to nonfunctional Oct4/Sox2 binding. This study highlights a complex interplay between Oct4 and Sox2 transcription factors and nucleosomes among different target genes, which may result in distinct patterns of stem cell gene regulation.

  20. A New Method for High-Resolution Apparent Thermal Inertia Mapping of Mars: Application to Valles Marineris

    Science.gov (United States)

    Kubiak, M.; Mège, D.; Gurgurewicz, J.; Ciążela, J.

    2014-12-01

    The minerals absorb and reflect thermal infrared (TIR) light of the different wavelengths depending on their composition and structure. Thus, every rock absorbs and reflects different wavelengths in TIR and has its own spectral signature. The TIR images are used in the thermal inertia mapping and in its approximation called apparent thermal inertia (ATI). We present the methodology and the high-resolution apparent thermal inertia maps for selected parts of Valles Marineris (Mars). ATI was calculated from surface albedo (A) and diurnal temperature difference (∆T) following the equation: ATI = (1 - A) / ∆T. Albedo was computed by dividing reflected radiation (IR) by incident radiation (II): A = IR / II. After introducing: II = F • cosIA, where F stands for solar constant and IA for incident angle (°), it develops to: A = IR / (F • cosIA). This formula allows us to calculate A on a horizontal surface. Calculating A on an inclined surface requires corrections of IA against relief characteristics (slopes, aspects): IAC = (IA - arctan(tans • cos(e + t • 15° - 180°))), where s is slope (°), e - aspect (°) and t - local solar time (h). A correction was made also for ∆T. The calibration process was more complex because it involved changes in incident radiation (II) over a given time interval (∆T = T13:00 - T6:00). II is a function of: Martian tilt, eccentricity, perihelium longitude, solar longitude (Ls, in °), latitude (φ, in °), local solar time and relief characteristics. Total II, integrated over the time interval, can be calculated following the equation [1]. The results were compared to the existing thermal inertia maps of Mars.

  1. Flood hazard mapping by integrating airborne laser scanning data, high resolution images and large scale maps: a case study

    OpenAIRE

    Fernandez, P.; G. Gonçalves; Gomes Pereira, L.; Moreira, M.

    2012-01-01

    The assessment and management of flood risks framework impose the mapping of flood hazard in potential flood risks areas. Floods in urban environments may happen due to rainfall extreme events and be exacerbated by saturated or impervious surfaces. Flood risk is greater in urban areas. (...)

  2. Statistical mechanics of nucleosomes

    Science.gov (United States)

    Chereji, Razvan V.

    Eukaryotic cells contain long DNA molecules (about two meters for a human cell) which are tightly packed inside the micrometric nuclei. Nucleosomes are the basic packaging unit of the DNA which allows this millionfold compactification. A longstanding puzzle is to understand the principles which allow cells to both organize their genomes into chromatin fibers in the crowded space of their nuclei, and also to keep the DNA accessible to many factors and enzymes. With the nucleosomes covering about three quarters of the DNA, their positions are essential because these influence which genes can be regulated by the transcription factors and which cannot. We study physical models which predict the genome-wide organization of the nucleosomes and also the relevant energies which dictate this organization. In the last five years, the study of chromatin knew many important advances. In particular, in the field of nucleosome positioning, new techniques of identifying nucleosomes and the competing DNA-binding factors appeared, as chemical mapping with hydroxyl radicals, ChIP-exo, among others, the resolution of the nucleosome maps increased by using paired-end sequencing, and the price of sequencing an entire genome decreased. We present a rigorous statistical mechanics model which is able to explain the recent experimental results by taking into account nucleosome unwrapping, competition between different DNA-binding proteins, and both the interaction between histones and DNA, and between neighboring histones. We show a series of predictions of our new model, all in agreement with the experimental observations.

  3. Object-oriented feature extraction approach for mapping supraglacial debris in Schirmacher Oasis using very high-resolution satellite data

    Science.gov (United States)

    Jawak, Shridhar D.; Jadhav, Ajay; Luis, Alvarinho J.

    2016-05-01

    Supraglacial debris was mapped in the Schirmacher Oasis, east Antarctica, by using WorldView-2 (WV-2) high resolution optical remote sensing data consisting of 8-band calibrated Gram Schmidt (GS)-sharpened and atmospherically corrected WV-2 imagery. This study is a preliminary attempt to develop an object-oriented rule set to extract supraglacial debris for Antarctic region using 8-spectral band imagery. Supraglacial debris was manually digitized from the satellite imagery to generate the ground reference data. Several trials were performed using few existing traditional pixel-based classification techniques and color-texture based object-oriented classification methods to extract supraglacial debris over a small domain of the study area. Multi-level segmentation and attributes such as scale, shape, size, compactness along with spectral information from the data were used for developing the rule set. The quantitative analysis of error was carried out against the manually digitized reference data to test the practicability of our approach over the traditional pixel-based methods. Our results indicate that OBIA-based approach (overall accuracy: 93%) for extracting supraglacial debris performed better than all the traditional pixel-based methods (overall accuracy: 80-85%). The present attempt provides a comprehensive improved method for semiautomatic feature extraction in supraglacial environment and a new direction in the cryospheric research.

  4. Disk and Envelope Structure in Class 0 Protostars: II. High Resolution Millimeter Mapping of the Serpens Sample

    CERN Document Server

    Enoch, M L; Duchene, G; Bock, D C; Bolatto, A D; Culverhouse, T L; Kwon, W; Lamb, J W; Leitch, E M; Marrone, D P; Muchovej, S J; Perez, L M; Scott, S L; Teuben, P J; Wright, M C H; Zauderer, B A

    2011-01-01

    We present high-resolution CARMA 230 GHz continuum imaging of nine deeply embedded protostars in the Serpens Molecular Cloud, including six of the nine known Class 0 protostars in Serpens. This work is part of a program to characterize disk and envelope properties for a complete sample of Class 0 protostars in nearby low-mass star forming regions. Here we present CARMA maps and visibility amplitudes as a function of uv-distance for the Serpens sample. Observations are made in the B, C, D, and E antenna configurations, with B configuration observations utilizing the CARMA Paired Antenna Calibration System. Combining data from multiple configurations provides excellent uv-coverage (4-500 klam), allowing us to trace spatial scales from 1e2 to 1e4 AU. We find evidence for compact disk components in all of the observed Class 0 protostars, suggesting that disks form at very early times (t 250 AU, but significant evidence of multiplicity on scales <2000 AU is seen in only one source.

  5. High-resolution elasticity maps and cytoskeletal dynamics of neurons measured by combined fluorescence and atomic force microscopy

    Science.gov (United States)

    Staii, Cristian

    2014-03-01

    Detailed knowledge of mechanical parameters such as cell elasticity, stiffness of the growth substrate, or traction stresses generated during axonal extensions is essential for understanding the mechanisms that control neuronal growth. Here I present results obtained in my research group, which combine Atomic Force Microscopy and Fluorescence Microscopy measurements to produce systematic, high-resolution elasticity maps for different types of live neuronal cells cultured on glass or biopolymer-based substrates. We measure how the stiffness of neurons changes both during neurite outgrowth and upon chemical modification (disruption of the cytoskeleton) of the cell. We find a reversible local stiffening of the cell during growth, and show that the increase in local elastic modulus is primarily due to the formation of microtubules in the cell soma. We also report a reversible shift in the elastic modulus of the cortical neurons cytoskeleton with temperature, from tubulin dominated regions at 37C to actin dominated regions at 25C. We demonstrate that the dominant mechanism by which the elasticity of the neuronal soma changes in response to temperature is the contractile stiffening of the actin component of the cytoskeleton induced by the activity of myosin II motors. We acknowledge financial support from NSF grant CBET 1067093.

  6. Geospatial mapping of Antarctic coastal oasis using geographic object-based image analysis and high resolution satellite imagery

    Science.gov (United States)

    Jawak, Shridhar D.; Luis, Alvarinho J.

    2016-04-01

    An accurate spatial mapping and characterization of land cover features in cryospheric regions is an essential procedure for many geoscientific studies. A novel semi-automated method was devised by coupling spectral index ratios (SIRs) and geographic object-based image analysis (OBIA) to extract cryospheric geospatial information from very high resolution WorldView 2 (WV-2) satellite imagery. The present study addresses development of multiple rule sets for OBIA-based classification of WV-2 imagery to accurately extract land cover features in the Larsemann Hills, east Antarctica. Multilevel segmentation process was applied to WV-2 image to generate different sizes of geographic image objects corresponding to various land cover features with respect to scale parameter. Several SIRs were applied to geographic objects at different segmentation levels to classify land mass, man-made features, snow/ice, and water bodies. We focus on water body class to identify water areas at the image level, considering their uneven appearance on landmass and ice. The results illustrated that synergetic usage of SIRs and OBIA can provide accurate means to identify land cover classes with an overall classification accuracy of ≍97%. In conclusion, our results suggest that OBIA is a powerful tool for carrying out automatic and semiautomatic analysis for most cryospheric remote-sensing applications, and the synergetic coupling with pixel-based SIRs is found to be a superior method for mining geospatial information.

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

    Science.gov (United States)

    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.

  8. Identification of submicroscopic genetic changes and precise breakpoint mapping in myelofibrosis using high resolution mate-pair sequencing.

    Science.gov (United States)

    Lasho, Terra; Johnson, Sarah H; Smith, David I; Crispino, John D; Pardanani, Animesh; Vasmatzis, George; Tefferi, Ayalew

    2013-09-01

    We used high resolution mate-pair sequencing (HRMPS) in 15 patients with primary myelofibrosis (PMF): eight with normal karyotype and seven with PMF-characteristic cytogenetic abnormalities, including der(6)t(1;6)(q21-23;p21.3) (n = 4), der(7)t(1;7)(q10;p10) (n = 2), del(20)(q11.2q13.3) (n = 3), and complex karyotype (n = 1). We describe seven novel deletions/translocations in five patients (including two with normal karyotype) whose breakpoints were PCR-validated and involved MACROD2, CACNA2D4, TET2, SGMS2, LRBA, SH3D19, INTS3, FOP (CHTOP), SCLT1, and PHF17. Deletions with breakpoints involving MACROD2 (lysine deacetylase; 20p12.1) were recurrent and found in two of the 15 study patients. A novel fusion transcript was found in one of the study patients (INTS3-CHTOP), and also in an additional non-study patient with PMF. In two patients with der(6)t(1;6)(q21-23;p21.3), we were able to map the precise translocation breakpoints, which involved KCNN3 and GUSBP2 in one case and HYDIN2 in another. This study demonstrates the utility of HRMPS in uncovering submicroscopic deletions/translocations/fusions, and precise mapping of breakpoints in those with overt cytogenetic abnormalities. The overall results confirm the genetic heterogeneity of PMF, given the low frequency of recurrent specific abnormalities, identified by this screening strategy. Currently, we are pursuing the pathogenetic relevance of some of the aforementioned findings.

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

    Science.gov (United States)

    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.

  10. The gastrointestinal electrical mapping suite (GEMS: software for analyzing and visualizing high-resolution (multi-electrode recordings in spatiotemporal detail

    Directory of Open Access Journals (Sweden)

    Yassi Rita

    2012-06-01

    Full Text Available Abstract Background Gastrointestinal contractions are controlled by an underlying bioelectrical activity. High-resolution spatiotemporal electrical mapping has become an important advance for investigating gastrointestinal electrical behaviors in health and motility disorders. However, research progress has been constrained by the low efficiency of the data analysis tasks. This work introduces a new efficient software package: GEMS (Gastrointestinal Electrical Mapping Suite, for analyzing and visualizing high-resolution multi-electrode gastrointestinal mapping data in spatiotemporal detail. Results GEMS incorporates a number of new and previously validated automated analytical and visualization methods into a coherent framework coupled to an intuitive and user-friendly graphical user interface. GEMS is implemented using MATLAB®, which combines sophisticated mathematical operations and GUI compatibility. Recorded slow wave data can be filtered via a range of inbuilt techniques, efficiently analyzed via automated event-detection and cycle clustering algorithms, and high quality isochronal activation maps, velocity field maps, amplitude maps, frequency (time interval maps and data animations can be rapidly generated. Normal and dysrhythmic activities can be analyzed, including initiation and conduction abnormalities. The software is distributed free to academics via a community user website and forum (http://sites.google.com/site/gimappingsuite. Conclusions This software allows for the rapid analysis and generation of critical results from gastrointestinal high-resolution electrical mapping data, including quantitative analysis and graphical outputs for qualitative analysis. The software is designed to be used by non-experts in data and signal processing, and is intended to be used by clinical researchers as well as physiologists and bioengineers. The use and distribution of this software package will greatly accelerate efforts to improve the

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

    Science.gov (United States)

    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.

  12. Chromosome landing at the ¤Mla¤ locus in barley (¤Hordeum vulgare¤ L.) by means of high-resolution mapping with AFLP markers

    DEFF Research Database (Denmark)

    Schwarz, G.; Michalek, W.; Mohler, V.

    1999-01-01

    to construct a high-resolution map of the Mla region. A fluorescence-based AFLP technique and bulked segregant analysis were applied to screen for polymorphic, tightly linked AFLP markers, Three AFLP markers were selected as suitable for a chromosome-landing strategy. One of these AFLP markers and a closely...

  13. A high-resolution comparative map between pig chromosome 17 and human chromosomes 4, 8, and 20: Identification of synteny breakpoints

    DEFF Research Database (Denmark)

    Lahbib-Mansais, Yvette; Karlskov-Mortensen, Peter; Mompart, Florence;

    2005-01-01

    We report on the construction of a high-resolution comparative map of porcine chromosome 17 (SSC17) focusing on evolutionary breakpoints with human chromosomes. The comparative map shows high homology with human chromosome 20 but suggests more limited homologies with other human chromosomes. SSC17...... is of particular interest in studies of chromosomal organization due to the presence of QTLs that affect meat quality and carcass composition. A total of 158 pig ESTs available in databases or developed by the Sino-Danish Pig Genome Sequencing Consortium were mapped using the INRA-University of Minnesota porcine...... radiation hydrid panel. The high-resolution map was further anchored by fluorescence in situ hybridization. This study confirmed the extensive conservation between SSC17 and HSA20 and enabled the gene order to be determined. The homology of the SSC17 pericentromeric region was extended to other human...

  14. High-Resolution Mapping of Sea Ice, Icebergs and Growlers in Kongsfjorden, Svalbard, using Ground Based Radar, Satellite, and UAV

    Science.gov (United States)

    Lauknes, T. R.; Rouyet, L.; Solbø, S. A.; Sivertsen, A.; Storvold, R.; Akbari, V.; Negrel, J.; Gerland, S.

    2016-12-01

    The dynamics of sea ­ice has a well­ recognized role in the climate system and its extent and evolution is impacted by the global warming. In addition, calving of icebergs and growlers at the tidewater glacier fronts is a component of the mass loss in polar regions. Understanding of calving and ice ­ocean interaction, in particular at tidewater glacier front remains elusive, and a problematic uncertainty in climate change projections. Studying the distribution, volumetry and motion of sea ­ice, icebergs and growlers is thus essential to understand their interactions with the environment in order to be able to predict at short­term their drifts, e.g. to mitigate the risk for shipping, and at longer term the multiple relations with climate changes. Here, we present the results from an arctic fieldwork campaign conducted in Kongsfjorden, Svalbard in April 2016, where we used different remote sensing instruments to observe dynamics of sea ice, icebergs, and growlers. We used a terrestrial radar system, imaging the study area every second minute during the observation period. At the front of the Kronebreen glacier, calving events can be detected and the drift of the generated icebergs and growlers tracked with unprecedented spatial and temporal resolution. During the field campaign, we collected four Radarsat-2 quad-pol images, that will be used to classify the different types of sea ice. In addition, we used small unmanned aircraft (UAS) instrumented with high resolution cameras capturing HD video and still pictures. This allows to map and measure the size of icebergs and ice floes. Such information is essential to validate sensitivity and detection limits from the ground and satellite based measurements.

  15. Fast terrain modelling for hydrogeological risk mapping and emergency management: the contribution of high-resolution satellite SAR imagery

    Directory of Open Access Journals (Sweden)

    A. Nascetti

    2015-07-01

    Full Text Available Geomatic tools fast terrain modelling play a relevant role in hydrogeological risk mapping and emergency management. Given their complete independence from logistic constraints on the ground (as for airborne data collection, illumination (daylight, and weather (clouds conditions, synthetic aperture radar (SAR satellite systems may provide important contributions in terms of digital surface models (DSMs and digital elevation models (DEMs. For this work we focused on the potential of high-resolution SAR satellite imagery for DSM generation using an interferometric (InSAR technique and using a revitalized radargrammetric stereomapping approach. The goal of this work was just methodological. Our goal was to illustrate both the fundamental advantages and drawbacks of the radargrammetric approach with respect to the InSAR technique for DSM generation, and to outline their possible joint role in hydrogeological risk mapping and emergency management. Here, it is worth mentioning that radargrammetry procedures are independent of image coherence (unlike the interferometric approach and phase unwrapping, as well as of parsimony (only a few images are necessary. Therefore, a short time is required for image collection (from tens of minutes to a few hours, thanks to the independence from illumination and weather. The most relevant obstacles of the technique are speckle and the lack of texture impact on image matching, as well as the well-known deformations of SAR imagery (layover and foreshortening, which may produce remarkable difficulties with complex morphologies and that must be accounted for during acquisition planning. Here, we discuss results obtained with InSAR and radargrammetry applied to a COSMO-SkyMed SpotLight triplet (two stereopairs suited for radargrammetry and InSAR, sharing one common image acquired over suburbs of San Francisco (United States, which are characterized by mixed morphology and land cover. We mainly focused on urban areas and

  16. High-resolution mapping of the NO2 spatial distribution over Belgian urban areas based on airborne APEX remote sensing

    Science.gov (United States)

    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.

  17. High resolution mapping of the tropospheric NO2 distribution in three Belgian cities based on airborne APEX remote sensing

    Science.gov (United States)

    Tack, Frederik; Merlaud, Alexis; Fayt, Caroline; Danckaert, Thomas; Iordache, Daniel; Meuleman, Koen; Deutsch, Felix; Adriaenssens, Sandy; Fierens, Frans; Van Roozendael, Michel

    2015-04-01

    An approach is presented to retrieve tropospheric nitrogen dioxide (NO2) vertical column densities (VCDs) and to map the NO2 two dimensional distribution at high resolution, based on Airborne Prism EXperiment (APEX) observations. APEX, developed by a Swiss-Belgian consortium on behalf of ESA (European Space Agency), is a pushbroom hyperspectral imager with a high spatial (approximately 3 m at 5000 m ASL), spectral (413 to 2421 nm in 533 narrow, contiguous spectral bands) and radiometric (14-bit) resolution. VCDs are derived, following a similar approach as described in the pioneering work of Popp et al. (2012), based on (1) spectral calibration and spatial binning of the observed radiance spectra in order to improve the spectral resolution and signal-to-noise ratio, (2) Differential Optical Absorption Spectroscopy (DOAS) analysis of the pre-processed spectra in the visible wavelength region, with a reference spectrum containing low NO2 absorption, in order to quantify the abundance of NO2 along the light path, based on its molecular absorption structures and (3) radiative transfer modeling for air mass factor calculation in order to convert slant to vertical columns. This study will be done in the framework of the BUMBA (Belgian Urban NO2 Monitoring Based on APEX hyperspectral data) project. Dedicated flights with APEX mounted in a Dornier DO-228 airplane, operated by Deutsches Zentrum für Luft- und Raumfahrt (DLR), are planned to be performed in Spring 2015 above the three largest and most heavily polluted Belgian cities, i.e. Brussels, Antwerp and Liège. The retrieved VCDs will be validated by comparison with correlative ground-based and car-based DOAS observations. Main objectives are (1) to assess the operational capabilities of APEX to map the NO2 field over an urban area at high spatial and spectral resolution in a relatively short time and cost-effective way, and to characterise all aspects of the retrieval approach; (2) to use the APEX NO2 measurements

  18. Integration of myocardial scar identified by preoperative delayed contrast-enhanced MRI into a high-resolution mapping system for planning and guidance of VT ablation procedures

    Science.gov (United States)

    Rettmann, M. E.; Suzuki, A.; Wang, S.; Pottinger, N.; Arter, J.; Netzer, A.; Parker, K.; Viker, K.; Packer, D. L.

    2017-03-01

    Myocardial scarring creates a substrate for reentrant circuits which can lead to ventricular tachycardia. In ventricular catheter ablation therapy, regions of myocardial scarring are targeted to interrupt arrhythmic electrical pathways. Low voltage regions are a surrogate for myocardial scar and are identified by generating an electro anatomic map at the start of the procedure. Recent efforts have focussed on integration of preoperative scar information generated from delayed contrast-enhanced MR imaging to augment intraprocedural information. In this work, we describe an initial feasibility study of integration of a preoperative MRI derived scar maps into a high-resolution mapping system to improve planning and guidance of VT ablation procedures.

  19. The songbird syrinx morphome: a three-dimensional, high-resolution, interactive morphological map of the zebra finch vocal organ

    DEFF Research Database (Denmark)

    During, D. N.; Ziegler, A.; Thompson, C. K.;

    2013-01-01

    and micro-computed tomography) and invasive techniques (histology and micro-dissection) to construct the annotated high-resolution three-dimensional dataset, or morphome, of the zebra finch (Taeniopygia guttata) syrinx. We identified and annotated syringeal cartilage, bone and musculature in situ...

  20. Strong nucleosomes of A. thaliana concentrate in centromere regions.

    Science.gov (United States)

    Salih, Bilal; Trifonov, Edward N

    2015-01-01

    Earlier identified strongest nucleosome DNA sequences of A. thaliana, those with visible 10-11 base sequence periodicity, are mapped along chromosomes. Resulting positional distributions reveal distinct maxima, one per chromosome, located in the centromere regions. Sequence-directed nucleosome mapping demonstrates that the strong nucleosomes (SNs) make tight arrays, several 'parallel' nucleosomes each, suggesting a columnar chromatin structure. The SNs represent a new class of centromeric nucleosomes, presumably, participating in synapsis of chromatids and securing the centromere architecture.

  1. 转录起始位点核小体定位的研究进展%Advances on Nucleosome Mapping Around TSS

    Institute of Scientific and Technical Information of China (English)

    王成爱

    2014-01-01

    核小体定位是参与真核生物基因表达调控的一种重要的表观遗传因素,深刻影响基因转录、DNA复制与修复等生物学过程。对于在许多基因位点,比如转录起始位点(TSS)、转录因子结合位点(TFBS)等处的核小体定位已有不少报道。主要介绍了核小体的定位特性,综述了转录起始位点处核小体的定位特征,分别从序列依赖性因素和DNA甲基化、组蛋白变体及修饰、染色质重塑、可变剪接等表观遗传因素较为详细地概括了转录起始位点核小体定位的研究进展。%Nucleosome mapping,an important epigenetic factor participating in regulating eukaryotic gene expression, deeply affects lots of biological processes,including gene transcription,DNA replication,DNA repair and so forth. The nucleosome mapping around TSS and TFBS has been reported properties of nucleosome mapping were introduced in this paper. Features in nucleosome mapping around TSS were summarized. Advances on nucleosome mapping around TSS from both the DNA sequence-dependent factor and some epigenetic factors including DNA methylation, variants and modification of histone, chromation remodeling,alternative splicing were reviewed.

  2. Mapping of Impervious Surfaces and Green Vegetation Fraction in Urban Areas Using High-Resolution Optical- and SAR- Data

    Science.gov (United States)

    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.

  3. High-resolution Rainfall Mapping in Dallas-Fort Worth (DFW) Urban Network of Radars at Multiple Frequencies

    Science.gov (United States)

    Chandra, Chandrasekar V.; Chen*, Haonan

    2015-04-01

    Urban flash flood is one of the most commonly encountered hazardous weather phenomena. Unfortunately, the rapid urbanization has made the densely populated areas even more vulnerable to flood risks. Hence, accurate and timely monitoring of rainfall at high spatiotemporal resolution is critical to severe weather warning and civil defense, especially in urban areas. However, it is still challenging to produce high-resolution products based on the large S-band National Weather Service (NWS) Next-Generation Weather Radar (NEXRAD), due to the sampling limitations and Earth curvature effect. Since 2012, the U.S. National Science Foundation Engineering Research Center (NSF-ERC) for Collaborative Adaptive Sensing of the Atmosphere (CASA) has initiated the development of Dallas-Fort Worth (DFW) radar remote sensing network for urban weather hazards mitigation. The DFW urban radar network consists of a combination of high-resolution X-band radars and a standard NWS NEXRAD radar operating at S-band frequency. High-resolution quantitative precipitation estimation (QPE) is one of the major research goals in the deployment of this urban radar network. It has been shown in the literature that the dual-polarization radar techniques can improve the QPE accuracy over traditional single-polarization radars by rendering more measurements to enhance the data quality, providing more information about rain drop size distribution (DSD), and implying more characteristics of different hydrometeor types. This paper will present the real-time dual-polarization CASA DFW QPE system, which is developed via fusion of observations from both the high-resolution X band radar network and the S-band NWS radar. The specific dual-polarization rainfall algorithms at different frequencies (i.e., S- and X-band) will be described in details. In addition, the fusion methodology combining observations at different temporal resolution will be presented. In order to demonstrate the capability of rainfall

  4. High-resolution cytogenetic mapping of 342 new cosmid markers including 43 RFLP markers on human chromosome 17 by fluorescence in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Inazawa, Johji; Ariyama, Takeshi; Abe, Tatsuo (Kyoto Prefectual Univ. of Medicine (Japan)); Saito, Hiroko; Nakamura, Yusuke (Cancer Institute, Tokyo (Japan))

    1993-07-01

    The authors have constructed a high-resolution cytogenetic map of human chromosome 17 with 342 cosmid markers, each newly isolated from a cosmid library constructed from a human-mouse hybrid cell line containing a single human chromosome 17. Direct mapping on R- and/or G-banded (pro)metaphase chromosomes by fluorescence in situ hybridization localized these markers throughout the chromosome, although density was highest in the R-band-dominant regions of 17p13, 17p11.2, 17q11.2-q12, 17q21.3, 17q23, and 17q25. By screening some of the cosmid clones, they identified 71 polymorphic systems with 43 markers; 11 of these are VNTRs. As the high-resolution cytogenetic map contains a large number of markers, it can provide useful landmarks for a contig map of chromosome 17. Furthermore, the map will contribute to positional cloning of aberrant genes responsible for inherited diseases such as Miller-Dieker syndrome (MDS), Smith-Magenis syndrome (SMS), and familial early-onset breast cancer, as well as putative tumor suppressor genes on this chromosome. 47 refs., 2 figs., 2 tabs.

  5. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

    OpenAIRE

    Zhang, Y; Moqtaderi, Z.; Rattner, BP; Euskirchen, G.; Snyder, M; Kadonaga, JT; Liu, XS; Struhl, K

    2009-01-01

    We assess the role of intrinsic histone-DNA interactions by mapping nucleosomes assembled in vitro on genomic DNA. Nucleosomes strongly prefer yeast DNA over Escherichia coli DNA, indicating that the yeast genome evolved to favor nucleosome formation. Many yeast promoter and terminator regions intrinsically disfavor nucleosome formation, and nucleosomes assembled in vitro show strong rotational positioning. Nucleosome arrays generated by the ACF assembly factor have fewer nucleosome-free regi...

  6. The design and construction of a high-resolution velocity-map imaging apparatus for photoelectron spectroscopy studies of size-selected clusters

    Science.gov (United States)

    León, Iker; Yang, Zheng; Liu, Hong-Tao; Wang, Lai-Sheng

    2014-08-01

    A new velocity-map imaging apparatus equipped with a laser-vaporization supersonic cluster source and a time-of-flight mass spectrometer is described for high-resolution photoelectron spectroscopy studies of size-selected cluster anions. Vibrationally cold anion clusters are produced using a laser-vaporization supersonic cluster source, size-selected by a time-of-flight mass spectrometer, and then focused co-linearly into the interaction zone of the high-resolution velocity-map imaging (VMI) system. The multilens VMI system is optimized via systematic simulations and can reach a resolution of 1.2 cm-1 (FWHM) for near threshold electrons while maintaining photoelectron kinetic energy resolutions (ΔKE/KE) of ˜0.53% for higher energy electrons. The new VMI lens has superior focusing power over a large energy range, yielding highly circular images with distortions no larger than 1.0025 between the long and short radii. The detailed design, simulation, construction, testing, and performance of the high-resolution VMI apparatus are presented.

  7. The design and construction of a high-resolution velocity-map imaging apparatus for photoelectron spectroscopy studies of size-selected clusters

    Energy Technology Data Exchange (ETDEWEB)

    León, Iker; Yang, Zheng; Liu, Hong-Tao; Wang, Lai-Sheng, E-mail: Lai-Sheng-Wang@brown.edu [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States)

    2014-08-15

    A new velocity-map imaging apparatus equipped with a laser-vaporization supersonic cluster source and a time-of-flight mass spectrometer is described for high-resolution photoelectron spectroscopy studies of size-selected cluster anions. Vibrationally cold anion clusters are produced using a laser-vaporization supersonic cluster source, size-selected by a time-of-flight mass spectrometer, and then focused co-linearly into the interaction zone of the high-resolution velocity-map imaging (VMI) system. The multilens VMI system is optimized via systematic simulations and can reach a resolution of 1.2 cm{sup −1} (FWHM) for near threshold electrons while maintaining photoelectron kinetic energy resolutions (ΔKE/KE) of ∼0.53% for higher energy electrons. The new VMI lens has superior focusing power over a large energy range, yielding highly circular images with distortions no larger than 1.0025 between the long and short radii. The detailed design, simulation, construction, testing, and performance of the high-resolution VMI apparatus are presented.

  8. High-resolution mapping based on an Unmanned Aerial Vehicle (UAV) to capture paleoseismic offsets along the Altyn-Tagh fault, China.

    Science.gov (United States)

    Gao, Mingxing; Xu, Xiwei; Klinger, Yann; van der Woerd, Jerome; Tapponnier, Paul

    2017-08-15

    The recent dramatic increase in millimeter- to centimeter- resolution topographic datasets obtained via multi-view photogrammetry raises the possibility of mapping detailed offset geomorphology and constraining the spatial characteristics of active faults. Here, for the first time, we applied this new method to acquire high-resolution imagery and generate topographic data along the Altyn Tagh fault, which is located in a remote high elevation area and shows preserved ancient earthquake surface ruptures. A digital elevation model (DEM) with a resolution of 0.065 m and an orthophoto with a resolution of 0.016 m were generated from these images. We identified piercing markers and reconstructed offsets based on both the orthoimage and the topography. The high-resolution UAV data were used to accurately measure the recent seismic offset. We obtained the recent offset of 7 ± 1 m. Combined with the high resolution satellite image, we measured cumulative offsets of 15 ± 2 m, 20 ± 2 m, 30 ± 2 m, which may be due to multiple paleo-earthquakes. Therefore, UAV mapping can provide fine-scale data for the assessment of the seismic hazards.

