Mapping Tree Density at the Global Scale

NASA Astrophysics Data System (ADS)

Covey, K. R.; Crowther, T. W.; Glick, H.; Bettigole, C.; Bradford, M.

2015-12-01

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global-scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical regions, with 0.74, and 0.61 trillion in boreal and temperate regions, respectively. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming impact of humans across most of the world. Based on our projected tree densities, we estimate that deforestation is currently responsible for removing over 15 billion trees each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

Redox potential distribution of an organic-rich contaminated site obtained by the inversion of self-potential data

NASA Astrophysics Data System (ADS)

Abbas, M.; Jardani, A.; Soueid Ahmed, A.; Revil, A.; Brigaud, L.; Bégassat, Ph.; Dupont, J. P.

2017-11-01

Mapping the redox potential of shallow aquifers impacted by hydrocarbon contaminant plumes is important for the characterization and remediation of such contaminated sites. The redox potential of groundwater is indicative of the biodegradation of hydrocarbons and is important in delineating the shapes of contaminant plumes. The self-potential method was used to reconstruct the redox potential of groundwater associated with an organic-rich contaminant plume in northern France. The self-potential technique is a passive technique consisting in recording the electrical potential distribution at the surface of the Earth. A self-potential map is essentially the sum of two contributions, one associated with groundwater flow referred to as the electrokinetic component, and one associated with redox potential anomalies referred to as the electroredox component (thermoelectric and diffusion potentials are generally negligible). A groundwater flow model was first used to remove the electrokinetic component from the observed self-potential data. Then, a residual self-potential map was obtained. The source current density generating the residual self-potential signals is assumed to be associated with the position of the water table, an interface characterized by a change in both the electrical conductivity and the redox potential. The source current density was obtained through an inverse problem by minimizing a cost function including a data misfit contribution and a regularizer. This inversion algorithm allows the determination of the vertical and horizontal components of the source current density taking into account the electrical conductivity distribution of the saturated and non-saturated zones obtained independently by electrical resistivity tomography. The redox potential distribution was finally determined from the inverted residual source current density. A redox map was successfully built and the estimated redox potential values correlated well with in-situ measurements.

TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits.

PubMed

Farabella, Irene; Vasishtan, Daven; Joseph, Agnel Praveen; Pandurangan, Arun Prasad; Sahota, Harpal; Topf, Maya

2015-08-01

Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed. TEMPy (template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature of TEMPy helps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists.

An integrated and highly sensitive ultrafast acoustoelectric imaging system for biomedical applications

NASA Astrophysics Data System (ADS)

Berthon, Beatrice; Dansette, Pierre-Marc; Tanter, Mickaël; Pernot, Mathieu; Provost, Jean

2017-07-01

Direct imaging of the electrical activation of the heart is crucial to better understand and diagnose diseases linked to arrhythmias. This work presents an ultrafast acoustoelectric imaging (UAI) system for direct and non-invasive ultrafast mapping of propagating current densities using the acoustoelectric effect. Acoustoelectric imaging is based on the acoustoelectric effect, the modulation of the medium’s electrical impedance by a propagating ultrasonic wave. UAI triggers this effect with plane wave emissions to image current densities. An ultrasound research platform was fitted with electrodes connected to high common-mode rejection ratio amplifiers and sampled by up to 128 independent channels. The sequences developed allow for both real-time display of acoustoelectric maps and long ultrafast acquisition with fast off-line processing. The system was evaluated by injecting controlled currents into a saline pool via copper wire electrodes. Sensitivity to low current and low acoustic pressure were measured independently. Contrast and spatial resolution were measured for varying numbers of plane waves and compared to line per line acoustoelectric imaging with focused beams at equivalent peak pressure. Temporal resolution was assessed by measuring time-varying current densities associated with sinusoidal currents. Complex intensity distributions were also imaged in 3D. Electrical current densities were detected for injected currents as low as 0.56 mA. UAI outperformed conventional focused acoustoelectric imaging in terms of contrast and spatial resolution when using 3 and 13 plane waves or more, respectively. Neighboring sinusoidal currents with opposed phases were accurately imaged and separated. Time-varying currents were mapped and their frequency accurately measured for imaging frame rates up to 500 Hz. Finally, a 3D image of a complex intensity distribution was obtained. The results demonstrated the high sensitivity of the UAI system proposed. The plane wave based approach provides a highly flexible trade-off between frame rate, resolution and contrast. In conclusion, the UAI system shows promise for non-invasive, direct and accurate real-time imaging of electrical activation in vivo.

The Arizona Radio Observatory CO Mapping Survey of Galactic Molecular Clouds. V. The Sh2-235 Cloud in CO J=2-1, 13CO J=2-1, and CO J=3-2

NASA Astrophysics Data System (ADS)

Bieging, John H.; Patel, Saahil; Peters, William L.; Toth, L. Viktor; Marton, Gábor; Zahorecz, Sarolta

2016-09-01

We present the results of a program to map the Sh2-235 molecular cloud complex in the CO and 13CO J = 2 - 1 transitions using the Heinrich Hertz Submillimeter Telescope. The map resolution is 38″ (FWHM), with an rms noise of 0.12 K brightness temperature, for a velocity resolution of 0.34 km s-1. With the same telescope, we also mapped the CO J = 3 - 2 line at a frequency of 345 GHz, using a 64 beam focal plane array of heterodyne mixers, achieving a typical rms noise of 0.5 K brightness temperature with a velocity resolution of 0.23 km s-1. The three spectral line data cubes are available for download. Much of the cloud appears to be slightly sub-thermally excited in the J = 3 level, except for in the vicinity of the warmest and highest column density areas, which are currently forming stars. Using the CO and 13CO J = 2 - 1 lines, we employ an LTE model to derive the gas column density over the entire mapped region. Examining a 125 pc2 region centered on the most active star formation in the vicinity of Sh2-235, we find that the young stellar object surface density scales as approximately the 1.6-power of the gas column density. The area distribution function of the gas is a steeply declining exponential function of gas column density. Comparison of the morphology of ionized and molecular gas suggests that the cloud is being substantially disrupted by expansion of the H II regions, which may be triggering current star formation.

Brain serotonin transporter density and aggression in abstinent methamphetamine abusers.

PubMed

Sekine, Yoshimoto; Ouchi, Yasuomi; Takei, Nori; Yoshikawa, Etsuji; Nakamura, Kazuhiko; Futatsubashi, Masami; Okada, Hiroyuki; Minabe, Yoshio; Suzuki, Katsuaki; Iwata, Yasuhide; Tsuchiya, Kenji J; Tsukada, Hideo; Iyo, Masaomi; Mori, Norio

2006-01-01

In animals, methamphetamine is known to have a neurotoxic effect on serotonin neurons, which have been implicated in the regulation of mood, anxiety, and aggression. It remains unknown whether methamphetamine damages serotonin neurons in humans. To investigate the status of brain serotonin neurons and their possible relationship with clinical characteristics in currently abstinent methamphetamine abusers. Case-control analysis. A hospital research center. Twelve currently abstinent former methamphetamine abusers (5 women and 7 men) and 12 age-, sex-, and education-matched control subjects recruited from the community. The brain regional density of the serotonin transporter, a structural component of serotonin neurons, was estimated using positron emission tomography and trans-1,2,3,5,6,10-beta-hexahydro-6-[4-(methylthio)phenyl]pyrrolo-[2,1-a]isoquinoline ([(11)C](+)McN-5652). Estimates were derived from region-of-interest and statistical parametric mapping methods, followed by within-case analysis using the measures of clinical variables. The duration of methamphetamine use, the magnitude of aggression and depressive symptoms, and changes in serotonin transporter density represented by the [(11)C](+)McN-5652 distribution volume. Methamphetamine abusers showed increased levels of aggression compared with controls. Region-of-interest and statistical parametric mapping analyses revealed that the serotonin transporter density in global brain regions (eg, the midbrain, thalamus, caudate, putamen, cerebral cortex, and cerebellum) was significantly lower in methamphetamine abusers than in control subjects, and this reduction was significantly inversely correlated with the duration of methamphetamine use. Furthermore, statistical parametric mapping analyses indicated that the density in the orbitofrontal, temporal, and anterior cingulate areas was closely associated with the magnitude of aggression in methamphetamine abusers. Protracted abuse of methamphetamine may reduce the density of the serotonin transporter in the brain, leading to elevated aggression, even in currently abstinent abusers.

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

NASA Technical Reports Server (NTRS)

Manista, E. J.

1972-01-01

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

Abnormalities of P300 cortical current density in unmedicated depressed patients revealed by LORETA analysis of event-related potentials.

PubMed

Kawasaki, Toshihiko; Tanaka, Shin; Wang, Jijun; Hokama, Hiroto; Hiramatsu, Kenichi

2004-02-01

The purpose of the present study was to investigate the neural substrates underlying event-related potential (ERP) abnormalities, with respect to the generators of the ERP components in depressed patients. Using an oddball paradigm, ERP from auditory stimuli were recorded from 22 unmedicated patients with current depressive episodes and compared with those from 22 age- and gender-matched normal controls. Cortical current densities of the N100 and P300 components were analyzed using low-resolution electromagnetic tomography (LORETA). Group differences in cortical current density were mapped on a 3-D cortex model. The results revealed that N100 cortical current densities did not differ between the two groups, while P300 cortical current densities were significantly lower in depressed patients over the bilateral temporal lobes, the left frontal region, and the right temporal-parietal area. Furthermore, the cortical area in which the group difference in P300 current density had been identified was remarkably larger over the right than the left hemisphere, thus supporting the hypothesis of right hemisphere dysfunction in depression.

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

Fertig, Fabian, E-mail: fabian.fertig@ise.fraunhofer.de; Greulich, Johannes; Rein, Stefan

We present a spatially resolved method to determine the short-circuit current density of crystalline silicon solar cells by means of lock-in thermography. The method utilizes the property of crystalline silicon solar cells that the short-circuit current does not differ significantly from the illuminated current under moderate reverse bias. Since lock-in thermography images locally dissipated power density, this information is exploited to extract values of spatially resolved current density under short-circuit conditions. In order to obtain an accurate result, one or two illuminated lock-in thermography images and one dark lock-in thermography image need to be recorded. The method can be simplifiedmore » in a way that only one image is required to generate a meaningful short-circuit current density map. The proposed method is theoretically motivated, and experimentally validated for monochromatic illumination in comparison to the reference method of light-beam induced current.« less

Charge and Spin Currents in Open-Shell Molecules:  A Unified Description of NMR and EPR Observables.

PubMed

Soncini, Alessandro

2007-11-01

The theory of EPR hyperfine coupling tensors and NMR nuclear magnetic shielding tensors of open-shell molecules in the limit of vanishing spin-orbit coupling (e.g., for organic radicals) is analyzed in terms of spin and charge current density vector fields. The ab initio calculation of the spin and charge current density response has been implemented at the Restricted Open-Shell Hartree-Fock, Unrestricted Hartree-Fock, and unrestricted GGA-DFT level of theory. On the basis of this formalism, we introduce the definition of nuclear hyperfine coupling density, a scalar function of position providing a partition of the EPR observable over the molecular domain. Ab initio maps of spin and charge current density and hyperfine coupling density for small radicals are presented and discussed in order to illustrate the interpretative advantages of the newly introduced approach. Recent NMR experiments providing evidence for the existence of diatropic ring currents in the open-shell singlet pancake-bonded dimer of the neutral phenalenyl radical are directly assessed via the visualization of the induced current density.

Quantitative Phase Fraction Detection in Organic Photovoltaic Materials through EELS Imaging

DOE PAGES

Dyck, Ondrej; Hu, Sheng; Das, Sanjib; ...

2015-11-24

Organic photovoltaic materials have recently seen intense interest from the research community. Improvements in device performance are occurring at an impressive rate; however, visualization of the active layer phase separation still remains a challenge. Our paper outlines the application of two electron energy-loss spectroscopic (EELS) imaging techniques that can complement and enhance current phase detection techniques. Specifically, the bulk plasmon peak position, often used to produce contrast between phases in energy filtered transmission electron microscopy (EFTEM), is quantitatively mapped across a sample cross section. One complementary spectrum image capturing the carbon and sulfur core loss edges is compared with themore » plasmon peak map and found to agree quite well, indicating that carbon and sulfur density differences between the two phases also allows phase discrimination. Additionally, an analytical technique for determining absolute atomic areal density is used to produce an absolute carbon and sulfur areal density map. We also show how these maps may be re-interpreted as a phase ratio map, giving quantitative information about the purity of the phases within the junction.« less

High-resolution carbon mapping on the million-hectare Island of Hawaii

Treesearch

Gregory P. Asner; R. Flint Hughes; Joseph Mascaro; Amanda L. Uowolo; David E. Knapp; James Jacobson; Ty Kennedy-Bowdoin; John K . Clark

2011-01-01

Current markets and international agreements for reducing emissions from deforestation and forest degradation (REDD) rely on carbon (C) monitoring techniques. Combining field measurements, airborne light detection and ranging (LiDAR)-based observations, and satellite-based imagery, we developed a 30-meter-resolution map of aboveground C density spanning 40 vegetation...

Electric currents and coronal heating in NOAA active region 6952

NASA Technical Reports Server (NTRS)

Metcalf, T. R.; Canfield, R. C.; Hudson, H. S.; Mickey, D. L.; Wulser, J. -P.; Martens, P. C. H.; Tsuneta, S.

1994-01-01

We examine the spatial and temporal relationship between coronal structures observed with the soft X-ray telescope (SXT) on board the Yohkoh spacecraft and the vertical electric current density derived from photospheric vector magnetograms obtained using the Stokes Polarimeter at the Mees Solar Observatory. We focus on a single active region: AR 6952 which we observed on 7 days during 1991 December. For 11 independent maps of the vertical electric current density co-aligned with non-flaring X-ray images, we search for a morphological relationship between sites of high vertical current density in the photosphere and enhanced X-ray emission in the overlying corona. We find no compelling spatial or temporal correlation between the sites of vertical current and the bright X-ray structures in this active region.

Transport and sedimentation in unconfined experimental dilute pyroclastic density currents

NASA Astrophysics Data System (ADS)

Ramirez, G.; Andrews, B. J.; Dennen, R. L.

2013-12-01

We present results from experiments conducted in a new facility that permits the study of large, unconfined particle laden density currents that are dynamically similar to natural dilute pyroclastic density currents (PDCs). Experiments were run in a sealed, air-filled tank measuring 8.5 m long by 6.1 m wide by 2.6 m tall. Currents were generated by feeding mixture of heated particles (5 μm aluminum oxide, 25 μm talc, 27 μm walnut shell, 76 μm glass beads) down a chute at controlled rates to produce dilute, turbulent gravity currents. Comparison of experimental currents with natural PDCs shows good agreement between Froude, densimetric and thermal Richardson, and particle Stokes and settling numbers; experimental currents have lower Reynolds numbers than natural PDCs, but are fully turbulent. Currents were illuminated with 3 orthogonal laser sheets (650, 532, and 450 nm wavelengths) and recorded with an array of HD video cameras and a high speed camera (up to 3000 fps). Deposits were mapped using a grid of sedimentation traps. We observe distinct differences between ambient temperature and warm currents: * warm currents have shorter run out distances, narrow map view distributions of currents and deposits, thicken with distance from the source, and lift off to form coignimbrite plumes; * ambient temperature currents typically travel farther, spread out radially, do not thicken greatly with transport distance, and do not form coignimbrite plumes. Long duration currents (600 s compared to 30-100 s) oscillate laterally with time (e.g. transport to the right, then the left, and back); this oscillation happens prior to any interaction with the tank walls. Isopach maps of the deposits show predictable trends in sedimentation versus distance in response to eruption parameters (eruption rate, duration, temperature, and initial current mass), but all sedimentation curves can be fit with 2nd order polynomials (R2>.9). Proximal sedimentation is similar in comparable warm and ambient temperature currents, but distal sedimentation (beyond the current runout) increases in warm currents reflecting deposition from coignimbrite plumes. We are currently developing analytical models to link the observed transport and sedimentation results.

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

NASA Astrophysics Data System (ADS)

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

2011-04-01

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

Updating Mars-GRAM to Increase the Accuracy of Sensitivity Studies at Large Optical Depths

NASA Technical Reports Server (NTRS)

Justh, Hiliary L.; Justus, C. G.; Badger, Andrew M.

2010-01-01

The Mars Global Reference Atmospheric Model (Mars-GRAM) is an engineering-level atmospheric model widely used for diverse mission applications. Mars-GRAM s perturbation modeling capability is commonly used, in a Monte-Carlo mode, to perform high fidelity engineering end-to-end simulations for entry, descent, and landing (EDL). During the Mars Science Laboratory (MSL) site selection process, it was discovered that Mars-GRAM, when used for sensitivity studies for MapYear=0 and large optical depth values such as tau=3, is less than realistic. From the surface to 80 km altitude, Mars-GRAM is based on the NASA Ames Mars General Circulation Model (MGCM). MGCM results that were used for Mars-GRAM with MapYear set to 0 were from a MGCM run with a fixed value of tau=3 for the entire year at all locations. This has resulted in an imprecise atmospheric density at all altitudes. As a preliminary fix to this pressure-density problem, density factor values were determined for tau=0.3, 1 and 3 that will adjust the input values of MGCM MapYear 0 pressure and density to achieve a better match of Mars-GRAM MapYear 0 with Thermal Emission Spectrometer (TES) observations for MapYears 1 and 2 at comparable dust loading. Currently, these density factors are fixed values for all latitudes and Ls. Results will be presented from work being done to derive better multipliers by including variation with latitude and/or Ls by comparison of MapYear 0 output directly against TES limb data. The addition of these more precise density factors to Mars-GRAM 2005 Release 1.4 will improve the results of the sensitivity studies done for large optical depths.

Four-dimensional ultrasound current source density imaging of a dipole field

NASA Astrophysics Data System (ADS)

Wang, Z. H.; Olafsson, R.; Ingram, P.; Li, Q.; Qin, Y.; Witte, R. S.

2011-09-01

Ultrasound current source density imaging (UCSDI) potentially transforms conventional electrical mapping of excitable organs, such as the brain and heart. For this study, we demonstrate volume imaging of a time-varying current field by scanning a focused ultrasound beam and detecting the acoustoelectric (AE) interaction signal. A pair of electrodes produced an alternating current distribution in a special imaging chamber filled with a 0.9% NaCl solution. A pulsed 1 MHz ultrasound beam was scanned near the source and sink, while the AE signal was detected on remote recording electrodes, resulting in time-lapsed volume movies of the alternating current distribution.

Nuclear Resonance Fluorescence and Isotopic Mapping of Containers

NASA Astrophysics Data System (ADS)

Johnson, Micah S.; McNabb, Dennis P.

2009-03-01

National security programs have expressed interest in developing systems to isotopically map shipping containers, fuel assemblies, and waste barrels for various materials including special nuclear material (SNM). Current radiographic systems offer little more than an ambiguous density silhouette of a container's contents. In this paper we will present a system being developed at LLNL to isotopically map containers using the nuclear resonance fluorescence (NRF) method. Recent experimental measurements on NRF strengths in SNM are discussed.

A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna.

PubMed

Dukić, Marinela; Berner, Daniel; Roesti, Marius; Haag, Christoph R; Ebert, Dieter

2016-10-13

Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome. A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates. Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.