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

    Science.gov (United States)

    2016-04-01

    collecting co-located soil cores with follow on high-resolution soil sampling for both field DNAPL screening using Oil -Red-O dye shake tests and quantitative...use of HRSC techniques in order to develop accurate CSMs and effective remediation strategies. Selective and targeted soil sampling at key locations...outer edges): o One sub-core was collected for field screening with Oil -Red-O. The Oil -O-Red screening was completed by ejecting the soil into a pre

  10. A 1-dimensional statistical mechanics model for nucleosome positioning on genomic DNA

    CERN Document Server

    Tesoro, S; Morozov, A N; Sulaiman, N; Marenduzzo, D

    2015-01-01

    The first level of folding of DNA in eukaryotes is provided by the so called '10nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging 'bead on a string' structure. In this work we present a one dimensional statistical mechanics model to study nucleosome positioning within one such 10 nm fibre. We consider both the case of homogeneous DNA, where the problem can be mapped to a Tonks gas, and that of genomic sheep DNA, where our modelling is informed by high-resolution nucleosome positioning data. First, we consider the simple, analytically solvable, case where nucleosomes are assumed to be point like. Then, we perform numerical simulations to gauge the effect of their finite size on the nucleosomal distribution probabilities. Finally, we compare nucleosome distributions and simulated nuclease digestion patterns for the two cases (homogeneous and sheep DNA), thereby providing testable predictions of the effect of sequence on ...

  11. A Versatile, Production-Oriented Approach to High-Resolution Tree-Canopy Mapping in Urban and Suburban Landscapes Using GEOBIA and Data Fusion

    Directory of Open Access Journals (Sweden)

    Jarlath O'Neil-Dunne

    2014-12-01

    Full Text Available The benefits of tree canopy in urban and suburban landscapes are increasingly well known: stormwater runoff control, air-pollution mitigation, temperature regulation, carbon storage, wildlife habitat, neighborhood cohesion, and other social indicators of quality of life. However, many urban areas lack high-resolution tree canopy maps that document baseline conditions or inform tree-planting programs, limiting effective study and management. This paper describes a GEOBIA approach to tree-canopy mapping that relies on existing public investments in LiDAR, multispectral imagery, and thematic GIS layers, thus eliminating or reducing data acquisition costs. This versatile approach accommodates datasets of varying content and quality, first using LiDAR derivatives to identify aboveground features and then a combination of LiDAR and imagery to differentiate trees from buildings and other anthropogenic structures. Initial tree canopy objects are then refined through contextual analysis, morphological smoothing, and small-gap filling. Case studies from locations in the United States and Canada show how a GEOBIA approach incorporating data fusion and enterprise processing can be used for producing high-accuracy, high-resolution maps for large geographic extents. These maps are designed specifically for practical application by planning and regulatory end users who expect not only high accuracy but also high realism and visual coherence.

  12. High-resolution mapping of a major effect QTL from wild tomato Solanum habrochaites that influences water relations under root chilling.

    Science.gov (United States)

    Arms, Erin M; Bloom, Arnold J; St Clair, Dina A

    2015-09-01

    QTL stm9 controlling rapid-onset water stress tolerance in S. habrochaites was high-resolution mapped to a chromosome 9 region that contains genes associated with abiotic stress tolerances. Wild tomato (Solanum habrochaites) exhibits tolerance to abiotic stresses, including drought and chilling. Root chilling (6 °C) induces rapid-onset water stress by impeding water movement from roots to shoots. S. habrochaites responds to such changes by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) fails to close stomata and wilts. This response (shoot turgor maintenance under root chilling) is controlled by a major QTL (designated stm9) on chromosome 9, which was previously fine-mapped to a 2.7-cM region. Recombinant sub-near-isogenic lines for chromosome 9 were marker-selected, phenotyped for shoot turgor maintenance under root chilling in two sets of replicated experiments (Fall and Spring), and the data were used to high-resolution map QTL stm9 to a 0.32-cM region. QTL mapping revealed a single QTL that was coincident for both the Spring and Fall datasets, suggesting that the gene or genes contributing to shoot turgor maintenance under root chilling reside within the marker interval H9-T1673. In the S. lycopersicum reference genome sequence, this chromosome 9 region is gene-rich and contains representatives of gene families that have been associated with abiotic stress tolerance.

  13. High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus.

    Science.gov (United States)

    Lu, Xia; Luan, Sheng; Hu, Long Yang; Mao, Yong; Tao, Ye; Zhong, Sheng Ping; Kong, Jie

    2016-06-01

    The Kuruma prawn, Marsupenaeus japonicus, is one of the most promising marine invertebrates in the industry in Asia, Europe and Australia. However, the increasing global temperatures result in considerable economic losses in M. japonicus farming. In the present study, to select genetically improved animals for the sustainable development of the Kuruma prawn industry, a high-resolution genetic linkage map and quantitative trait locus (QTL) identification were performed using the RAD technology. The maternal map contained 5849 SNP markers and spanned 3127.23 cM, with an average marker interval of 0.535 cM. Instead, the paternal map contained 3927 SNP markers and spanned 3326.19 cM, with an average marker interval of 0.847 cM. The consensus map contained 9289 SNP markers and spanned 3610.90 cM, with an average marker interval of 0.388 cM and coverage of 99.06 % of the genome. The markers were grouped into 41 linkage groups in the maps. Significantly, negative correlation was detected between high-temperature tolerance (UTT) and body weight (BW). The QTL mapping revealed 129 significant QTL loci for UTT and four significant QTL loci for BW at the genome-wide significance threshold. Among these QTLs, 129 overlapped with linked SNPs, and the remaining four were located in regions between contiguous SNPs. They explained the total phenotypic variance ranging from 8.9 to 12.4 %. Because of a significantly negative correlation between growth and high-temperature tolerance, we demonstrate that this high-resolution linkage map and QTLs would be useful for further marker-assisted selection in the genetic improvement of M. japonicus.

  14. Quaternary layer anomalies around the Carlsberg Fault zone mapped with high-resolution shear-wave seismics south of Copenhagen

    DEFF Research Database (Denmark)

    Kammann, Janina; Hübscher, Christian; Nielsen, Lars

    . In the Upper Cretaceous growth faulting documents continued rifting. This finding contrasts the Late Cretaceous to Paleogene inversion tectonics in neighboring structures, as the Tornquist Zone. The high-resolution shear-wave seismic method was used to image structures in Quaternary layers in the Carlsberg....... In the shear-wave profile, we imaged the 30 m of the upward continuation of the Carlsberg Fault zone. In our area of investigation, the fault zone appears to comprise normal block faults and one reverse block fault showing the complexity of the fault zone. The observed faults appear to affect both the Danian......The Carlsberg Fault zone is located in the N-S striking Höllviken Graben and traverses the city of Copenhagen. The fault zone is a NNW-SSE striking structure in direct vicinity to the transition zone of the Danish Basin and the Baltic Shield. Recent small earthquakes indicate activity in the area...

  15. Multi-dimensional water quality assessment of an urban drinking water source elucidated by high resolution underwater towed vehicle mapping.

    Science.gov (United States)

    Lock, Alan; Spiers, Graeme; Hostetler, Blair; Ray, James; Wallschläger, Dirk

    2016-04-15

    Spatial surveys of Ramsey Lake, Sudbury, Ontario water quality were conducted using an innovative underwater towed vehicle (UTV) equipped with a multi-parameter probe providing real-time water quality data. The UTV revealed underwater vent sites through high resolution monitoring of different spatial chemical characteristics using common sensors (turbidity, chloride, dissolved oxygen, and oxidation/reduction sensors) that would not be feasible with traditional water sampling methods. Multi-parameter probe vent site identification is supported by elevated alkalinity and silica concentrations at these sites. The identified groundwater vent sites appear to be controlled by bedrock fractures that transport water from different sources with different contaminants of concern. Elevated contaminants, such as, arsenic and nickel and/or nutrient concentrations are evident at the vent sites, illustrating the potential of these sources to degrade water quality.

  16. Nucleosome Organization in Human Embryonic Stem Cells.

    Directory of Open Access Journals (Sweden)

    Puya G Yazdi

    Full Text Available The fundamental repeating unit of eukaryotic chromatin is the nucleosome. Besides being involved in packaging DNA, nucleosome organization plays an important role in transcriptional regulation and cellular identity. Currently, there is much debate about the major determinants of the nucleosome architecture of a genome and its significance with little being known about its role in stem cells. To address these questions, we performed ultra-deep sequencing of nucleosomal DNA in two human embryonic stem cell lines and integrated our data with numerous epigenomic maps. Our analyses have revealed that the genome is a determinant of nucleosome organization with transcriptionally inactive regions characterized by a "ground state" of nucleosome profiles driven by underlying DNA sequences. DNA sequence preferences are associated with heterogeneous chromatin organization around transcription start sites. Transcription, histone modifications, and DNA methylation alter this "ground state" by having distinct effects on both nucleosome positioning and occupancy. As the transcriptional rate increases, nucleosomes become better positioned. Exons transcribed and included in the final spliced mRNA have distinct nucleosome profiles in comparison to exons not included at exon-exon junctions. Genes marked by the active modification H3K4m3 are characterized by lower nucleosome occupancy before the transcription start site compared to genes marked by the inactive modification H3K27m3, while bivalent domains, genes associated with both marks, lie exactly in the middle. Combinatorial patterns of epigenetic marks (chromatin states are associated with unique nucleosome profiles. Nucleosome organization varies around transcription factor binding in enhancers versus promoters. DNA methylation is associated with increasing nucleosome occupancy and different types of methylations have distinct location preferences within the nucleosome core particle. Finally, computational

  17. Nucleosome Organization in Human Embryonic Stem Cells.

    Science.gov (United States)

    Yazdi, Puya G; Pedersen, Brian A; Taylor, Jared F; Khattab, Omar S; Chen, Yu-Han; Chen, Yumay; Jacobsen, Steven E; Wang, Ping H

    2015-01-01

    The fundamental repeating unit of eukaryotic chromatin is the nucleosome. Besides being involved in packaging DNA, nucleosome organization plays an important role in transcriptional regulation and cellular identity. Currently, there is much debate about the major determinants of the nucleosome architecture of a genome and its significance with little being known about its role in stem cells. To address these questions, we performed ultra-deep sequencing of nucleosomal DNA in two human embryonic stem cell lines and integrated our data with numerous epigenomic maps. Our analyses have revealed that the genome is a determinant of nucleosome organization with transcriptionally inactive regions characterized by a "ground state" of nucleosome profiles driven by underlying DNA sequences. DNA sequence preferences are associated with heterogeneous chromatin organization around transcription start sites. Transcription, histone modifications, and DNA methylation alter this "ground state" by having distinct effects on both nucleosome positioning and occupancy. As the transcriptional rate increases, nucleosomes become better positioned. Exons transcribed and included in the final spliced mRNA have distinct nucleosome profiles in comparison to exons not included at exon-exon junctions. Genes marked by the active modification H3K4m3 are characterized by lower nucleosome occupancy before the transcription start site compared to genes marked by the inactive modification H3K27m3, while bivalent domains, genes associated with both marks, lie exactly in the middle. Combinatorial patterns of epigenetic marks (chromatin states) are associated with unique nucleosome profiles. Nucleosome organization varies around transcription factor binding in enhancers versus promoters. DNA methylation is associated with increasing nucleosome occupancy and different types of methylations have distinct location preferences within the nucleosome core particle. Finally, computational analysis of nucleosome

  18. A high-resolution InDel (insertion-deletion markers-anchored consensus genetic map identifies major QTLs governing pod number and seed yield in chickpea

    Directory of Open Access Journals (Sweden)

    Rishi Srivastava

    2016-09-01

    Full Text Available Development and large-scale genotyping of user-friendly informative genome/gene-derived InDel markers in natural and mapping populations is vital for accelerating genomics-assisted breeding applications of chickpea with minimal resource expenses. The present investigation employed a high-throughput whole genome NGS (next-generation sequencing resequencing strategy in low and high pod number parental accessions and homozygous individuals constituting the bulks from each of two inter-specific mapping populations [(Pusa 1103 x ILWC 46 and (Pusa 256 x ILWC 46] to develop non-erroneous InDel markers at a genome-wide scale. Comparing these high-quality genomic sequences, 82360 InDel markers with reference to kabuli genome and 13891 InDel markers exhibiting differentiation between low and high pod number parental accessions and bulks of aforementioned mapping populations were developed. These informative markers were structurally and functionally annotated in diverse coding and non-coding sequence components of genome/genes of kabuli chickpea. The functional significance of regulatory and coding (frameshift and large-effect mutations InDel markers for establishing marker-trait linkages through association/genetic mapping was apparent. The markers detected a greater amplification (97% and intra-specific polymorphic potential (58-87% among a diverse panel of cultivated desi, kabuli and wild accessions even by using a simpler cost-efficient agarose gel-based assay implicating their utility in large-scale genetic analysis especially in domesticated chickpea with narrow genetic base. Two high-density inter-specific genetic linkage maps generated using aforesaid mapping populations were integrated to construct a consensus 1479 InDel markers-anchored high-resolution (inter-marker distance: 0.66 cM genetic map for efficient molecular mapping of major QTLs governing pod number and seed yield per plant in chickpea. Utilizing these high-density genetic maps as

  19. Using object-oriented classification and high-resolution imagery to map fuel types in a Mediterranean region.

    Science.gov (United States)

    L. Arroyo; S.P. Healey; W.B. Cohen; D. Cocero; J.A. Manzanera

    2006-01-01

    Knowledge of fuel load and composition is critical in fighting, preventing, and understanding wildfires. Commonly, the generation of fuel maps from remotely sensed imagery has made use of medium-resolution sensors such as Landsat. This paper presents a methodology to generate fuel type maps from high spatial resolution satellite data through object-oriented...

  20. High-resolution three-dimensional macromolecular proton fraction mapping for quantitative neuroanatomical imaging of the rodent brain in ultra-high magnetic fields.

    Science.gov (United States)

    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

  1. NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps.

    Science.gov (United States)

    Suhre, Karsten; Navaza, Jorge; Sanejouand, Yves Henri

    2006-09-01

    This paper describes a freely available software suite that allows the modelling of large conformational changes of high-resolution three-dimensional protein structures under the constraint of a low-resolution electron-density map. Typical applications are the interpretation of electron-microscopy data using atomic scale X-ray structural models. The software package provided should enable the interested user to perform flexible fitting on new cases without encountering major technical difficulties. The NORMA software suite including three fully executable reference cases and extensive user instructions are available at http://www.elnemo.org/NORMA/.

  2. ‘‘Blind'' mapping of genic DNA sequence polymorphisms in Lolium perenne L. by high resolution melting curve analysis

    DEFF Research Database (Denmark)

    Studer, Bruno; Jensen, Louise Bach; Fiil, Alice;

    2009-01-01

    in vernalization response successfully discriminated genotypes in absence of allelic sequence information, and allowed to determine allele segregation in VrnA. Here we introduce the concept of "blind" mapping based on HRM as a powerful, fast and cheap method to map any DNA sequence polymorphisms without prior...... curves. In this study, HRM was used for simultaneous screening and genotyping of genic DNA sequence polymorphisms identified in the Lolium perenne F2 mapping population VrnA. Melting profiles of PCR products amplified from previously published gene loci and from a novel gene putatively involved...

  3. THE PANCHROMATIC HUBBLE ANDROMEDA TREASURY. VIII. A WIDE-AREA, HIGH-RESOLUTION MAP OF DUST EXTINCTION IN M31

    Energy Technology Data Exchange (ETDEWEB)

    Dalcanton, Julianne J.; Fouesneau, Morgan; Weisz, Daniel R.; Williams, Benjamin F. [Department of Astronomy, Box 351580, University of Washington, Seattle, WA 98195 (United States); Hogg, David W. [Center for Cosmology and Particle Physics, Department of Physics, New York University, 4 Washington Pl #424, New York, NY 10003 (United States); Lang, Dustin [McWilliams Center for Cosmology, Department of Physics, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213 (United States); Leroy, Adam K. [National Radio Astronomy Observatory, 520 Edgemont Road, Charlottesville, VA 22903 (United States); Gordon, Karl D.; Gilbert, Karoline M. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Sandstrom, Karin [Steward Observatory, University of Arizona, 933 N Cherry Ave, Tucson, AZ 85721 (United States); Bell, Eric F. [Department of Astronomy, University of Michigan, 500 Church St., Ann Arbor, MI 48109 (United States); Dong, Hui; Lauer, Tod R. [National Optical Astronomy Observatory, 950 North Cherry Avenue, Tucson, AZ 85719 (United States); Gouliermis, Dimitrios A. [Max Planck Institute für Astronomie, Königstuhl 17, D-69117, Heidelberg (Germany); Guhathakurta, Puragra [Department of Astronomy and Astrophysics, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 (United States); Schruba, Andreas [California Institute of Technology, Cahill Center for Astrophysics, 1200 E. California Blvd, Pasadena, CA 91125 (United States); Seth, Anil C. [University of Utah, Salt Lake City, UT (United States); Skillman, Evan D., E-mail: jd@astro.washington.edu [Minnesota Institute for Astrophysics, University of Minnesota, 116 Church Street SE, Minneapolis, MN 55455 (United States)

    2015-11-20

    We map the distribution of dust in M31 at 25 pc resolution using stellar photometry from the Panchromatic Hubble Andromeda Treasury survey. The map is derived with a new technique that models the near-infrared color–magnitude diagram (CMD) of red giant branch (RGB) stars. The model CMDs combine an unreddened foreground of RGB stars with a reddened background population viewed through a log-normal column density distribution of dust. Fits to the model constrain the median extinction, the width of the extinction distribution, and the fraction of reddened stars in each 25 pc cell. The resulting extinction map has a factor of ≳4 times better resolution than maps of dust emission, while providing a more direct measurement of the dust column. There is superb morphological agreement between the new map and maps of the extinction inferred from dust emission by Draine et al. However, the widely used Draine and Li dust models overpredict the observed extinction by a factor of ∼2.5, suggesting that M31's true dust mass is lower and that dust grains are significantly more emissive than assumed in Draine et al. The observed factor of ∼2.5 discrepancy is consistent with similar findings in the Milky Way by the Plank Collaboration et al., but we find a more complex dependence on parameters from the Draine and Li dust models. We also show that the the discrepancy with the Draine et al. map is lowest where the current interstellar radiation field has a harder spectrum than average. We discuss possible improvements to the CMD dust mapping technique, and explore further applications in both M31 and other galaxies.

  4. The Panchromatic Hubble Andromeda Treasury VIII: A Wide-Area, High-Resolution Map of Dust Extinction in M31

    CERN Document Server

    Dalcanton, Julianne J; Hogg, David W; Lang, Dustin; Leroy, Adam K; Gordon, Karl D; Sandstrom, Karin; Weisz, Daniel R; Williams, Benjamin F; Bell, Eric F; Dong, Hui; Gilbert, Karoline M; Gouliermis, Dimitrious A; Guhathakurta, Puragra; Lauer, Tod R; Schruba, Andreas; Seth, Anil C; Skillman, Evan D

    2015-01-01

    We map the distribution of dust in M31 at 25pc resolution, using stellar photometry from the Panchromatic Hubble Andromeda Treasury. We develop a new mapping technique that models the NIR color-magnitude diagram (CMD) of red giant branch (RGB) stars. The model CMDs combine an unreddened foreground of RGB stars with a reddened background population viewed through a log-normal column density distribution of dust. Fits to the model constrain the median extinction, the width of the extinction distribution, and the fraction of reddened stars. The resulting extinction map has >4 times better resolution than maps of dust emission, while providing a more direct measurement of the dust column. There is superb morphological agreement between the new map and maps of the extinction inferred from dust emission by Draine et al. 2014. However, the widely-used Draine & Li (2007) dust models overpredict the observed extinction by a factor of ~2.5, suggesting that M31's true dust mass is lower and that dust grains are sign...

  5. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C.

    Science.gov (United States)

    Mifsud, Borbala; Tavares-Cadete, Filipe; Young, Alice N; Sugar, Robert; Schoenfelder, Stefan; Ferreira, Lauren; Wingett, Steven W; Andrews, Simon; Grey, William; Ewels, Philip A; Herman, Bram; Happe, Scott; Higgs, Andy; LeProust, Emily; Follows, George A; Fraser, Peter; Luscombe, Nicholas M; Osborne, Cameron S

    2015-06-01

    Transcriptional control in large genomes often requires looping interactions between distal DNA elements, such as enhancers and target promoters. Current chromosome conformation capture techniques do not offer sufficiently high resolution to interrogate these regulatory interactions on a genomic scale. Here we use Capture Hi-C (CHi-C), an adapted genome conformation assay, to examine the long-range interactions of almost 22,000 promoters in 2 human blood cell types. We identify over 1.6 million shared and cell type-restricted interactions spanning hundreds of kilobases between promoters and distal loci. Transcriptionally active genes contact enhancer-like elements, whereas transcriptionally inactive genes interact with previously uncharacterized elements marked by repressive features that may act as long-range silencers. Finally, we show that interacting loci are enriched for disease-associated SNPs, suggesting how distal mutations may disrupt the regulation of relevant genes. This study provides new insights and accessible tools to dissect the regulatory interactions that underlie normal and aberrant gene regulation.

  6. Geographic Object-based Image Analysis for Developing Cryospheric Surface Mapping Application using Remotely Sensed High-Resolution Satellite Imagery

    Science.gov (United States)

    Jawak, S. D.; Luis, A. J.

    2015-12-01

    A novel semi-automated method was devised by coupling spectral index ratios (SIRs) and geographic object-based image analysis (GEOBIA) to extract cryospheric geoinformation from very high resolution WorldView 2 (WV-2) satellite imagery. The present study addresses development of multiple rule sets for GEOBIA-based classification of WV-2 imagery to accurately extract land cover features in the Larsemann Hills, Antarctica. Multi-level segmentation process was applied to WV-2 image to generate different sizes of geographic image objects corresponding to various land cover features w.r.t scale parameter. Several SIRs were applied to geographic objects at different segmentation levels to classify landmass, man-made features, snow/ice, and water bodies. A specific attention was paid to water body class to identify water areas at the image level, considering their uneven appearance on landmass and ice. The results illustrated that synergetic usage of SIRs and GEOBIA can provide accurate means to identify land cover classes with an overall classification accuracy of ≈97%. In conclusion, the results suggest that GEOBIA is a powerful tool for carrying out automatic and semiautomatic analysis for most cryospheric remote-sensing applications, and the synergetic coupling with pixel-based SIRs is found to be a superior method for mining geoinformation.

  7. Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.

    Directory of Open Access Journals (Sweden)

    So Yeon Kwon

    2016-04-01

    Full Text Available NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions.

  8. Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.

    Directory of Open Access Journals (Sweden)

    So Yeon Kwon

    2016-04-01

    Full Text Available NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions.

  9. Flood Damage Modeling on the Basis of Urban Structure Mapping Using High-Resolution Remote Sensing Data

    Directory of Open Access Journals (Sweden)

    Tina Gerl

    2014-08-01

    Full Text Available The modeling of flood damage is an important component for risk analyses, which are the basis for risk-oriented flood management, risk mapping, and financial appraisals. An automatic urban structure type mapping approach was applied on a land use/land cover classification generated from multispectral Ikonos data and LiDAR (Light Detection And Ranging data in order to provide spatially detailed information about the building stock of the case study area of Dresden, Germany. The multi-parameter damage models FLEMOps (Flood Loss Estimation Model for the private sector and regression-tree models have been adapted to the information derived from remote sensing data and were applied on the basis of the urban structure map. To evaluate this approach, which is suitable for risk analyses, as well as for post-disaster event analyses, an estimation of the flood losses caused by the Elbe flood in 2002 was undertaken. The urban structure mapping approach delivered a map with a good accuracy of 74% and on this basis modeled flood losses for the Elbe flood in 2002 in Dresden were in the same order of magnitude as official damage data. It has been shown that single-family houses suffered significantly higher damages than other urban structure types. Consequently, information on their specific location might significantly improve damage modeling, which indicates a high potential of remote sensing methods to further improve risk assessments.

  10. Soil depth map definition on a terraced slope for a following distributed, high resolution, numerical modelling analysis

    Science.gov (United States)

    Camera, C.; Apuani, T.; Mele, M.; Kuriakose, S. L.; Giudici, M.

    2012-04-01

    The soil thickness represents a key data for every environmental analysis involving soil, but its determination is not always simple. In this particular case, the study area is represented by a small terraced slope (0.6 km2) of Valtellina (Northern Italy), and the soil depth map is necessary for a coupled hydrogeological-stability analysis in a raster environment. During this work geometrical/morphological and geostatistical interpolation techniques were tested to obtain a satisfying soil depth map. At the end, the final product has been validated with geo-electrical resistivity inverse models. In this particular context, the presence of dry-stone retaining walls is of primary importance, since they have an influence on the morphology of the entire area as well as on the physical processes of water infiltration and slope stability. In order to consider the dry-stone walls in the analysis, it is necessary to have base maps with an adequate resolution (cells 1 m x 1 m). Assuming that the walls might be founded on bedrock or in its proximity, it was decided to use the heights of walls and the distribution of rock outcrops as soil depth input data. It was impossible to obtain direct measures with the knocking pole method, being pebbles frequently presents in the backfill soil . Except zero depth values, 682 measures were performed. The initial data set was divided into two subsets in order to use one as training points (76 % of the total) and the second as test points (24 %). Various techniques were tested, from linear multiple regressions with environmental predictors, to ordinary kriging, regression kriging with the same environmental variables, and Gaussian stochastic simulations. At the end, the best result was obtained with co-kriging, using a soil depth class map drawn from the field measures as co-variable. The result is a little bit guided but it was the only solution to obtain a map that partially takes into account the morphology of the slope. To verify the

  11. Vegetation mapping in the St Lucia estuary using very high-resolution multispectral imagery and LiDAR

    CSIR Research Space (South Africa)

    Lück-Vogel, Melanie

    2016-05-01

    Full Text Available (visible plus near infrared) in 0.65 m resolution. 397 Similarly, Swamp forest was consistently mapped with very high accuracies, apart from the 398 DEM-including runs 2 and 4 of the RapidEye images. In contrast, the class Grass and Shrubs 399 frequently... mapping in the St Lucia estuary using very high 1 resolution multispectral imagery and LiDAR 2 Melanie Lück-Vogel a, c,*, Cikizwa Mbolambi a, Kelly Rautenbach b, Janine Adams b, Lara 3 van Niekerk a 4 a Council for Scientific and Industrial Research, P...

  12. Ultra-high Resolution Mapping of the Inner Crater of the Active Kick'em Jenny Volcano

    Science.gov (United States)

    Hart, L.; Scott, C.; Tominaga, M.; Smart, C.; Vaughn, I.; Roman, C.; Carey, S.; German, C. R.; Participants, T.

    2015-12-01

    We conducted high-resolution geological characterization of a 0.015km^2 region of the inner crater of the most active submarine volcano in the Caribbean, Kick'em Jenny, located 8 km off Grenada in the Lesser Antilles Island Arc. We obtained digital still images and microbathymetery at an altitude of 3 m from the seafloor by using stereo cameras and a BlueView system mounted on Remotely Operated Vehicle (ROV) Hercules during the NA054 cruise on E/V Nautilus (Sept. - Oct. 2014). The seafloor images were processed to construct 2-D photo mosaics of the survey area using Standard Hercules Imaging Suite. We systematically classified the photographed seafloor geology based on the distribution of seafloor morphology and the observable rock fragment and outcrop sizes. The center of the crater floor shows a smooth, coherent texture with little variation in sea floor morphology. From immediately outside this area toward the crater rim, we observe an extensive area covered with outcrops, small rocks, and sediment: and within this area, (1) the north section is partially covered by uneven outcrops with elongated lineaments and a course, rugged seafloor with individual rock fragments observable; (2) the middle section contains high variability and heterogeneity in seafloor morphology in a non-systematic manner; and (3) overall, the southern most section displays subdued seafloor features both in space and variability compared to the other areas. The distributions of rock fragments were classified into four distinct sizes. We observe: (i) little variation in size distribution near the center of the crater floor; and (ii) rock fragment size increasing toward the rim of the crater. To obtain a better understanding of the link between variation in seafloor morphology, rock size distribution, and other in situ processes, we compare our observations on the digital photo mosaic to bathymetry data and ROV visuals (e.g. vents and bacterial mats).

  13. The songbird syrinx morphome: a three-dimensional, high-resolution, interactive morphological map of the zebra finch vocal organ

    Directory of Open Access Journals (Sweden)

    Düring Daniel N

    2013-01-01

    Full Text Available Abstract Background Like human infants, songbirds learn their species-specific vocalizations through imitation learning. The birdsong system has emerged as a widely used experimental animal model for understanding the underlying neural mechanisms responsible for vocal production learning. However, how neural impulses are translated into the precise motor behavior of the complex vocal organ (syrinx to create song is poorly understood. First and foremost, we lack a detailed understanding of syringeal morphology. Results To fill this gap we combined non-invasive (high-field magnetic resonance imaging and micro-computed tomography and invasive techniques (histology and micro-dissection to construct the annotated high-resolution three-dimensional dataset, or morphome, of the zebra finch (Taeniopygia guttata syrinx. We identified and annotated syringeal cartilage, bone and musculature in situ in unprecedented detail. We provide interactive three-dimensional models that greatly improve the communication of complex morphological data and our understanding of syringeal function in general. Conclusions Our results show that the syringeal skeleton is optimized for low weight driven by physiological constraints on song production. The present refinement of muscle organization and identity elucidates how apposed muscles actuate different syringeal elements. Our dataset allows for more precise predictions about muscle co-activation and synergies and has important implications for muscle activity and stimulation experiments. We also demonstrate how the syrinx can be stabilized during song to reduce mechanical noise and, as such, enhance repetitive execution of stereotypic motor patterns. In addition, we identify a cartilaginous structure suited to play a crucial role in the uncoupling of sound frequency and amplitude control, which permits a novel explanation of the evolutionary success of songbirds.

  14. Vegetation Fraction Mapping with Artificial Neural Network and High Resolution Multispectral Aerial Imagery Acquired During BEAREX07

    Science.gov (United States)

    Kersh, K. L.; Gowda, P. H.; Basu, S.; Howell, T. A.; O'Shaughnessy, S.; Rajan, N.; Akasheh, O. Z.

    2009-12-01

    Land surface models use vegetation fraction to more accurately partition latent, sensible and soil heat fluxes for a partial vegetated surface as it affects energy and moisture exchanges between the earth’s surface and atmosphere. In recent years, there is interest to integrate vegetation fraction data into intelligent irrigation scheduling systems to avoid false positive signals to irrigate. Remote sensing can facilitate the rapid collection of vegetation fraction information on individual fields over large areas in a timely and cost-effective manner. In this study, we developed a set of vegetation fraction models using least square regression and artificial neural network (ANN) techniques and evaluated using the data collected during Bushland Evapotranspiration and Agricultural Remote sensing Experiment 2007 (BEAREX07). During the BEAREX07, six aircraft campaigns were made covering bare soil to full crop cover conditions. High resolution multispectral data include 0.5-m visible (green and red) and near infrared images and 1.8-m thermal infrared images over the USDA-ARS-Conservation and Production Research Laboratory in Bushland, Texas [350 11' N, 1020 06' W; 1,170 m elevation MSL]. Atmospheric corrections were applied on these images before extracting spectral signatures for 40 ground truth locations. Field data collection in ground truth locations during the aircraft campaigns included digital pictures of crop cover using a Red/Infrared camera. Vegetation fraction information was derived from digital photos using a supervised classification. Comparison of performance statistics indicate that ANN performed slightly better than least square regression models. Newly developed fraction vegetation models will be used in the evaluation of land surface energy balance based evapotranspiration models.