Density-functional theory for internal magnetic fields

NASA Astrophysics Data System (ADS)

Tellgren, Erik I.

2018-01-01

A density-functional theory is developed based on the Maxwell-Schrödinger equation with an internal magnetic field in addition to the external electromagnetic potentials. The basic variables of this theory are the electron density and the total magnetic field, which can equivalently be represented as a physical current density. Hence, the theory can be regarded as a physical current density-functional theory and an alternative to the paramagnetic current density-functional theory due to Vignale and Rasolt. The energy functional has strong enough convexity properties to allow a formulation that generalizes Lieb's convex analysis formulation of standard density-functional theory. Several variational principles as well as a Hohenberg-Kohn-like mapping between potentials and ground-state densities follow from the underlying convex structure. Moreover, the energy functional can be regarded as the result of a standard approximation technique (Moreau-Yosida regularization) applied to the conventional Schrödinger ground-state energy, which imposes limits on the maximum curvature of the energy (with respect to the magnetic field) and enables construction of a (Fréchet) differentiable universal density functional.

Time and space resolved current density mapping in three dimensions using magnetic field probe array in a high voltage coaxial gap

NASA Astrophysics Data System (ADS)

Cordaro, S. W.; Bott-Suzuki, S. C.

2017-12-01

We present an experimental analysis of the symmetry of current density in a coaxial geometry, diagnosed using a magnetic field probe array and calculations of the Fowler-Nordheim enhancement factor. Data were collected on the coaxial gap breakdown device (240 A, 25 kV, 150 ns, ˜0.1 Hz), and data from experiments using 2 different gap sizes and different penetration depths are compared over runs comprising 50 shots for each case. The magnetic field probe array quantifies the distribution of current density at three axial locations, on either sides of a vacuum breakdown, and tracks the evolution with time and space. The results show asymmetries in current density, which can be influenced by changes in the gap size and the penetration depth (of the center electrode into the outer electrode). For smaller gap sizes (400 μm), symmetric current profiles were not observed, and the change in the penetration depth changes both the symmetric behavior of the current density and the enhancement factor. For larger gaps (900 μm), current densities were typically more uniform and less influenced by the penetration depth, which is reflected in the enhancement factor values. It is possible that the change in inductance caused by the localization of current densities plays a role in the observed behavior.

Influence of the Yukon River on the Bering Sea

NASA Technical Reports Server (NTRS)

Dean, K.; Mcroy, C. P.

1986-01-01

The purpose is to use satellite data to study relationships between discharge of the Yukon River to currents and biologic productivity in the northern Bering Sea. Amended specific objectives are: to develop thermal, sediment and chlorophyll surface maps using thematic mapping (TM) data of the discharge of the Yukon River and the Alaska Coastal Current during the ice free season; to develop a historical model of the distribution of the Yukon River discharge and the Alaska Coastal Current using LANDSAT multispectral scanner (MMS) and NOAA satellite imagery; and to use high resolution TM data to define the surface dynamics of the front between the Alaska Coastal Current and the Bering Shelf/Anadyr Current. LANDSAT MSS and TM, and Advanced Very High Resolution Radiometer (AVHRR) data were recorded during the 1985 ice-free period. The satellite data coincided with shipboard measurements acquired by Inner Self Transfer and Recycling scientists. Circumstances were such, that on July 5 and July 22, all three sensors recorded data that has been registered to a common map projection and map base, then contrast stretched, color composited, and density sliced.

Crystallographic orientation mapping with an electron backscattered diffraction technique in (Bi, Pb)2Sr2Ca2Cu3O10 superconductor tapes

NASA Astrophysics Data System (ADS)

Tan, T. T.; Li, S.; Oh, J. T.; Gao, W.; Liu, H. K.; Dou, S. X.

2001-02-01

It is believed that grain boundaries act as weak links in limiting the critical current density (Jc) of bulk high-Tc superconductors. The weak-link problem can be greatly reduced by elimination or minimization of large-angle grain boundaries. It has been reported that the distribution of the Jc in (Bi, Pb)2Sr2Ca2Cu3O10+x (Bi2223) superconductor tapes presents a parabolic relationship in the transverse cross section of the tapes, with the lowest currents occurring at the centre of the tapes. It was proposed that the Jc distribution is strongly dependent on the local crystallographic orientation distribution of the Bi2223 oxides. However, the local three-dimensional crystallographic orientation distribution of Bi2223 crystals in (Bi, Pb)2Sr2Ca2Cu3O10+x superconductor tapes has not yet been experimentally determined. In this work, the electron backscattered diffraction technique was employed to map the crystallographic orientation distribution, determine the misorientation of grain boundaries and also map the misorientation distribution in Bi2223 superconductor tapes. Through crystallographic orientation mapping, the relationship between the crystallographic orientation distribution, the boundary misorientation distribution and the fabrication parameters may be understood. This can be used to optimize the fabrication processes thus increasing the critical current density in Bi2223 superconductor tapes.

Software Toolbox for Low-Frequency Conductivity and Current Density Imaging Using MRI.

PubMed

Sajib, Saurav Z K; Katoch, Nitish; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

2017-11-01

Low-frequency conductivity and current density imaging using MRI includes magnetic resonance electrical impedance tomography (MREIT), diffusion tensor MREIT (DT-MREIT), conductivity tensor imaging (CTI), and magnetic resonance current density imaging (MRCDI). MRCDI and MREIT provide current density and isotropic conductivity images, respectively, using current-injection phase MRI techniques. DT-MREIT produces anisotropic conductivity tensor images by incorporating diffusion weighted MRI into MREIT. These current-injection techniques are finding clinical applications in diagnostic imaging and also in transcranial direct current stimulation (tDCS), deep brain stimulation (DBS), and electroporation where treatment currents can function as imaging currents. To avoid adverse effects of nerve and muscle stimulations due to injected currents, conductivity tensor imaging (CTI) utilizes B1 mapping and multi-b diffusion weighted MRI to produce low-frequency anisotropic conductivity tensor images without injecting current. This paper describes numerical implementations of several key mathematical functions for conductivity and current density image reconstructions in MRCDI, MREIT, DT-MREIT, and CTI. To facilitate experimental studies of clinical applications, we developed a software toolbox for these low-frequency conductivity and current density imaging methods. This MR-based conductivity imaging (MRCI) toolbox includes 11 toolbox functions which can be used in the MATLAB environment. The MRCI toolbox is available at http://iirc.khu.ac.kr/software.html . Its functions were tested by using several experimental datasets, which are provided together with the toolbox. Users of the toolbox can focus on experimental designs and interpretations of reconstructed images instead of developing their own image reconstruction softwares. We expect more toolbox functions to be added from future research outcomes. Low-frequency conductivity and current density imaging using MRI includes magnetic resonance electrical impedance tomography (MREIT), diffusion tensor MREIT (DT-MREIT), conductivity tensor imaging (CTI), and magnetic resonance current density imaging (MRCDI). MRCDI and MREIT provide current density and isotropic conductivity images, respectively, using current-injection phase MRI techniques. DT-MREIT produces anisotropic conductivity tensor images by incorporating diffusion weighted MRI into MREIT. These current-injection techniques are finding clinical applications in diagnostic imaging and also in transcranial direct current stimulation (tDCS), deep brain stimulation (DBS), and electroporation where treatment currents can function as imaging currents. To avoid adverse effects of nerve and muscle stimulations due to injected currents, conductivity tensor imaging (CTI) utilizes B1 mapping and multi-b diffusion weighted MRI to produce low-frequency anisotropic conductivity tensor images without injecting current. This paper describes numerical implementations of several key mathematical functions for conductivity and current density image reconstructions in MRCDI, MREIT, DT-MREIT, and CTI. To facilitate experimental studies of clinical applications, we developed a software toolbox for these low-frequency conductivity and current density imaging methods. This MR-based conductivity imaging (MRCI) toolbox includes 11 toolbox functions which can be used in the MATLAB environment. The MRCI toolbox is available at http://iirc.khu.ac.kr/software.html . Its functions were tested by using several experimental datasets, which are provided together with the toolbox. Users of the toolbox can focus on experimental designs and interpretations of reconstructed images instead of developing their own image reconstruction softwares. We expect more toolbox functions to be added from future research outcomes.

High-speed mapping of grown-in defects and their influence in large-area silicon photovoltaic devices

NASA Astrophysics Data System (ADS)

Sopori, Bhushan; Wei, Chen; Yi, Zhang; Madjdpour, Jamal

2000-03-01

A scanning system for mapping defects, and for measuring their influence on the photovoltaic of Si solar cells, is described. The system uses optical scattering patterns to identify the nature of defects. The local density of the defects is statistically determined from the integrated scattered light. The optical system can also measure the reflectance and the light-induced current which is then used to yield maps of the internal photoresponse of the device.

Statistical density modification using local pattern matching

DOEpatents

Terwilliger, Thomas C.

2007-01-23

A computer implemented method modifies an experimental electron density map. A set of selected known experimental and model electron density maps is provided and standard templates of electron density are created from the selected experimental and model electron density maps by clustering and averaging values of electron density in a spherical region about each point in a grid that defines each selected known experimental and model electron density maps. Histograms are also created from the selected experimental and model electron density maps that relate the value of electron density at the center of each of the spherical regions to a correlation coefficient of a density surrounding each corresponding grid point in each one of the standard templates. The standard templates and the histograms are applied to grid points on the experimental electron density map to form new estimates of electron density at each grid point in the experimental electron density map.

THE ARIZONA RADIO OBSERVATORY CO MAPPING SURVEY OF GALACTIC MOLECULAR CLOUDS. V. THE SH2-235 CLOUD IN CO J  = 2 − 1, {sup 13}CO J  = 2 − 1, AND CO J  = 3 − 2

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

Bieging, John H.; Peters, William L.; Patel, Saahil

We present the results of a program to map the Sh2-235 molecular cloud complex in the CO and {sup 13}CO  J  = 2 − 1 transitions using the Heinrich Hertz Submillimeter Telescope. The map resolution is 38″ (FWHM), with an rms noise of 0.12 K brightness temperature, for a velocity resolution of 0.34 km s{sup −1}. With the same telescope, we also mapped the CO J  = 3 − 2 line at a frequency of 345 GHz, using a 64 beam focal plane array of heterodyne mixers, achieving a typical rms noise of 0.5 K brightness temperature with a velocity resolution of 0.23 km s{sup −1}.more » The three spectral line data cubes are available for download. Much of the cloud appears to be slightly sub-thermally excited in the J  = 3 level, except for in the vicinity of the warmest and highest column density areas, which are currently forming stars. Using the CO and {sup 13}CO  J  = 2 − 1 lines, we employ an LTE model to derive the gas column density over the entire mapped region. Examining a 125 pc{sup 2} region centered on the most active star formation in the vicinity of Sh2-235, we find that the young stellar object surface density scales as approximately the 1.6-power of the gas column density. The area distribution function of the gas is a steeply declining exponential function of gas column density. Comparison of the morphology of ionized and molecular gas suggests that the cloud is being substantially disrupted by expansion of the H ii regions, which may be triggering current star formation.« less

Steady-State Density Functional Theory for Finite Bias Conductances.

PubMed

Stefanucci, G; Kurth, S

2015-12-09

In the framework of density functional theory, a formalism to describe electronic transport in the steady state is proposed which uses the density on the junction and the steady current as basic variables. We prove that, in a finite window around zero bias, there is a one-to-one map between the basic variables and both local potential on as well as bias across the junction. The resulting Kohn-Sham system features two exchange-correlation (xc) potentials, a local xc potential, and an xc contribution to the bias. For weakly coupled junctions the xc potentials exhibit steps in the density-current plane which are shown to be crucial to describe the Coulomb blockade diamonds. At small currents these steps emerge as the equilibrium xc discontinuity bifurcates. The formalism is applied to a model benzene junction, finding perfect agreement with the orthodox theory of Coulomb blockade.

New Mars free-air and Bouguer gravity: Correlation with topography, geology and large impact basins

NASA Technical Reports Server (NTRS)

Frey, Herbert; Bills, Bruce G.; Kiefer, Walter S.; Nerem, R. Steven; Roark, James H.; Zuber, Maria T.

1993-01-01

Free-air and Bouguer gravity anomalies from a 50x50 field (MGM635), derived at the Goddard Space Flight Center, with global topography, geology, and the distribution of large impact basins was compared. The free-air gravity anomalies were derived from re-analysis of Viking Orbiter and Mariner 9 tracking data and have a spatial resolution of 250-300 km. Bouguer anomalies were calculated using a 50x50 expansion of the current Mars topography and the GSFC degree 50 geoid as the equipotential reference surface. Rotational flattening was removed using a moment of inertia of 0.365 and the corrections from Table B2 of Sleep and Phillips. Crustal density and mean density were assumed to be 2.9 and 3.93 gm/cm(sup 3). The spherical harmonic topography used has zero mean elevation, and differs from the USGS maps by about 2 km. Comparisons with global geology use a simplified map with about 1/3 the number of units on the current maps. For correlation with impact basins, the recent compilation by Schultz and Frey was used.

A beam current density monitor for intense electron beams

NASA Astrophysics Data System (ADS)

Fiorito, R. B.; Raleigh, M.; Seltzer, S. M.

1983-12-01

The authors describe a new type of electric probe for mapping the radial current density profile of high-energy, high current electron beams. The idea of developing an electrically sensitive probe for these conditions was originally suggested to one of the authors during a year's visit to the Lawrence Livermore National Laboratory. The resulting probe is intended for use on the Experimental Test Accelerator (ETA) and the Advanced Test Accelerator at that laboratory. This report discusses in detail: the mechanical design, the electrical response, and temperature effects, as they pertain to the electric probe, and describe the first experimental results obtained using this probe on ETA.

Optical characteristics of lightning and thunderstorm currents

NASA Technical Reports Server (NTRS)

Krider, E. P.; Blakeslee, R. J.

1985-01-01

Researchers determined that lightning can be used to determine the diurnal variations of thunderstorms, i.e., storms that produce audible thunder, and that these variations are also in good agreement with diurnal variations in rainfall and convective activity. Measurements of the Maxwell current density, J sub m, under active thunderstorms show that this physical quantity is quasi-steady between lightning discharges and that lightning does not produce large changes in J sub m. Maps of J sub m show contours of iso-current density that are consistent with the locations of radar echos and the locations of where lightning has altered the cloud charge distribution.

Formation of current singularity in a topologically constrained plasma

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

Zhou, Yao; Huang, Yi-Min; Qin, Hong

2016-02-01

Recently a variational integrator for ideal magnetohydrodynamics in Lagrangian labeling has been developed. Its built-in frozen-in equation makes it optimal for studying current sheet formation. We use this scheme to study the Hahm-Kulsrud-Taylor problem, which considers the response of a 2D plasma magnetized by a sheared field under sinusoidal boundary forcing. We obtain an equilibrium solution that preserves the magnetic topology of the initial field exactly, with a fluid mapping that is non-differentiable. Unlike previous studies that examine the current density output, we identify a singular current sheet from the fluid mapping. These results are benchmarked with a constrained Grad-Shafranovmore » solver. The same signature of current singularity can be found in other cases with more complex magnetic topologies.« less

Globally optimal superconducting magnets part II: symmetric MSE coil arrangement.

PubMed

Tieng, Quang M; Vegh, Viktor; Brereton, Ian M

2009-01-01

A globally optimal superconducting magnet coil design procedure based on the Minimum Stored Energy (MSE) current density map is outlined. The method has the ability to arrange coils in a manner that generates a strong and homogeneous axial magnetic field over a predefined region, and ensures the stray field external to the assembly and peak magnetic field at the wires are in acceptable ranges. The outlined strategy of allocating coils within a given domain suggests that coils should be placed around the perimeter of the domain with adjacent coils possessing alternating winding directions for optimum performance. The underlying current density maps from which the coils themselves are derived are unique, and optimized to possess minimal stored energy. Therefore, the method produces magnet designs with the lowest possible overall stored energy. Optimal coil layouts are provided for unshielded and shielded short bore symmetric superconducting magnets.

The North Alabama Lightning Warning Product

NASA Technical Reports Server (NTRS)

Buechler, Dennis E.; Blakeslee, R. J.; Stano, G. T.

2009-01-01

The North Alabama Lightning Mapping Array NALMA has been collecting total lightning data on storms in the Tennessee Valley region since 2001. Forecasters from nearby National Weather Service (NWS) offices have been ingesting this data for display with other AWIPS products. The current lightning product used by the offices is the lightning source density plot. The new product provides a probabalistic, short-term, graphical forecast of the probability of lightning activity occurring at 5 min intervals over the next 30 minutes . One of the uses of the current lightning source density product by the Huntsville National Weather Service Office is to identify areas of potential for cloud-to-ground flashes based on where LMA total lightning is occurring. This product quantifies that observation. The Lightning Warning Product is derived from total lightning observations from the Washington, D.C. (DCLMA) and North Alabama Lightning Mapping Arrays and cloud-to-ground lightning flashes detected by the National Lightning Detection Network (NLDN). Probability predictions are provided for both intracloud and cloud-to-ground flashes. The gridded product can be displayed on AWIPS workstations in a manner similar to that of the lightning source density product.

Digital mining claim density map for federal lands in Nevada: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Nevada as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate Bureau of Land Management (BLM) State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Utah: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Utah as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Wyoming: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Wyoming as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Colorado: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Colorado as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in California: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in California as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in New Mexico: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in New Mexico as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Washington: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Washington as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Arizona: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Arizona as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Automatically Generated Vegetation Density Maps with LiDAR Survey for Orienteering Purpose

NASA Astrophysics Data System (ADS)

Petrovič, Dušan

2018-05-01

The focus of our research was to automatically generate the most adequate vegetation density maps for orienteering purpose. Application Karttapullatuin was used for automated generation of vegetation density maps, which requires LiDAR data to process an automatically generated map. A part of the orienteering map in the area of Kazlje-Tomaj was used to compare the graphical display of vegetation density. With different settings of parameters in the Karttapullautin application we changed the way how vegetation density of automatically generated map was presented, and tried to match it as much as possible with the orienteering map of Kazlje-Tomaj. Comparing more created maps of vegetation density the most suitable parameter settings to automatically generate maps on other areas were proposed, too.

Human population, urban settlement patterns and their impact on Plasmodium falciparum malaria endemicity.