  15. High-Resolution fMRI of Auditory Cortical Map Changes in Unilateral Hearing Loss and Tinnitus

    NARCIS (Netherlands)

    Ghazaleh, Naghmeh; Van der Zwaag, W.; Clarke, Stephanie; Ville, Dimitri Van De; Maire, Raphael; Saenz, Melissa

    2017-01-01

    Animal models of hearing loss and tinnitus observe pathological neural activity in the tonotopic frequency maps of the primary auditory cortex. Here, we applied ultra high-field fMRI at 7 T to test whether human patients with unilateral hearing loss and tinnitus also show altered functional activity

  16. Enhancing hydrologic mapping using LIDAR and high resolution aerial photos on the Frances Marion National Forest in coastal South Carolina

    Science.gov (United States)

    Andy Maceyka; William F. Hansen

    2016-01-01

    Evaluating hydrology within coastal marine terrace features has always been problematic as watershed boundaries and stream detail are difficult to determine in low gradient terrain with dense bottomland forests. Various studies have improved hydrologic detail using USGS Topographic Contour Maps (Hansen 2001, Eidson and others 2005) or Light Detection and Ranging (LIDAR...

  17. High-resolution precipitation mapping in a mountainous watershed: ground truth for evaluating uncertainty in a national precipitation dataset

    Science.gov (United States)

    Christopher Daly; Melissa E. Slater; Joshua A. Roberti; Stephanie H. Laseter; Lloyd W. Swift

    2017-01-01

    A 69-station, densely spaced rain gauge network was maintained over the period 1951–1958 in the Coweeta Hydrologic Laboratory, located in the southern Appalachians in western North Carolina, USA. This unique dataset was used to develop the first digital seasonal and annual precipitation maps for the Coweeta basin, using elevation regression functions and...

  18. Large-scale, high-resolution wind resource mapping for wind farm planning and development in South Africa

    DEFF Research Database (Denmark)

    Mortensen, Niels Gylling; Badger, Jake; Hansen, Jens Carsten

    2014-01-01

    Numerical wind atlas data at 5 km resolution have been used to map the wind resources of the Wind Atlas for South Africa (WASA) domain in great detail: mean wind speed, mean wind power density, elevation and ruggedness index for every 250 metres over an area of 350,000 square kilometres. The wind...

  19. High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations.

    Science.gov (United States)

    2014-12-11

    Cassava (Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400-500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculenta Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. We used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selection-enhanced breeding of this important crop.

  20. High-resolution AUV mapping and sampling of a deep hydrocarbon plume in the Gulf of Mexico

    Science.gov (United States)

    Ryan, J. P.; Zhang, Y.; Thomas, H.; Rienecker, E.; Nelson, R.; Cummings, S.

    2010-12-01

    During NOAA cruise GU-10-02 on the Ship Gordon Gunter, the Monterey Bay Aquarium Research Institute (MBARI) autonomous underwater vehicle (AUV) Dorado was deployed to map and sample a deep (900-1200 m) volume centered approximately seven nautical miles southwest of the Deepwater Horizon wellhead. Dorado was equipped to detect optical and chemical signals of hydrocarbons and to acquire targeted samples. The primary sensor reading used for hydrocarbon detection was colored dissolved organic matter (CDOM) fluorescence (CF). On June 2 and 3, ship cast and subsequent AUV surveys detected elevated CF in a layer between 1100 and 1200 m depth. While the deep volume was mapped in a series of parallel vertical sections, the AUV ran a peak-capture algorithm to target sample acquisition at layer signal peaks. Samples returned by ship CTD/CF rosette sampling and by AUV were preliminarily examined at sea, and they exhibited odor and fluorometric signal consistent with oil. More definitive and detailed results on these samples are forthcoming from shore-based laboratory analyses. During post-cruise analysis, all of the CF data were analyzed to objectively define and map the deep plume feature. Specifically, the maximum expected background CF over the depth range 1000-1200 m was extrapolated from a linear relationship between depth and maximum CF over the depth range 200 to 1000 m. Values exceeding the maximum expected background in the depth range 1000-1200 m were interpreted as signal from a hydrocarbon-enriched plume. Using this definition we examine relationships between CF and other AUV measurements within the plume, illustrate the three-dimensional structure of the plume boundary region that was mapped, describe small-scale layering on isopycnals, and examine short-term variations in plume depth, intensity and hydrographic relationships. Three-dimensional representation of part of a deep hydrocarbon plume mapped and sampled by AUV on June 2-3, 2010.

  1. High Resolution Urban Land Cover Mapping Using NAIP Aerial Photography and Image Processing for the USEPA National Atlas of Sustainability and Ecosystem Services

    Science.gov (United States)

    Pilant, A. N.; Baynes, J.; Dannenberg, M.

    2012-12-01

    The US EPA National Atlas for Sustainability is a web-based, easy-to-use, mapping application that allows users to view and analyze multiple ecosystem services in a specific region. The Atlas provides users with a visual method for interpreting ecosystem services and understanding how they can be conserved and enhanced for a sustainable future. The Urban Atlas component of the National Atlas will provide fine-scale information linking human health and well-being to environmental conditions such as urban heat islands, near-road pollution, resource use, access to recreation, drinking water quality and other quality of life indicators. The National Land Cover Data (NLCD) derived from 30 m scale 2006 Landsat imagery provides the land cover base for the Atlas. However, urban features and phenomena occur at finer spatial scales, so higher spatial resolution and more current LC maps are required. We used 4 band USDA NAIP imagery (1 m pixel size) and various classification approaches to produce urban land cover maps with these classes: impervious surface, grass and herbaceous, trees and forest, soil and barren, and water. Here we present the remote sensing methods used and results from four pilot cities in this effort, highlighting the pros and cons of the approach, and the benefits to sustainability and ecosystem services analysis. Example of high resolution land cover map derived from USDA NAIP aerial photo. Compare 30 m and 1 m resolution land cover maps of downtown Durham, NC.

  2. Combined high-resolution aeromagnetic and radiometric mapping of uranium mineralization and tectonic settings in Northeastern Nigeria

    Science.gov (United States)

    Adepelumi, A. A.; Falade, A. H.

    2017-09-01

    Geological lineaments, depths to the basement, uranium concentrations, and remobilization in parts of the Upper Benue Trough, covering about 55 × 55 km2 (longitudes 11°30'-12°00'E and 10°30'-10°30'N), Northeastern Nigeria were investigated using integrated High-Resolution Aeromagnetic Data (HRAD) and radiometric data. This was with a view to identifying the potential zones of uranium occurrence in the area. The HRAD was processed to accentuate anomalies of interest and depths estimate of 150-1941 m were obtained from source parameter imaging technique. The results from the superposition of the horizontal gradient magnitude, analytical signal amplitude, first vertical derivative, and 3D Euler solutions of the HRAD revealed that the study area was dissected by linear structures that trend ENE-WSW, NE-SW, E-W, NNE-SSW, WNW-ESE, and NW-SE; among which the ENE-WSW and NE-SW trends dominated. Analyses of radiometric data showed that uranium ores in the study area were possibly remobilized epigenetically from the granitic rocks, and were later deposited into sedimentary rocks (Bima formation). Burashika group (Bongna hills) and Wawa area of the study area showed vein-type deposits, while the anatectic migmatite in the northeastern region and the uranium rich Bima formation showed both fault/fracture and contact types of deposition. It was also observed the northwesterly and southeasterly, dominant dip direction, dipping faults dip in the same direction as the paleocurrent direction (direction of depositions of sediments), and trend in a direction perpendicular to the hypothetical direction of uranium deposition. The study concluded that the studied area is dissected by several linear structures and the studied area possibly contains deposits of uranium ore, which are likely to be found in: the Bima Sandstones of Wade, Shinga, Bima hill, Wuyo, Teli, Bryel, Dali, Barkan, Gasi, Kunkun, Boragara, Deba, and Gberundi localities; the anatectic migmatite at Kubuku, Whada

  3. Mapping the Structure of the Lithosphere-Asthenosphere System Under the Alpine Orogen with High-Resolution Teleseismic Tomography

    Science.gov (United States)

    Lippitsch, R.; Kissling, E.; Ansorge, J.

    2001-12-01

    Understanding the evolution of the Alpine orogen and the interaction between different lithospheric blocks requires precise knowledge of the structure of the lithosphere-asthenosphere system. To assess the gross features of the uppermost mantel we perform high-resolution teleseismic tomography. The data base encompasses 5000 manually picked first P-arrivals from 220 teleseismic events with even azimuthal distribution recorded at permanent and temporary seismic networks in the greater Alpine area. The tomographic study consists of these components: (1) Corrections for the contribution of the Alpine crust to travel-times of incoming wave fields that may account for up to 50% of the observed travel-time residuals. The 3-D crustal model established from controlled-source seismology data represents the large-scale Alpine crustal structure which clearly reflects the effects of the African-European plate collision. (2) Tests with synthetic data document that the combination of non-linear inversions, high-quality teleseismic data, and usage of an a priori 3-D crustal model allows reliable resolution of cells at 50km*50km*30km with a velocity variation in the order of +/- 3% in the upper mantle. (3) Our tomographic images illuminate the structure of the uppermost mantle to depth of 400 km reflecting the complex processes that formed the Alpine orogen when three different plates were amalgamated (European, Adriatic, and Ligurian plates). In the western Alps, the inversion results show a steep W-E dipping high-velocity anomaly which we interpret as the subducting European plate. In the eastern Alps we find high-velocity anomalies in a depth range of 150 km to 300 km beneath the axis of the orogen. At present, the relation of this material with European or Adriatic lithosphere remains unclear. Our results are in general agreement with earlier lithospheric studies. However, the increase in resolution illuminates significantly more complex lithospheric slab geometries, which

  4. High resolution three-dimensional magnetization mapping in Tokachidake Volcano using low altitude airborne magnetic survey data

    Science.gov (United States)

    Iwata, M.; Mogi, T.; Okuma, S.; Nakatsuka, T.

    2016-12-01

    Tokachidake Volcano, central Hokkaido, Japan erupted in 1926, 1962 and 1988-1989 in the 20th century from the central part. In recent years, expansions of the edifice of the volcano at shallow depth and increases of the volcanic smoke in the Taisho crater were observed (Meteorological Agency of Japan, 2014). Magnetic changes were observed at the 62-2 crater by repeated magnetic measurements in 2008-2009, implying a demagnetization beneath the crater (Hashimoto at al., 2010). Moreover, a very low resistivity part was found right under the 62-2 crater from an AMT survey (Yamaya et al., 2010). However, since the station numbers of the survey are limited, the area coverage is not sufficient. In this study, we have re-analyzed high-resolution aeromagnetic data to delineate the three-dimensional magnetic structure of the volcano to understand the nature of other craters.A low altitude airborne magnetic survey was conducted in 2014 mainly over the active areas of the volcano by the Ministry of Land, Infrastructure, Transport and Tourism to manage land slide risk in the volcano. The survey was flown at an altitude of 60 m above ground by a helicopter with a Cesium magnetometer in the towed-bird 30m below the helicopter. The low altitude survey enables us to delineate the detailed magnetic structure. We calculated magnetic anomaly distribution on a smooth surface assuming equivalent anomalies below the observation surface. Then the 3D magnetic imaging method (Nakatsuka and Okuma, 2014) was applied to the magnetic anomalies to reveal the three-dimensional magnetic structure.As a result, magnetization highs were seen beneath the Ground crater, Suribachi crater and Kitamuki crater. This implies that magmatic activity occurred in the past at these craters. These magma should have already solidified and acquired strong remanent magnetization. Relative magnetization lows were seen beneath the 62-2 crater and the Taisho crater where fumarolic activity is active. However a

  5. High-resolution maps of the 1.5 GHz emission from Jupiter's disk and radiation belt

    Science.gov (United States)

    Roberts, J. A.; Berge, G. L.; Bignell, R. C.

    1984-01-01

    VLA maps of four different faces of Jupiter made with a resolution of about 0.3 Jovian radius show new features of the radiation belt emission. A synchrotron model which reproduces these features serves to define the major characteristics of the relativistic electrons in the radiation belt. The observations provide the best determination to date of the atmospheric emission at 1.5 GHz and yield a disk brightness temperature of 425 + or - 100 K.

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

    OpenAIRE

    Guyon, Richard; Rakotomanga, Michaelle; Azzouzi, Naoual; Coutanceau, Jean Pierre; Bonillo, Celine; D’Cotta, Helena; Pepey, Elodie; Soler, Lucile; Rodier-Goud, Marguerite; D’Hont, Angelique; Conte, Matthew A; van Bers, Nikkie EM; Penman, David J.; Hitte, Christophe; Crooijmans, Richard Pma

    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 en...

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

    OpenAIRE

    Guyon, Richard; Rakotomanga, Michaëlle; Azzouzi, Naoual; Coutanceau, Jean-Pierre; Bonillo, Celine; D'Cotta, Helena; Pepey, Elodie; Soler, Lucile; Rodier-Goud, Marguerite; D'Hont, Angélique; Conte, Matthew,; Van Bers, Nikkie; Penman, David,; Hitte, Christophe; Crooijmans, Richard P M A

    2012-01-01

    BACKGROUND: The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. Itis also an important model for studies of fish physiology, particularly because of its broadtolerance to an array of environments. It is a good model to study evolutionary mechanismsin vertebrates, because of its close relationship to haplochromine cichlids, which haveundergone rapid speciation in East Africa. The existing genomic resources for Nile tilapiainclude a genetic map, BAC end se...

  8. The eastern arm of M83 revisited : High-resolution mapping of (CO)-C-12 1-0 emission

    NARCIS (Netherlands)

    Rand, RJ; Lord, SD; Higdon, JL

    1999-01-01

    We have used the Owens Valley Millimeter Array to map (CO)-C-12 (J = 1-0) along a 3.5 kpc segment of the eastern spiral arm of M83 at resolutions of 6 ".5 x 3 ".5, 10 ", and 16 ". The CO emission in most of this segment lies along the sharp dust lane demarcating the inner edge of the spiral arm, but

  9. Development of New Accurate, High Resolution DEMs and Merged Topographic-Bathymetric Grids for Inundation Mapping in Seward Alaska

    Science.gov (United States)

    Marriott, D.; Suleimani, E.; Hansen, R.

    2004-05-01

    The Geophysical Institute of the University of Alaska Fairbanks and the Alaska Division of Geological and Geophysical Surveys continue to participate in the National Tsunami Hazard Mitigation Program by evaluating and mapping potential inundation of selected coastal communities in Alaska. Seward, the next Alaskan community to be mapped, has excellent bathymetric data but very poor topographic data available. Since one of the most significant sources of errors in tsunami inundation mapping is inaccuracy of topographic and bathymetric data, the Alaska Tsunami Modeling Team cooperated with the local USGS glaciology office to perform photogrammetry in the Seward area to produce a new DEM. Using ten air photos and the APEX photogrammetry and analysis software, along with several precisely located GPS points, we developed a new georeferenced and highly accurate DEM with a 5-meter grid spacing. A variety of techniques were used to remove the effects of buildings and trees to yield a bald earth model. Finally, we resampled the new DEM to match the finest resolution model grid, and combined it with all other data, using the most recent and accurate data in each region. The new dataset has contours that deviate by more than 100 meters in some places from the contours in the previous dataset, showing significant improvement in accuracy for the purpose of tsunami modeling.

  10. Scalable, incremental learning with MapReduce parallelization for cell detection in high-resolution 3D microscopy data

    KAUST Repository

    Sung, Chul

    2013-08-01

    Accurate estimation of neuronal count and distribution is central to the understanding of the organization and layout of cortical maps in the brain, and changes in the cell population induced by brain disorders. High-throughput 3D microscopy techniques such as Knife-Edge Scanning Microscopy (KESM) are enabling whole-brain survey of neuronal distributions. Data from such techniques pose serious challenges to quantitative analysis due to the massive, growing, and sparsely labeled nature of the data. In this paper, we present a scalable, incremental learning algorithm for cell body detection that can address these issues. Our algorithm is computationally efficient (linear mapping, non-iterative) and does not require retraining (unlike gradient-based approaches) or retention of old raw data (unlike instance-based learning). We tested our algorithm on our rat brain Nissl data set, showing superior performance compared to an artificial neural network-based benchmark, and also demonstrated robust performance in a scenario where the data set is rapidly growing in size. Our algorithm is also highly parallelizable due to its incremental nature, and we demonstrated this empirically using a MapReduce-based implementation of the algorithm. We expect our scalable, incremental learning approach to be widely applicable to medical imaging domains where there is a constant flux of new data. © 2013 IEEE.

  11. Epicardial-endocardial breakthrough during stable atrial macroreentry: Evidence from ultra-high-resolution 3-dimensional mapping.

    Science.gov (United States)

    Pathik, Bhupesh; Lee, Geoffrey; Sacher, Frédéric; Haïssaguerre, Michel; Jaïs, Pierre; Massoullié, Grégoire; Derval, Nicolas; Sanders, Prashanthan; Kistler, Peter; Kalman, Jonathan M

    2017-08-01

    Evidence for epicardial-endocardial breakthrough (EEB) is derived from mapping inferences in patients with atrial fibrillation who may also have focal activations. The purpose of this study was to investigate whether EEB could be discerned during stable right atrial (RA) macroreentry using high-density high-spatial resolution 3-dimensional mapping. Macroreentry was diagnosed using 3-dimensional mapping and entrainment. Bipolar maps were reviewed for EEB defined as (1) presence of focal endocardial activation with radial spread unaccounted for by an endocardial wavefront and (2) present with the same timing on every tachycardia cycle. The EEB site was always in proximity to a line of endocardial conduction slowing or block. Distance and conduction velocity from the line of block to the EEB site was calculated. Electrograms at EEB sites were individually analyzed for morphology and to confirm direction of activation. Entrainment was performed at EEB sites. Twenty-six patients were studied. Fourteen examples of EEB were seen: 11 at the posterior RA (4 at the superior portion of the posterior wall and 7 at the inferior section) and 1 each at the cavotricuspid isthmus postablation, RA septum, and inferolateral RA. The mean area of the EEB site was 0.6 ± 0.2 cm(2). A mean of 79.5% ± 18.6% of unipolar electrograms at the EEB site demonstrated an rS morphology. The mean distance and conduction velocity from the line of endocardial block to the EEB site at the posterior RA was 13.6 ± 2.3 mm and 59.3 ± 12.3 cm/s, respectively. In 4 patients, entrainment demonstrated that EEB sites were within the circuit and in 1 of these patients critical to arrhythmia maintenance. Activation maps during tachycardia and coronary sinus pacing demonstrated EEB at the same anatomic site. EEB sites were demonstrated in stable atrial macroreentry supported by systematic entrainment confirmation and demonstration of the same phenomenon during pacing. Copyright © 2017 Heart Rhythm Society

  12. A High-Resolution InDel (Insertion–Deletion) Markers-Anchored Consensus Genetic Map Identifies Major QTLs Governing Pod Number and Seed Yield in Chickpea

    Science.gov (United States)

    Srivastava, Rishi; Singh, Mohar; Bajaj, Deepak; Parida, Swarup K.

    2016-01-01

    Development and large-scale genotyping of user-friendly informative genome/gene-derived InDel markers in natural and mapping populations is vital for accelerating genomics-assisted breeding applications of chickpea with minimal resource expenses. The present investigation employed a high-throughput whole genome next-generation resequencing strategy in low and high pod number parental accessions and homozygous individuals constituting the bulks from each of two inter-specific mapping populations [(Pusa 1103 × ILWC 46) and (Pusa 256 × ILWC 46)] to develop non-erroneous InDel markers at a genome-wide scale. Comparing these high-quality genomic sequences, 82,360 InDel markers with reference to kabuli genome and 13,891 InDel markers exhibiting differentiation between low and high pod number parental accessions and bulks of aforementioned mapping populations were developed. These informative markers were structurally and functionally annotated in diverse coding and non-coding sequence components of genome/genes of kabuli chickpea. The functional significance of regulatory and coding (frameshift and large-effect mutations) InDel markers for establishing marker-trait linkages through association/genetic mapping was apparent. The markers detected a greater amplification (97%) and intra-specific polymorphic potential (58–87%) among a diverse panel of cultivated desi, kabuli, and wild accessions even by using a simpler cost-efficient agarose gel-based assay implicating their utility in large-scale genetic analysis especially in domesticated chickpea with narrow genetic base. Two high-density inter-specific genetic linkage maps generated using aforesaid mapping populations were integrated to construct a consensus 1479 InDel markers-anchored high-resolution (inter-marker distance: 0.66 cM) genetic map for efficient molecular mapping of major QTLs governing pod number and seed yield per plant in chickpea. Utilizing these high-density genetic maps as anchors, three major

  13. High-resolution genetic mapping in the diversity outbred mouse population identifies Apobec1 as a candidate gene for atherosclerosis.

    Science.gov (United States)

    Smallwood, Tangi L; Gatti, Daniel M; Quizon, Pamela; Weinstock, George M; Jung, Kuo-Chen; Zhao, Liyang; Hua, Kunjie; Pomp, Daniel; Bennett, Brian J

    2014-10-23

    Inbred mice exhibit strain-specific variation in susceptibility to atherosclerosis and dyslipidemia that renders them useful in dissecting the genetic architecture of these complex diseases. Traditional quantitative trait locus (QTL) mapping studies using inbred strains often identify large genomic regions, containing many genes, due to limited recombination and/or sample size. This hampers candidate gene identification and translation of these results into possible risk factors and therapeutic targets. An alternative approach is the use of multiparental outbred lines for genetic mapping, such as the Diversity Outbred (DO) mouse panel, which can be more informative than traditional two-parent crosses and can aid in the identification of causal genes and variants associated with QTL. We fed 292 female DO mice either a high-fat, cholesterol-containing (HFCA) diet, to induce atherosclerosis, or a low-fat, high-protein diet for 18 wk and measured plasma lipid levels before and after diet treatment. We measured markers of atherosclerosis in the mice fed the HFCA diet. The mice were genotyped on a medium-density single-nucleotide polymorphism array and founder haplotypes were reconstructed using a hidden Markov model. The reconstructed haplotypes were then used to perform linkage mapping of atherosclerotic lesion size as well as plasma total cholesterol, triglycerides, insulin, and glucose. Among our highly significant QTL we detected a ~100 kb QTL interval for atherosclerosis on Chromosome 6, as well as a 1.4 Mb QTL interval on Chromosome 9 for triglyceride levels at baseline and a coincident 22.2 Mb QTL interval on Chromosome 9 for total cholesterol after dietary treatment. One candidate gene within the Chromosome 6 peak region associated with atherosclerosis is Apobec1, the apolipoprotein B (ApoB) mRNA-editing enzyme, which plays a role in the regulation of ApoB, a critical component of low-density lipoprotein, by editing ApoB mRNA. This study demonstrates the value

  14. High Resolution Mapping and Interpretation of Channel and Floodplain Topography With a Narrow-Beam Terrestrial-Aquatic Lidar

    Science.gov (United States)

    McKean, J.; Isaak, D.; Tonina, D.; Wright, W.; Kinzel, P.

    2007-12-01

    Basic description of channel and floodplain topography remains a fundamental challenge for modeling flow and sediment transport or even simply mapping habitat. Standard field wading and boat surveys of stream topography are limited by costs and logistics to relatively small sample reaches and floodplain maps are seldom well- integrated with channel bathymetry. We used the NASA Experimental Advanced Airborne Research Lidar (EAARL) to map channel and floodplain topography and investigate geomorphic controls on physical habitat in two diverse channels in the watershed of the Middle Fork Salmon River, Idaho. Bear Valley Creek is a small low-gradient gravel-bed stream flowing across an unconfined valley filled with glacial outwash materials. A hierarchy of nested geomorphic features is evident in this channel with the broadest fluvial domains a legacy of ~15,000 years of post-glacial valley evolution. Contemporary hydraulics operate on this broad template and control two smaller scales of pool-riffle morphology. Salmon spawning patterns closely reflect these nested physical domains, demonstrating how geomorphic history can influence modern distributions of aquatic habitat and organisms. In contrast, Big Creek is a higher-gradient stream predominately confined by steep side slopes in a deep valley. Here, the distribution of geomorphic domains and physical habitat is controlled by modern erosion processes and rock quality. Tributaries and valley walls contribute coarse debris, up to large boulders, to the channel, resulting in very rough and poorly organized bed topography. Tributary fans also function as local grade control with sediment deposition in lower-gradient reaches upstream of fans. A GIS toolkit is under development to extract at-a-station channel metrics from EAARL data, including for example, cross section and longitudinal profile characteristics. A new investigation has also begun to further investigate the quality of EAARL data. This study will explore the

  15. Terrane daylight mapping on large dip-slope terrain based on high-resolution DTM and semi-automatic geoprocessing processes

    Science.gov (United States)

    Yeh, Chih-Hsiang; Lin, Ming-Lang; Chan, Yu-Chang; Chang, Kuo-Jen; Hsieh, Yu-Chung

    2015-04-01

    "Daylight" in slope engineering means a lineament appearing on the ground surface casued by a internal weak plane of a rock slope. The morphology of the daylight implies the free surface condition of the rock mass upper the weak plane, directly affecting the slope stability and safety. Traditionally, the reconnaissance of daylight employs field investigation and drillings in local dip slope area, but when mapping in large area, it would be subjected to vegetation cover and budget limitation to get a simply result not used for engineering applications. Therefore, the purpose of this study is to develop a rapid and reliable mapping program based on high-resolution DTM, and to generate a large-scale daylight map for large dip slope area. The methodology can be divided into two phases: the first is re-mapping terrane boundary lineaments using LiDAR data and 3D GIS mapping technology; the second is automatically mapping daylight tracks by trend surface analysis and python scripts based on above terrane boundary lineaments. This study takes the area of Keelung River north bank, which is mainly cuesta topography, for an example. Recently, in the area, the frequency of dip slope landslide occurrence becomes more higher because of human development. One major reason to cause the daylight appearing on downslope is the slope toe cutting or river incision. Hereby, according to the final results of the daylight map, we can assess where the potential landsides dip slops are, and further differentiate three different risks of dip slope from the daylight's morphology, expecting to provide more detail engineering and geological information for furture engineering site selection and the design and application of disaster prevention.

  16. VLA High Resolution 1.4 and 8.4 GHz Mapping of the Barred Galaxy NGC 3367

    CERN Document Server

    García-Barreto, J A; Rudnick, L; Franco, Jose; Rudnick, Larry

    2002-01-01

    We report new radio continuum observations with an angular resolution of 2''.1 at 1.4 GHz and 0''.28 at 8.4 GHz of the barred galaxy NGC 3367. In the map at 1.4 GHz the central nuclear region connects to the SW lobe, with a projected structure at a position angle of PA = 230 forming a jet-like structure. The map at 8.4 GHz shows a compact unresolved source (smaller than 65 pc in diameter) associated with emission from the nucleus and several compact sources located within a radius of about 300 pc, forming a circumnuclear structure. The compact core, jet, and lobes form a small, low power counterpart to radio galaxies, with a flow axis that is out of the plane of the galaxy. The flow axis (PA=230) coincides with the PA of the major axis of the galaxy and is thus inclined to the rotation axis of the disk. In addition, the flow axis differs by about 20 deg. from the major axis of the stellar bar. Assuming that the stellar bar rotates counterclockwise (ie. assuming trailing spiral arms), this difference in angle ...

  17. Experiment LEND of the NASA Lunar Reconnaissance Orbiter for high-resolution mapping of neutron emission of the Moon.

    Science.gov (United States)

    Mitrofanov, I G; Sanin, A B; Golovin, D V; Litvak, M L; Konovalov, A A; Kozyrev, A S; Malakhov, A V; Mokrousov, M I; Tretyakov, V I; Troshin, V S; Uvarov, V N; Varenikov, A B; Vostrukhin, A A; Shevchenko, V V; Shvetsov, V N; Krylov, A R; Timoshenko, G N; Bobrovnitsky, Y I; Tomilina, T M; Grebennikov, A S; Kazakov, L L; Sagdeev, R Z; Milikh, G N; Bartels, A; Chin, G; Floyd, S; Garvin, J; Keller, J; McClanahan, T; Trombka, J; Boynton, W; Harshman, K; Starr, R; Evans, L

    2008-08-01

    The scientific objectives of neutron mapping of the Moon are presented as 3 investigation tasks of NASA's Lunar Reconnaissance Orbiter mission. Two tasks focus on mapping hydrogen content over the entire Moon and on testing the presence of water-ice deposits at the bottom of permanently shadowed craters at the lunar poles. The third task corresponds to the determination of neutron contribution to the total radiation dose at an altitude of 50 km above the Moon. We show that the Lunar Exploration Neutron Detector (LEND) will be capable of carrying out all 3 investigations. The design concept of LEND is presented together with results of numerical simulations of the instrument's sensitivity for hydrogen detection. The sensitivity of LEND is shown to be characterized by a hydrogen detection limit of about 100 ppm for a polar reference area with a radius of 5 km. If the presence of ice deposits in polar "cold traps" is confirmed, a unique record of many millions of years of lunar history would be obtained, by which the history of lunar impacts could be discerned from the layers of water ice and dust. Future applications of a LEND-type instrument for Mars orbital observations are also discussed.

  18. LAND-COVER DENSITY-BASED APPROACH TO URBAN LAND USE MAPPING USING HIGH-RESOLUTION IMAGERY

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiu-ying; FENG Xue-zhi; DENG Hui

    2005-01-01

    Nowadays, remote sensing imagery, especially with its high spatial resolution, has become an indispensable tool to provide timely up-gradation of urban land use and land cover information, which is a prerequisite for proper urban planning and management. The possible method described in the present paper to obtain urban land use types is based on the principle that land use can be derived from the land cover existing in a neighborhood. Here, moving window is used to represent the spatial pattern of land cover within a neighborhood and seven window sizes (61m×61 m,68m×68m, 75m×75m, 87m×87m, 99m×99m, 110m×110m and 121m×121m) are applied to determining the most proper window size. Then, the unsupervised method of ISODATA is employed to classify the layered land cover density maps obtained by the moving window. The results of accuracy evaluation show that the window size of 99m×99m is proper to infer urban land use categories and the proposed method has produced a land use map with a total accuracy of 85%.

  19. Genome-wide high-resolution mapping of UV-induced mitotic recombination events in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Yi Yin

    2013-10-01

    Full Text Available In the yeast Saccharomyces cerevisiae and most other eukaryotes, mitotic recombination is important for the repair of double-stranded DNA breaks (DSBs. Mitotic recombination between homologous chromosomes can result in loss of heterozygosity (LOH. In this study, LOH events induced by ultraviolet (UV light are mapped throughout the genome to a resolution of about 1 kb using single-nucleotide polymorphism (SNP microarrays. UV doses that have little effect on the viability of diploid cells stimulate crossovers more than 1000-fold in wild-type cells. In addition, UV stimulates recombination in G1-synchronized cells about 10-fold more efficiently than in G2-synchronized cells. Importantly, at high doses of UV, most conversion events reflect the repair of two sister chromatids that are broken at approximately the same position whereas at low doses, most conversion events reflect the repair of a single broken chromatid. Genome-wide mapping of about 380 unselected crossovers, break-induced replication (BIR events, and gene conversions shows that UV-induced recombination events occur throughout the genome without pronounced hotspots, although the ribosomal RNA gene cluster has a significantly lower frequency of crossovers.