PubMed

Tatem, Andrew J; Guerra, Carlos A; Kabaria, Caroline W; Noor, Abdisalan M; Hay, Simon I

2008-10-27

The efficient allocation of financial resources for malaria control and the optimal distribution of appropriate interventions require accurate information on the geographic distribution of malaria risk and of the human populations it affects. Low population densities in rural areas and high population densities in urban areas can influence malaria transmission substantially. Here, the Malaria Atlas Project (MAP) global database of Plasmodium falciparum parasite rate (PfPR) surveys, medical intelligence and contemporary population surfaces are utilized to explore these relationships and other issues involved in combining malaria risk maps with those of human population distribution in order to define populations at risk more accurately. First, an existing population surface was examined to determine if it was sufficiently detailed to be used reliably as a mask to identify areas of very low and very high population density as malaria free regions. Second, the potential of international travel and health guidelines (ITHGs) for identifying malaria free cities was examined. Third, the differences in PfPR values between surveys conducted in author-defined rural and urban areas were examined. Fourth, the ability of various global urban extent maps to reliably discriminate these author-based classifications of urban and rural in the PfPR database was investigated. Finally, the urban map that most accurately replicated the author-based classifications was analysed to examine the effects of urban classifications on PfPR values across the entire MAP database. Masks of zero population density excluded many non-zero PfPR surveys, indicating that the population surface was not detailed enough to define areas of zero transmission resulting from low population densities. In contrast, the ITHGs enabled the identification and mapping of 53 malaria free urban areas within endemic countries. Comparison of PfPR survey results showed significant differences between author-defined 'urban' and 'rural' designations in Africa, but not for the remainder of the malaria endemic world. The Global Rural Urban Mapping Project (GRUMP) urban extent mask proved most accurate for mapping these author-defined rural and urban locations, and further sub-divisions of urban extents into urban and peri-urban classes enabled the effects of high population densities on malaria transmission to be mapped and quantified. The availability of detailed, contemporary census and urban extent data for the construction of coherent and accurate global spatial population databases is often poor. These known sources of uncertainty in population surfaces and urban maps have the potential to be incorporated into future malaria burden estimates. Currently, insufficient spatial information exists globally to identify areas accurately where population density is low enough to impact upon transmission. Medical intelligence does however exist to reliably identify malaria free cities. Moreover, in Africa, urban areas that have a significant effect on malaria transmission can be mapped.

Improving Mars-GRAM: Increasing the Accuracy of Sensitivity Studies at Large Optical Depths

NASA Technical Reports Server (NTRS)

Justh, Hilary L.; Justus, C. G.; Badger, Andrew M.

2010-01-01

Extensively utilized for numerous mission applications, the Mars Global Reference Atmospheric Model (Mars-GRAM) is an engineering-level atmospheric model. In a Monte-Carlo mode, Mars-GRAM's perturbation modeling capability is used to perform high fidelity engineering end-to-end simulations for entry, descent, and landing (EDL). Mars-GRAM has been found to be inexact when used during the Mars Science Laboratory (MSL) site selection process for sensitivity studies for MapYear=0 and large optical depth values such as tau=3. Mars-GRAM is based on the NASA Ames Mars General Circulation Model (MGCM) from the surface to 80 km altitude. Mars-GRAM with the MapYear parameter set to 0 utilizes results from a MGCM run with a fixed value of tau=3 at all locations for the entire year. Imprecise atmospheric density and pressure at all altitudes is a consequence of this use of MGCM with tau=3. Density factor values have been determined for tau=0.3, 1 and 3 as a preliminary fix to this pressure-density problem. These factors adjust the input values of MGCM MapYear 0 pressure and density to achieve a better match of Mars-GRAM MapYear 0 with Thermal Emission Spectrometer (TES) observations for MapYears 1 and 2 at comparable dust loading. These density factors are fixed values for all latitudes and Ls and are included in Mars-GRAM Release 1.3. Work currently being done, to derive better multipliers by including variations with latitude and/or Ls by comparison of MapYear 0 output directly against TES limb data, will be highlighted in the presentation. The TES limb data utilized in this process has been validated by a comparison study between Mars atmospheric density estimates from Mars-GRAM and measurements by Mars Global Surveyor (MGS). This comparison study was undertaken for locations on Mars of varying latitudes, Ls, and LTST. The more precise density factors will be included in Mars-GRAM 2005 Release 1.4 and thus improve the results of future sensitivity studies done for large optical depths.

Mapping Air Population

NASA Astrophysics Data System (ADS)

Peterson, Michael P.; Hunt, Paul; Weiß, Konrad

2018-05-01

"Air population" refers to the total number of people flying above the earth at any point in time. The total number of passengers can then be estimated by multiplying the number of seats for each aircraft by the current seat occupancy rate. Using this method, the estimated air population is determined by state for the airspace over the United States. In the interactive, real-time mapping system, maps are provided to show total air population, the density of air population (air population / area of state), and the ratio of air population to ground population.

Derivation of a northern-hemispheric biomass map for use in global carbon cycle models

NASA Astrophysics Data System (ADS)

Thurner, Martin; Beer, Christian; Santoro, Maurizio; Carvalhais, Nuno; Wutzler, Thomas; Schepaschenko, Dmitry; Shvidenko, Anatoly; Kompter, Elisabeth; Levick, Shaun; Schmullius, Christiane

2013-04-01

Quantifying the state and the change of the World's forests is crucial because of their ecological, social and economic value. Concerning their ecological importance, forests provide important feedbacks on the global carbon, energy and water cycles. In addition to their influence on albedo and evapotranspiration, they have the potential to sequester atmospheric carbon dioxide and thus to mitigate global warming. The current state and inter-annual variability of forest carbon stocks remain relatively unexplored, but remote sensing can serve to overcome this shortcoming. While for the tropics wall-to-wall estimates of above-ground biomass have been recently published, up to now there was a lack of similar products covering boreal and temperate forests. Recently, estimates of forest growing stock volume (GSV) were derived from ENVISAT ASAR C-band data for latitudes above 30° N. Utilizing a wood density and a biomass compartment database, a forest carbon density map covering North-America, Europe and Asia with 0.01° resolution could be derived out of this dataset. Allometric functions between stem, branches, root and foliage biomass were fitted and applied for different leaf types (broadleaf, needleleaf deciduous, needleleaf evergreen forest). Additionally, this method enabled uncertainty estimation of the resulting carbon density map. Intercomparisons with inventory-based biomass products in Russia, Europe and the USA proved the high accuracy of this approach at a regional scale (r2 = 0.70 - 0.90). Based on the final biomass map, the forest carbon stocks and densities (excluding understorey vegetation) for three biomes were estimated across three continents. While 40.7 ± 15.7 Gt of carbon were found to be stored in boreal forests, temperate broadleaf/mixed forests and temperate conifer forests contain 24.5 ± 9.4 Gt(C) and 14.5 ± 4.8 Gt(C), respectively. In terms of carbon density, most of the carbon per area is stored in temperate conifer (62.1 ± 20.7 Mg(C)/ha(Forest)) and broadleaf/mixed forests (58.0 ± 22.1 Mg(C)/ha(Forest)), whereas boreal forests have a carbon density of only 40.0 ± 15.4 Mg(C)/ha(Forest). While European forest carbon stocks are relatively small, the carbon density is higher compared to the other continents. The derived biomass map substantially improves the knowledge on the current carbon stocks of the northern-hemispheric boreal and temperate forests, serving as a new benchmark for spatially explicit and consistent biomass mapping with moderate spatial resolution. This product can be of great value for global carbon cycle models as well as national carbon monitoring systems. Further investigations concentrate on improving biomass parameterizations and representations in such kind of models. The presented map will help to improve the simulation of biomass spatial patterns and variability and enables identifying the dominant influential factors like climatic conditions and disturbances.

Quantifying volcanic hazard at Campi Flegrei caldera (Italy) with uncertainty assessment: 2. Pyroclastic density current invasion maps

NASA Astrophysics Data System (ADS)

Neri, Augusto; Bevilacqua, Andrea; Esposti Ongaro, Tomaso; Isaia, Roberto; Aspinall, Willy P.; Bisson, Marina; Flandoli, Franco; Baxter, Peter J.; Bertagnini, Antonella; Iannuzzi, Enrico; Orsucci, Simone; Pistolesi, Marco; Rosi, Mauro; Vitale, Stefano

2015-04-01

Campi Flegrei (CF) is an example of an active caldera containing densely populated settlements at very high risk of pyroclastic density currents (PDCs). We present here an innovative method for assessing background spatial PDC hazard in a caldera setting with probabilistic invasion maps conditional on the occurrence of an explosive event. The method encompasses the probabilistic assessment of potential vent opening positions, derived in the companion paper, combined with inferences about the spatial density distribution of PDC invasion areas from a simplified flow model, informed by reconstruction of deposits from eruptions in the last 15 ka. The flow model describes the PDC kinematics and accounts for main effects of topography on flow propagation. Structured expert elicitation is used to incorporate certain sources of epistemic uncertainty, and a Monte Carlo approach is adopted to produce a set of probabilistic hazard maps for the whole CF area. Our findings show that, in case of eruption, almost the entire caldera is exposed to invasion with a mean probability of at least 5%, with peaks greater than 50% in some central areas. Some areas outside the caldera are also exposed to this danger, with mean probabilities of invasion of the order of 5-10%. Our analysis suggests that these probability estimates have location-specific uncertainties which can be substantial. The results prove to be robust with respect to alternative elicitation models and allow the influence on hazard mapping of different sources of uncertainty, and of theoretical and numerical assumptions, to be quantified.

On Galactic Density Modeling in the Presence of Dust Extinction

NASA Astrophysics Data System (ADS)

Bovy, Jo; Rix, Hans-Walter; Green, Gregory M.; Schlafly, Edward F.; Finkbeiner, Douglas P.

2016-02-01

Inferences about the spatial density or phase-space structure of stellar populations in the Milky Way require a precise determination of the effective survey volume. The volume observed by surveys such as Gaia or near-infrared spectroscopic surveys, which have good coverage of the Galactic midplane region, is highly complex because of the abundant small-scale structure in the three-dimensional interstellar dust extinction. We introduce a novel framework for analyzing the importance of small-scale structure in the extinction. This formalism demonstrates that the spatially complex effect of extinction on the selection function of a pencil-beam or contiguous sky survey is equivalent to a low-pass filtering of the extinction-affected selection function with the smooth density field. We find that the angular resolution of current 3D extinction maps is sufficient for analyzing Gaia sub-samples of millions of stars. However, the current distance resolution is inadequate and needs to be improved by an order of magnitude, especially in the inner Galaxy. We also present a practical and efficient method for properly taking the effect of extinction into account in analyses of Galactic structure through an effective selection function. We illustrate its use with the selection function of red-clump stars in APOGEE using and comparing a variety of current 3D extinction maps.

Automated MRI segmentation for individualized modeling of current flow in the human head.

PubMed

Huang, Yu; Dmochowski, Jacek P; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C

2013-12-01

High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of the brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images requires labor-intensive manual segmentation, even when utilizing available automated segmentation tools. Also, accurate placement of many high-density electrodes on an individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. A fully automated segmentation technique based on Statical Parametric Mapping 8, including an improved tissue probability map and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on four healthy subjects and seven stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets. The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly. Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials.

Resonant inelastic soft x-ray scattering of CdS: a two-dimensional electronic structure map approach

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

Weinhardt, L.; Fuchs, O.; Fleszar, A.

2008-09-24

Resonant inelastic x-ray scattering (RIXS) with soft x-rays is uniquely suited to study the elec-tronic structure of a variety of materials, but is currently limited by low (fluorescence yield) count rates. This limitation is overcome with a new high-transmission spectrometer that allows to measure soft x-ray RIXS"maps." The S L2,3 RIXS map of CdS is discussed and compared with density functional calculations. The map allows the extraction of decay channel-specific"absorp-tion spectra," giving detailed insight into the wave functions of occupied and unoccupied elec-tronic states.

Two dimensional thermal and charge mapping of power thyristors

NASA Technical Reports Server (NTRS)

Hu, S. P.; Rabinovici, B. M.

1975-01-01

The two dimensional static and dynamic current density distributions within the junction of semiconductor power switching devices and in particular the thyristors were obtained. A method for mapping the thermal profile of the device junctions with fine resolution using an infrared beam and measuring the attenuation through the device as a function of temperature were developed. The results obtained are useful in the design and quality control of high power semiconductor switching devices.

Pyroclastic density current hazard maps at Campi Flegrei caldera (Italy): the effects of event scale, vent location and time forecasts.

NASA Astrophysics Data System (ADS)

Bevilacqua, Andrea; Neri, Augusto; Esposti Ongaro, Tomaso; Isaia, Roberto; Flandoli, Franco; Bisson, Marina

2016-04-01

Today hundreds of thousands people live inside the Campi Flegrei caldera (Italy) and in the adjacent part of the city of Naples making a future eruption of such volcano an event with huge consequences. Very high risks are associated with the occurrence of pyroclastic density currents (PDCs). Mapping of background or long-term PDC hazard in the area is a great challenge due to the unknown eruption time, scale and vent location of the next event as well as the complex dynamics of the flow over the caldera topography. This is additionally complicated by the remarkable epistemic uncertainty on the eruptive record, affecting the time of past events, the location of vents as well as the PDCs areal extent estimates. First probability maps of PDC invasion were produced combining a vent-opening probability map, statistical estimates concerning the eruptive scales and a Cox-type temporal model including self-excitement effects, based on the eruptive record of the last 15 kyr. Maps were produced by using a Monte Carlo approach and adopting a simplified inundation model based on the "box model" integral approximation tested with 2D transient numerical simulations of flow dynamics. In this presentation we illustrate the independent effects of eruption scale, vent location and time of forecast of the next event. Specific focus was given to the remarkable differences between the eastern and western sectors of the caldera and their effects on the hazard maps. The analysis allowed to identify areas with elevated probabilities of flow invasion as a function of the diverse assumptions made. With the quantification of some sources of uncertainty in relation to the system, we were also able to provide mean and percentile maps of PDC hazard levels.

Integrating multisource imagery and GIS analysis for mapping Bermuda`s benthic habitats

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

Vierros, M.K.

1997-06-01

Bermuda is a group of isolated oceanic situated in the northwest Atlantic Ocean and surrounded by the Sargasso Sea. Bermuda possesses the northernmost coral reefs and mangroves in the Atlantic Ocean, and because of its high population density, both the terrestrial and marine environments are under intense human pressure. Although a long record of scientific research exists, this study is the first attempt to comprehensively map the area`s benthic habitats, despite the need for such a map for resource assessment and management purposes. Multi-source and multi-date imagery were used for producing the habitat map due to lack of a completemore » up-to-date image. Classifications were performed with SPOT data, and the results verified from recent aerial photography and current aerial video, along with extensive ground truthing. Stratification of the image into regions prior to classification reduced the confusing effects of varying water depth. Classification accuracy in shallow areas was increased by derivation of a texture pseudo-channel, while bathymetry was used as a classification tool in deeper areas, where local patterns of zonation were well known. Because of seasonal variation in extent of seagrasses, a classification scheme based on density could not be used. Instead, a set of classes based on the seagrass area`s exposure to the open ocean were developed. The resulting habitat map is currently being assessed for accuracy with promising preliminary results, indicating its usefulness as a basis for future resource assessment studies.« less

Markedly divergent estimates of Amazon forest carbon density from ground plots and satellites.

PubMed

Mitchard, Edward T A; Feldpausch, Ted R; Brienen, Roel J W; Lopez-Gonzalez, Gabriela; Monteagudo, Abel; Baker, Timothy R; Lewis, Simon L; Lloyd, Jon; Quesada, Carlos A; Gloor, Manuel; Ter Steege, Hans; Meir, Patrick; Alvarez, Esteban; Araujo-Murakami, Alejandro; Aragão, Luiz E O C; Arroyo, Luzmila; Aymard, Gerardo; Banki, Olaf; Bonal, Damien; Brown, Sandra; Brown, Foster I; Cerón, Carlos E; Chama Moscoso, Victor; Chave, Jerome; Comiskey, James A; Cornejo, Fernando; Corrales Medina, Massiel; Da Costa, Lola; Costa, Flavia R C; Di Fiore, Anthony; Domingues, Tomas F; Erwin, Terry L; Frederickson, Todd; Higuchi, Niro; Honorio Coronado, Euridice N; Killeen, Tim J; Laurance, William F; Levis, Carolina; Magnusson, William E; Marimon, Beatriz S; Marimon Junior, Ben Hur; Mendoza Polo, Irina; Mishra, Piyush; Nascimento, Marcelo T; Neill, David; Núñez Vargas, Mario P; Palacios, Walter A; Parada, Alexander; Pardo Molina, Guido; Peña-Claros, Marielos; Pitman, Nigel; Peres, Carlos A; Poorter, Lourens; Prieto, Adriana; Ramirez-Angulo, Hirma; Restrepo Correa, Zorayda; Roopsind, Anand; Roucoux, Katherine H; Rudas, Agustin; Salomão, Rafael P; Schietti, Juliana; Silveira, Marcos; de Souza, Priscila F; Steininger, Marc K; Stropp, Juliana; Terborgh, John; Thomas, Raquel; Toledo, Marisol; Torres-Lezama, Armando; van Andel, Tinde R; van der Heijden, Geertje M F; Vieira, Ima C G; Vieira, Simone; Vilanova-Torre, Emilio; Vos, Vincent A; Wang, Ophelia; Zartman, Charles E; Malhi, Yadvinder; Phillips, Oliver L

2014-08-01

The accurate mapping of forest carbon stocks is essential for understanding the global carbon cycle, for assessing emissions from deforestation, and for rational land-use planning. Remote sensing (RS) is currently the key tool for this purpose, but RS does not estimate vegetation biomass directly, and thus may miss significant spatial variations in forest structure. We test the stated accuracy of pantropical carbon maps using a large independent field dataset. Tropical forests of the Amazon basin. The permanent archive of the field plot data can be accessed at: http://dx.doi.org/10.5521/FORESTPLOTS.NET/2014_1. Two recent pantropical RS maps of vegetation carbon are compared to a unique ground-plot dataset, involving tree measurements in 413 large inventory plots located in nine countries. The RS maps were compared directly to field plots, and kriging of the field data was used to allow area-based comparisons. The two RS carbon maps fail to capture the main gradient in Amazon forest carbon detected using 413 ground plots, from the densely wooded tall forests of the north-east, to the light-wooded, shorter forests of the south-west. The differences between plots and RS maps far exceed the uncertainties given in these studies, with whole regions over- or under-estimated by > 25%, whereas regional uncertainties for the maps were reported to be < 5%. Pantropical biomass maps are widely used by governments and by projects aiming to reduce deforestation using carbon offsets, but may have significant regional biases. Carbon-mapping techniques must be revised to account for the known ecological variation in tree wood density and allometry to create maps suitable for carbon accounting. The use of single relationships between tree canopy height and above-ground biomass inevitably yields large, spatially correlated errors. This presents a significant challenge to both the forest conservation and remote sensing communities, because neither wood density nor species assemblages can be reliably mapped from space.

Markedly divergent estimates of Amazon forest carbon density from ground plots and satellites

PubMed Central

Mitchard, Edward T A; Feldpausch, Ted R; Brienen, Roel J W; Lopez-Gonzalez, Gabriela; Monteagudo, Abel; Baker, Timothy R; Lewis, Simon L; Lloyd, Jon; Quesada, Carlos A; Gloor, Manuel; ter Steege, Hans; Meir, Patrick; Alvarez, Esteban; Araujo-Murakami, Alejandro; Aragão, Luiz E O C; Arroyo, Luzmila; Aymard, Gerardo; Banki, Olaf; Bonal, Damien; Brown, Sandra; Brown, Foster I; Cerón, Carlos E; Chama Moscoso, Victor; Chave, Jerome; Comiskey, James A; Cornejo, Fernando; Corrales Medina, Massiel; Da Costa, Lola; Costa, Flavia R C; Di Fiore, Anthony; Domingues, Tomas F; Erwin, Terry L; Frederickson, Todd; Higuchi, Niro; Honorio Coronado, Euridice N; Killeen, Tim J; Laurance, William F; Levis, Carolina; Magnusson, William E; Marimon, Beatriz S; Marimon Junior, Ben Hur; Mendoza Polo, Irina; Mishra, Piyush; Nascimento, Marcelo T; Neill, David; Núñez Vargas, Mario P; Palacios, Walter A; Parada, Alexander; Pardo Molina, Guido; Peña-Claros, Marielos; Pitman, Nigel; Peres, Carlos A; Poorter, Lourens; Prieto, Adriana; Ramirez-Angulo, Hirma; Restrepo Correa, Zorayda; Roopsind, Anand; Roucoux, Katherine H; Rudas, Agustin; Salomão, Rafael P; Schietti, Juliana; Silveira, Marcos; de Souza, Priscila F; Steininger, Marc K; Stropp, Juliana; Terborgh, John; Thomas, Raquel; Toledo, Marisol; Torres-Lezama, Armando; van Andel, Tinde R; van der Heijden, Geertje M F; Vieira, Ima C G; Vieira, Simone; Vilanova-Torre, Emilio; Vos, Vincent A; Wang, Ophelia; Zartman, Charles E; Malhi, Yadvinder; Phillips, Oliver L

2014-01-01

Aim The accurate mapping of forest carbon stocks is essential for understanding the global carbon cycle, for assessing emissions from deforestation, and for rational land-use planning. Remote sensing (RS) is currently the key tool for this purpose, but RS does not estimate vegetation biomass directly, and thus may miss significant spatial variations in forest structure. We test the stated accuracy of pantropical carbon maps using a large independent field dataset. Location Tropical forests of the Amazon basin. The permanent archive of the field plot data can be accessed at: http://dx.doi.org/10.5521/FORESTPLOTS.NET/2014_1 Methods Two recent pantropical RS maps of vegetation carbon are compared to a unique ground-plot dataset, involving tree measurements in 413 large inventory plots located in nine countries. The RS maps were compared directly to field plots, and kriging of the field data was used to allow area-based comparisons. Results The two RS carbon maps fail to capture the main gradient in Amazon forest carbon detected using 413 ground plots, from the densely wooded tall forests of the north-east, to the light-wooded, shorter forests of the south-west. The differences between plots and RS maps far exceed the uncertainties given in these studies, with whole regions over- or under-estimated by > 25%, whereas regional uncertainties for the maps were reported to be < 5%. Main conclusions Pantropical biomass maps are widely used by governments and by projects aiming to reduce deforestation using carbon offsets, but may have significant regional biases. Carbon-mapping techniques must be revised to account for the known ecological variation in tree wood density and allometry to create maps suitable for carbon accounting. The use of single relationships between tree canopy height and above-ground biomass inevitably yields large, spatially correlated errors. This presents a significant challenge to both the forest conservation and remote sensing communities, because neither wood density nor species assemblages can be reliably mapped from space. PMID:26430387

Digital mining claim density map for federal lands in Idaho: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Idaho as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill and tunnel sites must be recorded at the appropriate Bureau of Land Management (BLM) State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Oregon: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Oregon as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill and tunnel sites must be recorded at the appropriate Bureau of Land Management (BLM) State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

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

Fertig, Fabian, E-mail: fabian.fertig@ise.fraunhofer.de; Greulich, Johannes; Rein, Stefan

Spatially resolved determination of solar cell parameters is beneficial for loss analysis and optimization of conversion efficiency. One key parameter that has been challenging to access by an imaging technique on solar cell level is short-circuit current density. This work discusses the robustness of a recently suggested approach to determine short-circuit current density spatially resolved based on a series of lock-in thermography images and options for a simplified image acquisition procedure. For an accurate result, one or two emissivity-corrected illuminated lock-in thermography images and one dark lock-in thermography image have to be recorded. The dark lock-in thermography image can bemore » omitted if local shunts are negligible. Furthermore, it is shown that omitting the correction of lock-in thermography images for local emissivity variations only leads to minor distortions for standard silicon solar cells. Hence, adequate acquisition of one image only is sufficient to generate a meaningful map of short-circuit current density. Beyond that, this work illustrates the underlying physics of the recently proposed method and demonstrates its robustness concerning varying excitation conditions and locally increased series resistance. Experimentally gained short-circuit current density images are validated for monochromatic illumination in comparison to the reference method of light-beam induced current.« less

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

PubMed Central

Ganal, Martin W.; Durstewitz, Gregor; Polley, Andreas; Bérard, Aurélie; Buckler, Edward S.; Charcosset, Alain; Clarke, Joseph D.; Graner, Eva-Maria; Hansen, Mark; Joets, Johann; Le Paslier, Marie-Christine; McMullen, Michael D.; Montalent, Pierre; Rose, Mark; Schön, Chris-Carolin; Sun, Qi; Walter, Hildrun; Martin, Olivier C.; Falque, Matthieu

2011-01-01

SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection. We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes, were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations – IBM (B73×Mo17) and LHRF (F2×F252) – were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the array's high quality, it will be a valuable resource for maize genetics and many aspects of maize breeding. PMID:22174790

Three-dimensional scanning force/tunneling spectroscopy at room temperature.

PubMed

Sugimoto, Yoshiaki; Ueda, Keiichi; Abe, Masayuki; Morita, Seizo

2012-02-29

We simultaneously measured the force and tunneling current in three-dimensional (3D) space on the Si(111)-(7 × 7) surface using scanning force/tunneling microscopy at room temperature. The observables, the frequency shift and the time-averaged tunneling current were converted to the physical quantities of interest, i.e. the interaction force and the instantaneous tunneling current. Using the same tip, the local density of states (LDOS) was mapped on the same surface area at constant height by measuring the time-averaged tunneling current as a function of the bias voltage at every lateral position. LDOS images at negative sample voltages indicate that the tip apex is covered with Si atoms, which is consistent with the Si-Si covalent bonding mechanism for AFM imaging. A measurement technique for 3D force/current mapping and LDOS imaging on the equivalent surface area using the same tip was thus demonstrated.

ON GALACTIC DENSITY MODELING IN THE PRESENCE OF DUST EXTINCTION

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

Bovy, Jo; Rix, Hans-Walter; Schlafly, Edward F.

Inferences about the spatial density or phase-space structure of stellar populations in the Milky Way require a precise determination of the effective survey volume. The volume observed by surveys such as Gaia or near-infrared spectroscopic surveys, which have good coverage of the Galactic midplane region, is highly complex because of the abundant small-scale structure in the three-dimensional interstellar dust extinction. We introduce a novel framework for analyzing the importance of small-scale structure in the extinction. This formalism demonstrates that the spatially complex effect of extinction on the selection function of a pencil-beam or contiguous sky survey is equivalent to amore » low-pass filtering of the extinction-affected selection function with the smooth density field. We find that the angular resolution of current 3D extinction maps is sufficient for analyzing Gaia sub-samples of millions of stars. However, the current distance resolution is inadequate and needs to be improved by an order of magnitude, especially in the inner Galaxy. We also present a practical and efficient method for properly taking the effect of extinction into account in analyses of Galactic structure through an effective selection function. We illustrate its use with the selection function of red-clump stars in APOGEE using and comparing a variety of current 3D extinction maps.« less

Energy content of stormtime ring current from phase space mapping simulations

NASA Technical Reports Server (NTRS)

Chen, Margaret W.; Schulz, Michael; Lyons, Larry R.

1993-01-01

We perform a phase space mapping study to estimate the enhancement in energy content that results from stormtime particle transport in the equatorial magnetosphere. Our pre-storm phase space distribution is based on a steady-state transport model. Using results from guiding-center simulations of ion transport during model storms having main phases of 3 hr, 6 hr, and 12 hr, we map phase space distributions of ring current protons from the pre-storm distribution in accordance with Liouville's theorem. We find that transport can account for the entire ten to twenty-fold increase in magnetospheric particle energy content typical of a major storm if a realistic stormtime enhancement of the phase space density f is imposed at the nightside tail plasma sheet (represented by an enhancement of f at the neutral line in our model).

Computational prediction of atomic structures of helical membrane proteins aided by EM maps.

PubMed

Kovacs, Julio A; Yeager, Mark; Abagyan, Ruben

2007-09-15

Integral membrane proteins pose a major challenge for protein-structure prediction because only approximately 100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane alpha-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of alpha-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts along the density rods; 2), fast optimization of side chains and scoring of the resulting conformations; and 3), refinement of the lowest-scoring conformations with internal coordinate mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional, and solvation energy contributions. In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the alpha-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL.

Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping

PubMed Central

Schlautman, Brandon; Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Iorizzo, Massimo; Polashock, James; Grygleski, Edward; Vorsa, Nicholi; Zalapa, Juan

2017-01-01

The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry. PMID:28250016

Cosmic Topology: Studying The Shape And Size Of Our Universe

NASA Astrophysics Data System (ADS)

Yzaguirre, Amelia; Hajian, A.

2010-01-01

The question of the size and the shape of our universe is a very old problem that has received considerable attention over the past few years. The simplest cosmological model predicts that the mean density of the universe is very close to the critical density, admitting a local geometry of the universe that is flat. Current results from different cosmological observations confirm this to the percent level accuracy. General Relativity (being a local theory) only determines local geometry, which allows for the possibility of a multiply connected universe with a zero (or small) curvature. To study the global shape, or topology, of the universe, one can use cosmological observations on large scales. In this project we investigate the possibility of a ``small universe'', that is, a compact finite space, by searching for planar symmetries in the CMB anisotropy maps provided by the five-year WMAP observations in two foreground cleaned maps (WMAP ILC map and the Tegmark, et al. (TOH) map ). Our results strongly suggest that the small universe model is not a viable topology for the universe.

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

PubMed

Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert; Tanyolac, Bahattin

2018-01-01

Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39). The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations

PubMed Central

Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert

2018-01-01

Background Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. Materials and methods A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including “CDC Redberry” x “ILL7502” (LR8), “ILL8006” x “CDC Milestone” (LR11) and “PI320937” x “Eston” (LR39). Results The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. Conclusion This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data. PMID:29351563

Atomic-scale diffractive imaging of sub-cycle electron dynamics in condensed matter

PubMed Central

Yakovlev, Vladislav S.; Stockman, Mark I.; Krausz, Ferenc; Baum, Peter

2015-01-01

For interaction of light with condensed-matter systems, we show with simulations that ultrafast electron and X-ray diffraction can provide a time-dependent record of charge-density maps with sub-cycle and atomic-scale resolutions. Using graphene as an example material, we predict that diffraction can reveal localised atomic-scale origins of optical and electronic phenomena. In particular, we point out nontrivial relations between microscopic electric current and density in undoped graphene. PMID:26412407

Atomic-scale diffractive imaging of sub-cycle electron dynamics in condensed matter

DOE PAGES

Yakovlev, Vladislav S.; Stockman, Mark I.; Krausz, Ferenc; ...

2015-09-28

For interaction of light with condensed-matter systems, we show with simulations that ultrafast electron and X-ray diffraction can provide a time-dependent record of charge-density maps with sub-cycle and atomic-scale resolutions. Using graphene as an example material, we predict that diffraction can reveal localised atomic-scale origins of optical and electronic phenomena. Here, we point out nontrivial relations between microscopic electric current and density in undoped graphene.

Activity of left inferior frontal gyrus related to word repetition effects: LORETA imaging with 128-channel EEG and individual MRI.

PubMed

Kim, Young Youn; Lee, Boreom; Shin, Yong Wook; Kwon, Jun Soo; Kim, Myung-Sun

2006-02-01

We investigated the brain substrate of word repetition effects on the implicit memory task using low-resolution electromagnetic tomography (LORETA) with high-density 128-channel EEG and individual MRI as a realistic head model. Thirteen right-handed, healthy subjects performed a word/non-word discrimination task, in which the words and non-words were presented visually, and some of the words appeared twice with a lag of one or five items. All of the subjects exhibited word repetition effects with respect to the behavioral data, in which a faster reaction time was observed to the repeated word (old word) than to the first presentation of the word (new word). The old words elicited more positive-going potentials than the new words, beginning at 200 ms and lasting until 500 ms post-stimulus. We conducted source reconstruction using LORETA at a latency of 400 ms with the peak mean global field potentials and used statistical parametric mapping for the statistical analysis. We found that the source elicited by the old words exhibited a statistically significant current density reduction in the left inferior frontal gyrus. This is the first study to investigate the generators of word repetition effects using voxel-by-voxel statistical mapping of the current density with individual MRI and high-density EEG.

Identification of irrigated crop types from ERTS-1 density contour maps and color infrared aerial photography. [Wyoming

NASA Technical Reports Server (NTRS)

Marrs, R. W.; Evans, M. A.

1974-01-01

The author has identified the following significant results. The crop types of a Great Plains study area were mapped from color infrared aerial photography. Each field was positively identified from field checks in the area. Enlarged (50x) density contour maps were constructed from three ERTS-1 images taken in the summer of 1973. The map interpreted from the aerial photography was compared to the density contour maps and the accuracy of the ERTS-1 density contour map interpretations were determined. Changes in the vegetation during the growing season and harvest periods were detectable on the ERTS-1 imagery. Density contouring aids in the detection of such charges.

Method for removing atomic-model bias in macromolecular crystallography

DOEpatents

Terwilliger, Thomas C [Santa Fe, NM

2006-08-01

Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

Mapping Physiological Suitability Limits for Malaria in Africa Under Climate Change.

PubMed

Ryan, Sadie J; McNally, Amy; Johnson, Leah R; Mordecai, Erin A; Ben-Horin, Tal; Paaijmans, Krijn; Lafferty, Kevin D

2015-12-01

We mapped current and future temperature suitability for malaria transmission in Africa using a published model that incorporates nonlinear physiological responses to temperature of the mosquito vector Anopheles gambiae and the malaria parasite Plasmodium falciparum. We found that a larger area of Africa currently experiences the ideal temperature for transmission than previously supposed. Under future climate projections, we predicted a modest increase in the overall area suitable for malaria transmission, but a net decrease in the most suitable area. Combined with human population density projections, our maps suggest that areas with temperatures suitable for year-round, highest-risk transmission will shift from coastal West Africa to the Albertine Rift between the Democratic Republic of Congo and Uganda, whereas areas with seasonal transmission suitability will shift toward sub-Saharan coastal areas. Mapping temperature suitability places important bounds on malaria transmissibility and, along with local level demographic, socioeconomic, and ecological factors, can indicate where resources may be best spent on malaria control.

Mapping physiological suitability limits for malaria in Africa under climate change

USGS Publications Warehouse

Ryan, Sadie J.; McNally, Amy; Johnson, Leah R.; Mordecai, Erin A.; Ben-Horin, Tal; Paaijmans, Krijn P.; Lafferty, Kevin D.

2015-01-01

We mapped current and future temperature suitability for malaria transmission in Africa using a published model that incorporates nonlinear physiological responses to temperature of the mosquito vector Anopheles gambiae and the malaria parasite Plasmodium falciparum. We found that a larger area of Africa currently experiences the ideal temperature for transmission than previously supposed. Under future climate projections, we predicted a modest increase in the overall area suitable for malaria transmission, but a net decrease in the most suitable area. Combined with human population density projections, our maps suggest that areas with temperatures suitable for year-round, highest-risk transmission will shift from coastal West Africa to the Albertine Rift between the Democratic Republic of Congo and Uganda, whereas areas with seasonal transmission suitability will shift toward sub-Saharan coastal areas. Mapping temperature suitability places important bounds on malaria transmissibility and, along with local level demographic, socioeconomic, and ecological factors, can indicate where resources may be best spent on malaria control.

Comparison of current map data with data from STS-99 SRTM

NASA Image and Video Library

2000-02-04

JSC2000E01552 (January 2000) --- This chart compares currently available global map data with the data which will be provided by SRTM during STS-99. The area depicted is the California coast. The SRTM mission will have approximately 1,000 scheduled data takes (every time Endeavour is over land). Data acquisition will be conducted in excess of 80 hours. The recording rate for data will be 180 Mbits/sec for C-band, 90 Mbits/sec for X-band. Total raw radar data will be approximately 9.8 terabytes (15,000 CDs). The mission will utilize some 300 high-density tapes (each tape records 30 min. of C-band, or 60 min. of X-band data).

Measuring the acoustoelectric interaction constant using ultrasound current source density imaging

NASA Astrophysics Data System (ADS)

Li, Qian; Olafsson, Ragnar; Ingram, Pier; Wang, Zhaohui; Witte, Russell

2012-10-01

Ultrasound current source density imaging (UCSDI) exploits the acoustoelectric (AE) effect, an interaction between ultrasound pressure and electrical resistivity, to map electrical conduction in the heart. The conversion efficiency for UCSDI is determined by the AE interaction constant K, a fundamental property of all materials; K directly affects the magnitude of the detected voltage signal in UCSDI. This paper describes a technique for measuring K in biological tissue, and reports its value for the first time in cadaver hearts. A custom chamber was designed and fabricated to control the geometry for estimating K, which was measured in different ionic salt solutions and seven cadaver rabbit hearts. We found K to be strongly dependent on concentration for the divalent salt CuSO4, but not for the monovalent salt NaCl, consistent with their different chemical properties. In the rabbit heart, K was determined to be 0.041±0.012%/MPa, similar to the measurement of K in physiological saline (0.034±0.003%/MPa). This study provides a baseline estimate of K for modeling and experimental studies that involve UCSDI to map cardiac conduction and reentry currents associated with arrhythmias.

Mapping radon-prone areas using γ-radiation dose rate and geological information.

PubMed

García-Talavera, M; García-Pérez, A; Rey, C; Ramos, L

2013-09-01

Identifying radon-prone areas is key to policies on the control of this environmental carcinogen. In the current paper, we present the methodology followed to delineate radon-prone areas in Spain. It combines information from indoor radon measurements with γ-radiation and geological maps. The advantage of the proposed approach is that it lessens the requirement for a high density of measurements by making use of commonly available information. It can be applied for an initial definition of radon-prone areas in countries committed to introducing a national radon policy or to improving existing radon maps in low population regions.

Talbot-Lau x-ray deflectometry phase-retrieval methods for electron density diagnostics in high-energy density experiments.

PubMed

Valdivia, Maria Pia; Stutman, Dan; Stoeckl, Christian; Mileham, Chad; Begishev, Ildar A; Bromage, Jake; Regan, Sean P

2018-01-10

Talbot-Lau x-ray interferometry uses incoherent x-ray sources to measure refraction index changes in matter. These measurements can provide accurate electron density mapping through phase retrieval. An adaptation of the interferometer has been developed in order to meet the specific requirements of high-energy density experiments. This adaptation is known as a moiré deflectometer, which allows for single-shot capabilities in the form of interferometric fringe patterns. The moiré x-ray deflectometry technique requires a set of object and reference images in order to provide electron density maps, which can be costly in the high-energy density environment. In particular, synthetic reference phase images obtained ex situ through a phase-scan procedure, can provide a feasible solution. To test this procedure, an object phase map was retrieved from a single-shot moiré image obtained from a plasma-produced x-ray source. A reference phase map was then obtained from phase-stepping measurements using a continuous x-ray tube source in a small laboratory setting. The two phase maps were used to retrieve an electron density map. A comparison of the moiré and phase-stepping phase-retrieval methods was performed to evaluate single-exposure plasma electron density mapping for high-energy density and other transient plasma experiments. It was found that a combination of phase-retrieval methods can deliver accurate refraction angle mapping. Once x-ray backlighter quality is optimized, the ex situ method is expected to deliver electron density mapping with improved resolution. The steps necessary for improved diagnostic performance are discussed.

Automated MRI Segmentation for Individualized Modeling of Current Flow in the Human Head

PubMed Central

Huang, Yu; Dmochowski, Jacek P.; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C.