  20. High resolution spectroscopic mapping imaging applied in situ to multilayer structures for stratigraphic identification of painted art objects

    Science.gov (United States)

    Karagiannis, Georgios Th.

    2016-04-01

    The development of non-destructive techniques is a reality in the field of conservation science. These techniques are usually not so accurate, as the analytical micro-sampling techniques, however, the proper development of soft-computing techniques can improve their accuracy. In this work, we propose a real-time fast acquisition spectroscopic mapping imaging system that operates from the ultraviolet to mid infrared (UV/Vis/nIR/mIR) area of the electromagnetic spectrum and it is supported by a set of soft-computing methods to identify the materials that exist in a stratigraphic structure of paint layers. Particularly, the system acquires spectra in diffuse-reflectance mode, scanning in a Region-Of-Interest (ROI), and having wavelength range from 200 up to 5000 nm. Also, a fuzzy c-means clustering algorithm, i.e., the particular soft-computing algorithm, produces the mapping images. The evaluation of the method was tested on a byzantine painted icon.

  1. A high-resolution linkage map of the citrus tristeza virus resistance gene region in Poncirus trifoliata (L.) Raf.

    Science.gov (United States)

    Fang, D Q; Federici, C T; Roose, M L

    1998-10-01

    Resistance to citrus tristeza virus (CTV) was evaluated in 554 progeny of 10 populations derived from Poncirus trifoliata. A dominant gene (Ctv) controlled CTV resistance in P. trifoliata. Twenty-one dominant PCR-based DNA markers were identified as linked to Ctv by bulked segregant analysis. Of the 11 closest markers to Ctv, only 2 segregated in all populations. Ten of these markers were cloned and sequenced, and codominant RFLP markers were developed. Seven RFLP markers were then evaluated in 10 populations. Marker orders were consistent in all linkage maps based on data of single populations or on combined data of populations with similar segregation patterns. In a consensus map, the six closest marker loci spanned 5.3 cM of the Ctv region. Z16 cosegregated with Ctv. C19 and AD08 flanked Ctv at distances of 0.5 and 0.8 cM, respectively. These 3 markers were present as single copies in the Poncirus genome, and could be used directly for bacterial artificial chromosome library screening to initiate a walk toward Ctv. BLAST searches of the GenBank database revealed high sequence similarities between 2 markers and known plant disease resistance genes, indicating that a resistance gene cluster exists in the Ctv region in P. trifoliata.

  2. High-resolution topography along surface rupture of the 16 October 1999 Hector Mine, California (Mw 7.1) from airborne laser swath mapping

    Science.gov (United States)

    Hudnutt, K.W.; Borsa, A.; Glennie, C.; Minster, J.-B.

    2002-01-01

    In order to document surface rupture associated with the Hector Mine earthquake, in particular, the area of maximum slip and the deformed surface of Lavic Lake playa, we acquired high-resolution data using relatively new topographic-mapping methods. We performed a raster-laser scan of the main surface breaks along the entire rupture zone, as well as along an unruptured portion of the Bullion fault. The image of the ground surface produced by this method is highly detailed, comparable to that obtained when geologists make particularly detailed site maps for geomorphic or paleoseismic studies. In this case, however, for the first time after a surface-rupturing earthquake, the detailed mapping is along the entire fault zone rather than being confined to selected sites. These data are geodetically referenced, using the Global Positioning System, thus enabling more accurate mapping of the rupture traces. In addition, digital photographs taken along the same flight lines can be overlaid onto the precise topographic data, improving terrain visualization. We demonstrate the potential of these techniques for measuring fault-slip vectors.

  3. Urban land use/land cover mapping with high-resolution SAR imagery by integrating support vector machines into object-based analysis

    Science.gov (United States)

    Hu, Hongtao; Ban, Yifang

    2008-10-01

    This paper investigates the capability of high-resolution SAR data for urban landuse/land-cover mapping by integrating support vector machines (SVMs) into object-based analysis. Five-date RADARSAT fine-beam C-HH SAR images with a pixel spacing of 6.25 meter were acquired over the rural-urban fringe of the Great Toronto Area (GTA) during May to August in 2002. First, the SAR images were segmented using multi-resolution segmentation algorithm and two segmentation levels were created. Next, a range of spectral, shape and texture features were selected and calculated for all image objects on both levels. The objects on the lower level then inherited features of their super objects. In this way, the objects on the lower level received detailed descriptions about their neighbours and contexts. Finally, SVM classifiers were used to classify the image objects on the lower level based on the selected features. For training the SVM, sample image objects on the lower level were used. One-against-one approach was chosen to apply SVM to multiclass classification of SAR images in this research. The results show that the proposed method can achieve a high accuracy for the classification of high-resolution SAR images over urban areas.

  4. THE OLKHON GEODYNAMIC PROVING GROUND (LAKE BAIKAL: HIGH RESOLUTION SATELLITE DATA AND GEOLOGICAL MAPS OF NEW GENERATION

    Directory of Open Access Journals (Sweden)

    Valentin S. Fedorovsky

    2015-09-01

    Full Text Available The Olkhon region of the Western Pribaikalie is highly attractive for geologists due to the presence of diverse metamorphic complexes and highly complicated combinations of folded structures in this region. The Olkhon region is located within the area of the Pribaikalsky National Park of Russia. At abundant outcrops in the subject area, various geological aspects resulting from the Early Palaeozoic collision system can be studied in detail. By its parameters, the subject area can be considered a «geodynamic proving ground». In recent years, abundant aerospace materials on the area have been accumulated, and long-term field studies resulted in many discoveries and findings which encourage critical revision of the initial conceptions. The material available allows compilation of a new package of geological maps in hard and electronic versions.

  5. High-Resolution Mapping Using a Sub-Audio Magnetic Survey at the Comet Gold Mine, Western Australia

    Directory of Open Access Journals (Sweden)

    Piyaphong Chenrai

    2011-01-01

    Full Text Available The Comet Gold Mine in the Murchison mineral field lies within the Yilgarn Craton of Western Australia. Gold mineralization in this area is associated with a series of north-northeasterly trending structures, and has a long exploration history with some previous geophysical information. Other exploration information, such as geology and drill hole data, are integrated with the geophysical results to study the geophysical responses and generate a geophysical interpretation map. The response from the sub-audio magnetic (SAM survey was investigated over an area of 13 sq km. The SAM survey was completed using a transmitter current of 5 - 8 Amp with a 50 o/o duty cycle at 4 Hz frequency, which was considered a good instrumental setting for the Comet area. SAM anomalies were compared to results obtained from other geophysical methods and then integrated with geological data to generate a geophysical interpretation map at a 1 : 5000 scale. The new interpretation of geological units and structures at the Comet area should provide a better understanding of the geological and structural setting for mineralization in the Comet area. Our results show that the Comet Fault represents a faulted limb of the Comet fold structure that has both limbs dipping to the southeast and a plunge to the northeast. Magnetic anomalies associated with sedimentary iron formation (SIF are considered to be well correlated with some gold bearing horizons and the location of the Comet Fault, which has become more siliceous and has been altered by sulphide minerals and magnetite minerals.

  6. High-Resolution Precipitation Mapping in a Mountainous Watershed: Ground Truth for Evaluating Uncertainty in a National Precipitation Dataset

    Science.gov (United States)

    Daly, C.; Slater, M. E.; Roberti, J. A.; Laseter, S. H.; Swift, L. W.

    2016-12-01

    A 69-station, densely-spaced rain gauge network was maintained over the period 1951-1958 in the Coweeta Hydrologic Laboratory, located in the southern Appalachians in western North Carolina, USA. This unique dataset was used to develop the first digital seasonal and annual precipitation maps for the Coweeta basin, using elevation regression functions and residual interpolation. It was found that a 10-m elevation grid filtered to an approximately 7-km effective wavelength explained the most variance in precipitation (R2 = 0.82-0.95). A "dump zone" of locally high precipitation a short distance downwind from the mountain crest marking the southern border of the basin was the main feature that was not explained well by the precipitation-elevation relationship. These data and maps provided a rare "ground-truth" for estimating uncertainty in the national-scale Parameter-elevation Relationships on Independent Slopes Model (PRISM) precipitation grids for this location and time period. Differences between PRISM and ground-truth were compared to uncertainty estimates produced by the PRISM model and cross-validation errors. Potential sources of uncertainty in the national PRISM grids were evaluated, including the effects of coarse grid resolution, limited station data, and imprecise station locations. The PRISM national grids matched closely (within five percent) with the Coweeta dataset. The PRISM regression prediction interval, which includes the influence of stations in an area of tens of km around a given location, overestimated the local error at Coweeta (12-20 percent). Offsetting biases and generally low error rates made it difficult to isolate major sources of uncertainty in the PRISM grids. However, station density and selection, and mis-location of stations were identified as likely sources of error. The methods used in this study can be repeated in other areas where high-density data exist to gain a more comprehensive picture of the uncertainties in national

  7. Geo-Correction of High-Resolution Imagery Using Fast Template Matching on a GPU in Emergency Mapping Contexts

    Directory of Open Access Journals (Sweden)

    Martina Giovalli

    2013-09-01

    Full Text Available The increasing availability of satellite imagery acquired by existing and new sensors allows a wide variety of new applications that depend on the use of diverse spectral and spatial resolution data sets. One of the pre-conditions for the use of hybrid image data sets is a consistent geo-correction capacity. We demonstrate how a novel fast template matching approach implemented on a graphics processing unit (GPU allows us to accurately and rapidly geo-correct imagery in an automated way. The key difference with existing geo-correction approaches, which do not use a GPU, is the possibility to match large source image segments (8,192 by 8,192 pixels with relatively large templates (512 by 512 pixels significantly faster. Our approach is sufficiently robust to allow for the use of various reference data sources. The need for accelerated processing is relevant in our application context, which relates to mapping activities in the European Copernicus emergency management service. Our new method is demonstrated over an area northwest of Valencia (Spain for a large forest fire event in July 2012. We use the Disaster Monitoring Constellation’s (DMC DEIMOS-1 and RapidEye imagery for the delineation of burnt scar extent. Automated geo-correction of each full resolution image set takes approximately one minute. The reference templates are taken from the TerraColor data set and the Spanish national ortho-imagery database, through the use of dedicated web map services. Geo-correction results are compared to the vector sets derived in the Copernicus emergency service activation request.

  8. A one-dimensional statistical mechanics model for nucleosome positioning on genomic DNA.

    Science.gov (United States)

    Tesoro, S; Ali, I; Morozov, A N; Sulaiman, N; Marenduzzo, D

    2016-02-12

    The first level of folding of DNA in eukaryotes is provided by the so-called '10 nm chromatin fibre', where DNA wraps around histone proteins (∼10 nm in size) to form nucleosomes, which go on to create a zig-zagging bead-on-a-string structure. In this work we present a one-dimensional statistical mechanics model to study nucleosome positioning within one such 10 nm fibre. We focus on the case of genomic sheep DNA, and we start from effective potentials valid at infinite dilution and determined from high-resolution in vitro salt dialysis experiments. We study positioning within a polynucleosome chain, and compare the results for genomic DNA to that obtained in the simplest case of homogeneous DNA, where the problem can be mapped to a Tonks gas. First, we consider the simple, analytically solvable, case where nucleosomes are assumed to be point-like. Then, we perform numerical simulations to gauge the effect of their finite size on the nucleosomal distribution probabilities. Finally we compare nucleosome distributions and simulated nuclease digestion patterns for the two cases (homogeneous and sheep DNA), thereby providing testable predictions of the effect of sequence on experimentally observable quantities in experiments on polynucleosome chromatin fibres reconstituted in vitro.

  9. Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber.

    Science.gov (United States)

    Lou, Qunfeng; He, Yuhua; Cheng, Chunyan; Zhang, Zhonghua; Li, Ji; Huang, Sanwen; Chen, Jinfeng

    2013-01-01

    Cucumber is an important model crop and the first species sequenced in Cucurbitaceae family. Compared to the fast increasing genetic and genomics resources, the molecular cytogenetic researches in cucumber are still very limited, which results in directly the shortage of relation between plenty of physical sequences or genetic data and chromosome structure. We mapped twenty-three fosmids anchored by SSR markers from LG-3, the longest linkage group, and LG-4, the shortest linkage group on pachytene chromosomes 3 and 4, using uorescence in situ hybridization (FISH). Integrated molecular cytogenetic maps of chromosomes 3 and 4 were constructed. Except for three SSR markers located on heterochromatin region, the cytological order of markers was concordant with those on the linkage maps. Distinct structural differences between chromosomes 3 and 4 were revealed by the high resolution pachytene chromosomes. The extreme difference of genetic length between LG-3 and LG-4 was mainly attributed to the difference of overall recombination frequency. The significant differentiation of heterochromatin contents in chromosomes 3 and 4 might have a direct correlation with recombination frequency. Meanwhile, the uneven distribution of recombination frequency along chromosome 4 was observed, and recombination frequency of the long arm was nearly 3.5 times higher than that of the short arm. The severe suppression of recombination was exhibited in centromeric and heterochromatin domains of chromosome 4. Whereas a close correlation between the gene density and recombination frequency was observed in chromosome 4, no significant correlation was observed between them along chromosome 3. The comparison between cytogenetic and sequence maps revealed a large gap on the pericentromeric heterochromatin region of sequence map of chromosome 4. These results showed that integrated molecular cytogenetic maps can provide important information for the study of genetic and genomics in cucumber.

  10. Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber.

    Directory of Open Access Journals (Sweden)

    Qunfeng Lou

    Full Text Available Cucumber is an important model crop and the first species sequenced in Cucurbitaceae family. Compared to the fast increasing genetic and genomics resources, the molecular cytogenetic researches in cucumber are still very limited, which results in directly the shortage of relation between plenty of physical sequences or genetic data and chromosome structure. We mapped twenty-three fosmids anchored by SSR markers from LG-3, the longest linkage group, and LG-4, the shortest linkage group on pachytene chromosomes 3 and 4, using uorescence in situ hybridization (FISH. Integrated molecular cytogenetic maps of chromosomes 3 and 4 were constructed. Except for three SSR markers located on heterochromatin region, the cytological order of markers was concordant with those on the linkage maps. Distinct structural differences between chromosomes 3 and 4 were revealed by the high resolution pachytene chromosomes. The extreme difference of genetic length between LG-3 and LG-4 was mainly attributed to the difference of overall recombination frequency. The significant differentiation of heterochromatin contents in chromosomes 3 and 4 might have a direct correlation with recombination frequency. Meanwhile, the uneven distribution of recombination frequency along chromosome 4 was observed, and recombination frequency of the long arm was nearly 3.5 times higher than that of the short arm. The severe suppression of recombination was exhibited in centromeric and heterochromatin domains of chromosome 4. Whereas a close correlation between the gene density and recombination frequency was observed in chromosome 4, no significant correlation was observed between them along chromosome 3. The comparison between cytogenetic and sequence maps revealed a large gap on the pericentromeric heterochromatin region of sequence map of chromosome 4. These results showed that integrated molecular cytogenetic maps can provide important information for the study of genetic and genomics

  11. High-Resolution Mapping of Homologous Recombination Events in rad3 Hyper-Recombination Mutants in Yeast

    Science.gov (United States)

    Dominska, Margaret; Moriel-Carretero, María; Herrera-Moyano, Emilia; Aguilera, Andrés; Petes, Thomas D.

    2016-01-01

    The Saccharomyces cerevisae RAD3 gene is the homolog of human XPD, an essential gene encoding a DNA helicase of the TFIIH complex involved in both nucleotide excision repair (NER) and transcription. Some mutant alleles of RAD3 (rad3-101 and rad3-102) have partial defects in DNA repair and a strong hyper-recombination (hyper-Rec) phenotype. Previous studies showed that the hyper-Rec phenotype associated with rad3-101 and rad3-102 can be explained as a consequence of persistent single-stranded DNA gaps that are converted to recombinogenic double-strand breaks (DSBs) by replication. The systems previously used to characterize the hyper-Rec phenotype of rad3 strains do not detect the reciprocal products of mitotic recombination. We have further characterized these events using a system in which the reciprocal products of mitotic recombination are recovered. Both rad3-101 and rad3-102 elevate the frequency of reciprocal crossovers about 100-fold. Mapping of these events shows that three-quarters of these crossovers reflect DSBs formed at the same positions in both sister chromatids (double sister-chromatid breaks, DSCBs). The remainder reflects DSBs formed in single chromatids (single chromatid breaks, SCBs). The ratio of DSCBs to SCBs is similar to that observed for spontaneous recombination events in wild-type cells. We mapped 216 unselected genomic alterations throughout the genome including crossovers, gene conversions, deletions, and duplications. We found a significant association between the location of these recombination events and regions with elevated gamma-H2AX. In addition, there was a hotspot for deletions and duplications at the IMA2 and HXT11 genes near the left end of chromosome XV. A comparison of these data with our previous analysis of spontaneous mitotic recombination events suggests that a sub-set of spontaneous events in wild-type cells may be initiated by incomplete NER reactions, and that DSCBs, which cannot be repaired by sister

  12. Segmentation and classification of high resolution imagery for mapping individual species in a closed canopy, deciduous forest

    Institute of Scientific and Technical Information of China (English)

    Timothy; A.; Warner; James; B.; McGraw; Rick; Landenberger

    2006-01-01

    In this paper we investigate the use of a shadow-based delineation program for identifying segments in imagery of a closed canopy, deciduous forest, in West Virginia, USA, as a way to reduce the noise associated with per-pixel classification in forested environments. Shadows typically cluster along the boundaries of trees and therefore can be used to provide a network of nodes for the delineation of segments. A minimum cost path algorithm, where cost is defined as the cumulative sum of brightness values traversed along the connecting route, was used to connect shadow clumps. To test this approach, a series of classifications was undertaken using a multispectral digital aerial image of a six hectare test site and a minimum cost path segmentation. Three species were mapped: oaks, red maple and yellow poplar. The accuracy of an aspatial maximum likelihood classification (termed PERPIXEL classification) was 68.5%, compared to 74.0% for classification using the mean vector of the segments identified with the minimum cost path algorithm (MEAN_SEG), and 78% when the most common class present in the segment is assigned to the entire segment (POSTCLASS_SEG). By comparison, multispectral classification of the multispectral data using the field-mapped polygons of individual trees as segments, produced an accuracy of 82.3% when the mean vector of the polygon was used for classification (MEAN_TREE), and 85.7% when the most common class was assigned to the entire polygon (POSTCLASS_TREE). A moving window-based post-classification majority filter (POSTCLASS_MAJ5BY5) produced an intermediate accuracy value, 73.8%. The minimum cost path segmentation algorithm was found to correctly delineate approximately 28% of the trees. The remaining trees were either segmented, aggregated, or a combination of both segmented and aggregated. Varying the threshold that was used to discriminate shadows appeared to have little effect on the number of correctly delineated trees, or on the overall

  13. High-resolution threshold photoelectron study of the propargyl radical by the vacuum ultraviolet laser velocity-map imaging method

    Science.gov (United States)

    Gao, Hong; Xu, Yuntao; Yang, Lei; Lam, Chow-Shing; Wang, Hailing; Zhou, Jingang; Ng, C. Y.

    2011-12-01

    By employing the vacuum ultraviolet (VUV) laser velocity-map imaging (VMI) photoelectron scheme to discriminate energetic photoelectrons, we have measured the VUV-VMI-threshold photoelectrons (VUV-VMI-TPE) spectra of propargyl radical [C3H3({tilde X}{}^2B_1)] near its ionization threshold at photoelectron energy bandwidths of 3 and 7 cm-1 (full-width at half-maximum, FWHM). The simulation of the VUV-VMI-TPE spectra thus obtained, along with the Stark shift correction, has allowed the determination of a precise value 70 156 ± 4 cm-1 (8.6982 ± 0.0005 eV) for the ionization energy (IE) of C3H3. In the present VMI-TPE experiment, the Stark shift correction is determined by comparing the VUV-VMI-TPE and VUV laser pulsed field ionization-photoelectron (VUV-PFI-PE) spectra for the origin band of the photoelectron spectrum of the {tilde X}^ + {- tilde X} transition of chlorobenzene. The fact that the FWHMs for this origin band observed using the VUV-VMI-TPE and VUV-PFI-PE methods are nearly the same indicates that the energy resolutions achieved in the VUV-VMI-TPE and VUV-PFI-PE measurements are comparable. The IE(C3H3) value obtained based on the VUV-VMI-TPE measurement is consistent with the value determined by the VUV laser PIE spectrum of supersonically cooled C3H3({tilde X}{}^2B_1) radicals, which is also reported in this article.

  14. It's all in the pixels: high resolution remote sensing data and the mapping and analysis of the archaeological and historical landscape

    Directory of Open Access Journals (Sweden)

    Erwin Meylemans

    2017-03-01

    Full Text Available In Flanders (Belgium a large amount of remote-sensing data has been acquired and processed over the past few years, including high-resolution lidar and multi/hyperspectral aerial photography. These new data are contributing to the detection of archaeological sites and the characterisation of the cultural/historical landscape. Of particular use in historically stable areas under forest and pasture, lidar demonstrates the presence of a large number of previously unknown features and sites. The analysis and modelling of these data, combined with other landscape data such as soil maps, augering data, geological and historical maps, and aerial photographs, also provide possible new instruments for the characterisation and evaluation of prehistoric and historic landscapes. This vast amount of new remote-sensing data, plus the information it delivers, however, presents not only obvious opportunities but also a number of challenges. A centralised online system was developed by the 'GIS-Flanders agency', storing both processed and raw data from multispectral recordings, airborne lidar, mobile mapping images etc., and presenting several download and visualisation possibilities and tools. A new system has also been set up to handle specific archaeological and cultural historical data (historical images and aerial photographs, archaeological field data. Dialogue is needed so that the preservation and management needs of the archaeological heritage are also included.

  15. Application of the High Resolution Melting analysis for genetic mapping of Sequence Tagged Site markers in narrow-leafed lupin (Lupinus angustifolius L.).

    Science.gov (United States)

    Kamel, Katarzyna A; Kroc, Magdalena; Święcicki, Wojciech

    2015-01-01

    Sequence tagged site (STS) markers are valuable tools for genetic and physical mapping that can be successfully used in comparative analyses among related species. Current challenges for molecular markers genotyping in plants include the lack of fast, sensitive and inexpensive methods suitable for sequence variant detection. In contrast, high resolution melting (HRM) is a simple and high-throughput assay, which has been widely applied in sequence polymorphism identification as well as in the studies of genetic variability and genotyping. The present study is the first attempt to use the HRM analysis to genotype STS markers in narrow-leafed lupin (Lupinus angustifolius L.). The sensitivity and utility of this method was confirmed by the sequence polymorphism detection based on melting curve profiles in the parental genotypes and progeny of the narrow-leafed lupin mapping population. Application of different approaches, including amplicon size and a simulated heterozygote analysis, has allowed for successful genetic mapping of 16 new STS markers in the narrow-leafed lupin genome.

  16. High-resolution fluorescence mapping of impurities in historical zinc oxide pigments: hard X-ray nanoprobe applications to the paints of Pablo Picasso

    Energy Technology Data Exchange (ETDEWEB)

    Casadio, Francesca [The Art Institute of Chicago, Chicago, IL (United States); Rose, Volker [Argonne National Laboratory, Advanced Photon Source and Center for Nanoscale Materials, Argonne, IL (United States)

    2013-04-15

    Here for the first time we describe the use of high resolution nanoprobe X-ray fluorescence (XRF) mapping for the analysis of artists' paints, hierarchically complex materials typically composed of binder, pigments, fillers, and other additives. The work undertaken at the nanoprobe sought to obtain highly spatially resolved, highly sensitive mapping of metal impurities (Pb, Cd, Fe, and other metals) in submicron particles of zinc oxide pigments used in early 20th century artists' tube paints and enamel paints, with particular emphasis on Ripolin, a popular brand of French house paint used extensively by Pablo Picasso and some of his contemporaries. Analysis revealed that the Zn oxide particles only contain a little Fe, proving that the highest quality Zn oxide pigment, free of Pb and Cd, was used for Ripolin house paints as well as artists' paints. Nanoprobe XRF mapping also demonstrated that artists' tube paints generally have more abundant fillers and additional whites (based on Pb, Ti, Ca) than Ripolin paints, which contain mostly pure zinc oxide. The chemical characterization of paints at the nanoscale opens the path to a better understanding of their fabrication and chemical reactivity. (orig.)

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. Mapping in vitro local material properties of intact and disrupted virions at high resolution using multi-harmonic atomic force microscopy

    Science.gov (United States)

    Cartagena, Alexander; Hernando-Pérez, Mercedes; Carrascosa, José L.; de Pablo, Pedro J.; Raman, Arvind

    2013-05-01

    Understanding the relationships between viral material properties (stiffness, strength, charge density, adhesion, hydration, viscosity, etc.), structure (protein sub-units, genome, surface receptors, appendages), and functions (self-assembly, stability, disassembly, infection) is of significant importance in physical virology and nanomedicine. Conventional Atomic Force Microscopy (AFM) methods have measured a single physical property such as the stiffness of the entire virus from nano-indentation at a few points which severely limits the study of structure-property-function relationships. We present an in vitro dynamic AFM technique operating in the intermittent contact regime which synthesizes anharmonic Lorentz-force excited AFM cantilevers to map quantitatively at nanometer resolution the local electro-mechanical force gradient, adhesion, and hydration layer viscosity within individual φ29 virions. Furthermore, the changes in material properties over the entire φ29 virion provoked by the local disruption of its shell are studied, providing evidence of bacteriophage depressurization. The technique significantly generalizes recent multi-harmonic theory (A. Raman, et al., Nat. Nanotechnol., 2011, 6, 809-814) and enables high-resolution in vitro quantitative mapping of multiple material properties within weakly bonded viruses and nanoparticles with complex structure that otherwise cannot be observed using standard AFM techniques.Understanding the relationships between viral material properties (stiffness, strength, charge density, adhesion, hydration, viscosity, etc.), structure (protein sub-units, genome, surface receptors, appendages), and functions (self-assembly, stability, disassembly, infection) is of significant importance in physical virology and nanomedicine. Conventional Atomic Force Microscopy (AFM) methods have measured a single physical property such as the stiffness of the entire virus from nano-indentation at a few points which severely limits the

  19. Evaluation of single-band snow-patch mapping using high-resolution microwave remote sensing: an application in the maritime Antarctic

    Science.gov (United States)

    Mora, Carla; Jiménez, Juan Javier; Pina, Pedro; Catalão, João; Vieira, Gonçalo

    2017-01-01

    The mountainous and ice-free terrains of the maritime Antarctic generate complex mosaics of snow patches, ranging from tens to hundreds of metres. These can only be accurately mapped using high-resolution remote sensing. In this paper we evaluate the application of radar scenes from TerraSAR-X in High Resolution SpotLight mode for mapping snow patches at a test area on Fildes Peninsula (King George Island, South Shetlands). Snow-patch mapping and characterization of snow stratigraphy were conducted at the time of image acquisition on 12 and 13 January 2012. Snow was wet in all studied snow patches, with coarse-grain and rounded crystals showing advanced melting and with frequent ice layers in the snow pack. Two TerraSAR-X scenes in HH and VV polarization modes were analysed, with the former showing the best results when discriminating between wet snow, lake water and bare soil. However, significant overlap in the backscattering signal was found. Average wet-snow backscattering was -18.0 dB in HH mode, with water showing -21.1 dB and bare soil showing -11.9 dB. Single-band pixel-based and object-oriented image classification methods were used to assess the classification potential of TerraSAR-X SpotLight imagery. The best results were obtained with an object-oriented approach using a watershed segmentation with a support vector machine (SVM) classifier, with an overall accuracy of 92 % and Kappa of 0.88. The main limitation was the west to north-west facing snow patches, which showed significant error, an issue related to artefacts from the geometry of satellite imagery acquisition. The results show that TerraSAR-X in SpotLight mode provides high-quality imagery for mapping wet snow and snowmelt in the maritime Antarctic. The classification procedure that we propose is a simple method and a first step to an implementation in operational mode if a good digital elevation model is available.

  20. High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6.

    Science.gov (United States)

    Szinay, Dóra; Chang, Song-Bin; Khrustaleva, Ludmila; Peters, Sander; Schijlen, Elio; Bai, Yuling; Stiekema, Willem J; van Ham, Roeland C H J; de Jong, Hans; Klein Lankhorst, René M

    2008-11-01

    Within the framework of the International Solanaceae Genome Project, the genome of tomato (Solanum lycopersicum) is currently being sequenced. We follow a 'BAC-by-BAC' approach that aims to deliver high-quality sequences of the euchromatin part of the tomato genome. BACs are selected from various libraries of the tomato genome on the basis of markers from the F2.2000 linkage map. Prior to sequencing, we validated the precise physical location of the selected BACs on the chromosomes by five-colour high-resolution fluorescent in situ hybridization (FISH) mapping. This paper describes the strategies and results of cytogenetic mapping for chromosome 6 using 75 seed BACs for FISH on pachytene complements. The cytogenetic map obtained showed discrepancies between the actual chromosomal positions of these BACs and their markers on the linkage group. These discrepancies were most notable in the pericentromere heterochromatin, thus confirming previously described suppression of cross-over recombination in that region. In a so called pooled-BAC FISH, we hybridized all seed BACs simultaneously and found a few large gaps in the euchromatin parts of the long arm that are still devoid of seed BACs and are too large for coverage by expanding BAC contigs. Combining FISH with pooled BACs and newly recruited seed BACs will thus aid in efficient targeting of novel seed BACs into these areas. Finally, we established the occurrence of repetitive DNA in heterochromatin/euchromatin borders by combining BAC FISH with hybridization of a labelled repetitive DNA fraction (Cot-100). This strategy provides an excellent means to establish the borders between euchromatin and heterochromatin in this chromosome.

  1. Mapping freshwater deltaic wetlands and aquatic habitats at multiple scales with high-resolution multispectral WorldView-2 imagery and Indicator Species Analysis

    Science.gov (United States)

    Lane, C.; Liu, H.; Anenkhonov, O.; Autrey, B.; Chepinoga, V.