2013-01-01

Objective High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography (HD-EEG) require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images (MRI) requires labor-intensive manual segmentation, even when leveraging available automated segmentation tools. Also, accurate placement of many high-density electrodes on individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. Approach A fully automated segmentation technique based on Statical Parametric Mapping 8 (SPM8), including an improved tissue probability map (TPM) and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on 4 healthy subjects and 7 stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets. Main results The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view (FOV) extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly. Significance Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials. PMID:24099977

Automated MRI segmentation for individualized modeling of current flow in the human head

NASA Astrophysics Data System (ADS)

Huang, Yu; Dmochowski, Jacek P.; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C.

2013-12-01

Objective. High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of the brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images requires labor-intensive manual segmentation, even when utilizing available automated segmentation tools. Also, accurate placement of many high-density electrodes on an individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. Approach. A fully automated segmentation technique based on Statical Parametric Mapping 8, including an improved tissue probability map and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on four healthy subjects and seven stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets.Main results. The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly.Significance. Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials.

Vector magnetic field and vector current density in and around the δ-spot NOAA 10808†

NASA Astrophysics Data System (ADS)

Bommier, Véronique; Landi Degl'Innocenti, Egidio; Schmieder, Brigitte; Gelly, Bernard

2011-08-01

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

A High Density Consensus Map of Rye (Secale cereale L.) Based on DArT Markers

PubMed Central

Myśków, Beata; Stojałowski, Stefan; Heller-Uszyńska, Katarzyna; Góralska, Magdalena; Brągoszewski, Piotr; Uszyński, Grzegorz; Kilian, Andrzej; Rakoczy-Trojanowska, Monika

2011-01-01

Background Rye (Secale cereale L.) is an economically important crop, exhibiting unique features such as outstanding resistance to biotic and abiotic stresses and high nutrient use efficiency. This species presents a challenge to geneticists and breeders due to its large genome containing a high proportion of repetitive sequences, self incompatibility, severe inbreeding depression and tissue culture recalcitrance. The genomic resources currently available for rye are underdeveloped in comparison with other crops of similar economic importance. The aim of this study was to create a highly saturated, multilocus linkage map of rye via consensus mapping, based on Diversity Arrays Technology (DArT) markers. Methodology/Principal Findings Recombinant inbred lines (RILs) from 5 populations (564 in total) were genotyped using DArT markers and subjected to linkage analysis using Join Map 4.0 and Multipoint Consensus 2.2 software. A consensus map was constructed using a total of 9703 segregating markers. The average chromosome map length ranged from 199.9 cM (2R) to 251.4 cM (4R) and the average map density was 1.1 cM. The integrated map comprised 4048 loci with the number of markers per chromosome ranging from 454 for 7R to 805 for 4R. In comparison with previously published studies on rye, this represents an eight-fold increase in the number of loci placed on a consensus map and a more than two-fold increase in the number of genetically mapped DArT markers. Conclusions/Significance Through the careful choice of marker type, mapping populations and the use of software packages implementing powerful algorithms for map order optimization, we produced a valuable resource for rye and triticale genomics and breeding, which provides an excellent starting point for more in-depth studies on rye genome organization. PMID:22163026

Usefulness of ventricular endocardial electric reconstruction from body surface potential maps to noninvasively localize ventricular ectopic activity in patients

NASA Astrophysics Data System (ADS)

Lai, Dakun; Sun, Jian; Li, Yigang; He, Bin

2013-06-01

As radio frequency (RF) catheter ablation becomes increasingly prevalent in the management of ventricular arrhythmia in patients, an accurate and rapid determination of the arrhythmogenic site is of important clinical interest. The aim of this study was to test the hypothesis that the inversely reconstructed ventricular endocardial current density distribution from body surface potential maps (BSPMs) can localize the regions critical for maintenance of a ventricular ectopic activity. Patients with isolated and monomorphic premature ventricular contractions (PVCs) were investigated by noninvasive BSPMs and subsequent invasive catheter mapping and ablation. Equivalent current density (CD) reconstruction (CDR) during symptomatic PVCs was obtained on the endocardial ventricular surface in six patients (four men, two women, years 23-77), and the origin of the spontaneous ectopic activity was localized at the location of the maximum CD value. Compared with the last (successful) ablation site (LAS), the mean and standard deviation of localization error of the CDR approach were 13.8 and 1.3 mm, respectively. In comparison, the distance between the LASs and the estimated locations of an equivalent single moving dipole in the heart was 25.5 ± 5.5 mm. The obtained CD distribution of activated sources extending from the catheter ablation site also showed a high consistency with the invasively recorded electroanatomical maps. The noninvasively reconstructed endocardial CD distribution is suitable to predict a region of interest containing or close to arrhythmia source, which may have the potential to guide RF catheter ablation.

Construction of an ultra-high density consensus genetic map, and enhancement of the physical map from genome sequencing in Lupinus angustifolius.

PubMed

Zhou, Gaofeng; Jian, Jianbo; Wang, Penghao; Li, Chengdao; Tao, Ye; Li, Xuan; Renshaw, Daniel; Clements, Jonathan; Sweetingham, Mark; Yang, Huaan

2018-01-01

An ultra-high density genetic map containing 34,574 sequence-defined markers was developed in Lupinus angustifolius. Markers closely linked to nine genes of agronomic traits were identified. A physical map was improved to cover 560.5 Mb genome sequence. Lupin (Lupinus angustifolius L.) is a recently domesticated legume grain crop. In this study, we applied the restriction-site associated DNA sequencing (RADseq) method to genotype an F 9 recombinant inbred line population derived from a wild type × domesticated cultivar (W × D) cross. A high density linkage map was developed based on the W × D population. By integrating sequence-defined DNA markers reported in previous mapping studies, we established an ultra-high density consensus genetic map, which contains 34,574 markers consisting of 3508 loci covering 2399 cM on 20 linkage groups. The largest gap in the entire consensus map was 4.73 cM. The high density W × D map and the consensus map were used to develop an improved physical map, which covered 560.5 Mb of genome sequence data. The ultra-high density consensus linkage map, the improved physical map and the markers linked to genes of breeding interest reported in this study provide a common tool for genome sequence assembly, structural genomics, comparative genomics, functional genomics, QTL mapping, and molecular plant breeding in lupin.

Plasma response to the injection of an electron beam

NASA Technical Reports Server (NTRS)

Singh, N.; Schunk, R. W.

1984-01-01

The results of Vlasov-Poisson-solver numerical simulations of the detailed temporal response of a Maxwellian plasma to the sudden injection of an electron beam are presented in graphs and maps and discussed. Phenomena characterized include ion bursts, electron shocks and holes, plasma heating and expulsion, density gradients; cavitons, deep-density-front and solitary-pulse propagation down the density gradient, and Bunemann-mode excitation leading to formation of a virtual cathode and double layers which are at first monotonic or have low-potential-side dips or high-potential-side bumps and become strong as the electron-current density decreases. The strength of the double layer is found to be roughly proportional to the beam energy.

Canopy Density Mapping on Ultracam-D Aerial Imagery in Zagros Woodlands, Iran

NASA Astrophysics Data System (ADS)

Erfanifard, Y.; Khodaee, Z.

2013-09-01

Canopy density maps express different characteristics of forest stands, especially in woodlands. Obtaining such maps by field measurements is so expensive and time-consuming. It seems necessary to find suitable techniques to produce these maps to be used in sustainable management of woodland ecosystems. In this research, a robust procedure was suggested to obtain these maps by very high spatial resolution aerial imagery. It was aimed to produce canopy density maps by UltraCam-D aerial imagery, newly taken in Zagros woodlands by Iran National Geographic Organization (NGO), in this study. A 30 ha plot of Persian oak (Quercus persica) coppice trees was selected in Zagros woodlands, Iran. The very high spatial resolution aerial imagery of the plot purchased from NGO, was classified by kNN technique and the tree crowns were extracted precisely. The canopy density was determined in each cell of different meshes with different sizes overlaid on the study area map. The accuracy of the final maps was investigated by the ground truth obtained by complete field measurements. The results showed that the proposed method of obtaining canopy density maps was efficient enough in the study area. The final canopy density map obtained by a mesh with 30 Ar (3000 m2) cell size had 80% overall accuracy and 0.61 KHAT coefficient of agreement which shows a great agreement with the observed samples. This method can also be tested in other case studies to reveal its capability in canopy density map production in woodlands.

Obsessive-compulsive dimension localized using low-resolution brain electromagnetic tomography (LORETA).

PubMed

Sherlin, Leslie; Congedo, Marco

2005-10-21

Electroencephalographic mapping techniques have been used to show differences between normal subjects and those diagnosed with various mental disorders. To date, there is no other research using the techniques of low-resolution brain electromagnetic tomography (LORETA) with the obsessive-compulsive disorder (OCD) population. The current investigation compares current source density measures of persons with OCD symptoms to an age-matched control group. The main finding is excess current source density in the Beta frequencies in the cingulate gyrus. This Beta activity is primarily located in the middle cingulate gyrus as well as adjacent frontal parieto-occipital regions. Lower frequency Beta is prominent more anteriorly in the cingulate gyrus whereas higher frequency Beta is seen more posteriorly. These preliminary findings indicate the utility of LORETA as a clinical and diagnostic tool.

Communication: Origin of the contributions to DNA structure in phages

PubMed Central

Myers, Christopher G.; Pettitt, B. Montgomery

2013-01-01

Cryo electron microscopy (cryo-EM) data of the interior of phages show ordering of the interior DNA that has been interpreted as a nearly perfectly ordered polymer. We show surface-induced correlations, excluded volume, and electrostatic forces are sufficient to predict most of the major features of the current structural data for DNA packaged within viral capsids without additional ordering due to elastic bending forces for the polymer. Current models assume highly-ordered, even spooled, hexagonally packed conformations based on interpretation of cryo-EM density maps. We show herein that the surface induced packing of short (6mer), unconnected DNA polymer segments is the only necessary ingredient in creating ringed densities consistent with experimental density maps. This implies the ensemble of possible conformations of polymeric DNA within the capsid that are consistent with cryo-EM data may be much larger than implied by traditional interpretations where such rings can only result from highly-ordered spool-like conformations. This opens the possibility of a more disordered, entropically-driven view of phage packaging thermodynamics. We also show the electrostatics of the DNA contributes a large portion of the internal hydrostatic and osmotic pressures of a phage virion, suggesting that nonlinear elastic anomalies might reduce the overall elastic bending enthalpy of more disordered conformations to have allowable free energies. PMID:23444988

Communication: Origin of the contributions to DNA structure in phages.

PubMed

Myers, Christopher G; Pettitt, B Montgomery

2013-02-21

Cryo electron microscopy (cryo-EM) data of the interior of phages show ordering of the interior DNA that has been interpreted as a nearly perfectly ordered polymer. We show surface-induced correlations, excluded volume, and electrostatic forces are sufficient to predict most of the major features of the current structural data for DNA packaged within viral capsids without additional ordering due to elastic bending forces for the polymer. Current models assume highly-ordered, even spooled, hexagonally packed conformations based on interpretation of cryo-EM density maps. We show herein that the surface induced packing of short (6mer), unconnected DNA polymer segments is the only necessary ingredient in creating ringed densities consistent with experimental density maps. This implies the ensemble of possible conformations of polymeric DNA within the capsid that are consistent with cryo-EM data may be much larger than implied by traditional interpretations where such rings can only result from highly-ordered spool-like conformations. This opens the possibility of a more disordered, entropically-driven view of phage packaging thermodynamics. We also show the electrostatics of the DNA contributes a large portion of the internal hydrostatic and osmotic pressures of a phage virion, suggesting that nonlinear elastic anomalies might reduce the overall elastic bending enthalpy of more disordered conformations to have allowable free energies.

Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping.

PubMed

Schlautman, Brandon; Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Iorizzo, Massimo; Polashock, James; Grygleski, Edward; Vorsa, Nicholi; Zalapa, Juan

2017-04-03

The American cranberry ( Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry. Copyright © 2017 Schlautman et al.

A comparison of photospheric electric current and ultraviolet and X-ray emission in a solar active region

NASA Astrophysics Data System (ADS)

Haisch, B. M.; Bruner, M. E.; Hagyard, M. J.; Bonnet, R. M.

1986-01-01

This paper presents an extensive set of coordinated observations of a solar active region, taking into account spectroheliograms obtained with the aid of the Solar Maximum Mission (SMM) Ultraviolet Spectrometer Polarimeter (UVSP) instrument, SMM soft X-ray polychromator (XRP) raster maps, and high spatial resolution ultraviolet images of the sun in Lyman-alpha and in the 1600 A continuum. These data span together the upper solar atmosphere from the temperature minimum to the corona. The data are compared to maps of the inferred photospheric electric current derived from the Marshall Space Flight Center (MSFC) vector magnetograph observations. Some empirical correlation is found between regions of inferred electric current density and the brightest features in the ultraviolet continuum and to a lesser extent those seen in Lyman-alpha within an active region.

Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix

PubMed Central

He, Jing; Zeil, Stephanie; Hallak, Hussam; McKaig, Kele; Kovacs, Julio; Wriggers, Willy

2016-01-01

Cryo-electron microscopy (cryo-EM) is an important biophysical technique that produces three-dimensional (3D) density maps at different resolutions. Because more and more models are being produced from cryo-EM density maps, validation of the models is becoming important. We propose a method for measuring local agreement between a model and the density map using the central axis of the helix. This method was tested using 19 helices from cryo-EM density maps between 5.5 Å and 7.2 Å resolution and 94 helices from simulated density maps. This method distinguished most of the well-fitting helices, although challenges exist for shorter helices. PMID:27280059

Computational Prediction of Atomic Structures of Helical Membrane Proteins Aided by EM Maps

PubMed Central

Kovacs, Julio A.; Yeager, Mark; Abagyan, Ruben

2007-01-01

Integral membrane proteins pose a major challenge for protein-structure prediction because only ≈100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane α-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of α-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts along the density rods; 2), fast optimization of side chains and scoring of the resulting conformations; and 3), refinement of the lowest-scoring conformations with internal coordinate mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional, and solvation energy contributions. In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the α-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL. PMID:17496035

Recent Results From Internal and Very-Near-Field Plasma Diagnostics of a High Specific Impulse Hall Thruster

NASA Technical Reports Server (NTRS)

Hofer, Richard R.; Gallimore, Alec D.; Jacobson, David (Technical Monitor)

2003-01-01

Floating potential and ion current density measurements were taken on the laboratory model NASA-173Mv2 in order to improve understanding of the physical processes affecting Hall thruster performance at high specific impulse. Floating potential was measured on discharge chamber centerline over axial positions spanning 10 mm from the anode to 100 mm downstream of the exit plane. Ion current density was mapped radially up to 300 mm from thruster centerline over axial positions in the very-near-field (10 to 250 mm from the exit plane). All data were collected using a planar probe in conjunction with a high-speed translation stage to minimize probe-induced thruster perturbations. Measurements of floating potential at a xenon flow rate of 10 mg/s have shown that the acceleration layer moved upstream 3 1 mm when the voltage increased from 300 to 600 V. The length of the acceleration layer was 14 2 mm and was approximately constant with voltage and magnetic field. Ion current density measurements indicated the annular ion beam crossed the thruster centerline 163 mm downstream of the exit plane. Radial integration of the ion current density at the cathode plane provided an estimate of the ion current fraction. At 500 V and 5 mg/s, the ion current fraction was calculated as 0.77.

Photospheric electric current and transition region brightness within an active region

NASA Technical Reports Server (NTRS)

Deloach, A. C.; Hagyard, M. J.; Rabin, D.; Moore, R. L.; Smith, B. J., Jr.; West, E. A.; Tandberg-Hanssen, E.

1984-01-01

Distributions of vertical electrical current density J(z) calculated from vector measurements of the photospheric magnetic field are compared with ultraviolet spectroheliograms to investigate whether resistive heating is an important source of enhanced emission in the transition region. The photospheric magnetic fields in Active Region 2372 were measured on April 6 and 7, 1980 with the Marshall Space Flight Center vector magnetograph; ultraviolet wavelength spectroheliograms (L-alpha and N V 1239 A) were obtained with the UV Spectrometer and Polarimeter experiment aboard the Solar Maximum Mission satellite. Spatial registration of the J(z) (5 arcsec resolution) and UV (3 arcsec resolution) maps indicates that the maximum current density is cospatial with a minor but persistent UV enhancement, but there is little detected current associated with other nearby bright areas. It is concluded that, although resistive heating may be important in the transition region, the currents responsible for the heating are largely unresolved in the present measurements and have no simple correlation with the residual current measured on 5-arcsec scales.

Trans fatty acids and cholesterol levels: an evidence map of the available science

USDA-ARS?s Scientific Manuscript database

High intakes of industrial trans fatty acids (iTFA) increase circulating low density lipoprotein cholesterol (LDL-C) levels, which has implicated iTFA in coronary heart disease (CHD) risk. Published data on iTFA and LDL-C, however, represent higher intake levels than the U.S. population currently co...

Tobacco retail outlet density and risk of youth smoking in New Zealand.

PubMed

Marsh, Louise; Ajmal, Ali; McGee, Rob; Robertson, Lindsay; Cameron, Claire; Doscher, Crile

2016-12-01

Evidence suggests inconsistent findings on the relationship between density of tobacco outlets around schools and risk of smoking among students. This study examines the density of tobacco outlets around secondary schools in New Zealand (NZ) and current smoking, experimental smoking, susceptibility to smoking, and attempted and successful tobacco purchasing. Smoking data came from the 2012 ASH Year 10 survey, a national survey of youth smoking in NZ. Geographic Information Systems were used to map tobacco retail outlets; a layer of secondary school locations was obtained from Koordinates.com. Logistic regression examined the relationship between density of outlets around schools and smoking behaviours, adjusting for individual-level and school-level confounders. Of the 27 238 students surveyed, 3.5% (952) were current smokers, 4.1% (n=1 128) were experimental smokers, and 39.8% (10 454) of nonsmokers were susceptible to smoking. An inverse relationship was found between the density of tobacco retail outlets and current smoking. Current smokers were significantly more likely to attempt to purchase tobacco if the density of tobacco retail outlets around their school was high. Non-smoking students were more likely to be susceptible to smoking if the density of tobacco outlets around their school was high. There was no statistically significant association between density of tobacco outlets and successful purchasing, nor experimental smoking. Restricting the permitted density of tobacco retail outlets around schools should be part of comprehensive tobacco control. In this regard, both smokers and non-smokers support the introduction of increased regulation of the tobacco retail environment to achieve our national smoke-free 2025 goal. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

polymapR - linkage analysis and genetic map construction from F1 populations of outcrossing polyploids.

PubMed

Bourke, Peter M; van Geest, Geert; Voorrips, Roeland E; Jansen, Johannes; Kranenburg, Twan; Shahin, Arwa; Visser, Richard G F; Arens, Paul; Smulders, Marinus J M; Maliepaard, Chris

2018-05-02

Polyploid species carry more than two copies of each chromosome, a condition found in many of the world's most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops. polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops. polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polymapR. Chris Maliepaard chris.maliepaard@wur.nl or Roeland E. Voorrips roeland.voorrips@wur.nl. Supplementary data are available at Bioinformatics online.

Knot soliton in DNA and geometric structure of its free-energy density.

PubMed

Wang, Ying; Shi, Xuguang

2018-03-01

In general, the geometric structure of DNA is characterized using an elastic rod model. The Landau model provides us a new theory to study the geometric structure of DNA. By using the decomposition of the arc unit in the helical axis of DNA, we find that the free-energy density of DNA is similar to the free-energy density of a two-condensate superconductor. By using the φ-mapping topological current theory, the torus knot soliton hidden in DNA is demonstrated. We show the relation between the geometric structure and free-energy density of DNA and the Frenet equations in differential geometry theory are considered. Therefore, the free-energy density of DNA can be expressed by the curvature and torsion of the helical axis.

Uniform magnetic fields in density-functional theory

NASA Astrophysics Data System (ADS)

Tellgren, Erik I.; Laestadius, Andre; Helgaker, Trygve; Kvaal, Simen; Teale, Andrew M.

2018-01-01

We construct a density-functional formalism adapted to uniform external magnetic fields that is intermediate between conventional density functional theory and Current-Density Functional Theory (CDFT). In the intermediate theory, which we term linear vector potential-DFT (LDFT), the basic variables are the density, the canonical momentum, and the paramagnetic contribution to the magnetic moment. Both a constrained-search formulation and a convex formulation in terms of Legendre-Fenchel transformations are constructed. Many theoretical issues in CDFT find simplified analogs in LDFT. We prove results concerning N-representability, Hohenberg-Kohn-like mappings, existence of minimizers in the constrained-search expression, and a restricted analog to gauge invariance. The issue of additivity of the energy over non-interacting subsystems, which is qualitatively different in LDFT and CDFT, is also discussed.

Uniform magnetic fields in density-functional theory.

PubMed

Tellgren, Erik I; Laestadius, Andre; Helgaker, Trygve; Kvaal, Simen; Teale, Andrew M

2018-01-14

We construct a density-functional formalism adapted to uniform external magnetic fields that is intermediate between conventional density functional theory and Current-Density Functional Theory (CDFT). In the intermediate theory, which we term linear vector potential-DFT (LDFT), the basic variables are the density, the canonical momentum, and the paramagnetic contribution to the magnetic moment. Both a constrained-search formulation and a convex formulation in terms of Legendre-Fenchel transformations are constructed. Many theoretical issues in CDFT find simplified analogs in LDFT. We prove results concerning N-representability, Hohenberg-Kohn-like mappings, existence of minimizers in the constrained-search expression, and a restricted analog to gauge invariance. The issue of additivity of the energy over non-interacting subsystems, which is qualitatively different in LDFT and CDFT, is also discussed.

A method for age-matched OCT angiography deviation mapping in the assessment of disease- related changes to the radial peripapillary capillaries.

PubMed

Pinhas, Alexander; Linderman, Rachel; Mo, Shelley; Krawitz, Brian D; Geyman, Lawrence S; Carroll, Joseph; Rosen, Richard B; Chui, Toco Y

2018-01-01

To present a method for age-matched deviation mapping in the assessment of disease-related changes to the radial peripapillary capillaries (RPCs). We reviewed 4.5x4.5mm en face peripapillary OCT-A scans of 133 healthy control eyes (133 subjects, mean 41.5 yrs, range 11-82 yrs) and 4 eyes with distinct retinal pathologies, obtained using spectral-domain optical coherence tomography angiography. Statistical analysis was performed to evaluate the impact of age on RPC perfusion densities. RPC density group mean and standard deviation maps were generated for each decade of life. Deviation maps were created for the diseased eyes based on these maps. Large peripapillary vessel (LPV; noncapillary vessel) perfusion density was also studied for impact of age. Average healthy RPC density was 42.5±1.47%. ANOVA and pairwise Tukey-Kramer tests showed that RPC density in the ≥60yr group was significantly lower compared to RPC density in all younger decades of life (p<0.01). Average healthy LPV density was 21.5±3.07%. Linear regression models indicated that LPV density decreased with age, however ANOVA and pairwise Tukey-Kramer tests did not reach statistical significance. Deviation mapping enabled us to quantitatively and visually elucidate the significance of RPC density changes in disease. It is important to consider changes that occur with aging when analyzing RPC and LPV density changes in disease. RPC density, coupled with age-matched deviation mapping techniques, represents a potentially clinically useful method in detecting changes to peripapillary perfusion in disease.

NeuroMap: A Spline-Based Interactive Open-Source Software for Spatiotemporal Mapping of 2D and 3D MEA Data

PubMed Central

Abdoun, Oussama; Joucla, Sébastien; Mazzocco, Claire; Yvert, Blaise

2010-01-01

A major characteristic of neural networks is the complexity of their organization at various spatial scales, from microscopic local circuits to macroscopic brain-scale areas. Understanding how neural information is processed thus entails the ability to study them at multiple scales simultaneously. This is made possible using microelectrodes array (MEA) technology. Indeed, high-density MEAs provide large-scale coverage (several square millimeters) of whole neural structures combined with microscopic resolution (about 50 μm) of unit activity. Yet, current options for spatiotemporal representation of MEA-collected data remain limited. Here we present NeuroMap, a new interactive Matlab-based software for spatiotemporal mapping of MEA data. NeuroMap uses thin plate spline interpolation, which provides several assets with respect to conventional mapping methods used currently. First, any MEA design can be considered, including 2D or 3D, regular or irregular, arrangements of electrodes. Second, spline interpolation allows the estimation of activity across the tissue with local extrema not necessarily at recording sites. Finally, this interpolation approach provides a straightforward analytical estimation of the spatial Laplacian for better current sources localization. In this software, coregistration of 2D MEA data on the anatomy of the neural tissue is made possible by fine matching of anatomical data with electrode positions using rigid-deformation-based correction of anatomical pictures. Overall, NeuroMap provides substantial material for detailed spatiotemporal analysis of MEA data. The package is distributed under GNU General Public License and available at http://sites.google.com/site/neuromapsoftware. PMID:21344013

NeuroMap: A Spline-Based Interactive Open-Source Software for Spatiotemporal Mapping of 2D and 3D MEA Data.

PubMed

Abdoun, Oussama; Joucla, Sébastien; Mazzocco, Claire; Yvert, Blaise

2011-01-01

A major characteristic of neural networks is the complexity of their organization at various spatial scales, from microscopic local circuits to macroscopic brain-scale areas. Understanding how neural information is processed thus entails the ability to study them at multiple scales simultaneously. This is made possible using microelectrodes array (MEA) technology. Indeed, high-density MEAs provide large-scale coverage (several square millimeters) of whole neural structures combined with microscopic resolution (about 50 μm) of unit activity. Yet, current options for spatiotemporal representation of MEA-collected data remain limited. Here we present NeuroMap, a new interactive Matlab-based software for spatiotemporal mapping of MEA data. NeuroMap uses thin plate spline interpolation, which provides several assets with respect to conventional mapping methods used currently. First, any MEA design can be considered, including 2D or 3D, regular or irregular, arrangements of electrodes. Second, spline interpolation allows the estimation of activity across the tissue with local extrema not necessarily at recording sites. Finally, this interpolation approach provides a straightforward analytical estimation of the spatial Laplacian for better current sources localization. In this software, coregistration of 2D MEA data on the anatomy of the neural tissue is made possible by fine matching of anatomical data with electrode positions using rigid-deformation-based correction of anatomical pictures. Overall, NeuroMap provides substantial material for detailed spatiotemporal analysis of MEA data. The package is distributed under GNU General Public License and available at http://sites.google.com/site/neuromapsoftware.

The frequency-domain approach for apparent density mapping

NASA Astrophysics Data System (ADS)

Tong, T.; Guo, L.

2017-12-01

Apparent density mapping is a technique to estimate density distribution in the subsurface layer from the observed gravity data. It has been widely applied for geologic mapping, tectonic study and mineral exploration for decades. Apparent density mapping usually models the density layer as a collection of vertical, juxtaposed prisms in both horizontal directions, whose top and bottom surfaces are assumed to be horizontal or variable-depth, and then inverts or deconvolves the gravity anomalies to determine the density of each prism. Conventionally, the frequency-domain approach, which assumes that both top and bottom surfaces of the layer are horizontal, is usually utilized for fast density mapping. However, such assumption is not always valid in the real world, since either the top surface or the bottom surface may be variable-depth. Here, we presented a frequency-domain approach for apparent density mapping, which permits both the top and bottom surfaces of the layer to be variable-depth. We first derived the formula for forward calculation of gravity anomalies caused by the density layer, whose top and bottom surfaces are variable-depth, and the formula for inversion of gravity anomalies for the density distribution. Then we proposed the procedure for density mapping based on both the formulas of inversion and forward calculation. We tested the approach on the synthetic data, which verified its effectiveness. We also tested the approach on the real Bouguer gravity anomalies data from the central South China. The top surface was assumed to be flat and was on the sea level, and the bottom surface was considered as the Moho surface. The result presented the crustal density distribution, which was coinciding well with the basic tectonic features in the study area.

Mapping Wintering Waterfowl Distributions Using Weather Surveillance Radar

PubMed Central

Buler, Jeffrey J.; Randall, Lori A.; Fleskes, Joseph P.; Barrow, Wylie C.; Bogart, Tianna; Kluver, Daria

2012-01-01

The current network of weather surveillance radars within the United States readily detects flying birds and has proven to be a useful remote-sensing tool for ornithological study. Radar reflectivity measures serve as an index to bird density and have been used to quantitatively map landbird distributions during migratory stopover by sampling birds aloft at the onset of nocturnal migratory flights. Our objective was to further develop and validate a similar approach for mapping wintering waterfowl distributions using weather surveillance radar observations at the onset of evening flights. We evaluated data from the Sacramento, CA radar (KDAX) during winters 1998–1999 and 1999–2000. We determined an optimal sampling time by evaluating the accuracy and precision of radar observations at different times during the onset of evening flight relative to observed diurnal distributions of radio-marked birds on the ground. The mean time of evening flight initiation occurred 23 min after sunset with the strongest correlations between reflectivity and waterfowl density on the ground occurring almost immediately after flight initiation. Radar measures became more spatially homogeneous as evening flight progressed because birds dispersed from their departure locations. Radars effectively detected birds to a mean maximum range of 83 km during the first 20 min of evening flight. Using a sun elevation angle of −5° (28 min after sunset) as our optimal sampling time, we validated our approach using KDAX data and additional data from the Beale Air Force Base, CA (KBBX) radar during winter 1998–1999. Bias-adjusted radar reflectivity of waterfowl aloft was positively related to the observed diurnal density of radio-marked waterfowl locations on the ground. Thus, weather radars provide accurate measures of relative wintering waterfowl density that can be used to comprehensively map their distributions over large spatial extents. PMID:22911816

Mapping wintering waterfowl distributions using weather surveillance radar.

PubMed

Buler, Jeffrey J; Randall, Lori A; Fleskes, Joseph P; Barrow, Wylie C; Bogart, Tianna; Kluver, Daria

2012-01-01

The current network of weather surveillance radars within the United States readily detects flying birds and has proven to be a useful remote-sensing tool for ornithological study. Radar reflectivity measures serve as an index to bird density and have been used to quantitatively map landbird distributions during migratory stopover by sampling birds aloft at the onset of nocturnal migratory flights. Our objective was to further develop and validate a similar approach for mapping wintering waterfowl distributions using weather surveillance radar observations at the onset of evening flights. We evaluated data from the Sacramento, CA radar (KDAX) during winters 1998-1999 and 1999-2000. We determined an optimal sampling time by evaluating the accuracy and precision of radar observations at different times during the onset of evening flight relative to observed diurnal distributions of radio-marked birds on the ground. The mean time of evening flight initiation occurred 23 min after sunset with the strongest correlations between reflectivity and waterfowl density on the ground occurring almost immediately after flight initiation. Radar measures became more spatially homogeneous as evening flight progressed because birds dispersed from their departure locations. Radars effectively detected birds to a mean maximum range of 83 km during the first 20 min of evening flight. Using a sun elevation angle of -5° (28 min after sunset) as our optimal sampling time, we validated our approach using KDAX data and additional data from the Beale Air Force Base, CA (KBBX) radar during winter 1998-1999. Bias-adjusted radar reflectivity of waterfowl aloft was positively related to the observed diurnal density of radio-marked waterfowl locations on the ground. Thus, weather radars provide accurate measures of relative wintering waterfowl density that can be used to comprehensively map their distributions over large spatial extents.

Surface Current Density Mapping for Identification of Gastric Slow Wave Propagation

PubMed Central

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

2009-01-01

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

Comparison of photospheric electric current and ultraviolet and x-ray emission in a solar active region

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

Haisch, B.M.; Bruner, M.E.; Hagyard, M.J.

This paper presents an extensive set of coordinated observations of a solar active region, taking into account spectroheliograms obtained with the aid of the Solar Maximum Mission (SMM) Ultraviolet Spectrometer Polarimeter (UVSP) instrument, SMM soft x-ray polychromator (XRP) raster maps, and high spatial resolution ultraviolet images of the sun in Lyman-alpha and in the 1600 A continuum. These data span together the upper solar atmosphere from the temperature minimum to the corona. The data are compared to maps of the inferred photospheric electric current derived from the Marshall Space Flight Center (MSFC) vector magnetograph observations. Some empirical correlation is foundmore » between regions of inferred electric current density and the brightest features in the ultraviolet continuum and to a lesser extent those seen in Lyman-alpha within an active region. 29 references.« less

Seismo-electromagnetic anomalies observed by Fomosat-1 and GIM TEC during January 27 1999 to July 2004

NASA Astrophysics Data System (ADS)

Yu, C. Y.; Liu, J. Y. G.

2014-12-01

In this study, we examine the pre-earthquake ionospheric anomalies (PEIAs) by the electron density (Ne) and ion temperature (Ti) observed by FORMOSAT-1 (ROCSAT-1) satellite during magnitude greater than 7.0 worldwide earthquakes during 1999-2004. Meanwhile, PEIAs is also currently investigated to have a better understanding of the spatial distribution of the ROCSAT-1 SIPs. Total electron density (TEC) of the global ionosphere map (GIM) confirm that the anomalous feature appear near the epicenters before the earthquakes.

The Density of Mid-sized Kuiper Belt Objects from ALMA Thermal Observations

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

Brown, Michael E.; Butler, Bryan J.

The densities of mid-sized Kuiper Belt objects (KBOs) are a key constraint in understanding the assembly of objects in the outer solar system. These objects are critical for understanding the currently unexplained transition from the smallest KBOs with densities lower than that of water, to the largest objects with significant rock content. Mapping this transition is made difficult by the uncertainties in the diameters of these objects, which maps into an even larger uncertainty in volume and thus density. The substantial collecting area of the Atacama Large Millimeter Array allows significantly more precise measurements of thermal emission from outer solarmore » system objects and could potentially greatly improve the density measurements. Here we use new thermal observations of four objects with satellites to explore the improvements possible with millimeter data. We find that effects due to effective emissivity at millimeter wavelengths make it difficult to use the millimeter data directly to find diameters and thus volumes for these bodies. In addition, we find that when including the effects of model uncertainty, the true uncertainties on the sizes of outer solar system objects measured with radiometry are likely larger than those previously published. Substantial improvement in object sizes will likely require precise occultation measurements.« less

Plume characteristics of MPD thrusters: A preliminary examination

NASA Technical Reports Server (NTRS)

Myers, Roger M.

1989-01-01

A diagnostics facility for MPD thruster plume measurements was built and is currently undergoing testing. The facility includes electrostatic probes for electron temperature and density measurements, Hall probes for magnetic field and current distribution mapping, and an imaging system to establish the global distribution of plasma species. Preliminary results for MPD thrusters operated at power levels between 30 and 60 kW with solenoidal applied magnetic fields show that the electron density decreases exponentially from 1x10(2) to 2x10(18)/cu m over the first 30 cm of the expansion, while the electron temperature distribution is relatively uniform, decreasing from approximately 2.5 eV to 1.5 eV over the same distance. The radiant intensity of the ArII 4879 A line emission also decays exponentially. Current distribution measurements indicate that a significant fraction of the discharge current is blown into the plume region, and that its distribution depends on the magnitudes of both the discharge current and the applied magnetic field.

Results of rocket measurements of D-region ionization over Thumba in MAP

NASA Technical Reports Server (NTRS)

Chakrabarty, D. K.; Beig, G.; Garg, S. C.; Subrahmanyam, P.; Zalpuri, K. S.; Somayajulu, Y. V.; Rao, M. N. M.; Tandel, C. B.; Murlikrishna, T. R.

1989-01-01

Under MAP, two rockets were launched from Thumba (8.5 N, 76.8 E) around 1030 hrs Lt with identical payloads on 7 and 10 March 1986 for D region studies. Positive ion densities were measured by spherical probe and Gerdien condenser and electron densities were measured by Langmuir probe and propagation experiments. In both flights a valley in ionization height profile was noticed around 83 km. The density of ionization at this altitude was about 4 x 10(2) cu cm. A detailed positive ion-chemical scheme was used to reproduce the measured ionization height profiles. The density of NO needed to reproduce the valley in ionization at 83 km came around 5 x 10(5) cu cm. A photochemical treatment without diffusion process was found inadequate to explain this value of NO. Calculations showed that the value of vertical eddy diffusion needed to reproduce the value of NO was around 10(6)sq cm/s. Interestingly, the same value of eddy diffusion coefficient was obtained when derived in the manner described by Thrane and his coworkers using only the positive ion current data of spherical probes.

Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping.

PubMed

Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Schlautman, Brandon; Deutsch, Joseph; Salazar, Walter; Hernandez-Ochoa, Miguel; Grygleski, Edward; Steffan, Shawn; Iorizzo, Massimo; Polashock, James; Vorsa, Nicholi; Zalapa, Juan

2016-06-13

The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species. GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS).

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

PubMed Central

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

2016-01-01

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

Molecular surface mesh generation by filtering electron density map.

PubMed

Giard, Joachim; Macq, Benoît

2010-01-01

Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface.

Long-Term Variability of Jupiter's Magnetodisk and Implications for the Aurora

NASA Astrophysics Data System (ADS)

Vogt, Marissa F.; Bunce, Emma J.; Nichols, Jonathan D.; Clarke, John T.; Kurth, William S.

2017-12-01

Observations of Jupiter's UV auroral emissions collected over several years show that the ionospheric positions of the main emission and the Ganymede footprint can vary by as much as 3° in latitude. One explanation for this shift is a change of Jupiter's current sheet current density, which would alter the amount of field line stretching and displace the ionospheric mapping of field lines from a given radial distance in the magnetosphere. In this study we measure the long-term variability of Jupiter's magnetodisk using Galileo magnetometer data collected from 1996 to 2003. Using the Connerney et al. (1981) current sheet model, we calculate the current sheet density parameter that gives the best fit to the data from each orbit and find that the current density parameter varies by about 15% of its average value during the Galileo era. We investigate possible relationships between the observed current sheet variability and quantities such as Io's plasma torus production rate inferred from volcanic activity and external solar wind conditions extrapolated from data at 1 AU but find only a weak correlation. Finally, we trace Khurana (1997) model field lines to show that the observed changes in Jupiter's current sheet are sufficient to shift the ionospheric footprint of Ganymede and main auroral emission by a few degrees of latitude, consistent with the magnitude of auroral variability observed by Hubble Space Telescope (HST). However, we find that the measured auroral shifts in HST images are not consistent with concurrent changes in the current density parameter measured by Galileo.