    2012-12-01

    Remote sensing technology has long been used in wetland inventory and monitoring though derived wetland maps were limited in applicability and often unsatisfactory largely due to the relatively coarse spatial resolution of conventional satellite imagery. The advent of high-resolution multispectral satellite systems presents new and exciting capabilities in mapping wetland systems with unprecedented accuracy and spatial detail. This research explores and evaluates the use of high-resolution WorldView-2 (WV2) multispectral imagery in identifying and classifying freshwater deltaic wetland vegetation and aquatic habitats in the Selenga River Delta, a Ramsar Wetland of International Importance that drains into Lake Baikal, Russia - a United Nations World Heritage site. A hybrid approach was designed and applied for WV2 image classification consisting of initial unsupervised classification, training data acquisition and analysis, indicator species analysis, and final supervised classification. A hierarchical scheme was defined and adopted for classifying aquatic habitats and wetland vegetation at genus and community levels at a fine scale, while at a coarser scale representing wetland systems as broad substrate and vegetation classes for regional comparisons under various existing wetland classification systems. Rigorous radiometric correction of WV2 images and orthorectification based on GPS-derived ground control points and an ASTER global digital elevation model resulted in 2- to 3-m positional accuracy. We achieved overall classification accuracy of 86.5% for 22 classes of wetland and aquatic habitats at the finest scale and >91% accuracy for broad vegetation and aquatic classes at more generalized scales. At the finest scale, the addition of four new WV2 spectral bands contributed to a classification accuracy increase of 3.5%. The coastal band of WV2 was found to increase the separation between different open water and aquatic habitats, while yellow, red-edge, and

  2. Full hierarchic versus non-hierarchic classification approaches for mapping sealed surfaces at the rural-urban fringe using high-resolution satellite data.

    Science.gov (United States)

    De Roeck, Tim; Van de Voorde, Tim; Canters, Frank

    2009-01-01

    Since 2008 more than half of the world population is living in cities and urban sprawl is continuing. Because of these developments, the mapping and monitoring of urban environments and their surroundings is becoming increasingly important. In this study two object-oriented approaches for high-resolution mapping of sealed surfaces are compared: a standard non-hierarchic approach and a full hierarchic approach using both multi-layer perceptrons and decision trees as learning algorithms. Both methods outperform the standard nearest neighbour classifier, which is used as a benchmark scenario. For the multi-layer perceptron approach, applying a hierarchic classification strategy substantially increases the accuracy of the classification. For the decision tree approach a one-against-all hierarchic classification strategy does not lead to an improvement of classification accuracy compared to the standard all-against-all approach. Best results are obtained with the hierarchic multi-layer perceptron classification strategy, producing a kappa value of 0.77. A simple shadow reclassification procedure based on characteristics of neighbouring objects further increases the kappa value to 0.84.

  3. High-resolution mapping of Martian water ice clouds using Mars Express OMEGA observations - Derivation of the diurnal cloud life cycle

    Science.gov (United States)

    Szantai, Andre; Audouard, Joachim; Madeleine, Jean-Baptiste; Forget, Francois; Pottier, Alizée; Millour, Ehouarn; Gondet, Brigitte; Langevin, Yves; Bibring, Jean-Pierre

    2016-10-01

    The mapping in space and time of water ice clouds can help to explain the Martian water cycle and atmospheric circulation. For this purpose, an ice cloud index (ICI) corresponding to the depth of a water ice absorption band at 3.4 microns is derived from a series of OMEGA images (spectels) covering 5 Martian years. The ICI values for the corresponding pixels are then binned on a high-resolution regular grid (1° longitude x 1° latitude x 5° Ls x 1 h local time) and averaged. Inside each bin, the cloud cover is calculated by dividing the number of pixels considered as cloudy (after comparison to a threshold) to the number of all (valid) pixelsWe compare the maps of clouds obtained around local time 14:00 with collocated TES cloud observations (which were only obtained around this time of the day). A good agreement is found.Averaged ICI compared to the water ice column variable from the Martian Climate Database (MCD) show a correct correlation (~0.5) , which increases when values limited to the tropics only are compared.The number of gridpoints containing ICI values is small ( ~1%), but by taking several neighbor gridpoints and over longer periods, we can observe a cloud life cycle during daytime. An example in the the tropics, around the northern summer solstice, shows a decrease of cloudiness in the morning followed by an increase in the afternoon.

  4. Comparison Effectiveness of Pixel Based Classification and Object Based Classification Using High Resolution Image In Floristic Composition Mapping (Study Case: Gunung Tidar Magelang City)

    Science.gov (United States)

    Ardha Aryaguna, Prama; Danoedoro, Projo

    2016-11-01

    Developments of analysis remote sensing have same way with development of technology especially in sensor and plane. Now, a lot of image have high spatial and radiometric resolution, that's why a lot information. Vegetation object analysis such floristic composition got a lot advantage of that development. Floristic composition can be interpreted using a lot of method such pixel based classification and object based classification. The problems for pixel based method on high spatial resolution image are salt and paper who appear in result of classification. The purpose of this research are compare effectiveness between pixel based classification and object based classification for composition vegetation mapping on high resolution image Worldview-2. The results show that pixel based classification using majority 5×5 kernel windows give the highest accuracy between another classifications. The highest accuracy is 73.32% from image Worldview-2 are being radiometric corrected level surface reflectance, but for overall accuracy in every class, object based are the best between another methods. Reviewed from effectiveness aspect, pixel based are more effective then object based for vegetation composition mapping in Tidar forest.

  5. A comparison of gold versus silver electrode contacts for high-resolution gastric electrical mapping using flexible printed circuit board arrays.

    Science.gov (United States)

    O'Grady, G; Paskaranandavadivel, N; Angeli, T R; Du, P; Windsor, J A; Cheng, L K; Pullan, A J

    2011-03-01

    Stomach contractions are initiated and coordinated by electrical events termed slow waves, and slow wave abnormalities contribute to gastric motility disorders. Recently, flexible printed circuit board (PCB) multi-electrode arrays were introduced, facilitating high-resolution mapping of slow wave activity in humans. However PCBs with gold contacts have shown a moderately inferior signal quality to previous custom-built silver-wire platforms, potentially limiting analyses. This study determined if using silver instead of gold contacts improved flexible PCB performance. In a salt-bath test, modestly higher stimulus amplitudes were recorded from silver PCBs (mean 312, s.d. 89 µV) than those from gold (mean 281, s.d. 85 µV) (p < 0.001); however, the signal-to-noise ratio (SNR) was similar (p = 0.26). In eight in vivo experimental studies, involving gastric serosal recordings from five pigs, no silver versus gold differences were found in terms of slow wave amplitudes (mean 677 versus 682 µV; p = 0.91), SNR (mean 8.8 versus 8.8 dB; p = 0.94) or baseline drift (NRMS; mean 12.0 versus 12.1; p = 0.97). Under the prescribed conditions, flexible PCBs with silver or gold contacts provide comparable results in vivo, and contact material difference does not explain the performance difference between current-generation slow wave mapping platforms. Alternative explanations for this difference and the implications for electrode design are discussed.

  6. A comparison of gold vs silver electrode contacts for high-resolution gastric electrical mapping using flexible printed circuit board arrays

    Science.gov (United States)

    O’Grady, G; Paskaranandavadivel, N; Angeli, T R; Du, P; Windsor, J A; Cheng, L K; Pullan, A J

    2014-01-01

    Stomach contractions are initiated and coordinated by electrical events termed slow waves, and slow wave abnormalities contribute to gastric motility disorders. Recently, flexible printed circuit board (PCB) multi-electrode arrays were introduced, facilitating high-resolution mapping of slow wave activity in humans. However PCBs with gold-contacts have shown a moderately inferior signal quality to previous custom-built silver-wire platforms, potentially limiting analyses. This study determined if using silver instead of gold contacts improved flexible PCB performance. In a salt-bath test, modestly higher stimulus amplitudes were recorded from silver PCBs (mean 312 s.d. 89 μV) than gold (mean 281 s.d. 85 μV) (p<0.001); however the signal to noise ratio (SNR) was similar (p=0.26). In eight in-vivo experimental studies, involving gastric serosal recordings from five pigs, no silver vs gold differences were found in terms of slow wave amplitudes (mean 677 vs 682 μV; p=0.91), SNR (mean 8.8 vs 8.8 dB; p=0.94) or baseline drift (NMRS; mean 12.0 vs 12.1; p=0.97). Under the prescribed conditions, flexible PCBs with silver or gold contacts provide comparable results in-vivo, and contact material difference does not explain the performance difference between current-generation slow wave mapping platforms. Alternative explanations for this difference and the implications for electrode design are discussed. PMID:21252419

  7. High-resolution ALMA continuum mapping of submillimeter galaxies detected by the LABOCA/ACT Survery of Clusters al All Redshifts.

    Science.gov (United States)

    Aguirre, Paula; Gonzalez-Lopez, Jorge; Baker, Andrew

    2015-08-01

    The LABOCA/ACT Survey of Clusters at All Red- shifts, LASCAR, obtained new 870 μm LABOCA and 2.1 GHz ATCA mapping for a set of ten massive SZE-selected galaxy clusters from the ACT southern survey, and Herschel PACS/SPIRE data for a sample subset (6 and 5 clusters respectively), with the aim of studying the properties of the clusters’ SZE signals and of the background SMG population from the same dataset.The submillimeter observations resulted in the detection of 48 submillimeter galaxies, of which 30 have been recently mapped at high resolution in the continuum with ALMA Band 7; preliminary results show that most LABOCA sources are actuallly resolved into 2 or even 3 fainter sources. In this work we will present an analysis of the SMGs' flux densities, counts and multi-component configurations revealed by ALMA data, and we will combine submillimeter measurements with complementary radio, Herschel/SPIRE, Herschel/PACS, Spitzer/IRAC and ground-based optical imaging to model the spectral energy distribution and estimate photometric redsfhits for individual components in each SMG system.

  8. High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding.

    Science.gov (United States)

    Rabbi, Ismail Y; Hamblin, Martha T; Kumar, P Lava; Gedil, Melaku A; Ikpan, Andrew S; Jannink, Jean-Luc; Kulakow, Peter A

    2014-06-24

    Cassava mosaic disease (CMD), caused by different species of cassava mosaic geminiviruses (CMGs), is the most important disease of cassava in Africa and the Indian sub-continent. The cultivated cassava species is protected from CMD by polygenic resistance introgressed from the wild species Manihot glaziovii and a dominant monogenic type of resistance, named CMD2, discovered in African landraces. The ability of the monogenic resistance to confer high levels of resistance in different genetic backgrounds has led recently to its extensive usage in breeding across Africa as well as pre-emptive breeding in Latin America. However, most of the landraces carrying the monogenic resistance are morphologically very similar and come from a geographically restricted area of West Africa, raising the possibility that the diversity of the single-gene resistance could be very limited, or even located at a single locus. Several mapping studies, employing bulk segregant analysis, in different genetic backgrounds have reported additional molecular markers linked to supposedly new resistance genes. However, it is not possible to tell if these are indeed new genes in the absence adequate genetic map framework or allelism tests. To address this important question, a high-density single nucleotide polymorphism (SNP) map of cassava was developed through genotyping-by-sequencing a bi-parental mapping population (N=180) that segregates for the dominant monogenic resistance to CMD. Virus screening using PCR showed that CMD symptoms and presence of virus were strongly correlated (r=0.98). Genome-wide scan and high-resolution composite interval mapping using 6756 SNPs uncovered a single locus with large effect (R(2)=0.74). Projection of the previously published resistance-linked microsatellite markers showed that they co-occurred in the same chromosomal location surrounding the presently mapped resistance locus. Moreover, their relative distance to the mapped resistance locus correlated with

  9. Terrane mapping on the dip-slope based on high-resolution DTM and its geological implications at the Huafan University campus in northern Taiwan

    Science.gov (United States)

    Tseng, C. H.; Chan, Y. C.; Jeng, C. J.; Hsieh, Y. C.

    2016-12-01

    Analyses of slope stability is a critical issue in mountainous areas in Taiwan, for slope failure often causes great damage to local and even regional communities. A dip-slope about 20° toward southwest has been confirmed, on which the Huafan University campus is founded in the northern end of the Western Foothill belt in northern Taiwan. Continuous monitoring systems for the dip-slope by means of inclinometers and groundwater gauges have been set up within the campus for 15 years. Furthermore, a numerical three dimensional modeling for the landslide runout of the dip-slope has also been achieved and proposes potential failure mechanisms. Nevertheless, geomorphic and geological conditions which may be related to the slop failure in the study area were unclear owing to dense vegetation and artificial objects. A 3-D GIS mapping method on the basis of a high-resolution digital terrane model (DTM) derived from LiDAR technology is applied to this area. The high-resolution DTM can be used to distinguish small-scale natural morphology of geomorphic and geological features and structures. Results of the analyses reveal several bulges existing at lower part of the dip-slope, implying potential creeping behavior. In addition, narrow and small gullies are also found on one of the flanks of the dip-slope, and may raise instability if erosional processes continue within the gullies on both lateral sides of the slope mass. On the other hand, traces of a potential fault striking NNE-SSW through the campus is also proposed. The existence of the potential fault can explain the phenomena of groundwater exudation in some places within and outside the campus. Furthermore, bedding plane traces of the bedrock formations by the 3-D mapping method perform inconsistent attitudes within the campus and adjacent regions, resulting in a concave morphology of the landform. It is thus assumed that the potential fault and fold-like structures probably resulted from tectonic stress coming from

  10. A New Method of Providing Communities With High-Resolution Maps of Present and Future Inundation Pathways: Two Examples From Massachusetts

    Science.gov (United States)

    Borrelli, M.; Mague, S. T.; Smith, T. L.

    2015-12-01

    A new method of mapping storm-tide (inundation) pathways and linking those data with tidal elevations in real-time for local managers is being developed. Separate, ongoing studies in two coastal towns in Massachusetts have demonstrated the strengths of this method. High-resolution lidar datasets are imported into 3D data visualization software and water levels are raised incrementally from the highest spring tide of the year to the storm of record +1 m. This range was identified to include 'nuisance flooding' as well as present and future inundation pathways not yet observed by local authorities caused by storms superimposed on projected sea level rise. Potential storm-tide pathways are identified using Lidar data but are then verified with extensive fieldwork using RTK-GPS instruments (tested vertical accuracy of 4.9 cm at 95%) to overcome the vertical uncertainty associated with Lidar data. The fieldwork serves two purposes, first is to field check the lidar data with the highest resolution instrument available and, second to verify and document the presence or absence of a storm-tide pathway. Having developed the map of storm tide pathways within a GIS environment referenced to a geodetic datum (NAVD88), a tide gauge or staff is installed in the town's harbor or other sheltered coastal area and the elevations of all storm tide pathways are then referenced to the local tidal datum. The benefit here is three-fold. First, local officials can use the high-resolution data set that is tied to a local tidal datum to autonomously monitor predicted storm surges and be prepared for inundation at sites prior to flooding. Second, storm-tide pathways that have heretofore never been inundated can be identified and steps can be taken to remove or minimize flooding hazards. Finally, identification of present and future storm tide pathways can be used to prioritize and budget proactive solutions in response to increases in chronic, nuisance and more frequent flooding associated

  11. 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.

    Science.gov (United States)

    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.

  12. High resolution genetic mapping uncovers chitin synthase-1 as the target-site of the structurally diverse mite growth inhibitors clofentezine, hexythiazox and etoxazole in Tetranychus urticae

    Science.gov (United States)

    Demaeght, Peter; Osborne, Edward J.; Odman-Naresh, Jothini; Grbić, Miodrag; Nauen, Ralf; Merzendorfer, Hans

    2014-01-01

    The acaricides clofentezine, hexythiazox and etoxazole are commonly referred to as ‘mite growth inhibitors’, and clofentezine and hexythiazox have been used successfully for the integrated control of plant mite pests for decades. Although they are still important today, their mode of action has remained elusive. Recently, a mutation in chitin synthase 1 (CHS1) was linked to etoxazole resistance. In this study, we identified and investigated a T. urticae strain (HexR) harboring recessive, monogenic resistance to each of hexythiazox, clofentezine, and etoxazole. To elucidate if there is a common genetic basis for the observed cross-resistance, we adapted a previously developed bulk segregant analysis method to map with high resolution a single, shared resistance locus for all three compounds. This finding indicates that the underlying molecular basis for resistance to all three compounds is identical. This locus is centered on the CHS1 gene, and as supported by additional genetic and biochemical studies, a non-synonymous variant (I1017F) in CHS1 associates with resistance to each of the tested acaricides in HexR. Our findings thus demonstrate a shared molecular mode of action for the chemically diverse mite growth inhibitors clofentezine, hexythiazox and etoxazole as inhibitors of an essential, non-catalytic activity of CHS1. Given the previously documented cross-resistance between clofentezine, hexythiazox and the benzyolphenylurea compounds flufenoxuron and cycloxuron, CHS1 should be also considered as a potential target-site of insecticidal BPUs. PMID:24859419

  13. High Resolution Elevation Contours

    Data.gov (United States)

    Minnesota Department of Natural Resources — This dataset contains contours generated from high resolution data sources such as LiDAR. Generally speaking this data is 2 foot or less contour interval.

  14. Genome-Wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map

    Science.gov (United States)

    Nimmakayala, Padma; Tomason, Yan R.; Abburi, Venkata L.; Alvarado, Alejandra; Saminathan, Thangasamy; Vajja, Venkata G.; Salazar, Germania; Panicker, Girish K.; Levi, Amnon; Wechter, William P.; McCreight, James D.; Korol, Abraham B.; Ronin, Yefim; Garcia-Mas, Jordi; Reddy, Umesh K.

    2016-01-01

    Melon (Cucumis melo L.) is a phenotypically diverse eudicot diploid (2n = 2x = 24) has climacteric and non-climacteric morphotypes and show wide variation for fruit firmness, an important trait for transportation and shelf life. We generated 13,789 SNP markers using genotyping-by-sequencing (GBS) and anchored them to chromosomes to understand genome-wide fixation indices (Fst) between various melon morphotypes and genomewide linkage disequilibrium (LD) decay. The FST between accessions of cantalupensis and inodorus was 0.23. The FST between cantalupensis and various agrestis accessions was in a range of 0.19–0.53 and between inodorus and agrestis accessions was in a range of 0.21–0.59 indicating sporadic to wide ranging introgression. The EM (Expectation Maximization) algorithm was used for estimation of 1436 haplotypes. Average genome-wide LD decay for the melon genome was noted to be 9.27 Kb. In the current research, we focused on the genome-wide divergence underlying diverse melon horticultural groups. A high-resolution genetic map with 7153 loci was constructed. Genome-wide segregation distortion and recombination rate across various chromosomes were characterized. Melon has climacteric and non-climacteric morphotypes and wide variation for fruit firmness, a very important trait for transportation and shelf life. Various levels of QTLs were identified with high to moderate stringency and linked to fruit firmness using both genome-wide association study (GWAS) and biparental mapping. Gene annotation revealed some of the SNPs are located in β-D-xylosidase, glyoxysomal malate synthase, chloroplastic anthranilate phosphoribosyltransferase, and histidine kinase, the genes that were previously characterized for fruit ripening and softening in other crops. PMID:27713759

  15. Mapping Intra-Field Yield Variation Using High Resolution Satellite Imagery to Integrate Bioenergy and Environmental Stewardship in an Agricultural Watershed

    Directory of Open Access Journals (Sweden)

    Yuki Hamada

    2015-07-01

    Full Text Available Biofuels are important alternatives for meeting our future energy needs. Successful bioenergy crop production requires maintaining environmental sustainability and minimum impacts on current net annual food, feed, and fiber production. The objectives of this study were to: (1 determine under-productive areas within an agricultural field in a watershed using a single date; high resolution remote sensing and (2 examine impacts of growing bioenergy crops in the under-productive areas using hydrologic modeling in order to facilitate sustainable landscape design. Normalized difference indices (NDIs were computed based on the ratio of all possible two-band combinations using the RapidEye and the National Agricultural Imagery Program images collected in summer 2011. A multiple regression analysis was performed using 10 NDIs and five RapidEye spectral bands. The regression analysis suggested that the red and near infrared bands and NDI using red-edge and near infrared that is known as the red-edge normalized difference vegetation index (RENDVI had the highest correlation (R2 = 0.524 with the reference yield. Although predictive yield map showed striking similarity to the reference yield map, the model had modest correlation; thus, further research is needed to improve predictive capability for absolute yields. Forecasted impact using the Soil and Water Assessment Tool model of growing switchgrass (Panicum virgatum on under-productive areas based on corn yield thresholds of 3.1, 4.7, and 6.3 Mg·ha−1 showed reduction of tile NO3-N and sediment exports by 15.9%–25.9% and 25%–39%, respectively. Corresponding reductions in water yields ranged from 0.9% to 2.5%. While further research is warranted, the study demonstrated the integration of remote sensing and hydrologic modeling to quantify the multifunctional value of projected future landscape patterns in a context of sustainable bioenergy crop production.

  16. Detection of degenerative cartilage disease: comparison of high-resolution morphological MR and quantitative T2 mapping at 3.0 Tesla.

    Science.gov (United States)

    Apprich, S; Welsch, G H; Mamisch, T C; Szomolanyi, P; Mayerhoefer, M; Pinker, K; Trattnig, S

    2010-09-01

    The aim of the study was to investigate the association of T2 relaxation times of the knee with early degenerative cartilage changes. Furthermore the impact of unloading the knee on T2 values was evaluated. Forty-three patients with knee pain and an ICRS (International Cartilage Repair Society) cartilage defect grade Morphological cartilage grading was based on high-resolution proton-density (PD), turbo-spin-echo (TSE) and three-dimensional (3D) isotropic True fast imaging with steady-state precession (FISP) images of slices covering the cartilage layer above the posterior horn of the meniscus. T2 maps were calculated from a multi-echo, spin-echo (MESE) sequence, performed at the beginning and at the end of the scan (time interval 40 min). Influence of cartilage defect grading on deep, superficial, and global T2 values as well as on T2 values for zonal variation was assessed using analysis of variance (ANOVA) and Spearman rank correlation test. Differences among both T2 measurements were compared using paired t-test. Global and superficial T2 values significantly increased with cartilage defect grade regardless of the time elapsed from unloading (global T2: ICRS grade 0, 38.9 and 40.1 ms; grade 1, 41.2 and 44.5 ms; grade 2, 47.7 and 53.4 ms; P=0.041 and 0.008) with stronger correlation for second T2 measurement. In contrast there were no significant differences among grades in the zonal variation at any time. Significant differences for T2 values between the two subsequent measurements were consistently found. T2 mapping might be a sensitive method for the detection of early cartilage degeneration. From our results we would recommend to measure T2 after unloading. Copyright 2010. Published by Elsevier Ltd.

  17. The impact of surgical excisions on human gastric slow wave conduction, defined by high-resolution electrical mapping and in-silico modeling

    Science.gov (United States)

    Du, Peng; Hameed, Ahmer; Angeli, Timothy R.; Lahr, Christopher; Abell, Thomas L.; Cheng, Leo K.; O’Grady, Gregory

    2015-01-01

    Background Gastric contractions are coordinated by slow waves, generated by interstitial cells of Cajal (ICC). Gastric surgery affects slow wave conduction, potentially contributing to post-operative gastric dysfunction. However, the impact of gastric cuts on slow waves has not been comprehensively evaluated. This study aimed to define consequences of surgical excisions on gastric slow waves by applying high-resolution (HR) electrical mapping and in-silico modeling. Methods Patients undergoing gastric stimulator implantation (n=10) underwent full-thickness stapled excisions (25×15 mm, distal corpus) for histological evaluation, enabling HR mapping (256 electrodes; 36cm2) over and adjacent to excisions. A biophysically-based in-silico model of bi-directionally coupled ICC networks was developed and applied to investigate the underlying conduction mechanisms and importance of excision orientation. Results Normal gastric slow waves propagated aborally (3.0±0.2 cycles/min). Excisions induced complete conduction block and wavelets that rotated around blocks, then propagated rapidly circumferentially distal to blocks (8.5±1.2 vs normal 3.6±0.4 mm s−1; ppropagating gastric wavefronts distal to excisions. Excisions were associated with complex dysrhythmias in 5 patients: retrograde propagation (3/10), ectopics (3/10), functional blocks (2/10) and collisions (1/10). Simulations demonstrated conduction anisotropy emerged from bidirectional coupling within ICC layers and showed transverse incision length and orientation correlated to degree of conduction distortion. Conclusions Orienting incisions in the longitudinal gastric axis causes least disruption to electrical conduction and motility. However, if transverse incisions are made, a homeostatic mechanism of gastric conduction anisotropy compensates by restoring aborally-propagating wavefronts. Complex dysrhythmias accompanying excisions could modify post-operative recovery in susceptible patients. PMID:26251163

  18. The impact of surgical excisions on human gastric slow wave conduction, defined by high-resolution electrical mapping and in silico modeling.

    Science.gov (United States)

    Du, P; Hameed, A; Angeli, T R; Lahr, C; Abell, T L; Cheng, L K; O'Grady, G

    2015-10-01

    Gastric contractions are coordinated by slow waves, generated by interstitial cells of Cajal (ICC). Gastric surgery affects slow wave conduction, potentially contributing to postoperative gastric dysfunction. However, the impact of gastric cuts on slow waves has not been comprehensively evaluated. This study aimed to define consequences of surgical excisions on gastric slow waves by applying high-resolution (HR) electrical mapping and in silico modeling. Patients undergoing gastric stimulator implantation (n = 10) underwent full-thickness stapled excisions (25 × 15 mm, distal corpus) for histological evaluation, enabling HR mapping (256 electrodes; 36 cm(2) ) over and adjacent to excisions. A biophysically based in silico model of bidirectionally coupled ICC networks was developed and applied to investigate the underlying conduction mechanisms and importance of excision orientation. Normal gastric slow waves propagated aborally (3.0 ± 0.2 cpm). Excisions induced complete conduction block and wavelets that rotated around blocks, then propagated rapidly circumferentially distal to the blocks (8.5 ± 1.2 vs normal 3.6 ± 0.4 mm/s; p propagating gastric wavefronts distal to excisions. Excisions were associated with complex dysrhythmias in five patients: retrograde propagation (3/10), ectopics (3/10), functional blocks (2/10), and collisions (1/10). Simulations demonstrated conduction anisotropy emerged from bidirectional coupling within ICC layers and showed transverse incision length and orientation correlated with the degree of conduction distortion. Orienting incisions in the longitudinal gastric axis causes least disruption to electrical conduction and motility. However, if transverse incisions are made, a homeostatic mechanism of gastric conduction anisotropy compensates by restoring aborally propagating wavefronts. Complex dysrhythmias accompanying excisions could modify postoperative recovery in susceptible patients. © 2015 John Wiley & Sons Ltd.

  19. Mapping bare soil in South West Wales, UK, using high resolution colour infra-red aerial photography for water quality and flood risk management applications

    Science.gov (United States)

    Sykes, Helena; Neale, Simon; Coe, Sarah

    2016-04-01

    Natural Resources Wales is a UK government body responsible for environmental regulation, among other areas. River walks in Water Framework Directive (WFD) priority catchments in South West Wales, UK, identified soil entering water courses due to poaching and bank erosion, leading to deterioration in the water quality and jeopardising the water quality meeting legal minimum standards. Bare soil has also been shown to cause quicker and higher hydrograph peaks in rural catchments than if those areas were vegetated, which can lead to flooding of domestic properties during peak storm flows. The aim was to target farm visits by operational staff to advise on practices likely to improve water quality and to identify areas where soft engineering solutions such as revegetation could alleviate flood risk in rural areas. High resolution colour-infrared aerial photography, 25cm in the three colour bands and 50cm in the near infrared band, was used to map bare soil in seven catchments using supervised classification of a five band stack including the Normalised Difference Vegetation Index (NDVI). Mapping was combined with agricultural land use and field boundary data to filter out arable fields, which are supposed to bare soil for part of their cycle, and was very successful when compared to ground truthing, with the exception of silage fields which contained sparse, no or unproductive vegetation at the time the imagery was acquired leading to spectral similarity to bare soil. A raindrop trace model was used to show the path sediment from bare soil areas would take when moving through the catchment to a watercourse, with hedgerows inserted as barriers following our observations from ground truthing. The findings have been used to help farmers gain funding for improvements such as fencing to keep animals away from vulnerable river banks. These efficient and automated methods can be rolled out to more catchments in Wales and updated using aerial imagery acquired more recently to

  20. SU-E-CAMPUS-I-04: Automatic Skin-Dose Mapping for An Angiographic System with a Region-Of-Interest, High-Resolution Detector

    Energy Technology Data Exchange (ETDEWEB)

    Vijayan, S; Rana, V [Department of Physiology and Biophysics, Toshiba Stroke and Vascular Research Center (United States); Setlur Nagesh, S [Toshiba Stroke and Vascular Research Center (United States); Ionita, C [Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, NY (United States); Rudin, S [Department of Radiology, Department of Physiology and Biophysics, Toshiba Stroke and Vascular Research Center, Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, NY (United States); Bednarek, D [Department of Radiology, Department of Physiology and Biophysics, Toshiba Stroke and Vascular Research Center (United States)

    2014-06-15

    Purpose: Our real-time skin dose tracking system (DTS) has been upgraded to monitor dose for the micro-angiographic fluoroscope (MAF), a high-resolution, small field-of-view x-ray detector. Methods: The MAF has been mounted on a changer on a clinical C-Arm gantry so it can be used interchangeably with the standard flat-panel detector (FPD) during neuro-interventional procedures when high resolution is needed in a region-of-interest. To monitor patient skin dose when using the MAF, our DTS has been modified to automatically account for the change in scatter for the very small MAF FOV and to provide separated dose distributions for each detector. The DTS is able to provide a color-coded mapping of the cumulative skin dose on a 3D graphic model of the patient. To determine the correct entrance skin exposure to be applied by the DTS, a correction factor was determined by measuring the exposure at the entrance surface of a skull phantom with an ionization chamber as a function of entrance beam size for various beam filters and kVps. Entrance exposure measurements included primary radiation, patient backscatter and table forward scatter. To allow separation of the dose from each detector, a parameter log is kept that allows a replay of the procedure exposure events and recalculation of the dose components.The graphic display can then be constructed showing the dose distribution from the MAF and FPD separately or together. Results: The DTS is able to provide separate displays of dose for the MAF and FPD with field-size specific scatter corrections. These measured corrections change from about 49% down to 10% when changing from the FPD to the MAF. Conclusion: The upgraded DTS allows identification of the patient skin dose delivered when using each detector in order to achieve improved dose management as well as to facilitate peak skin-dose reduction through dose spreading. Research supported in part by Toshiba Medical Systems Corporation and NIH Grants R43FD0158401, R44FD

  1. Improved mapping of flood extent and flood depth using space based SAR data in combination with very high resolution digital elevation data

    Science.gov (United States)

    Zwenzner, H.