Assessing future vent opening locations at the Somma-Vesuvio volcanic complex: 2. Probability maps of the caldera for a future Plinian/sub-Plinian event with uncertainty quantification

NASA Astrophysics Data System (ADS)

Tadini, A.; Bevilacqua, A.; Neri, A.; Cioni, R.; Aspinall, W. P.; Bisson, M.; Isaia, R.; Mazzarini, F.; Valentine, G. A.; Vitale, S.; Baxter, P. J.; Bertagnini, A.; Cerminara, M.; de Michieli Vitturi, M.; Di Roberto, A.; Engwell, S.; Esposti Ongaro, T.; Flandoli, F.; Pistolesi, M.

2017-06-01

In this study, we combine reconstructions of volcanological data sets and inputs from a structured expert judgment to produce a first long-term probability map for vent opening location for the next Plinian or sub-Plinian eruption of Somma-Vesuvio. In the past, the volcano has exhibited significant spatial variability in vent location; this can exert a significant control on where hazards materialize (particularly of pyroclastic density currents). The new vent opening probability mapping has been performed through (i) development of spatial probability density maps with Gaussian kernel functions for different data sets and (ii) weighted linear combination of these spatial density maps. The epistemic uncertainties affecting these data sets were quantified explicitly with expert judgments and implemented following a doubly stochastic approach. Various elicitation pooling metrics and subgroupings of experts and target questions were tested to evaluate the robustness of outcomes. Our findings indicate that (a) Somma-Vesuvio vent opening probabilities are distributed inside the whole caldera, with a peak corresponding to the area of the present crater, but with more than 50% probability that the next vent could open elsewhere within the caldera; (b) there is a mean probability of about 30% that the next vent will open west of the present edifice; (c) there is a mean probability of about 9.5% that the next medium-large eruption will enlarge the present Somma-Vesuvio caldera, and (d) there is a nonnegligible probability (mean value of 6-10%) that the next Plinian or sub-Plinian eruption will have its initial vent opening outside the present Somma-Vesuvio caldera.

A trace map comparison algorithm for the discrete fracture network models of rock masses

NASA Astrophysics Data System (ADS)

Han, Shuai; Wang, Gang; Li, Mingchao

2018-06-01

Discrete fracture networks (DFN) are widely used to build refined geological models. However, validating whether a refined model can match to reality is a crucial problem, concerning whether the model can be used for analysis. The current validation methods include numerical validation and graphical validation. However, the graphical validation, aiming at estimating the similarity between a simulated trace map and the real trace map by visual observation, is subjective. In this paper, an algorithm for the graphical validation of DFN is set up. Four main indicators, including total gray, gray grade curve, characteristic direction and gray density distribution curve, are presented to assess the similarity between two trace maps. A modified Radon transform and loop cosine similarity are presented based on Radon transform and cosine similarity respectively. Besides, how to use Bézier curve to reduce the edge effect is described. Finally, a case study shows that the new algorithm can effectively distinguish which simulated trace map is more similar to the real trace map.

A High-Density Linkage Map for Astyanax mexicanus Using Genotyping-by-Sequencing Technology

PubMed Central

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

2014-01-01

The Mexican tetra, Astyanax mexicanus, is a unique model system consisting of cave-adapted and surface-dwelling morphotypes that diverged >1 million years (My) ago. This remarkable natural experiment has enabled powerful genetic analyses of cave adaptation. Here, we describe the application of next-generation sequencing technology to the creation of a high-density linkage map. Our map comprises more than 2200 markers populating 25 linkage groups constructed from genotypic data generated from a single genotyping-by-sequencing project. We leveraged emergent genomic and transcriptomic resources to anchor hundreds of anonymous Astyanax markers to the genome of the zebrafish (Danio rerio), the most closely related model organism to our study species. This facilitated the identification of 784 distinct connections between our linkage map and the Danio rerio genome, highlighting several regions of conserved genomic architecture between the two species despite ∼150 My of divergence. Using a Mendelian cave-associated trait as a proof-of-principle, we successfully recovered the genomic position of the albinism locus near the gene Oca2. Further, our map successfully informed the positions of unplaced Astyanax genomic scaffolds within particular linkage groups. This ability to identify the relative location, orientation, and linear order of unaligned genomic scaffolds will facilitate ongoing efforts to improve on the current early draft and assemble future versions of the Astyanax physical genome. Moreover, this improved linkage map will enable higher-resolution genetic analyses and catalyze the discovery of the genetic basis for cave-associated phenotypes. PMID:25520037

Targeted carbon conservation at national scales with high-resolution monitoring

PubMed Central

Asner, Gregory P.; Knapp, David E.; Martin, Roberta E.; Tupayachi, Raul; Anderson, Christopher B.; Mascaro, Joseph; Sinca, Felipe; Chadwick, K. Dana; Higgins, Mark; Farfan, William; Llactayo, William; Silman, Miles R.

2014-01-01

Terrestrial carbon conservation can provide critical environmental, social, and climate benefits. Yet, the geographically complex mosaic of threats to, and opportunities for, conserving carbon in landscapes remain largely unresolved at national scales. Using a new high-resolution carbon mapping approach applied to Perú, a megadiverse country undergoing rapid land use change, we found that at least 0.8 Pg of aboveground carbon stocks are at imminent risk of emission from land use activities. Map-based information on the natural controls over carbon density, as well as current ecosystem threats and protections, revealed three biogeographically explicit strategies that fully offset forthcoming land-use emissions. High-resolution carbon mapping affords targeted interventions to reduce greenhouse gas emissions in rapidly developing tropical nations. PMID:25385593

Targeted carbon conservation at national scales with high-resolution monitoring.

PubMed

Asner, Gregory P; Knapp, David E; Martin, Roberta E; Tupayachi, Raul; Anderson, Christopher B; Mascaro, Joseph; Sinca, Felipe; Chadwick, K Dana; Higgins, Mark; Farfan, William; Llactayo, William; Silman, Miles R

2014-11-25

Terrestrial carbon conservation can provide critical environmental, social, and climate benefits. Yet, the geographically complex mosaic of threats to, and opportunities for, conserving carbon in landscapes remain largely unresolved at national scales. Using a new high-resolution carbon mapping approach applied to Perú, a megadiverse country undergoing rapid land use change, we found that at least 0.8 Pg of aboveground carbon stocks are at imminent risk of emission from land use activities. Map-based information on the natural controls over carbon density, as well as current ecosystem threats and protections, revealed three biogeographically explicit strategies that fully offset forthcoming land-use emissions. High-resolution carbon mapping affords targeted interventions to reduce greenhouse gas emissions in rapidly developing tropical nations.

The application of GBS markers for extending the dense genetic map of rye (Secale cereale L.) and the localization of the Rfc1 gene restoring male fertility in plants with the C source of sterility-inducing cytoplasm.

PubMed

Milczarski, Paweł; Hanek, Monika; Tyrka, Mirosław; Stojałowski, Stefan

2016-11-01

Genotyping by sequencing (GBS) is an efficient method of genotyping in numerous plant species. One of the crucial steps toward the application of GBS markers in crop improvement is anchoring them on particular chromosomes. In rye (Secale cereale L.), chromosomal localization of GBS markers has not yet been reported. In this paper, the application of GBS markers generated by the DArTseq platform for extending the high-density map of rye is presented. Additionally, their application is used for the localization of the Rfc1 gene that restores male fertility in plants with the C source of sterility-inducing cytoplasm. The total number of markers anchored on the current version of the map is 19,081, of which 18,132 were obtained from the DArTseq platform. Numerous markers co-segregated within the studied mapping population, so, finally, only 3397 unique positions were located on the map of all seven rye chromosomes. The total length of the map is 1593 cM and the average distance between markers is 0.47 cM. In spite of the resolution of the map being not very high, it should be a useful tool for further studies of the Secale cereale genome because of the presence on this map of numerous GBS markers anchored for the first time on rye chromosomes. The Rfc1 gene was located on high-density maps of the long arm of the 4R chromosome obtained for two mapping populations. Genetic maps were composed of DArT, DArTseq, and PCR-based markers. Consistent mapping results were obtained and DArTs tightly linked to the Rfc1 gene were successfully applied for the development of six new PCR-based markers useful in marker-assisted selection.

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

PubMed Central

2013-01-01

Background Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species. Results Genotyping by Sequencing (GBS) was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs) linked these results to published maps for cross-validation and map comparison. Conclusions GBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation distortion in R. idaeus, which may help to identify deleterious alleles that are the basis of inbreeding depression in the species. PMID:23324311

Neutral surfaces and potential vorticity in the world's oceans

NASA Astrophysics Data System (ADS)

You, Yuzhu; McDougall, Trevor J.

1990-08-01

Several neutral surfaces are mapped in this paper and their properties are contrasted with those of potential density surfaces. It is shown that the Pacific is relatively forgiving to the use of potential density, while more care must be taken in the Atlantic and Indian oceans because of the larger compensating lateral gradients of potential temperature and salinity along neutral surfaces in these oceans. The dynamically important tracer, neutral-surface potential vorticity (NSPV), defined to be proportional to f/h (where f is the Coriolis frequency and h is the height between two neutral surfaces), is mapped on several neutral surfaces in each of the world's oceans. At a depth of 1000m in the Atlantic and Indian oceans, the epineutral gradient of NSPV is different to the isopycnal variations of fN2 by as much as a factor of two (here N is the buoyancy frequency). Maps of isopycnal potential vorticity (IPV) resemble those of fN2, but the values of IPV are less by the simple factor μ, defined by μ = c[Rρ-1]/[Rρ-c], where Rρ is the stability ratio of the water column and c is the ratio of the values of α/β at the in situ pressure to that at the reference pressure (α and β being the thermal expansion and saline contraction coefficients, respectively). Layered models of the ocean circulation often take the vertical shear between layers (the thermal wind) to be given by the product of the interface slope and the contrast of potential density across the interface. The true thermal wind equation involves the interfaeial difference of in situ density, which is larger than the corresponding difference of potential density by the factor μ that is mapped in this paper, taking values up to 1.25 at a depth of 1000 m. This implies that the thermal wind is currently underestimated by up to 25% in layered ocean models. The differences between the slopes of neutral surfaces and potential density surfaces can be quantified Using the factory μ. The magnitudes of these slopes are illustrated here with contour maps and with vertical profiles, One would think that by choosing the reference pressure of potential density to be at the central pressure of a data set, the conservation equation of potential vorticity could be expressed with respect to these potential density surfaces with sufficient accuracy. Here it is shown that even the best potential density variable is significantly in error at thermoclinic frontal regions. This is linked to the fact that diapycnal velocities are not simply due to vertical mixing processes, but are also partly caused by epineutral mixing.

The Mesoscale Ionospheric Simulation Testbed (MIST) Regional Data Assimilation Model (Invited)

NASA Astrophysics Data System (ADS)

Comberiate, J.; Kelly, M. A.; Miller, E.; Paxton, L.

2013-12-01

The Mesoscale Ionospheric Simulation Testbed (MIST) provides a regional nowcast and forecast of electron density values and has sufficient resolution to include equatorial plasma bubbles. The SSUSI instrument on the DMSP F18 satellite has high-resolution nightly observations of plasma bubbles at 8 PM local time throughout the current solar maximum. MIST can assimilate SSUSI UV observations, GPS TEC measurements, and SCINDA S4 readings simultaneously into a single scintillation map over a region of interest. MIST also models ionospheric physics to provide a short-term UHF scintillation forecast based on assimilated data. We will present examples of electron density and scintillation maps from MIST. We will also discuss the potential to predict scintillation occurrence up to 6 hours in advance using observations of the equatorial arcs from SSUSI observations at 5:30 PM local time on the DMSP F17 satellite.

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

PubMed

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

2016-07-07

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

The energetics and mass structure of regions of star formation: S201

NASA Technical Reports Server (NTRS)

Thronson, H. A., Jr.; Smith, H. A.; Lada, C. J.; Glaccum, W.; Harper, D. A.; Loewenstein, R. F.; Smith, J.

1984-01-01

Theoretical predictions about dust and gas in star forming regions are tested by observing a 4 arcmin region surrounding the radio continuum source in 5201. The object was mapped in two far infrared wavelengths and found to show significant extended emission. Under the assumption that the molecular gas is heated solely via thermal coupling with the dust, the volume density was mapped in 5201. The ratios of infrared optical depth to CO column density were calculated for a number of positions in the source. Near the center of the cloud the values are found to be in good agreement with other determinations for regions with lower column density. In addition, the observations suggest significant molecular destruction in the outer parts of the object. Current models of gas heating were used to calculate a strong limit for the radius of the far infrared emitting grains, equal to or less than 0.15 micron. Grains of about this size are required by the observation of high temperature (T equal to or greater than 20 K) gas in many sources.

A model for heliospheric flux-ropes

NASA Astrophysics Data System (ADS)

Nieves-Chinchilla, T.; Linton, M.; Vourlidas, A.; Hidalgo, M. A. U.

2017-12-01

This work is presents an analytical flux-rope model, which explores different levels of complexity starting from a circular-cylindrical geometry. The framework of this series of models was established by Nieves-Chinchilla et al. 2016 with the circular-cylindrical analytical flux rope model. The model attempts to describe the magnetic flux rope topology with distorted cross-section as a possible consequence of the interaction with the solar wind. In this model, the flux rope is completely described in a non-orthogonal geometry. The Maxwell equations are solved using tensor calculus consistent with the geometry chosen, invariance along the axial direction, and with the assumption of no radial current density. The model is generalized in terms of the radial and azimuthal dependence of the poloidal current density component and axial current density component. The misalignment between current density and magnetic field is studied in detail for several example profiles of the axial and poloidal current density components. This theoretical analysis provides a map of the force distribution inside of the flux-rope. For reconstruction of the heliospheric flux-ropes, the circular-cylindrical reconstruction technique has been adapted to the new geometry and applied to in situ ICMEs with a flux-rope entrained and tested with cases with clear in situ signatures of distortion. The model adds a piece in the puzzle of the physical-analytical representation of these magnetic structures that should be evaluated with the ultimate goal of reconciling in-situ reconstructions with imaging 3D remote sensing CME reconstructions. Other effects such as axial curvature and/or expansion could be incorporated in the future to fully understand the magnetic structure.

Numerical modeling of a sub Plinian eruption at La Soufrière de Guadeloupe: implications for pyroclastic density currents hazard assessment.

NASA Astrophysics Data System (ADS)

Esposti Ongaro, Tomaso; Neri, Augusto; Komorowski, Jean-Christophe

2013-04-01

We present three-dimensional numerical simulations of a sub-Plinian eruptive scenario at La Soufrière de Guadeloupe, aimed at assessing the capability of pyroclastic density currents to reach the inhabited regions on the volcano slopes, in case of the future resumption of the explosive activity. The selected eruptive scenario is similar to that hypothesized for the 1530 a.D. eruption, but several eruptive conditions have been analyzed to account for different behaviours of the eruptive column and percentages of collapse. Numerical results describe, in 3D and in time, the formation, instability and partial collapse of the eruptive column, and the simultaneous formation of a convective plume and several branched pyroclastic density currents. The proximal volcano morphology, characterized by the presence of ancient caldera rims and the remnants of the old edifice, controls the areal distribution of the collapsed material and the paths of channelized flows along the incised topography. The analysis of the 3D runs suggests that partial collapse scenarios produce steeply stratified pyroclastic density currents, which are strongly controlled by the topography and whose propagation is likely driven by the dynamics of the dense, basal layer. Although vertical grid size still does not allow the resolution of the dynamics of such concentrated flows, preliminary georeferenced maps of pyroclastic density currents' hazardous actions (temperature and dynamic pressure) provide interesting and useful information which can serve as a basis for elaborating a quantitative framework for the assessment of their impact on vulnerable infrastructures, networks, and population.

Variants for HDL-C, LDL-C, and triglycerides identified from admixture mapping and fine-mapping analysis in African American families.

PubMed

Shetty, Priya B; Tang, Hua; Feng, Tao; Tayo, Bamidele; Morrison, Alanna C; Kardia, Sharon L R; Hanis, Craig L; Arnett, Donna K; Hunt, Steven C; Boerwinkle, Eric; Rao, Dabeeru C; Cooper, Richard S; Risch, Neil; Zhu, Xiaofeng

2015-02-01

Admixture mapping of lipids was followed-up by family-based association analysis to identify variants for cardiovascular disease in African Americans. The present study conducted admixture mapping analysis for total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. The analysis was performed in 1905 unrelated African American subjects from the National Heart, Lung and Blood Institute's Family Blood Pressure Program (FBPP). Regions showing admixture evidence were followed-up with family-based association analysis in 3556 African American subjects from the FBPP. The admixture mapping and family-based association analyses were adjusted for age, age(2), sex, body mass index, and genome-wide mean ancestry to minimize the confounding caused by population stratification. Regions that were suggestive of local ancestry association evidence were found on chromosomes 7 (low-density lipoprotein cholesterol), 8 (high-density lipoprotein cholesterol), 14 (triglycerides), and 19 (total cholesterol and triglycerides). In the fine-mapping analysis, 52 939 single-nucleotide polymorphisms (SNPs) were tested and 11 SNPs (8 independent SNPs) showed nominal significant association with high-density lipoprotein cholesterol (2 SNPs), low-density lipoprotein cholesterol (4 SNPs), and triglycerides (5 SNPs). The family data were used in the fine-mapping to identify SNPs that showed novel associations with lipids and regions, including genes with known associations for cardiovascular disease. This study identified regions on chromosomes 7, 8, 14, and 19 and 11 SNPs from the fine-mapping analysis that were associated with high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides for further studies of cardiovascular disease in African Americans. © 2014 American Heart Association, Inc.

Model-based local density sharpening of cryo-EM maps

PubMed Central

Jakobi, Arjen J; Wilmanns, Matthias

2017-01-01

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement. PMID:29058676

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

PubMed Central

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

2016-01-01

High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly. PMID:27225429

CRISM Multispectral and Hyperspectral Mapping Data - A Global Data Set for Hydrated Mineral Mapping

NASA Astrophysics Data System (ADS)

Seelos, F. P.; Hash, C. D.; Murchie, S. L.; Lim, H.

2017-12-01

The Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) is a visible through short-wave infrared hyperspectral imaging spectrometer (VNIR S-detector: 364-1055 nm; IR L-detector: 1001-3936 nm; 6.55 nm sampling) that has been in operation on the Mars Reconnaissance Orbiter (MRO) since 2006. Over the course of the MRO mission, CRISM has acquired 290,000 individual mapping observation segments (mapping strips) with a variety of observing modes and data characteristics (VNIR/IR; 100/200 m/pxl; multi-/hyper-spectral band selection) over a wide range of observing conditions (atmospheric state, observation geometry, instrument state). CRISM mapping data coverage density varies primarily with latitude and secondarily due to seasonal and operational considerations. The aggregate global IR mapping data coverage currently stands at 85% ( 80% at the equator with 40% repeat sampling), which is sufficient spatial sampling density to support the assembly of empirically optimized radiometrically consistent mapping mosaic products. The CRISM project has defined a number of mapping mosaic data products (e.g. Multispectral Reduced Data Record (MRDR) map tiles) with varying degrees of observation-specific processing and correction applied prior to mosaic assembly. A commonality among the mosaic products is the presence of inter-observation radiometric discrepancies which are traceable to variable observation circumstances or associated atmospheric/photometric correction residuals. The empirical approach to radiometric reconciliation leverages inter-observation spatial overlaps and proximal relationships to construct a graph that encodes the mosaic structure and radiometric discrepancies. The graph theory abstraction allows the underling structure of the msaic to be evaluated and the corresponding optimization problem configured so it is well-posed. Linear and non-linear least squares optimization is then employed to derive a set of observation- and wavelength- specific model parameters for a series of transform functions that minimize the total radiometric discrepancy across the mosaic. This empirical approach to CRISM data radiometric reconciliation and the utility of the resulting mapping data mosaic products for hydrated mineral mapping will be presented.