    2009-04-01

    Due to their capability to present a synoptic view of the spatial extent of floods, remote sensing technology, and especially synthetic aperture radar (SAR) systems, have been successfully applied for flood mapping and monitoring applications during the past decades. However, the quality and accuracy of the flood masks and derived flood parameters highly depend on the geometric precision of the satellite data as well as on the classification accuracy of the derived water mask. The incorporation of high resolution elevation data from LiDAR measurements for example can help to improve the plausibility and reliability of the flood masks. On the basis of the improved flood masks more sophisticated parameters such as inundation depth can be derived. A cross section approach is presented that allows the dynamic fitting of the position of the flood mask profiles according to the underlying terrain information from the DEM. The method was tested on the River Severn (UK), for which TerraSAR-X stripmap data with 3 meters pixel spacing acquired during the 2007 summer flood are used in combination with a LiDAR DEM of 2 meters pixel size. Initially, the cross sections were established perpendicularly to the major flow direction along the 7 km reach of the River Severn. The profile spacing was set to 50 meters. For each cross section profile the water level was extracted at the position of the left and the right border of the flood. On the basis of the longitudinal profile, which contains the sequence of all cross section profiles, a moving average was applied on the water levels in order to get a smooth water surface and to reduce single outliers. However, in case of obvious irregularities in the water levels illustrated in the longitudinal profile and caused by misclassification the respective cross-sections had to be excluded from further analysis. It must be taken into account, that the approach is mainly affected by possible classification errors in the dimension of more

  2. A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits

    Directory of Open Access Journals (Sweden)

    Laurent Pascal

    2006-03-01

    Full Text Available Abstract Background A number of different quantitative trait loci (QTL for various phenotypic traits, including milk production, functional, and conformation traits in dairy cattle as well as growth and body composition traits in meat cattle, have been mapped consistently in the middle region of bovine chromosome 6 (BTA6. Dense genetic and physical maps and, ultimately, a fully annotated genome sequence as well as their mutual connections are required to efficiently identify genes and gene variants responsible for genetic variation of phenotypic traits. A comprehensive high-resolution gene-rich map linking densely spaced bovine markers and genes to the annotated human genome sequence is required as a framework to facilitate this approach for the region on BTA6 carrying the QTL. Results Therefore, we constructed a high-resolution radiation hybrid (RH map for the QTL containing chromosomal region of BTA6. This new RH map with a total of 234 loci including 115 genes and ESTs displays a substantial increase in loci density compared to existing physical BTA6 maps. Screening the available bovine genome sequence resources, a total of 73 loci could be assigned to sequence contigs, which were already identified as specific for BTA6. For 43 loci, corresponding sequence contigs, which were not yet placed on the bovine genome assembly, were identified. In addition, the improved potential of this high-resolution RH map for BTA6 with respect to comparative mapping was demonstrated. Mapping a large number of genes on BTA6 and cross-referencing them with map locations in corresponding syntenic multi-species chromosome segments (human, mouse, rat, dog, chicken achieved a refined accurate alignment of conserved segments and evolutionary breakpoints across the species included. Conclusion The gene-anchored high-resolution RH map (1 locus/300 kb for the targeted region of BTA6 presented here will provide a valuable platform to guide high-quality assembling and

  3. The High Resolution Stereo Camera (HRSC) of Mars Express and its approach to science analysis and mapping for Mars and its satellites

    Science.gov (United States)

    Gwinner, K.; Jaumann, R.; Hauber, E.; Hoffmann, H.; Heipke, C.; Oberst, J.; Neukum, G.; Ansan, V.; Bostelmann, J.; Dumke, A.; Elgner, S.; Erkeling, G.; Fueten, F.; Hiesinger, H.; Hoekzema, N. M.; Kersten, E.; Loizeau, D.; Matz, K.-D.; McGuire, P. C.; Mertens, V.; Michael, G.; Pasewaldt, A.; Pinet, P.; Preusker, F.; Reiss, D.; Roatsch, T.; Schmidt, R.; Scholten, F.; Spiegel, M.; Stesky, R.; Tirsch, D.; van Gasselt, S.; Walter, S.; Wählisch, M.; Willner, K.

    2016-07-01

    The High Resolution Stereo Camera (HRSC) of ESA's Mars Express is designed to map and investigate the topography of Mars. The camera, in particular its Super Resolution Channel (SRC), also obtains images of Phobos and Deimos on a regular basis. As HRSC is a push broom scanning instrument with nine CCD line detectors mounted in parallel, its unique feature is the ability to obtain along-track stereo images and four colors during a single orbital pass. The sub-pixel accuracy of 3D points derived from stereo analysis allows producing DTMs with grid size of up to 50 m and height accuracy on the order of one image ground pixel and better, as well as corresponding orthoimages. Such data products have been produced systematically for approximately 40% of the surface of Mars so far, while global shape models and a near-global orthoimage mosaic could be produced for Phobos. HRSC is also unique because it bridges between laser altimetry and topography data derived from other stereo imaging instruments, and provides geodetic reference data and geological context to a variety of non-stereo datasets. This paper, in addition to an overview of the status and evolution of the experiment, provides a review of relevant methods applied for 3D reconstruction and mapping, and respective achievements. We will also review the methodology of specific approaches to science analysis based on joint analysis of DTM and orthoimage information, or benefitting from high accuracy of co-registration between multiple datasets, such as studies using multi-temporal or multi-angular observations, from the fields of geomorphology, structural geology, compositional mapping, and atmospheric science. Related exemplary results from analysis of HRSC data will be discussed. After 10 years of operation, HRSC covered about 70% of the surface by panchromatic images at 10-20 m/pixel, and about 97% at better than 100 m/pixel. As the areas with contiguous coverage by stereo data are increasingly abundant, we also

  4. High-resolution land topography

    Science.gov (United States)

    Massonnet, Didier; Elachi, Charles

    2006-11-01

    After a description of the background, methods of production and some scientific uses of high-resolution land topography, we present the current status and the prospect of radar interferometry, regarded as one of the best techniques for obtaining the most global and the most accurate topographic maps. After introducing briefly the theoretical aspects of radar interferometry - principles, limits of operation and various capabilities -, we will focus on the topographic applications that resulted in an almost global topographic map of the earth: the SRTM map. After introducing the Interferometric Cartwheel system, we will build on its expected performances to discuss the scientific prospects of refining a global topographic map to sub-metric accuracy. We also show how other fields of sciences such as hydrology may benefit from the products generated by interferometric radar systems. To cite this article: D. Massonnet, C. Elachi, C. R. Geoscience 338 (2006).

  5. Soil process-oriented modelling of within-field variability based on high-resolution 3D soil type distribution maps.

    Science.gov (United States)

    Bönecke, Eric; Lück, Erika; Gründling, Ralf; Rühlmann, Jörg; Franko, Uwe

    2016-04-01

    Today, the knowledge of within-field variability is essential for numerous purposes, including practical issues, such as precision and sustainable soil management. Therefore, process-oriented soil models have been applied for a considerable time to answer question of spatial soil nutrient and water dynamics, although, they can only be as consistent as their variation and resolution of soil input data. Traditional approaches, describe distribution of soil types, soil texture or other soil properties for greater soil units through generalised point information, e.g. from classical soil survey maps. Those simplifications are known to be afflicted with large uncertainties. Varying soil, crop or yield conditions are detected even within such homogenised soil units. However, recent advances of non-invasive soil survey and on-the-go monitoring techniques, made it possible to obtain vertical and horizontal dense information (3D) about various soil properties, particularly soil texture distribution which serves as an essential soil key variable affecting various other soil properties. Thus, in this study we based our simulations on detailed 3D soil type distribution (STD) maps (4x4 m) to adjacently built-up sufficient informative soil profiles including various soil physical and chemical properties. Our estimates of spatial STD are based on high-resolution lateral and vertical changes of electrical resistivity (ER), detected by a relatively new multi-sensor on-the-go ER monitoring device. We performed an algorithm including fuzzy-c-mean (FCM) logic and traditional soil classification to estimate STD from those inverted and layer-wise available ER data. STD is then used as key input parameter for our carbon, nitrogen and water transport model. We identified Pedological horizon depths and inferred hydrological soil variables (field capacity, permanent wilting point) from pedotransferfunctions (PTF) for each horizon. Furthermore, the spatial distribution of soil organic carbon

  6. A comparison of selected classification algorithms for mapping bamboo patches in lower Gangetic plains using very high resolution WorldView 2 imagery

    Science.gov (United States)

    Ghosh, Aniruddha; Joshi, P. K.

    2014-02-01

    Bamboo is used by different communities in India to develop indigenous products, maintain livelihood and sustain life. Indian National Bamboo Mission focuses on evaluation, monitoring and development of bamboo as an important plant resource. Knowledge of spatial distribution of bamboo therefore becomes necessary in this context. The present study attempts to map bamboo patches using very high resolution (VHR) WorldView 2 (WV 2) imagery in parts of South 24 Parganas, West Bengal, India using both pixel and object-based approaches. A combined layer of pan-sharpened multi-spectral (MS) bands, first 3 principal components (PC) of these bands and seven second order texture measures based Gray Level Co-occurrence Matrices (GLCM) of first three PC were used as input variables. For pixel-based image analysis (PBIA), recursive feature elimination (RFE) based feature selection was carried out to identify the most important input variables. Results of the feature selection indicate that the 10 most important variables include PC 1, PC 2 and their GLCM mean along with 6 MS bands. Three different sets of predictor variables (5 and 10 most important variables and all 32 variables) were classified with Support Vector Machine (SVM) and Random Forest (RF) algorithms. Producer accuracy of bamboo was found to be highest when 10 most important variables selected from RFE were classified with SVM (82%). However object-based image analysis (OBIA) achieved higher classification accuracy than PBIA using the same 32 variables, but with less number of training samples. Using object-based SVM classifier, the producer accuracy of bamboo reached 94%. The significance of this study is that the present framework is capable of accurately identifying bamboo patches as well as detecting other tree species in a tropical region with heterogeneous land use land cover (LULC), which could further aid the mandate of National Bamboo Mission and related programs.

  7. High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree.

    Directory of Open Access Journals (Sweden)

    Linnéa Smeds

    2016-05-01

    Full Text Available Recombination is an engine of genetic diversity and therefore constitutes a key process in evolutionary biology and genetics. While the outcome of crossover recombination can readily be detected as shuffled alleles by following the inheritance of markers in pedigreed families, the more precise location of both crossover and non-crossover recombination events has been difficult to pinpoint. As a consequence, we lack a detailed portrait of the recombination landscape for most organisms and knowledge on how this landscape impacts on sequence evolution at a local scale. To localize recombination events with high resolution in an avian system, we performed whole-genome re-sequencing at high coverage of a complete three-generation collared flycatcher pedigree. We identified 325 crossovers at a median resolution of 1.4 kb, with 86% of the events localized to <10 kb intervals. Observed crossover rates were in excellent agreement with data from linkage mapping, were 52% higher in male (3.56 cM/Mb than in female meiosis (2.28 cM/Mb, and increased towards chromosome ends in male but not female meiosis. Crossover events were non-randomly distributed in the genome with several distinct hot-spots and a concentration to genic regions, with the highest density in promoters and CpG islands. We further identified 267 non-crossovers, whose location was significantly associated with crossover locations. We detected a significant transmission bias (0.18 in favour of 'strong' (G, C over 'weak' (A, T alleles at non-crossover events, providing direct evidence for the process of GC-biased gene conversion in an avian system. The approach taken in this study should be applicable to any species and would thereby help to provide a more comprehensive portray of the recombination landscape across organism groups.

  8. Mapping primary gyrogenesis during fetal development in primate brains: high-resolution in utero structural MRI study of fetal brain development in pregnant baboons

    Directory of Open Access Journals (Sweden)

    Peter Kochunov

    2010-05-01

    Full Text Available The global and regional changes in the fetal cerebral cortex in primates were mapped during primary gyrification (PG; weeks 17-25 of 26 weeks total gestation. Studying pregnant baboons using high-resolution MRI in utero, measurements included cerebral volume, cortical surface area, gyrification index and length and depth of ten primary cortical sulci. Seven normally developing fetuses were imaged in two animals longitudinally and sequentially. We compared these results to those on PG that from the ferret studies and analyzed them in the context of our recent studies of phylogenetics of cerebral gyrification. We observed that in both primates and non-primates, the cerebrum undergoes a very rapid transformation into the gyrencephalic state, subsequently accompanied by an accelerated growth in brain volume and cortical surface area. However, PG trends in baboons exhibited some critical differences from those observed in ferrets. For example, in baboons, the growth along the long (length axis of cortical sulci was unrelated to the growth along the short (depth axis and far outpaced it. Additionally, the correlation between the rate of growth along the short sulcal axis and heritability of sulcal depth was negative and approached significance (r=-0.60;p<.10, while the same trend for long axis was positive and not significant (p=0.3;p=0.40. These findings, in an animal that shares a highly orchestrated pattern of PG with humans, suggest that ontogenic processes that influence changes in sulcal length and depth are diverse and possibly driven by different factors in primates than in non-primates.

  9. 3D-isotropic high-resolution morphological imaging and quantitative T2 mapping as biomarkers for gender related differences after matrix-associated autologous chondrocyte transplantation (MACT).

    Science.gov (United States)

    Pachowsky, Milena L; Werner, Sven; Marlovits, Stefan; Stelzeneder, David; Renner, Nina; Trattnig, Siegfried; Welsch, Goetz H

    2014-10-01

    The aim of this study was to determine in vivo high-resolution morphological and biochemical gender related differences in cartilage repair tissue (MACT). Forty patients were examined clinically and by MR scans at 3T-MRI (coronal 3D True-FISP sequence for morphologic assessment and multi-echo spin-echo T2-mapping for biochemical assessment of healthy cartilage and MACT cartilage). Mean T2 values in repair tissue in the deep zone showed significantly shorter T2 times in females (p = 0.009, female 43.5 ± 9.8 vs. male 48.2 ± 7.7 ms). The superficial zone showed higher T2 values than the deep zone in both the groups (female 48.5 ± 9.8, males 52.6 ± 11.0 ms) without significant difference between female and male patients. Native control cartilage showed no statistically significant differences for T2 between females and males. The subdivisions "structure of the repair tissue" and "subchondral bone" of the MOCART score showed statistically significant differences between females and males (p = 0.026 and p = 0.007) as well as the Lysholm score (p = 0.03). Our investigations revealed differences between female and male patients after MACT of the knee in clinical outcome and advanced morphological and biochemical MRI. The presented imaging biomarkers can depict subtle changes after cartilage regeneration procedures and might help to understand gender related differences after cartilage repair procedures. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  10. High-resolution meiotic and physical mapping of the Best`s vitelliform macular dystrophy (VMD2) locus to pericentromeric chromosome 11

    Energy Technology Data Exchange (ETDEWEB)

    Weber, B.H.F.; Vogt, G. [Institut fuer Humangenetik, Wuerzburg (Germany); Walker, D. [UBC, Vancouver (Canada)] [and others

    1994-09-01

    Vitelliform macular dystrophy, also known as Best`s disease, is a juvenile-onset macular degeneration with autosomal dominant inheritance. It is characterized by well-demarcated accumulation of lipofuscin-like material within and beneath the retinal pigment epithelium (RPE) and classically results in an egg yolk-like appearance of the macula. Typically, carriers of the disease gene show a specific electrophysiological sign which can be detected by electrooculography (EOG). The EOG measures a standing potential between the cornea and the retina which is primarily generated by the RPE. The histopathological findings as well as the EOG abnormalities suggest that Best`s disease is a generalized disorder of the RPE. The basic biochemical defect is still unknown. As a first step in the positional cloning of the defective gene, the Best`s disease locus was mapped to chromosome 11 between markers at D11S871 and INT2. Subsequently, his region was refined to a 3.7 cM interval flanked by loci D11S903 and PYGM. To further narrow the D11S903-PYGM interval and to obtain an estimate of the physical size of the minimal candidate region, we used a combination of high-resolution PCR hybrid mapping and analysis of recombinant Best`s disease chromosomes. We identified six markers from within the D11S903-PYGM interval that show no recombination with the defective gene in three multigeneration Best`s disease pedigrees. Our hybrid panel localizes these markers on either side of the centromere on chromosome 11. The closest markers flanking the disease gene are at D11S986 in band p12-11.22 and at D11S480 in band q13.2-13.3. Our study demonstrates that the physical size of the Best`s disease region is exceedingly larger than was previously estimated from the genetic data due to the proximity of the defective gene to the centromere of chromosome 11.

  11. DPNuc: Identifying Nucleosome Positions Based on the Dirichlet Process Mixture Model.

    Science.gov (United States)

    Chen, Huidong; Guan, Jihong; Zhou, Shuigeng

    2015-01-01

    Nucleosomes and the free linker DNA between them assemble the chromatin. Nucleosome positioning plays an important role in gene transcription regulation, DNA replication and repair, alternative splicing, and so on. With the rapid development of ChIP-seq, it is possible to computationally detect the positions of nucleosomes on chromosomes. However, existing methods cannot provide accurate and detailed information about the detected nucleosomes, especially for the nucleosomes with complex configurations where overlaps and noise exist. Meanwhile, they usually require some prior knowledge of nucleosomes as input, such as the size or the number of the unknown nucleosomes, which may significantly influence the detection results. In this paper, we propose a novel approach DPNuc for identifying nucleosome positions based on the Dirichlet process mixture model. In our method, Markov chain Monte Carlo (MCMC) simulations are employed to determine the mixture model with no need of prior knowledge about nucleosomes. Compared with three existing methods, our approach can provide more detailed information of the detected nucleosomes and can more reasonably reveal the real configurations of the chromosomes; especially, our approach performs better in the complex overlapping situations. By mapping the detected nucleosomes to a synthetic benchmark nucleosome map and two existing benchmark nucleosome maps, it is shown that our approach achieves a better performance in identifying nucleosome positions and gets a higher F-score. Finally, we show that our approach can more reliably detect the size distribution of nucleosomes.

  12. High-resolution headlamp

    Science.gov (United States)

    Gut, Carsten; Cristea, Iulia; Neumann, Cornelius

    2016-04-01

    The following article shall describe how human vision by night can be influenced. At first, front lighting systems that are already available on the market will be described, followed by their analysis with respect to the positive effects on traffic safety. Furthermore, how traffic safety by night can be increased since the introduction of high resolution headlamps shall be discussed.

  13. Z curve theory-based analysis of the dynamic nature of nucleosome positioning in Saccharomyces cerevisiae.

    Science.gov (United States)

    Wu, Xueting; Liu, Hui; Liu, Hongbo; Su, Jianzhong; Lv, Jie; Cui, Ying; Wang, Fang; Zhang, Yan

    2013-11-01

    Nucleosome is the elementary structural unit of eukaryotic chromatin. Instability of nucleosome positioning plays critical roles in chromatin remodeling in differentiation and disease. In this study, we investigated nucleosome dynamics in the Saccharomyces cerevisiae genome using a geometric model based on Z curve theory. We identified 52,941 stable nucleosomes and 7607 dynamic nucleosomes, compiling them into a genome-wide nucleosome dynamic positioning map and constructing a user-friendly visualization platform (http://bioinfo.hrbmu.edu.cn/nucleosome). Our approach achieved a sensitivity of 90.31% and a specificity of 87.76% for S. cerevisiae. Analysis revealed transcription factor binding sites (TFBSs) were enriched in linkers. And among the sparse nucleosomes around TFBSs, dynamic nucleosomes were slightly preferred. Gene Ontology (GO) enrichment analysis indicated that stable and dynamic nucleosomes were enriched on genes involved in different biological processes and functions. This study provides an approach for comprehending chromatin remodeling and transcriptional regulation of genes.

  14. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.

    Science.gov (United States)

    Zhang, Yong; Moqtaderi, Zarmik; Rattner, Barbara P; Euskirchen, Ghia; Snyder, Michael; Kadonaga, James T; Liu, X Shirley; Struhl, Kevin

    2009-08-01

    We assess the role of intrinsic histone-DNA interactions by mapping nucleosomes assembled in vitro on genomic DNA. Nucleosomes strongly prefer yeast DNA over Escherichia coli DNA, indicating that the yeast genome evolved to favor nucleosome formation. Many yeast promoter and terminator regions intrinsically disfavor nucleosome formation, and nucleosomes assembled in vitro show strong rotational positioning. Nucleosome arrays generated by the ACF assembly factor have fewer nucleosome-free regions, reduced rotational positioning and less translational positioning than obtained by intrinsic histone-DNA interactions. Notably, nucleosomes assembled in vitro have only a limited preference for specific translational positions and do not show the pattern observed in vivo. Our results argue against a genomic code for nucleosome positioning, and they suggest that the nucleosomal pattern in coding regions arises primarily from statistical positioning from a barrier near the promoter that involves some aspect of transcriptional initiation by RNA polymerase II.

  15. Developing a semi/automated protocol to post-process large volume, High-resolution airborne thermal infrared (TIR) imagery for urban waste heat mapping

    Science.gov (United States)

    Rahman, Mir Mustafizur

    In collaboration with The City of Calgary 2011 Sustainability Direction and as part of the HEAT (Heat Energy Assessment Technologies) project, the focus of this research is to develop a semi/automated 'protocol' to post-process large volumes of high-resolution (H-res) airborne thermal infrared (TIR) imagery to enable accurate urban waste heat mapping. HEAT is a free GeoWeb service, designed to help Calgary residents improve their home energy efficiency by visualizing the amount and location of waste heat leaving their homes and communities, as easily as clicking on their house in Google Maps. HEAT metrics are derived from 43 flight lines of TABI-1800 (Thermal Airborne Broadband Imager) data acquired on May 13--14, 2012 at night (11:00 pm--5:00 am) over The City of Calgary, Alberta (˜825 km 2) at a 50 cm spatial resolution and 0.05°C thermal resolution. At present, the only way to generate a large area, high-spatial resolution TIR scene is to acquire separate airborne flight lines and mosaic them together. However, the ambient sensed temperature within, and between flight lines naturally changes during acquisition (due to varying atmospheric and local micro-climate conditions), resulting in mosaicked images with different temperatures for the same scene components (e.g. roads, buildings), and mosaic join-lines arbitrarily bisect many thousands of homes. In combination these effects result in reduced utility and classification accuracy including, poorly defined HEAT Metrics, inaccurate hotspot detection and raw imagery that are difficult to interpret. In an effort to minimize these effects, three new semi/automated post-processing algorithms (the protocol) are described, which are then used to generate a 43 flight line mosaic of TABI-1800 data from which accurate Calgary waste heat maps and HEAT metrics can be generated. These algorithms (presented as four peer-reviewed papers)---are: (a) Thermal Urban Road Normalization (TURN)---used to mitigate the microclimatic

  16. High-resolution mapping of soil moisture at the field scale using ground-penetrating radar for improving remote sensing data products

    Science.gov (United States)

    Lambot, Sébastien; Mahmoudzadeh, Mohammad Reza; Phuong Tran, Anh; Nottebaere, Martijn; Leonard, Aline; Defourny, Pierre; Neyt, Xavier

    2014-05-01

    Characterizing the spatiotemporal distribution of soil moisture at various scales is essential in agricultural, hydrological, meteorological, and climatological research and applications. Soil moisture determines the boundary condition between the soil and the atmosphere and governs key processes of the hydrological cycle such as infiltration, runoff, root water uptake, evaporation, as well as energy exchanges between the Earth's surface and the atmosphere. In that respect, ground-penetrating radar (GPR) is of particular interest for field-scale soil moisture mapping as soil moisture is highly correlated to its permittivity, which controls radar wave propagation in the soil. Yet, accurate determination of the electrical properties of a medium using GPR requires full-wave inverse modeling, which has remained a major challenge in applied geophysics for many years. We present a new near-field radar modeling approach for wave propagation in layered media. Radar antennas are modeled using an equivalent set of infinitesimal electric dipoles and characteristic, frequency-dependent, global reflection and transmission coefficients. These coefficients determine wave propagation between the radar reference plane, point sources, and field points. The interactions between the antenna and the soil are inherently accounted for. The fields are calculated using three-dimensional Green's functions. We validated the model using both time and frequency domain radars. The radars were mounted on a quad and controlled by a computer for real-time radar and dGPS data acquisition. Several fields were investigated and time-lapse measurements were performed on some of them to analyze temporal stability in soil moisture patterns and the repeatability of the measurements. The results were compared to ground-truths. The proposed technique is presently being applied to improve space-borne remote sensing data products for soil moisture by providing high-resolution observational information that

  17. High-resolution mapping reveals linkage between genes in common bean cultivar Ouro Negro conferring resistance to the rust, anthracnose, and angular leaf spot diseases.

    Science.gov (United States)

    Valentini, Giseli; Gonçalves-Vidigal, Maria Celeste; Hurtado-Gonzales, Oscar P; de Lima Castro, Sandra Aparecida; Cregan, Perry B; Song, Qijian; Pastor-Corrales, Marcial A

    2017-08-01

    Co-segregation analysis and high-throughput genotyping using SNP, SSR, and KASP markers demonstrated genetic linkage between Ur-14 and Co-3 (4) /Phg-3 loci conferring resistance to the rust, anthracnose and angular leaf spot diseases of common bean. Rust, anthracnose, and angular leaf spot are major diseases of common bean in the Americas and Africa. The cultivar Ouro Negro has the Ur-14 gene that confers broad spectrum resistance to rust and the gene cluster Co-3 (4) /Phg-3 containing two tightly linked genes conferring resistance to anthracnose and angular leaf spot, respectively. We used co-segregation analysis and high-throughput genotyping of 179 F2:3 families from the Rudá (susceptible) × Ouro Negro (resistant) cross-phenotyped separately with races of the rust and anthracnose pathogens. The results confirmed that Ur-14 and Co-3 (4) /Phg-3 cluster in Ouro Negro conferred resistance to rust and anthracnose, respectively, and that Ur-14 and the Co-3 (4) /Phg-3 cluster were closely linked. Genotyping the F2:3 families, first with 5398 SNPs on the Illumina BeadChip BARCBEAN6K_3 and with 15 SSR, and eight KASP markers, specifically designed for the candidate region containing Ur-14 and Co-3 (4) /Phg-3, permitted the creation of a high-resolution genetic linkage map which revealed that Ur-14 was positioned at 2.2 cM from Co-3 (4) /Phg-3 on the short arm of chromosome Pv04 of the common bean genome. Five flanking SSR markers were tightly linked at 0.1 and 0.2 cM from Ur-14, and two flanking KASP markers were tightly linked at 0.1 and 0.3 cM from Co-3 (4) /Phg-3. Many other SSR, SNP, and KASP markers were also linked to these genes. These markers will be useful for the development of common bean cultivars combining the important Ur-14 and Co-3 (4) /Phg-3 genes conferring resistance to three of the most destructive diseases of common bean.

  18. Ultra high resolution tomography

    Energy Technology Data Exchange (ETDEWEB)

    Haddad, W.S.

    1994-11-15

    Recent work and results on ultra high resolution three dimensional imaging with soft x-rays will be presented. This work is aimed at determining microscopic three dimensional structure of biological and material specimens. Three dimensional reconstructed images of a microscopic test object will be presented; the reconstruction has a resolution on the order of 1000 A in all three dimensions. Preliminary work with biological samples will also be shown, and the experimental and numerical methods used will be discussed.

  19. High Resolution Acoustical Imaging

    Science.gov (United States)

    1989-05-01

    1028 (September 1982). 26 G. Arfken , Mathematical Methods for Physicists (Academic Press, New York, 1971), 2nd printing, pp.662-666. 27 W. R. Hahn...difference in the approach used by the two methods , as noted in the previous paragraph, forming a direct mathematical com- parison may be impossible...examines high resolution methods which use a linear array to locate stationary objects which have scattered the fressure waves. Several;- new methods

  20. Asymmetric nucleosomes flank promoters in the budding yeast genome.

    Science.gov (United States)

    Ramachandran, Srinivas; Zentner, Gabriel E; Henikoff, Steven

    2015-03-01

    Nucleosomes in active chromatin are dynamic, but whether they have distinct structural conformations is unknown. To identify nucleosomes with alternative structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed that 5% of budding yeast (Saccharomyces cerevisiae) nucleosome positions have asymmetric histone-DNA interactions. These asymmetric interactions are enriched at nucleosome positions that flank promoters. Micrococcal nuclease (MNase) sequence-based profiles of asymmetric nucleosome positions revealed a corresponding asymmetry in MNase protection near the dyad axis, suggesting that the loss of DNA contacts around H4S47 is accompanied by protection of the DNA from MNase. Chromatin immunoprecipitation mapping of selected nucleosome remodelers indicated that asymmetric nucleosomes are bound by the RSC chromatin remodeling complex, which is required for maintaining nucleosomes at asymmetric positions. These results imply that the asymmetric nucleosome-RSC complex is a metastable intermediate representing partial unwrapping and protection of nucleosomal DNA on one side of the dyad axis during chromatin remodeling.

  1. Saturn's rings - high resolution

    Science.gov (United States)

    1981-01-01

    Voyager 2 obtained this high-resolution picture of Saturn's rings Aug. 22, when the spacecraft was 4 million kilometers (2.5 million miles) away. Evident here are the numerous 'spoke' features, in the B-ring; their very sharp, narrow appearance suggests short formation times. Scientists think electromagnetic forces are responsible in some way for these features, but no detailed theory has been worked out. Pictures such as this and analyses of Voyager 2's spoke movies may reveal more clues about the origins of these complex structures. The Voyager project is managed for NASA by the Jet Propulsion Laboratory, Pasadena, Calif.

  2. High-resolution measurement and mapping of tungstate in waters, soils and sediments using the low-disturbance DGT sampling technique

    Energy Technology Data Exchange (ETDEWEB)

    Guan, Dong-Xing [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023 (China); Williams, Paul N. [Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 7BL (United Kingdom); Xu, Hua-Cheng [State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008 (China); Li, Gang [Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021 (China); Luo, Jun, E-mail: esluojun@nju.edu.cn [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023 (China); Ma, Lena Q. [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023 (China); Soil and Water Science Department, University of Florida, Gainesville, FL 32611 (United States)

    2016-10-05

    Highlights: • Two high-resolution diffusive gradients in thin-films samplers were characterized. • For the first time DGT was applied to study the bioavailability of W in soils. • 1D and 2D high resolution profiling of W fluxes across the SWI were obtained. • The apparent diffusion W fluxes across two micro-interfaces were calculated. - Abstract: Increasing tungsten (W) use for industrial and military applications has resulted in greater W discharge into natural waters, soils and sediments. Risk modeling of W transport and fate in the environment relies on measurement of the release/mobilization flux of W in the bulk media and the interfaces between matrix compartments. Diffusive gradients in thin-films (DGT) is a promising passive sampling technique to acquire such information. DGT devices equipped with the newly developed high-resolution binding gels (precipitated zirconia, PZ, or ferrihydrite, PF, gels) or classic/conventional ferrihydrite slurry gel were comprehensively assessed for measuring W in waters. {sup Ferrihydrite}DGT can measure W at various ionic strengths (0.001–0.5 mol L{sup −1} NaNO{sub 3}) and pH (4–8), while {sup PZ}DGT can operate across slightly wider environmental conditions. The three DGT configurations gave comparable results for soil W measurement, showing that typically W resupply is relatively poorly sustained. 1D and 2D high-resolution W profiling across sediment—water and hotspot—bulk media interfaces from Lake Taihu were obtained using {sup PZ}DGT coupled with laser ablation ICP–MS measurement, and the apparent diffusion fluxes across the interfaces were calculated using a numerical model.

  3. Dynamic nucleosome organization at hox promoters during zebrafish embryogenesis.

    Directory of Open Access Journals (Sweden)

    Steven E Weicksel

    Full Text Available Nucleosome organization at promoter regions plays an important role in regulating gene activity. Genome-wide studies in yeast, flies, worms, mammalian embryonic stem cells and transformed cell lines have found well-positioned nucleosomes flanking a nucleosome depleted region (NDR at transcription start sites. This nucleosome arrangement depends on DNA sequence (cis-elements as well as DNA binding factors and ATP-dependent chromatin modifiers (trans-factors. However, little is understood about how the nascent embryonic genome positions nucleosomes during development. This is particularly intriguing since the embryonic genome must undergo a broad reprogramming event upon fusion of sperm and oocyte. Using four stages of early embryonic zebrafish development, we map nucleosome positions at the promoter region of 37 zebrafish hox genes. We find that nucleosome arrangement at the hox promoters is a progressive process that takes place over several stages. At stages immediately after fertilization, nucleosomes appear to be largely disordered at hox promoter regions. At stages after activation of the embryonic genome, nucleosomes are detectable at hox promoters, with positions becoming more uniform and more highly occupied. Since the genomic sequence is invariant during embryogenesis, this progressive change in nucleosome arrangement suggests that trans-factors play an important role in organizing nucleosomes during embryogenesis. Separating hox genes into expressed and non-expressed groups shows that expressed promoters have better positioned and occupied nucleosomes, as well as distinct NDRs, than non-expressed promoters. Finally, by blocking the retinoic acid-signaling pathway, we disrupt early hox gene transcription, but observe no effect on nucleosome positions, suggesting that active hox transcription is not a driving force behind the arrangement of nucleosomes at the promoters of hox genes during early development.

  4. Uncovering the forces between nucleosomes using DNA origami

    Science.gov (United States)

    Funke, Jonas J.; Ketterer, Philip; Lieleg, Corinna; Schunter, Sarah; Korber, Philipp; Dietz, Hendrik

    2016-01-01

    Revealing the energy landscape for nucleosome association may contribute to the understanding of higher-order chromatin structures and their impact on genome regulation. We accomplish this in a direct measurement by integrating two nucleosomes into a DNA origami–based force spectrometer, which enabled subnanometer-resolution measurements of nucleosome-nucleosome distance frequencies via single-particle electron microscopy imaging. From the data, we derived the Boltzmann-weighted distance-dependent energy landscape for nucleosome pair interactions. We find a shallow but long-range (~6 nm) attractive nucleosome pair potential with a minimum of −1.6 kcal/mol close to direct contact distances. The relative nucleosome orientation had little influence, but histone H4 acetylation or removal of histone tails drastically decreased the interaction strength. Because of the weak and shallow pair potential, higher-order nucleosome assemblies will be compliant and experience dynamic shape fluctuations in the absence of additional cofactors. Our results contribute to a more accurate description of chromatin and our force spectrometer provides a powerful tool for the direct and high-resolution study of molecular interactions using imaging techniques. PMID:28138524

  5. Uncovering the forces between nucleosomes using DNA origami.

    Science.gov (United States)

    Funke, Jonas J; Ketterer, Philip; Lieleg, Corinna; Schunter, Sarah; Korber, Philipp; Dietz, Hendrik

    2016-11-01

    Revealing the energy landscape for nucleosome association may contribute to the understanding of higher-order chromatin structures and their impact on genome regulation. We accomplish this in a direct measurement by integrating two nucleosomes into a DNA origami-based force spectrometer, which enabled subnanometer-resolution measurements of nucleosome-nucleosome distance frequencies via single-particle electron microscopy imaging. From the data, we derived the Boltzmann-weighted distance-dependent energy landscape for nucleosome pair interactions. We find a shallow but long-range (~6 nm) attractive nucleosome pair potential with a minimum of -1.6 kcal/mol close to direct contact distances. The relative nucleosome orientation had little influence, but histone H4 acetylation or removal of histone tails drastically decreased the interaction strength. Because of the weak and shallow pair potential, higher-order nucleosome assemblies will be compliant and experience dynamic shape fluctuations in the absence of additional cofactors. Our results contribute to a more accurate description of chromatin and our force spectrometer provides a powerful tool for the direct and high-resolution study of molecular interactions using imaging techniques.

  6. High Resolution Laboratory Spectroscopy

    CERN Document Server

    Brünken, Sandra

    2016-01-01

    In this short review we will highlight some of the recent advancements in the field of high-resolution laboratory spectroscopy that meet the needs dictated by the advent of highly sensitive and broadband telescopes like ALMA and SOFIA. Among these is the development of broadband techniques for the study of complex organic molecules, like fast scanning conventional absorption spectroscopy based on multiplier chains, chirped pulse instrumentation, or the use of synchrotron facilities. Of similar importance is the extension of the accessible frequency range to THz frequencies, where many light hydrides have their ground state rotational transitions. Another key experimental challenge is the production of sufficiently high number densities of refractory and transient species in the laboratory, where discharges have proven to be efficient sources that can also be coupled to molecular jets. For ionic molecular species sensitive action spectroscopic schemes have recently been developed to overcome some of the limita...

  7. What controls nucleosome positions?

    Science.gov (United States)

    Segal, Eran; Widom, Jonathan

    2009-08-01

    The DNA of eukaryotic genomes is wrapped in nucleosomes, which strongly distort and occlude the DNA from access to most DNA-binding proteins. An understanding of the mechanisms that control nucleosome positioning along the DNA is thus essential to understanding the binding and action of proteins that carry out essential genetic functions. New genome-wide data on in vivo and in vitro nucleosome positioning greatly advance our understanding of several factors that can influence nucleosome positioning, including DNA sequence preferences, DNA methylation, histone variants and post-translational modifications, higher order chromatin structure, and the actions of transcription factors, chromatin remodelers and other DNA-binding proteins. We discuss how these factors function and ways in which they might be integrated into a unified framework that accounts for both the preservation of nucleosome positioning and the dynamic nucleosome repositioning that occur across biological conditions, cell types, developmental processes and disease.

  8. High-resolution measurement and mapping of tungstate in waters, soils and sediments using the low-disturbance DGT sampling technique.

    Science.gov (United States)

    Guan, Dong-Xing; Williams, Paul N; Xu, Hua-Cheng; Li, Gang; Luo, Jun; Ma, Lena Q

    2016-10-05

    Increasing tungsten (W) use for industrial and military applications has resulted in greater W discharge into natural waters, soils and sediments. Risk modeling of W transport and fate in the environment relies on measurement of the release/mobilization flux of W in the bulk media and the interfaces between matrix compartments. Diffusive gradients in thin-films (DGT) is a promising passive sampling technique to acquire such information. DGT devices equipped with the newly developed high-resolution binding gels (precipitated zirconia, PZ, or ferrihydrite, PF, gels) or classic/conventional ferrihydrite slurry gel were comprehensively assessed for measuring W in waters. (Ferrihydrite)DGT can measure W at various ionic strengths (0.001-0.5molL(-1) NaNO3) and pH (4-8), while (PZ)DGT can operate across slightly wider environmental conditions. The three DGT configurations gave comparable results for soil W measurement, showing that typically W resupply is relatively poorly sustained. 1D and 2D high-resolution W profiling across sediment-water and hotspot-bulk media interfaces from Lake Taihu were obtained using (PZ)DGT coupled with laser ablation ICP-MS measurement, and the apparent diffusion fluxes across the interfaces were calculated using a numerical model. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Nucleosome alterations caused by mutations at modifiable histone residues in Saccharomyces cerevisiae.

    Science.gov (United States)

    Liu, Hongde; Wang, Pingyan; Liu, Lingjie; Min, Zhu; Luo, Kun; Wan, Yakun

    2015-10-26

    Nucleosome organization exhibits dynamic properties depending on the cell state and environment. Histone proteins, fundamental components of nucleosomes, are subject to chemical modifications on particular residues. We examined the effect of substituting modifiable residues of four core histones with the non-modifiable residue alanine on nucleosome dynamics. We mapped the genome-wide nucleosomes in 22 histone mutants of Saccharomyces cerevisiae and compared the nucleosome alterations relative to the wild-type strain. Our results indicated that different types of histone mutation resulted in different phenotypes and a distinct reorganization of nucleosomes. Nucleosome occupancy was altered at telomeres, but not at centromeres. The first nucleosomes upstream (-1) and downstream (+1) of the transcription start site (TSS) were more dynamic than other nucleosomes. Mutations in histones affected the nucleosome array downstream of the TSS. Highly expressed genes, such as ribosome genes and genes involved in glycolysis, showed increased nucleosome occupancy in many types of histone mutant. In particular, the H3K56A mutant exhibited a high percentage of dynamic genomic regions, decreased nucleosome occupancy at telomeres, increased occupancy at the +1 and -1 nucleosomes, and a slow growth phenotype under stress conditions. Our findings provide insight into the influence of histone mutations on nucleosome dynamics.

  10. Controls of nucleosome positioning in the human genome.

    Directory of Open Access Journals (Sweden)

    Daniel J Gaffney

    Full Text Available Nucleosomes are important for gene regulation because their arrangement on the genome can control which proteins bind to DNA. Currently, few human nucleosomes are thought to be consistently positioned across cells; however, this has been difficult to assess due to the limited resolution of existing data. We performed paired-end sequencing of micrococcal nuclease-digested chromatin (MNase-seq from seven lymphoblastoid cell lines and mapped over 3.6 billion MNase-seq fragments to the human genome to create the highest-resolution map of nucleosome occupancy to date in a human cell type. In contrast to previous results, we find that most nucleosomes have more consistent positioning than expected by chance and a substantial fraction (8.7% of nucleosomes have moderate to strong positioning. In aggregate, nucleosome sequences have 10 bp periodic patterns in dinucleotide frequency and DNase I sensitivity; and, across cells, nucleosomes frequently have translational offsets that are multiples of 10 bp. We estimate that almost half of the genome contains regularly spaced arrays of nucleosomes, which are enriched in active chromatin domains. Single nucleotide polymorphisms that reduce DNase I sensitivity can disrupt the phasing of nucleosome arrays, which indicates that they often result from positioning against a barrier formed by other proteins. However, nucleosome arrays can also be created by DNA sequence alone. The most striking example is an array of over 400 nucleosomes on chromosome 12 that is created by tandem repetition of sequences with strong positioning properties. In summary, a large fraction of nucleosomes are consistently positioned--in some regions because they adopt favored sequence positions, and in other regions because they are forced into specific arrangements by chromatin remodeling or DNA binding proteins.

  11. Mapping 3D fault geometry in earthquakes using high-resolution topography: Examples from the 2010 El Mayor-Cucapah (Mexico) and 2013 Balochistan (Pakistan) earthquakes

    Science.gov (United States)

    Zhou, Yu; Walker, Richard T.; Elliott, John R.; Parsons, Barry

    2016-04-01

    Fault dips are usually measured from outcrops in the field or inferred through geodetic or seismological modeling. Here we apply the classic structural geology approach of calculating dip from a fault's 3-D surface trace using recent, high-resolution topography. A test study applied to the 2010 El Mayor-Cucapah earthquake shows very good agreement between our results and those previously determined from field measurements. To obtain a reliable estimate, a fault segment ≥120 m long with a topographic variation ≥15 m is suggested. We then applied this method to the 2013 Balochistan earthquake, getting dips similar to previous estimates. Our dip estimates show a switch from north to south dipping at the southern end of the main trace, which appears to be a response to local extension within a stepover. We suggest that this previously unidentified geometrical complexity may act as the endpoint of earthquake ruptures for the southern end of the Hoshab fault.

  12. HRSC: High resolution stereo camera

    Science.gov (United States)

    Neukum, G.; Jaumann, R.; Basilevsky, A.T.; Dumke, A.; Van Gasselt, S.; Giese, B.; Hauber, E.; Head, J. W.; Heipke, C.; Hoekzema, N.; Hoffmann, H.; Greeley, R.; Gwinner, K.; Kirk, R.; Markiewicz, W.; McCord, T.B.; Michael, G.; Muller, Jan-Peter; Murray, J.B.; Oberst, J.; Pinet, P.; Pischel, R.; Roatsch, T.; Scholten, F.; Willner, K.

    2009-01-01

    The High Resolution Stereo Camera (HRSC) on Mars Express has delivered a wealth of image data, amounting to over 2.5 TB from the start of the mapping phase in January 2004 to September 2008. In that time, more than a third of Mars was covered at a resolution of 10-20 m/pixel in stereo and colour. After five years in orbit, HRSC is still in excellent shape, and it could continue to operate for many more years. HRSC has proven its ability to close the gap between the low-resolution Viking image data and the high-resolution Mars Orbiter Camera images, leading to a global picture of the geological evolution of Mars that is now much clearer than ever before. Derived highest-resolution terrain model data have closed major gaps and provided an unprecedented insight into the shape of the surface, which is paramount not only for surface analysis and geological interpretation, but also for combination with and analysis of data from other instruments, as well as in planning for future missions. This chapter presents the scientific output from data analysis and highlevel data processing, complemented by a summary of how the experiment is conducted by the HRSC team members working in geoscience, atmospheric science, photogrammetry and spectrophotometry. Many of these contributions have been or will be published in peer-reviewed journals and special issues. They form a cross-section of the scientific output, either by summarising the new geoscientific picture of Mars provided by HRSC or by detailing some of the topics of data analysis concerning photogrammetry, cartography and spectral data analysis.

  13. Aggregated Habitat Cover Maps Depicting the Shallow-water Benthic Habitats of the Northwestern Hawaiian Islands Derived from High Resolution IKONOS Satellite Imagery

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Shallow-water, aggregated cover maps were produced by combining as many as four or more detailed habitat types into general cover categories. The original detailed...

  14. Aggregated Habitat Cover Maps Depicting the Shallow-water Benthic Habitats of the Northwestern Hawaiian Islands Derived from High Resolution IKONOS Satellite Imagery

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Shallow-water, aggregated cover maps were produced by combining as many as four or more detailed habitat types into general cover categories. The original detailed...

  15. Shallow-water Benthic Habitats of the Northwestern Hawaiian Islands from Aggregated Habitat Cover Maps Derived from High Resolution IKONOS Satellite Imagery (Draft)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Shallow-water, aggregated cover maps were produced by combining as many as four or more detailed habitat types into general cover categories. The original detailed...

  16. High Resolution Formaldehyde Photochemistry

    Science.gov (United States)

    Ernest, C. T.; Bauer, D.; Hynes, A. J.

    2010-12-01

    Formaldehyde (HCHO) is the most abundant and most important organic carbonyl compound in the atmosphere. The sources of formaldehyde are the oxidation of methane, isoprene, acetone, and other volatile organic compounds (VOCs); fossil fuel combustion; and biomass burning. The dominant loss mechanism for formaldehyde is photolysis which occurs via two pathways: (R1) HCHO + hv → HCO + H (R2) HCHO + hv → H2 + CO The first pathway (R1) is referred to as the radical channel, while the second pathway (R2) is referred to as the molecular channel. The products of both pathways play a significant role in atmospheric chemistry. The CO that is produced in the molecular channel undergoes further oxidation to produce CO2. Under atmospheric conditions, the H atom and formyl radical that are produced in the radical channel undergo rapid reactions with O2 to produce the hydroperoxyl radical (HO2) via (R3) and (R4). (R3) HCO + O2 → HO2 + CO (R4) H + O2 → HO2 Thus, for every photon absorbed, the photolysis of formaldehyde can contribute one CO2 molecule to the global greenhouse budget or two HO2 radicals to the tropospheric HOx (OH + HO2) cycle. The HO2 radicals produced during formaldehyde photolysis have also been implicated in the formation of photochemical smog. The HO2 radicals act as radical chain carriers and convert NO to NO2, which ultimately results in the catalytic production of O3. Constraining the yield of HO2 produced via HCHO photolysis is essential for improving tropospheric chemistry models. In this study, both the absorption cross section and the quantum yield of the radical channel (R1) were measured at high resolution over the tropospherically relevant wavelength range 304-330 nm. For the cross section measurements a narrow linewidth Nd:YAG pumped dye laser was used with a multi-pass cell. Partial pressures of HCHO were kept below 0.3 torr. Simultaneous measurement of OH LIF in a flame allowed absolute calibration of the wavelength scale. Pressure

  17. Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping.

    Science.gov (United States)

    Treweek, Jennifer B; Chan, Ken Y; Flytzanis, Nicholas C; Yang, Bin; Deverman, Benjamin E; Greenbaum, Alon; Lignell, Antti; Xiao, Cheng; Cai, Long; Ladinsky, Mark S; Bjorkman, Pamela J; Fowlkes, Charless C; Gradinaru, Viviana

    2015-11-01

    To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1-2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks.

  18. Mangrove Blue Carbon stocks and change estimation from PolInSAR, Lidar and High Resolution Stereo Imagery combined with Forest Cover change mapping

    Science.gov (United States)

    Zalles, V.; Fatoyinbo, T. E.; Simard, M.; Lagomasino, D.; Lee, S. K.; Trettin, C.; Feliciano, E. A.; Hansen, M.; John, P.

    2015-12-01

    Mangroves and tidal wetlands have the highest carbon density among terrestrial ecosystems. Although they only represent 3 % of the total forest area (or 0.01 % of land area), C emissions from mangrove destruction alone at current rates could be equivalent to 10 % of carbon emissions from deforestation. One of the main challenges to implementing carbon mitigation projects is measuring carbon, efficiently, effectively, and safely. In mangroves especially, the extreme difficulty of the terrain has hindered the establishment of sufficient field plots needed to accurately measure carbon on the scale necessary to relate remotely sensed measurements with field measurements at accuracies required for REDD and other C trading mechanisms. In this presentation we will showcase the methodologies for, and the remote sensing products necessary to implement MRV (monitoring, reporting and verification) systems in Coastal Blue Carbon ecosystems. Specifically, we will present new methods to estimate aboveground biomass stocks and change in mangrove ecosystems using remotely sensed data from Interferometric SAR from the TanDEM-X mission, commercial airborne Lidar, High Resolution Stereo-imagery, and timeseries analysis of Landsat imagery in combination with intensive field measurements of above and belowground carbon stocks. Our research is based on the hypothesis that by combining field measurements, commercial airborne Lidar, optical and Pol-InSAR data, we are able to estimate Mangrove blue carbon storage with an error under 20% at the project level and permit the evaluation of UNFCCC mechanisms for the mitigation of carbon emissions from coastal ecosystems.

  19. A high resolution melting real time PCR for mapping of filaria infection in domestic cats living in brugian filariosis-endemic areas.

    Science.gov (United States)

    Wongkamchai, Sirichit; Nochote, Hathai; Foongladda, Suporn; Dekumyoy, Paron; Thammapalo, Suvit; Boitano, John J; Choochote, Wej

    2014-03-17

    We present here a real time PCR with high resolution melting (HRM) analysis for determining the prevalence and distribution of filarial species in domestic cats residing in brugian filariosis endemic areas of Narathiwat province, Thailand. Filarial species can be clearly distinguished in a single well using a single pair of primers. Blood samples were taken from a total of 2039 domestic cats living in endemic areas. Microfilariae were detected in 5.7% of the sample, while the overall prevalence of filaria infection by HRM analysis was 6.6%. The filariae species found in the infected cats were Brugia malayi, Dirofilaria immitis, D. repens as well as Acanthocheilonema (Dipetalonema) reconditum. This is the first report of A. reconditum infection from Thailand. The study also observed an overlapping of the distribution areas of animal and human filariae. From a public health perspective, the distribution and prevalence of these nematodes warrant an appropriate drug-based prophylaxis to be administered to cats in the endemic areas to reduce the number of diseased carriers. Furthermore, this molecular approach is more sensitive than microfilariae detection, enables species identification and greatly facilitates the collection of epidemiological data. Thus, the present study may help to bridge human-animal interface by coordinating research outcomes with the control of zoonoses that is vitally important for human and veterinary public health.

  20. Predicting nucleosome positioning using a duration Hidden Markov Model

    Directory of Open Access Journals (Sweden)

    Widom Jonathan

    2010-06-01

    Full Text Available Abstract Background The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA sequence itself is highly predictive of nucleosome positioning genome-wide. Therefore a fast software tool for predicting nucleosome positioning can help understanding how a genome's nucleosome organization may facilitate genome function. Results We present a duration Hidden Markov model for nucleosome positioning prediction by explicitly modeling the linker DNA length. The nucleosome and linker models trained from yeast data are re-scaled when making predictions for other species to adjust for differences in base composition. A software tool named NuPoP is developed in three formats for free download. Conclusions Simulation studies show that modeling the linker length distribution and utilizing a base composition re-scaling method both improve the prediction of nucleosome positioning regarding sensitivity and false discovery rate. NuPoP provides a user-friendly software tool for predicting the nucleosome occupancy and the most probable nucleosome positioning map for genomic sequences of any size. When compared with two existing methods, NuPoP shows improved performance in sensitivity.

  1. Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations

    Science.gov (United States)

    Chang, Le; Takada, Shoji

    2016-01-01

    Histone tail acetylation is a key epigenetic marker that tends to open chromatin folding and activate transcription. Despite intensive studies, precise roles of individual lysine acetylation in chromatin folding have only been poorly understood. Here, we revealed structural dynamics of tri-nucleosomes with several histone tail acetylation states and analyzed histone tail interactions with DNA by performing molecular simulations at an unprecedentedly high resolution. We found versatile acetylation-dependent landscapes of tri-nucleosome. The H4 and H2A tail acetylation reduced the contact between the first and third nucleosomes mediated by the histone tails. The H3 tail acetylation reduced its interaction with neighboring linker DNAs resulting in increase of the distance between consecutive nucleosomes. Notably, two copies of the same histone in a single nucleosome have markedly asymmetric interactions with DNAs, suggesting specific pattern of nucleosome docking albeit high inherent flexibility. Estimated transcription factor accessibility was significantly high for the H4 tail acetylated structures. PMID:27698366

  2. Development of a high-resolution binational vegetation map of the Santa Cruz River riparian corridor and surrounding watershed, southern Arizona and northern Sonora, Mexico

    Science.gov (United States)

    Wallace, Cynthia S.A.; Villarreal, Miguel L.; Norman, Laura M.

    2011-01-01

    This report summarizes the development of a binational vegetation map developed for the Santa Cruz Watershed, which straddles the southern border of Arizona and the northern border of Sonora, Mexico. The map was created as an environmental input to the Santa Cruz Watershed Ecosystem Portfolio Model (SCWEPM) that is being created by the U.S. Geological Survey for the watershed. The SCWEPM is a map-based multicriteria evaluation tool that allows stakeholders to explore tradeoffs between valued ecosystem services at multiple scales within a participatory decision-making process. Maps related to vegetation type and are needed for use in modeling wildlife habitat and other ecosystem services. Although detailed vegetation maps existed for the U.S. side of the border, there was a lack of consistent data for the Santa Cruz Watershed in Mexico. We produced a binational vegetation classification of the Santa Cruz River riparian habitat and watershed vegetation based on NatureServe Terrestrial Ecological Systems (TES) units using Classification And Regression Tree (CART) modeling. Environmental layers used as predictor data were derived from a seasonal set of Landsat Thematic Mapper (TM) images (spring, summer, and fall) and from a 30-meter digital-elevation-model (DEM) grid. Because both sources of environmental data are seamless across the international border, they are particularly suited to this binational modeling effort. Training data were compiled from existing field data for the riparian corridor and data collected by the NM-GAP (New Mexico Gap Analysis Project) team for the original Southwest Regional Gap Analysis Project (SWReGAP) modeling effort. Additional training data were collected from core areas of the SWReGAP classification itself, allowing the extrapolation of the SWReGAP mapping into the Mexican portion of the watershed without collecting additional training data.

  3. Analysis of high-resolution HapMap of DTNBP1 (Dysbindin) suggests no consistency between reported common variant associations and schizophrenia.

    Science.gov (United States)

    Mutsuddi, Mousumi; Morris, Derek W; Waggoner, Skye G; Daly, Mark J; Scolnick, Edward M; Sklar, Pamela

    2006-11-01

    DTNBP1 was first identified as a putative schizophrenia-susceptibility gene in Irish pedigrees, with a report of association to common genetic variation. Several replication studies have reported confirmation of an association to DTNBP1 in independent European samples; however, reported risk alleles and haplotypes appear to differ between studies, and comparison among studies has been confounded because different marker sets were employed by each group. To facilitate evaluation of existing evidence of association and further work, we supplemented the extensive genotype data, available through the International HapMap Project (HapMap), about DTNBP1 by specifically typing all associated single-nucleotide polymorphisms reported in each of the studies of the Centre d'Etude du Polymorphisme Humain (CEPH)-derived HapMap sample (CEU). Using this high-density reference map, we compared the putative disease-associated haplotype from each study and found that the association studies are inconsistent with regard to the identity of the disease-associated haplotype at DTNBP1. Specifically, all five "replication" studies define a positively associated haplotype that is different from the association originally reported. We further demonstrate that, in all six studies, the European-derived populations studied have haplotype patterns and frequencies that are consistent with HapMap CEU samples (and each other). Thus, it is unlikely that population differences are creating the inconsistency of the association studies. Evidence of association is, at present, equivocal and unsatisfactory. The new dense map of the region may be valuable in more-comprehensive follow-up studies.

  4. Precise Visualization Method for Cultural Heritage-The Case of High-Resolution Read Relief Image Map Used for Study of Royal City of Angkor Thom, Cambodia

    Science.gov (United States)

    Chiba, T.; Shimoda, I.; Haraguchi, T.; Shimoda, M.

    2016-06-01

    To precisely visualize the Royal City of Angkor Thom, Cambodia, we used a new method in field of cultural heritage study. Read Relief Image Map (RRIM, Chiba et al., 2008) is a powerful method which has been used for geomorphological studies. In this study, using the LiDAR data conducted at the Angkor Archaeological Park in Cambodia in April 2012 (Evans et al., 2013), we visualized the Royal City of Angkor Thom and its vicinity (Shimoda et al., 2016). The RRIM provided a new visualization method of localizing, minute topographical changes in regions with large undulations over a wide area. It has proved to be effective in mapping, on a single wide-area map, the numerous buried remains that exist as comparable height differences or minute undulations measuring less than 1 meter in height, and provides a unique aerial view of their widespread distribution. Based on the RRIM map, past archaeological studies were referenced to reconstruct the layout of the water channel network system. Past studies revealed that a large number of ponds had been dug inside Angkor Thom. The RRIM expanded the investigation and revealed the existence of many ponds outside the royal capital indicating that a residential community had flourished outside the moat surrounded capital city.

  5. The Design and Compilation of High-Resolution Image Map of Cities and Administrative District of Shaanxi Province%陕西省设区市高分辨率影像地图的设计与编制

    Institute of Scientific and Technical Information of China (English)

    赵力彬; 周晓敏; 赵曦; 李庆东

    2013-01-01

    Image map is of the attributes of RS image and DLC, which can be absolutely clear at a glance and well understood by the readers without certain skills of mapping. Based on the design and compilation of high - resolution image map of 10 cities and administrative district of Shaanxi province, the author introduces the general idea about image map and the key technology and methods of image map compilation.%影像地图具有影像与线划地图的双重优势,读者无需专门的地图知识便能对图上的内容一目了然,受到广大读者的接受和喜爱.本文结合陕西省十个设区市高分辨率影像地图的设计与编制,介绍了影像地图的总体设计思想以及编制的关键技术和方法.

  6. High-Resolution Mass Spectrometers

    Science.gov (United States)

    Marshall, Alan G.; Hendrickson, Christopher L.

    2008-07-01

    Over the past decade, mass spectrometry has been revolutionized by access to instruments of increasingly high mass-resolving power. For small molecules up to ˜400 Da (e.g., drugs, metabolites, and various natural organic mixtures ranging from foods to petroleum), it is possible to determine elemental compositions (CcHhNnOoSsPp…) of thousands of chemical components simultaneously from accurate mass measurements (the same can be done up to 1000 Da if additional information is included). At higher mass, it becomes possible to identify proteins (including posttranslational modifications) from proteolytic peptides, as well as lipids, glycoconjugates, and other biological components. At even higher mass (˜100,000 Da or higher), it is possible to characterize posttranslational modifications of intact proteins and to map the binding surfaces of large biomolecule complexes. Here we review the principles and techniques of the highest-resolution analytical mass spectrometers (time-of-flight and Fourier transform ion cyclotron resonance and orbitrap mass analyzers) and describe some representative high-resolution applications.

  7. Mapping of invasive Acacia species in Brazilian Mussununga ecosystems using high- resolution IR remote sensing data acquired with an autonomous Unmanned Aerial System (UAS)

    Science.gov (United States)

    Lehmann, Jan Rudolf Karl; Zvara, Ondrej; Prinz, Torsten

    2015-04-01

    The biological invasion of Australian Acacia species in natural ecosystems outside Australia has often a negative impact on native and endemic plant species and the related biodiversity. In Brazil, the Atlantic rainforest of Bahia and Espirito Santo forms an associated type of ecosystem, the Mussununga. In our days this biologically diverse ecosystem is negatively affected by the invasion of Acacia mangium and Acacia auriculiformis, both introduced to Brazil by the agroforestry to increase the production of pulp and high grade woods. In order to detect the distribution of Acacia species and to monitor the expansion of this invasion the use of high-resolution imagery data acquired with an autonomous Unmanned Aerial System (UAS) proved to be a very promising approach. In this study, two types of datasets - CIR and RGB - were collected since both types provide different information. In case of CIR imagery attention was paid on spectral signatures related to plants, whereas in case of RGB imagery the focus was on surface characteristics. Orthophoto-mosaics and DSM/DTM for both dataset were extracted. RGB/IHS transformations of the imagery's colour space were utilized, as well as NDVIblue index in case of CIR imagery to discriminate plant associations. Next, two test areas were defined in order validate OBIA rule sets using eCognition software. In case of RGB dataset, a rule set based on elevation distinction between high vegetation (including Acacia) and low vegetation (including soils) was developed. High vegetation was classified using Nearest Neighbour algorithm while working with the CIR dataset. The IHS information was used to mask shadows, soils and low vegetation. Further Nearest Neighbour classification was used for distinction between Acacia and other high vegetation types. Finally an accuracy assessment was performed using a confusion matrix. One can state that the IHS information appeared to be helpful in Acacia detection while the surface elevation

  8. Integrating high-resolution mapping of the seafloor with sediment-transport measurements to understand coastal erosion in northern South Carolina

    Science.gov (United States)

    Barnhardt, W.; Baldwin, W.; Denny, J.; Schwab, W.; Paul, G.; Driscoll, N.; Warner, J.; Voulgaris, G.

    2006-12-01

    Shoreline behavior along the coast of Long Bay, South Carolina is dictated by waves, tidal currents, and sediment supply that act within the overall constraints of the regional geologic setting. This study examined the influence of the geologic framework on coastal evolution through the interpretation of high-resolution geophysical data (swath bathymetry, sidescan-sonar imagery, seismic-reflection profiles), bottom samples and cores. Interpreted geophysical data were used to form conceptual models of sediment flux in the nearshore area, which are being tested by conducting site-specific sediment transport and oceanographic measurements and modeling. The inner shelf of Long Bay extends from the shoreface to about 10 km offshore (5-15 m water depth). It is underlain by coastal-plain strata of Cretaceous/Tertiary age that are incised by large fluvial channels formed during the Pliocene and Pleistocene. The indurated coastal-plain and channel-fill deposits are exposed as hardgrounds over large expanses of the inner shelf, and locally overlain by a discontinuous veneer of sandy Holocene sediment generally less than 1-m thick. A regional unconformity, thought to represent erosion during the most recent marine transgression, coincides with the seafloor in these areas of sparse sediment. Minor bathymetric highs occur where relatively thicker accumulations of Holocene sediment lie above the low- relief, transgressive unconformity. One of the thickest accumulations of Holocene sediment is contained within an anomalous, shore-oblique sand body that lies 3 km offshore of Myrtle Beach and is not associated with a modern tidal inlet. The lobate deposit is approximately 11-km long, 3-km wide, and up to 3-m thick. Cores show that the shoal is a marine deposit less than 5000 years old with a gravelly lag at the base representing the transgressive surface. It contains an estimated volume of 26 million m3 of sediment, largely consisting of fine to medium, well sorted quartz sand and

  9. HATS (High Altitude Thermal Sounder): a passive sensor solution to 3D high-resolution mapping of upper atmosphere dynamics (Conference Presentation)

    Science.gov (United States)

    Gordley, Larry; Marshall, Benjamin T.; Lachance, Richard L.

    2016-10-01

    This presentation introduces a High Altitude Thermal Sensor (HATS) that has the potential to resolve the thermal structure of the upper atmosphere (cloud top to 100km) with both horizontal and vertical resolution of 5-7 km or better. This would allow the complete characterization of the wave structures that carry weather signature from the underlying atmosphere. Using a novel gas correlation technique, an extremely high-resolution spectral scan is accomplished by measuring a Doppler modulated signal as the atmospheric thermal scene passes through the HATS 2D FOV. This high spectral resolution, difficult to impossible to achieve with any other passive technique, enables the separation of radiation emanating at high altitudes from that emanating at low altitudes. A principal component analysis of these modulation signals then exposes the complete thermal structure of the upper atmosphere. We show that nadir sounding from low earth orbit, using various branches of CO2 emission in the 17 to 15 micron region, with sufficient spectral resolution and spectral measurement range, can distinguish thermal energy that peaks at various altitudes. By observing the up-welling atmospheric emission through a low pressure (Doppler broadened) gas cell, as the scene passes through our FOV, a modulation signal is created as the atmospheric emission lines are shifted through the spectral position of the gas cell absorption lines. The modulation signal is shown to be highly correlated to the emission coming from the spectral location of the gas cell lines relative to the atmospheric emission lines. This effectively produces a scan of the atmospheric emission with a Doppler line resolution. Similar to thermal sounding of the troposphere, a principal component analysis of the modulation signal can be used to produce an altitude resolved profile, given a reasonable a priori temperature profile. It is then shown that with the addition of a limb observation with one CO2 broadband channel

  10. Investigating the architecture of the Paganica Fault (2009 Mw 6.1 earthquake, central Italy) by integrating high-resolution multiscale refraction tomography and detailed geological mapping

    Science.gov (United States)

    Villani, F.; Improta, L.; Pucci, S.; Civico, R.; Bruno, P. P. G.; Pantosti, D.

    2017-01-01

    We present a 2-D subsurface image of the Paganica Fault from a high-resolution refraction tomography and detailed geological investigation carried out across part of the northwestern segment of the 20-km-long Paganica-San Demetrio fault-system, and which was responsible of the 2009 April 6 Mw 6.1 L'Aquila earthquake (central Italy). We acquired two seismic profiles crossing the Paganica basin with a dense-wide aperture configuration. More than 30 000 P wave first-arrival traveltimes were input to a non-linear tomographic inversion. The obtained 250-300 m deep 2-D Vp images illuminate the shallow portion of the Paganica Fault, and depict additional unreported splays defining a complex half-graben structure. We interpret local thickening of low-Vp (tectonic clastic wedges above a high-Vp (3800-5000 m s-1) carbonate basement. These results are condensed in a 4.2-km-long section across the Paganica basin, clearly indicating that the Paganica Fault is a mature normal fault cutting the whole upper ˜10 km of the crust. We evaluate a minimum cumulative net displacement of 650 ± 90 m and a total heave of 530 ± 65 m accomplished by the Paganica Fault, respectively. In the conservative hypothesis that the extension started during the Gelasian (1.80-2.59 Ma), we obtain a minimum long-term slip-rate of 0.30 ± 0.07 mm yr-1 and an extension-rate of 0.25 ± 0.06 mm yr-1, respectively. Considering the regional averaged extensional field of ˜1 mm yr-1 obtained from geodetic and geological analyses at 104 yr timescale, we infer that the Paganica Fault accounts for ˜20 per cent of the NE-extension affecting this zone of the central Apennines axis due to the concurrent activity of other parallel normal fault-systems nearby (e.g. the Liri, Velino-Magnola, L'Aquila-Celano and Gran Sasso fault-systems).

  11. Nucleosome Positioning and Epigenetics

    Science.gov (United States)

    Schwab, David; Bruinsma, Robijn

    2008-03-01

    The role of chromatin structure in gene regulation has recently taken center stage in the field of epigenetics, phenomena that change the phenotype without changing the DNA sequence. Recent work has also shown that nucleosomes, a complex of DNA wrapped around a histone octamer, experience a sequence dependent energy landscape due to the variation in DNA bend stiffness with sequence composition. In this talk, we consider the role nucleosome positioning might play in the formation of heterochromatin, a compact form of DNA generically responsible for gene silencing. In particular, we discuss how different patterns of nucleosome positions, periodic or random, could either facilitate or suppress heterochromatin stability and formation.

  12. Getting around Antarctica: new high-resolution mappings of the grounded and freely-floating boundaries of the Antarctic ice sheet created for the International Polar Year

    Directory of Open Access Journals (Sweden)

    R. Bindschadler

    2011-01-01

    Full Text Available The boundary of grounded ice and the location of ice transitioning to a freely floating state are mapped at 15-m resolution around the entire continent of Antarctica. These data products are produced by participants of the International Polar Year project ASAID using customized software combining Landsat-7 imagery and ICESat laser altimetry. The grounded ice boundary is 53 610 km long; 74% of it abuts to floating ice shelves or outlet glaciers, 19% is adjacent to open or sea-ice covered ocean, and 7% of the boundary are land terminations with bare rock. Elevations along each line are selected from 6 candidate digital elevation models: two created from the input ICESat laser altimetry and Landsat data, two from stereo satellite imagery, and two from compilations of primarily radar altimetry. Elevation selection and an assignment of confidence in the elevation value are based on agreement with ICESat elevation values and shape of the surface inferred from the Landsat imagery. Elevations along the freely-floating boundary (called the hydrostatic line are converted to ice thicknesses by applying a firn-correction factor and a flotation criterion. The relationship between the seaward offset of the hydrostatic line from the grounding line only weakly matches a prediction based on beam theory. Airborne data are used to validate the technique of grounding line mapping, elevation selection and ice thickness derivation. The mapped products along with the customized software to generate them and a variety of intermediate products are available from the National Snow and Ice Data Center.

  13. High Resolution Mapping of Soil Properties Using Remote Sensing Variables in South-Western Burkina Faso: A Comparison of Machine Learning and Multiple Linear Regression Models

    Science.gov (United States)

    Welp, Gerhard; Thiel, Michael

    2017-01-01

    Accurate and detailed spatial soil information is essential for environmental modelling, risk assessment and decision making. The use of Remote Sensing data as secondary sources of information in digital soil mapping has been found to be cost effective and less time consuming compared to traditional soil mapping approaches. But the potentials of Remote Sensing data in improving knowledge of local scale soil information in West Africa have not been fully explored. This study investigated the use of high spatial resolution satellite data (RapidEye and Landsat), terrain/climatic data and laboratory analysed soil samples to map the spatial distribution of six soil properties–sand, silt, clay, cation exchange capacity (CEC), soil organic carbon (SOC) and nitrogen–in a 580 km2 agricultural watershed in south-western Burkina Faso. Four statistical prediction models–multiple linear regression (MLR), random forest regression (RFR), support vector machine (SVM), stochastic gradient boosting (SGB)–were tested and compared. Internal validation was conducted by cross validation while the predictions were validated against an independent set of soil samples considering the modelling area and an extrapolation area. Model performance statistics revealed that the machine learning techniques performed marginally better than the MLR, with the RFR providing in most cases the highest accuracy. The inability of MLR to handle non-linear relationships between dependent and independent variables was found to be a limitation in accurately predicting soil properties at unsampled locations. Satellite data acquired during ploughing or early crop development stages (e.g. May, June) were found to be the most important spectral predictors while elevation, temperature and precipitation came up as prominent terrain/climatic variables in predicting soil properties. The results further showed that shortwave infrared and near infrared channels of Landsat8 as well as soil specific indices of

  14. A high-resolution map of genes, microsatellite markers, and new dinucleotide repeats from UBE1 to the GATA locus in the region Xp11.23

    Energy Technology Data Exchange (ETDEWEB)

    Kwan, Sau-Ping; Hagemann, T.L. [Rush Medical School, Chicago, IL (United States); Rosen, F.S. [Harvard Medical School, Boston, MA (United States)] [and others

    1995-09-01

    Several new genes and markers have recently been identified on the proximal short arm of the human X chromosome in the area of Xp11.23. We had previously generated at YAC contig in this region extending from UBE1 to the OATL1 locus. In this report two polymorphic dinucleotide repeats, DXS6949 and DXS6950, were isolated and characterized from the OATL1 locus. A panel of YAC deletion derivatives from the distal portion of the contig was used in conjunction with the rest of the YAC map to position the new microsatellites and order other markers localizing to this interval. The marker order was determined to be DXS1367-ZNF81-DXS6849-ZNF21-DXS6616-DXS6950-DXS6949. In the proximal region below OATL1, we have isolated a pair of YACs from the GATA locus, B1026 and C01160. Mapping within these YACs indicates the orientation of DXS1126 and DXS1240, while a cosmid near the OATL1 region reveals the overlap between the YAC contigs from the two loci. This cosmid contains the gene responsible for Wiskott-Aldrich syndrome (WAS) and localizes the disease gene between OATL1 and GATA. These data enable the expansion of the present physical map of the X chromosome from UBE1 to the GATA locus, covering a large portion of the Xp11.23 region. Genetic crossovers in Xp11.23 support the marker orientation and the position of WAS, contrary to previous reports. With the integration of both physical and genetic maps we have predicted the following marker order: Xpter-UBE1-SYN1/ARAF1/TIMP1/DXS1367-ZNF81-DXS-6849-ZNF21-DXSy6616-(OATL1, DXS6950-DXS6949)-WAS-(GATA,DXS1126)-DXS12410-Xcen. This orientation identifies DXS6949 and DXS1126 as the nearest flanking polymorphic markers for WAS and provides useful anchor positions for the analysis of other disease genes that have been localized to this area including three different retinal defects and X-linked nephrolithiasis. 39 refs., 3 figs., 1 tab.

  15. High Resolution Mapping of Soil Properties Using Remote Sensing Variables in South-Western Burkina Faso: A Comparison of Machine Learning and Multiple Linear Regression Models.

    Science.gov (United States)

    Forkuor, Gerald; Hounkpatin, Ozias K L; Welp, Gerhard; Thiel, Michael

    2017-01-01

    Accurate and detailed spatial soil information is essential for environmental modelling, risk assessment and decision making. The use of Remote Sensing data as secondary sources of information in digital soil mapping has been found to be cost effective and less time consuming compared to traditional soil mapping approaches. But the potentials of Remote Sensing data in improving knowledge of local scale soil information in West Africa have not been fully explored. This study investigated the use of high spatial resolution satellite data (RapidEye and Landsat), terrain/climatic data and laboratory analysed soil samples to map the spatial distribution of six soil properties-sand, silt, clay, cation exchange capacity (CEC), soil organic carbon (SOC) and nitrogen-in a 580 km2 agricultural watershed in south-western Burkina Faso. Four statistical prediction models-multiple linear regression (MLR), random forest regression (RFR), support vector machine (SVM), stochastic gradient boosting (SGB)-were tested and compared. Internal validation was conducted by cross validation while the predictions were validated against an independent set of soil samples considering the modelling area and an extrapolation area. Model performance statistics revealed that the machine learning techniques performed marginally better than the MLR, with the RFR providing in most cases the highest accuracy. The inability of MLR to handle non-linear relationships between dependent and independent variables was found to be a limitation in accurately predicting soil properties at unsampled locations. Satellite data acquired during ploughing or early crop development stages (e.g. May, June) were found to be the most important spectral predictors while elevation, temperature and precipitation came up as prominent terrain/climatic variables in predicting soil properties. The results further showed that shortwave infrared and near infrared channels of Landsat8 as well as soil specific indices of redness

  16. Heritability and coefficient of genetic variation analyses of phenotypic traits provide strong basis for high-resolution QTL mapping in the Collaborative Cross mouse genetic reference population.

    Science.gov (United States)

    Iraqi, Fuad A; Athamni, Hanifa; Dorman, Alexandra; Salymah, Yasser; Tomlinson, Ian; Nashif, Aysar; Shusterman, Ariel; Weiss, Ervin; Houri-Haddad, Yael; Mott, Richard; Soller, Morris

    2014-04-01

    Most biological traits of human importance are complex in nature; their manifestation controlled by the cumulative effect of many genetic factors interacting with one another and with the individual's life history. Because of this, mouse genetic reference populations (GRPs) consisting of collections of inbred lines or recombinant inbred lines (RIL) derived from crosses between inbred lines are of particular value in analysis of complex traits, since massive amounts of data can be accumulated on the individual lines. However, existing mouse GRPs are derived from inbred lines that share a common history, resulting in limited genetic diversity, and reduced mapping precision due to long-range gametic disequilibrium. To overcome these limitations, the Collaborative Cross (CC) a genetically highly diverse collection of mouse RIL was established. The CC, now in advanced stages of development, will eventually consist of about 500 RIL derived from reciprocal crosses of eight divergent founder strains of mice, including three wild subspecies. Previous studies have shown that the CC indeed contains enormous diversity at the DNA level, that founder haplotypes are inherited in expected frequency, and that long-range gametic disequilibrium is not present. We here present data, primarily from our own laboratory, documenting extensive genetic variation among CC lines as expressed in broad-sense heritability (H(2)) and by the well-known "coefficient of genetic variation," demonstrating the ability of the CC resource to provide unprecedented mapping precision leading to identification of strong candidate genes.

  17. Baculoviruses and nucleosome management.

    Science.gov (United States)

    Volkman, Loy E

    2015-02-01

    Negatively-supercoiled-ds DNA molecules, including the genomes of baculoviruses, spontaneously wrap around cores of histones to form nucleosomes when present within eukaryotic nuclei. Hence, nucleosome management should be essential for baculovirus genome replication and temporal regulation of transcription, but this has not been documented. Nucleosome mobilization is the dominion of ATP-dependent chromatin-remodeling complexes. SWI/SNF and INO80, two of the best-studied complexes, as well as chromatin modifier TIP60, all contain actin as a subunit. Retrospective analysis of results of AcMNPV time course experiments wherein actin polymerization was blocked by cytochalasin D drug treatment implicate actin-containing chromatin modifying complexes in decatenating baculovirus genomes, shutting down host transcription, and regulating late and very late phases of viral transcription. Moreover, virus-mediated nuclear localization of actin early during infection may contribute to nucleosome management.

  18. Environmental Risk Assessment Based on High-Resolution Spatial Maps of Potentially Toxic Elements Sampled on Stream Sediments of Santiago, Cape Verde

    Directory of Open Access Journals (Sweden)

    Marina M. S. Cabral Pinto

    2014-10-01

    Full Text Available Geochemical mapping is the base knowledge to identify the regions of the planet with critical contents of potentially toxic elements from either natural or anthropogenic sources. Sediments, soils and waters are the vehicles which link the inorganic environment to life through the supply of essential macro and micro nutrients. The chemical composition of surface geological materials may cause metabolic changes which may favor the occurrence of endemic diseases in humans. In order to better understand the relationships between environmental geochemistry and public health, we present environmental risk maps of some harmful elements (As, Cd, Co, Cr, Cu, Hg, Mn, Ni, Pb, V, and Zn in the stream sediments of Santiago, Cape Verde, identifying the potentially harmful areas in this island. The Estimated Background Values (EBV of Cd, Co, Cr, Ni and V were found to be above the Canadian guidelines for any type of use of stream sediments and also above the target values of the Dutch and United States guidelines. The Probably Effect Concentrations (PEC, above which harmful effects are likely in sediment dwelling organisms, were found for Cr and Ni. Some associations between the geological formations of the island and the composition of stream sediments were identified and confirmed by descriptive statistics and by Principal Component Analysis (PCA. The EBV spatial distribution of the metals and the results of PCA allowed us to establish relationships between the EBV maps and the geological formations. The first two PCA modes indicate that heavy metals in Santiago stream sediments are mainly originated from weathering of underlying bedrocks. The first metal association (Co, V, Cr, and Mn; first PCA mode consists of elements enriched in basic rocks and compatible elements. The second association of variables (Zn and Cd as opposed to Ni; second PCA mode appears to be strongly controlled by the composition of alkaline volcanic rocks and pyroclastic rocks. So, the

  19. Mapping the bathymetry of supraglacial lakes and streams on the Greenland Ice Sheet using field measurements and high resolution satellite images

    Directory of Open Access Journals (Sweden)

    C. J. Legleiter

    2013-09-01

    Full Text Available Recent melt events on the Greenland Ice Sheet (GrIS accentuate the need to constrain estimates of sea level rise through improved characterization of meltwater pathways. This effort will require more precise estimates of the volume of water stored on the surface of the GrIS. We assessed the potential to obtain such information by mapping the bathymetry of supraglacial lakes and streams from WorldView2 (WV2 satellite images. Simultaneous {in situ} observations of depth and reflectance from two streams and a lake with measured depths up to 10.45 m were used to test a spectrally-based depth retrieval algorithm. We performed Optimal Band Ratio Analysis (OBRA of continuous field spectra and spectra convolved to the bands of the WV2, Landsat, MODIS, and ASTER sensors. The field spectra yielded a strong relationship with depth (R2 = 0.94, and OBRA R2 values were nearly as high (0.87–0.92 for convolved spectra, suggesting that these sensors' broader bands would be sufficient for depth retrieval. Our field measurements thus indicated that remote sensing of supraglacial bathymetry is not only feasible but potentially highly accurate. OBRA of spectra from 2 m-pixel WV2 images acquired within 3–72 h of our field observations produced an optimal R2 value of 0.92 and unbiased, precise depth estimates, with mean and root-mean square errors < 1% and 10–25% of the mean depth. Bathymetric maps produced by applying OBRA relations revealed subtle features of lake and channel morphology. In addition to providing refined storage volume estimates for lakes of various sizes, this approach can help provide estimates of the transient flux of meltwater through streams.

  20. High resolution linkage disequilibrium and haplotype maps for the genes in the centromeric region of chromo- some 15 in Tibetans and comparisons with Han population

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Genetic variations and their functional implications have been one of the focuses in recent genome research. With the release of the HapMap by the International Consortium, and the availability of the ultra-high-volume genotyping platform, it will soon be possible to use genome-wide association approach to identify genetic variations responsible for complex traits/diseases. While the power of this approach is generally agreed, it is a debated issue as to how much population difference should be exploited, and how best it should be applied. To address this issue we have sequenced 7 genes in the centromeric region of chromosome 15, investigated their SNPs, SNP frequencies, tagSNPs, LD structures, and haplotypes in 50 Tibetan subjects, and compared them with those from the Han population. Genetic diversities between the two populations were also quantified. Our results show that the overall genetic variation between the two populations is very little, but there are differences, primarily in allele frequencies, which is a dominating factor for haplotypes and tagSNPs. In general Tibetans have longer LD and less diversity in the region studied. These data provide genetic evidence for the close relationship between the two populations, and support the idea that all populations are fundamentally the same, but also indicate population variations, particularly in allele frequency, should be taken into account in complex traits/ diseases analysis. Data obtained in this investigation not only help us understand the genome region, but also provide road maps for variation study in the genes/ region in Tibetan population.

  1. From amplification to gene in thyroid cancer: A high-resolution mapped bacterial-artificial-chromosome resource for cancer chromosome aberrations guides gene discovery after comparative genome hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Chen, X.N.; Gonsky, R.; Korenberg, J.R. [UCLA School of Medicine, Los Angeles, CA (United States). Cedars-Sinai Research Inst.; Knauf, J.A.; Fagin, J.A. [Univ. of Cincinnati, OH (United States). Div. of Endocrinology/Metabolism; Wang, M.; Lai, E.H. [Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Pharmacology; Chissoe, S. [Washington Univ. School of Medicine, St. Louis, MO (United States). Genome Sequencing

    1998-08-01

    Chromosome rearrangements associated with neoplasms provide a rich resource for definition of the pathways of tumorigenesis. The power of comparative genome hybridization (CGH) to identify novel genes depends on the existence of suitable markers, which are lacking throughout most of the genome. The authors now report a general approach that translates CGH data into higher-resolution genomic-clone data that are then used to define the genes located in aneuploid regions. They used CGH to study 33 thyroid-tumor DNAs and two tumor-cell-line DNAs. The results revealed amplifications of chromosome band 2p21, with less-intense amplification on 2p13, 19q13.1, and 1p36 and with least-intense amplification on 1p34, 1q42, 5q31, 5q33-34, 9q32-34, and 14q32. To define the 2p21 region amplified, a dense array of 373 FISH-mapped chromosome 2 bacterial artificial chromosomes (BACs) was constructed, and 87 of these were hybridized to a tumor-cell line. Four BACs carried genomic DNA that was amplified in these cells. The maximum amplified region was narrowed to 3--6 Mb by multicolor FISH with the flanking BACs, and the minimum amplicon size was defined by a contig of 420 kb. Sequence analysis of the amplified BAC 1D9 revealed a fragment of the gene, encoding protein kinase C epsilon (PKC{epsilon}), that was then shown to be amplified and rearranged in tumor cells. In summary, CGH combined with a dense mapped resource of BACs and large-scale sequencing has led directly to the definition of PKC{epsilon} as a previously unmapped candidate gene involved in thyroid tumorigenesis.

  2. Baculoviruses and nucleosome management

    Energy Technology Data Exchange (ETDEWEB)

    Volkman, Loy E., E-mail: lvolkman@berkeley.edu

    2015-02-15

    Negatively-supercoiled-ds DNA molecules, including the genomes of baculoviruses, spontaneously wrap around cores of histones to form nucleosomes when present within eukaryotic nuclei. Hence, nucleosome management should be essential for baculovirus genome replication and temporal regulation of transcription, but this has not been documented. Nucleosome mobilization is the dominion of ATP-dependent chromatin-remodeling complexes. SWI/SNF and INO80, two of the best-studied complexes, as well as chromatin modifier TIP60, all contain actin as a subunit. Retrospective analysis of results of AcMNPV time course experiments wherein actin polymerization was blocked by cytochalasin D drug treatment implicate actin-containing chromatin modifying complexes in decatenating baculovirus genomes, shutting down host transcription, and regulating late and very late phases of viral transcription. Moreover, virus-mediated nuclear localization of actin early during infection may contribute to nucleosome management. - Highlights: • Baculoviruses have negatively-supercoiled, circular ds DNA. • Negatively-supercoiled DNA spontaneously forms nucleosomes in the nucleus. • Nucleosomes must be mobilized for replication and transcription to proceed. • Actin-containing chromatin modifiers participate in baculovirus replication.

  3. High resolution deformation maps of Volcán de Colima, Mexico, derived from a year-long TerraSAR-X Spotlight time series

    Science.gov (United States)

    Salzer, Jacqueline; Nikkhoo, Mehdi; Walter, Thomas R.

    2015-04-01

    atmospheric contribution by applying a linear correction to each small baseline interferogram. In combination with a high resolution LIDAR digital elevation model the spotlight data allows the detection and quantification of slow deformation in the region of the dome in an unprecedented spatial and temporal resolution, considerably higher than those achieved by other methods. The results from the PS approach are compared to those from processing the interferograms using the GAMMA software, and deriving the time series from the filtered, unwrapped and geocoded interferograms using GIAnT. We find that, in this scenario, using GIAnT offers disctinct advanages, in particular the faster processing time and overall spatially smoother results. The velocities in either look direction reach up to 10cm/year in line of sight, the maximum subsidence being directed towards the centre of the dome, but very low velocities at its borders. The velocities in the center of the dome strongly decrease over the time period analysed, with only a fraction of the total displacements occuring the last months of 2012. We explore whether this pattern may be explained with cooling, the collapse of bubbles in the viscous dome material, or even presents a first sign for the looming renewal of volcanic activity at the beginning of 2013 [4]. 1. González, M.B., J.J. Ramı'rez, and C. Navarro, Summary of the historical eruptive activity of Volcán De Colima, Mexico 1519-2000. Journal of Volcanology and Geothermal Research, 2002. 117(1-2): p. 21-46. 2. Borselli, L., et al., Flank collapse scenarios at Volcán de Colima, Mexico: A relative instability analysis. Journal of Volcanology and Geothermal Research, 2011. 208(1-2): p. 51-65. 3. Jendryke, M., et al., Using Open-Source Components to Process Interferometric TerraSAR-X Spotlight Data. International Journal of Antennas and Propagation, 2013. 2013: p. 13. 4. Salzer, J.T., et al., Satellite radar data reveal short-term pre-explosive displacements and a

  4. High-resolution mapping of a genetic locus regulating preferential carbohydrate intake, total kilocalories, and food volume on mouse chromosome 17.

    Directory of Open Access Journals (Sweden)

    Rodrigo Gularte-Mérida

    Full Text Available The specific genes regulating the quantitative variation in macronutrient preference and food intake are virtually unknown. We fine mapped a previously identified mouse chromosome 17 region harboring quantitative trait loci (QTL with large effects on preferential macronutrient intake-carbohydrate (Mnic1, total kilcalories (Kcal2, and total food volume (Tfv1 using interval-specific strains. These loci were isolated in the [C57BL/6J.CAST/EiJ-17.1-(D17Mit19-D17Mit50; B6.CAST-17.1] strain, possessing a ∼ 40.1 Mb region of CAST DNA on the B6 genome. In a macronutrient selection paradigm, the B6.CAST-17.1 subcongenic mice eat 30% more calories from the carbohydrate-rich diet, ∼ 10% more total calories, and ∼ 9% more total food volume per body weight. In the current study, a cross between carbohydrate-preferring B6.CAST-17.1 and fat-preferring, inbred B6 mice was used to generate a subcongenic-derived F2 mapping population; genotypes were determined using a high-density, custom SNP panel. Genetic linkage analysis substantially reduced the 95% confidence interval for Mnic1 (encompassing Kcal2 and Tfv1 from 40.1 to 29.5 Mb and more precisely established its boundaries. Notably, no genetic linkage for self-selected fat intake was detected, underscoring the carbohydrate-specific effect of this locus. A second key finding was the separation of two energy balance QTLs: Mnic1/Kcal2/Tfv1 for food intake and a newly discovered locus regulating short term body weight gain. The Mnic1/Kcal2/Tfv1 QTL was further de-limited to 19.0 Mb, based on the absence of nutrient intake phenotypes in subcongenic HQ17IIa mice. Analyses of available sequence data and gene ontologies, along with comprehensive expression profiling in the hypothalamus of non-recombinant, cast/cast and b6/b6 F2 controls, focused our attention on candidates within the QTL interval. Zfp811, Zfp870, and Btnl6 showed differential expression and also contain stop codons, but have no known biology

  5. Getting around Antarctica: new high-resolution mappings of the grounded and freely-floating boundaries of the Antarctic ice sheet created for the International Polar Year

    Directory of Open Access Journals (Sweden)

    R. Bindschadler

    2011-07-01

    Full Text Available Two ice-dynamic transitions of the Antarctic ice sheet – the boundary of grounded ice features and the freely-floating boundary – are mapped at 15-m resolution by participants of the International Polar Year project ASAID using customized software combining Landsat-7 imagery and ICESat/GLAS laser altimetry. The grounded ice boundary is 53 610 km long; 74 % abuts to floating ice shelves or outlet glaciers, 19 % is adjacent to open or sea-ice covered ocean, and 7 % of the boundary ice terminates on land. The freely-floating boundary, called here the hydrostatic line, is the most landward position on ice shelves that expresses the full amplitude of oscillating ocean tides. It extends 27 521 km and is discontinuous. Positional (one-sigma accuracies of the grounded ice boundary vary an order of magnitude ranging from ±52 m for the land and open-ocean terminating segments to ±502 m for the outlet glaciers. The hydrostatic line is less well positioned with errors over 2 km. Elevations along each line are selected from 6 candidate digital elevation models based on their agreement with ICESat elevation values and surface shape inferred from the Landsat imagery. Elevations along the hydrostatic line are converted to ice thicknesses by applying a firn-correction factor and a flotation criterion. BEDMAP-compiled data and other airborne data are compared to the ASAID elevations and ice thicknesses to arrive at quantitative (one-sigma uncertainties of surface elevations of ±3.6, ±9.6, ±11.4, ±30 and ±100 m for five ASAID-assigned confidence levels. Over one-half of the surface elevations along the grounded ice boundary and over one-third of the hydrostatic line elevations are ranked in the highest two confidence categories. A comparison between ASAID-calculated ice shelf thicknesses and BEDMAP-compiled data indicate a thin-ice bias of 41.2 ± 71.3 m for the ASAID ice thicknesses. The relationship between the seaward offset of the hydrostatic line

  6. Getting around Antarctica: New High-Resolution Mappings of the Grounded and Freely-Floating Boundaries of the Antarctic Ice Sheet Created for the International Polar Year

    Science.gov (United States)

    Bindschadler, R.; Choi, H.; Wichlacz, A.; Bingham, R.; Bohlander, J.; Brunt, K.; Corr, H.; Drews, R.; Fricker, H.; Hall, M.; Hindmarsh, R.; Kohler, J.; Padman, L.; Rack, W.; Rotschkly, G.; Urbini, S.; Vornberger, P.; Young, N.

    2011-01-01

    Two ice-dynamic transitions of the Antarctic ice sheet - the boundary of grounded ice features and the freely-floating boundary - are mapped at 15-m resolution by participants of the International Polar Year project ASAID using customized software combining Landsat-7 imagery and ICESat/GLAS laser altimetry. The grounded ice boundary is 53 610 km long; 74% abuts to floating ice shelves or outlet glaciers, 19% is adjacent to open or sea-ice covered ocean, and 7% of the boundary ice terminates on land. The freely-floating boundary, called here the hydrostatic line, is the most landward position on ice shelves that expresses the full amplitude of oscillating ocean tides. It extends 27 521 km and is discontinuous. Positional (one-sigma) accuracies of the grounded ice boundary vary an order of magnitude ranging from +/- 52m for the land and open-ocean terminating segments to +/- 502m for the outlet glaciers. The hydrostatic line is less well positioned with errors over 2 km. Elevations along each line are selected from 6 candidate digital elevation models based on their agreement with ICESat elevation values and surface shape inferred from the Landsat imagery. Elevations along the hydrostatic line are converted to ice thicknesses by applying a firn-correction factor and a flotation criterion. BEDMAP-compiled data and other airborne data are compared to the ASAID elevations and ice thicknesses to arrive at quantitative (one-sigma) uncertainties of surface elevations of +/-3.6, +/-9.6, +/-11.4, +/-30 and +/-100m for five ASAID-assigned confidence levels. Over one-half of the surface elevations along the grounded ice boundary and over one-third of the hydrostatic line elevations are ranked in the highest two confidence categories