Merging field mapping and modeling to interpret the lithofacies variations from unsteady ash-rich pyroclastic density currents on uneven topography

NASA Astrophysics Data System (ADS)

Doronzo, Domenico; Dellino, Pierfrancesco; Sulpizio, Roberto; Lucchi, Federico

2017-04-01

In order to obtain significant volcanological results from computer simulations of explosive eruptions, one either needs a systematic statistical approach to test a wide range of initial and boundary conditions, or needs using a well-constrained field case study. Here we followed the second approach, using data obtained from field mapping of the Grotta dei Palizzi 2 pyroclastic deposits (Vulcano Island, Italy) as input for numerical modeling. This case study deals with impulsive phreatomagmatic explosions that generated ash-rich pyroclastic density currents, interacting with the high topographic obstacle of the La Fossa Caldera rim. We demonstrate that by merging field data with 3D numerical simulation it is possible to highlight the details of the dynamical current-terrain interaction, and to interpret the lithofacies variations of the associated deposits as a function of topography-induced sedimentation rate. Results suggest that a value of the sedimentation rate lower than 5 kg/m2s at the bed load can still be sheared by the overlying current, producing tractional structures in the deposit. Instead, a sedimentation rate in excess of that threshold can preclude the formation of tractional structures, producing thick massive deposits. We think that the approach used in this study could be applied to other case studies to confirm or refine such threshold value of the sedimentation rate, which is to be considered as an upper value as for the limitations of the numerical model.

Insights Into Upland Cotton (Gossypium hirsutum L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents. Genomics Insights

USDA-ARS?s Scientific Manuscript database

High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement; high-density linkage maps are especially important in paleopolyploids with exce...

Mapping the Baby Universe

NASA Technical Reports Server (NTRS)

Wanjek, Christopher

2003-01-01

In June, NASA plans to launch the Microwave Anisotropy Probe (MAP) to survey the ancient radiation in unprecedented detail. MAP will map slight temperature fluctuations within the microwave background that vary by only 0.00001 C across a chilly radiation that now averages 2.73 C above absolute zero. The temperature differences today point back to density differences in the fiery baby universe, in which there was a little more matter here and a little less matter there. Areas of slightly enhanced density had stronger gravity than low-density areas. The high-density areas pulled back on the background radiation, making it appear slightly cooler in those directions.

Simulations of phase space distributions of storm time proton ring current

NASA Technical Reports Server (NTRS)

Chen, Margaret W.; Lyons, Larry R.; Schulz, Michael

1994-01-01

We use results of guiding-center simulations of ion transport to map phase space densities of the stormtime proton ring current. We model a storm as a sequence of substorm-associated enhancements in the convection electric field. Our pre-storm phase space distribution is an analytical solution to a steady-state transport model in which quiet-time radial diffusion balances charge exchange. This pre-storm phase space spectra at L approximately 2 to 4 reproduce many of the features found in observed quiet-time spectra. Using results from simulations of ion transport during model storms having main phases of 3, 6, and 12 hr, we map phase space distributions from the pre-storm distribution in accordance with Liouville's theorem. We find stormtime enhancements in the phase space densities at energies E approximately 30-160 keV for L approximately 2.5 to 4. These enhancements agree well with the observed stormtime ring current. For storms with shorter main phases (approximately 3 hr), the enhancements are caused mainly by the trapping of ions injected from open night side trajectories, and diffusive transport of higher-energy (greater than or approximately 160 keV) ions contributes little to the stormtime ring current. However, the stormtime ring current is augmented also by the diffusive transport of higher-energy ions (E greater than or approximately 160 keV) durinng stroms having longer main phases (greater than or approximately 6 hr). In order to account for the increase in Dst associated with the formation of the stormtime ring current, we estimate the enhancement in particle-energy content that results from stormtime ion transport in the equatorial magnetosphere. We find that transport alone cannot account for the entire increase in absolute value of Dst typical of a major storm. However, we can account for the entire increase in absolute value of Dst by realistically increasing the stormtime outer boundary value of the phase space density relative to the quiet-time value. We compute the magnetic field produced by the ring current itself and find that radial profiles of the magnetic field depression resemble those obtained from observational data.

The effects of vent location, event scale and time forecasts on pyroclastic density current hazard maps at Campi Flegrei caldera (Italy)

NASA Astrophysics Data System (ADS)

Bevilacqua, Andrea; Neri, Augusto; Bisson, Marina; Esposti Ongaro, Tomaso; Flandoli, Franco; Isaia, Roberto; Rosi, Mauro; Vitale, Stefano

2017-09-01

This study presents a new method for producing long-term hazard maps for pyroclastic density currents (PDC) originating at Campi Flegrei caldera. Such method is based on a doubly stochastic approach and is able to combine the uncertainty assessments on the spatial location of the volcanic vent, the size of the flow and the expected time of such an event. The results are obtained by using a Monte Carlo approach and adopting a simplified invasion model based on the box model integral approximation. Temporal assessments are modelled through a Cox-type process including self-excitement effects, based on the eruptive record of the last 15 kyr. Mean and percentile maps of PDC invasion probability are produced, exploring their sensitivity to some sources of uncertainty and to the effects of the dependence between PDC scales and the caldera sector where they originated. Conditional maps representative of PDC originating inside limited zones of the caldera, or of PDC with a limited range of scales are also produced. Finally, the effect of assuming different time windows for the hazard estimates is explored, also including the potential occurrence of a sequence of multiple events. Assuming that the last eruption of Monte Nuovo (A.D. 1538) marked the beginning of a new epoch of activity similar to the previous ones, results of the statistical analysis indicate a mean probability of PDC invasion above 5% in the next 50 years on almost the entire caldera (with a probability peak of 25% in the central part of the caldera). In contrast, probability values reduce by a factor of about 3 if the entire eruptive record is considered over the last 15 kyr, i.e. including both eruptive epochs and quiescent periods.

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

PubMed

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

2016-04-01

Most agricultural traits are controlled by quantitative trait loci (QTLs); however, there are few studies on QTL mapping of horticultural traits in pepper (Capsicum spp.) due to the lack of high-density molecular maps and the sequence information. In this study, an ultra-high-density map and 120 recombinant inbred lines (RILs) derived from a cross between C. annuum'Perennial' and C. annuum'Dempsey' were used for QTL mapping of horticultural traits. Parental lines and RILs were resequenced at 18× and 1× coverage, respectively. Using a sliding window approach, an ultra-high-density bin map containing 2,578 bins was constructed. The total map length of the map was 1,372 cM, and the average interval between bins was 0.53 cM. A total of 86 significant QTLs controlling 17 horticultural traits were detected. Among these, 32 QTLs controlling 13 traits were major QTLs. Our research shows that the construction of bin maps using low-coverage sequence is a powerful method for QTL mapping, and that the short intervals between bins are helpful for fine-mapping of QTLs. Furthermore, bin maps can be used to improve the quality of reference genomes by elucidating the genetic order of unordered regions and anchoring unassigned scaffolds to linkage groups. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Covariance and correlation estimation in electron-density maps.

PubMed

Altomare, Angela; Cuocci, Corrado; Giacovazzo, Carmelo; Moliterni, Anna; Rizzi, Rosanna

2012-03-01

Quite recently two papers have been published [Giacovazzo & Mazzone (2011). Acta Cryst. A67, 210-218; Giacovazzo et al. (2011). Acta Cryst. A67, 368-382] which calculate the variance in any point of an electron-density map at any stage of the phasing process. The main aim of the papers was to associate a standard deviation to each pixel of the map, in order to obtain a better estimate of the map reliability. This paper deals with the covariance estimate between points of an electron-density map in any space group, centrosymmetric or non-centrosymmetric, no matter the correlation between the model and target structures. The aim is as follows: to verify if the electron density in one point of the map is amplified or depressed as an effect of the electron density in one or more other points of the map. High values of the covariances are usually connected with undesired features of the map. The phases are the primitive random variables of our probabilistic model; the covariance changes with the quality of the model and therefore with the quality of the phases. The conclusive formulas show that the covariance is also influenced by the Patterson map. Uncertainty on measurements may influence the covariance, particularly in the final stages of the structure refinement; a general formula is obtained taking into account both phase and measurement uncertainty, valid at any stage of the crystal structure solution.

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

USDA-ARS?s Scientific Manuscript database

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

Anthropogenic Transformation of the Biomes, 1700 to 2000

NASA Astrophysics Data System (ADS)

Ellis, E. C.; Lightman, D.; Klein Goldewijk, K.; Ramankutty, N.

2008-12-01

Current global patterns of terrestrial ecosystem form and process are now predominantly anthropogenic as a result of land use and other direct human interactions with ecosystems. This study investigates anthropogenic transformation of the terrestrial biosphere over the course of the industrial revolution by mapping and characterizing global transitions between wild and anthropogenic biomes between 1700 and 2000. A global map of potential natural vegetation was used to represent wild biomes. Anthropogenic biomes were mapped for 1700, 1800, 1900 and 2000 using rule-based classification of current and historical global data for human population density, urban area and percent land cover by cultivated crops (rainfed, irrigated, and rice) and pastures. By assuming that wild, climate-driven, biome patterns have been relatively constant since 1700, transitions between wild and anthropogenic biomes were characterized between 1700 and 2000 at century intervals. Historical analysis of wild to anthropogenic biome transitions reveal the global transition from a primarily wild to a primarily anthropogenic terrestrial biosphere. Moreover, by mapping and examining global transitions between wild and anthropogenic biome classes, we provide a simple framework for assessing and modeling both past and future global biotic and ecological patterns in the light of the extent, intensity and duration of their modification by humans.

Mapping Error in Southern Ocean Transport Computed from Satellite Altimetry and Argo

NASA Astrophysics Data System (ADS)

Kosempa, M.; Chambers, D. P.

2016-02-01

Argo profiling floats afford basin-scale coverage of the Southern Ocean since 2005. When density estimates from Argo are combined with surface geostrophic currents derived from satellite altimetry, one can estimate integrated geostrophic transport above 2000 dbar [e.g., Kosempa and Chambers, JGR, 2014]. However, the interpolation techniques relied upon to generate mapped data from Argo and altimetry will impart a mapping error. We quantify this mapping error by sampling the high-resolution Southern Ocean State Estimate (SOSE) at the locations of Argo floats and Jason-1, and -2 altimeter ground tracks, then create gridded products using the same optimal interpolation algorithms used for the Argo/altimetry gridded products. We combine these surface and subsurface grids to compare the sampled-then-interpolated transport grids to those from the original SOSE data in an effort to quantify the uncertainty in volume transport integrated across the Antarctic Circumpolar Current (ACC). This uncertainty is then used to answer two fundamental questions: 1) What is the minimum linear trend that can be observed in ACC transport given the present length of the instrument record? 2) How long must the instrument record be to observe a trend with an accuracy of 0.1 Sv/year?

A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus

PubMed Central

2011-01-01

Background Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. Results SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome. Conclusions The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping with a concurrent objective of reducing microarray costs. HIgh-density gene-rich maps represent a powerful resource to assist gene discovery endeavors when used in combination with QTL and association mapping and should be especially valuable to assist the assembly of reference genome sequences soon to come for several plant and animal species. PMID:21492453

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

PubMed Central

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

2016-01-01

Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp. PMID:27345016

Strategies to Improve the Accuracy of Mars-GRAM Sensitivity Studies at Large Optical Depths

NASA Technical Reports Server (NTRS)

Justh, Hilary L.; Justus, Carl G.; Badger, Andrew M.

2009-01-01

The Mars Global Reference Atmospheric Model (Mars-GRAM) is an engineering-level atmospheric model widely used for diverse mission applications. Mars-GRAM s perturbation modeling capability is commonly used, in a Monte-Carlo mode, to perform high fidelity engineering end-to-end simulations for entry, descent, and landing (EDL). It has been discovered during the Mars Science Laboratory (MSL) site selection process that Mars-GRAM when used for sensitivity studies for MapYear=0 and large optical depth values such as tau=3 is less than realistic. A comparison study between Mars atmospheric density estimates from Mars- GRAM and measurements by Mars Global Surveyor (MGS) has been undertaken for locations of varying latitudes, Ls, and LTST on Mars. The preliminary results from this study have validated the Thermal Emission Spectrometer (TES) limb data. From the surface to 80 km altitude, Mars- GRAM is based on the NASA Ames Mars General Circulation Model (MGCM). MGCM results that were used for Mars-GRAM with MapYear=0 were from a MGCM run with a fixed value of tau=3 for the entire year at all locations. Unrealistic energy absorption by uniform atmospheric dust leads to an unrealistic thermal energy balance on the polar caps. The outcome is an inaccurate cycle of condensation/sublimation of the polar caps and, as a consequence, an inaccurate cycle of total atmospheric mass and global-average surface pressure. Under an assumption of unchanged temperature profile and hydrostatic equilibrium, a given percentage change in surface pressure would produce a corresponding percentage change in density at all altitudes. Consequently, the final result of a change in surface pressure is an imprecise atmospheric density at all altitudes. To solve this pressure-density problem, a density factor value was determined for tau=.3, 1 and 3 that will adjust the input values of MGCM MapYear 0 pressure and density to achieve a better match of Mars-GRAM MapYear=0 with MapYears 1 and 2 MGCM output at comparable dust loading. Currently, these density factors are fixed values for all latitudes and Ls. Results will be presented of the work underway to derive better multipliers by including possible variation with latitude and/or Ls. This is achieved by comparison of Mars-GRAM MapYear=0 output with TES limb data. The addition of these density factors to Mars-GRAM will improve the results of the sensitivity studies done for large optical depths. Answers may also be provided to the issues raised in a recent study by Desai(2008). Desai has shown that the actual landing sites of Mars Pathfinder, the Mars Exploration Rovers and the Phoenix Mars Lander have been further downrange than predicted by models prior to landing. Desai s reconstruction of their entries into the Martian atmosphere showed that the models consistently predicted higher densities than those found upon EDL. The solution of this problem would be important to the Mars Program since future exploration of Mars by landers and rovers will require more accurate landing capabilities, especially for the proposed Mars Sample Return mission.

Application of gamma ray spectrometric measurements and VLF-EM data for tracing vein type uranium mineralization

NASA Astrophysics Data System (ADS)

Gaafar, Ibrahim

2015-12-01

This study is an attempt to use the gamma ray spectrometric measurements and VLF-EM data to identify the subsurface structure and map uranium mineralization along El Sela shear zone, South Eastern Desert of Egypt. Many injections more or less mineralized with uranium and associated with alteration processes were recorded in El Sela shear zone. As results from previous works, the emplacement of these injections is structurally controlled and well defined by large shear zones striking in an ENE-WSW direction and crosscut by NW-SE to NNW-SSE fault sets. VLF method has been applied to map the structure and the presence of radioactive minerals that have been delineated by the detection of high uranium mineralization. The electromagnetic survey was carried out to detect the presence of shallow and deep conductive zones that cross the granites along ENE-WSW fracturing directions and to map its spatial distribution. The survey comprised seventy N-S spectrometry and VLF-EM profiles with 20 m separation. The resulted data were displayed as composite maps for K, eU and eTh as well as VLF-Fraser map. Twelve profiles with 100 m separation were selected for detailed description. The VLF-EM data were interpreted qualitatively as well as quantitatively using the Fraser and the Karous-Hjelt filters. Fraser filtered data and relative current density pseudo-sections indicate the presence of shallow and deep conductive zones that cross the granites along ENE-WSW shearing directions. High uranium concentrations found just above the higher apparent current-density zones that coincide with El-Sela shear zone indicate a positive relation between conductivity and uranium minerals occurrence. This enables to infer that the anomalies detected by VLF-EM data are due to the highly conductive shear zone enriched with uranium mineralization extending for more than 80 m.

Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

PubMed Central

Serin, Elise A. R.; Snoek, L. B.; Nijveen, Harm; Willems, Leo A. J.; Jiménez-Gómez, Jose M.; Hilhorst, Henk W. M.; Ligterink, Wilco

2017-01-01

High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches. PMID:29259624

Improving experimental phases for strong reflections prior to density modification

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

Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.

Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D 61, 899–902], the impact of identifying optimized phases for a small numbermore » of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

Improving experimental phases for strong reflections prior to density modification

DOE PAGES

Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; ...

2013-09-20

Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D 61, 899–902], the impact of identifying optimized phases for a small numbermore » of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

The effects of intragrain defects on the local photoresponse of polycrystalline silicon solar cells

NASA Astrophysics Data System (ADS)

Inoue, N.; Wilmsen, C. W.; Jones, K. A.

1981-02-01

Intragrain defects in Wacker cast and Monsanto zone-refined polycrystalline silicon materials were investigated using the electron-beam-induced current (EBIC) technique. The EBIC response maps were compared with etch pit, local diffusion length and local photoresponse measurements. It was determined that the Wacker polycrystalline silicon has a much lower density of defects than does the Monsanto polycrystalline silicon and that most of the defects in the Wacker material are not active recombination sites. A correlation was found between the recombination site density, as determined by EBIC, and the local diffusion length. It is shown that a large density of intragrain recombination sites greatly reduces the minority carrier diffusion length and thus can significantly reduce the photoresponse of solar cells.

Genotyping-by-Sequencing derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat

USDA-ARS?s Scientific Manuscript database

Hard red winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) was used to develop a recombinant inbred population to identify genomic regions associated with drought and adaptation. To precisely map genomic regions high-density linkage maps are a prerequisite. In this s...

Enhancing superconducting critical current by randomness

DOE PAGES

Wang, Y. L.; Thoutam, L. R.; Xiao, Z. L.; ...

2016-01-11

The key ingredient of high critical currents in a type-II superconductor is defect sites that pin vortices. Here, we demonstrate that a random pinscape, an overlooked pinning system in nanopatterned superconductors, can lead to a substantially larger critical current enhancement at high magnetic fields than an ordered array of vortex pin sites. We reveal that the better performance of a random pinscape is due to the variation of the local density of its pinning sites, which mitigates the motion of vortices. This is confirmed by achieving even higher enhancement of the critical current through a conformally mapped random pinscape, wheremore » the distribution of the local density of pinning sites is further enlarged. Our findings highlight the potential of random pinscapes in enhancing the superconducting critical currents of applied superconductors in which random pin sites of nanoscale defects emerging in the materials synthesis process or through ex-situ irradiation are the only practical choice for large-scale production. Our results may also stimulate research on effects of a random pinscape in other complementary systems such as colloidal crystals, Bose-Einstein condensates, and Luttinger liquids.« less

A Comprehensive Investigation of Facility Effects on the Testing of High-Power Monolithic and Clustered Hall Thruster Systems

DTIC Science & Technology

2004-09-02

path for developing high-power EP systems is somewhat certain given NASA’s recent success with its 70+ kW NASA-457M Hall thruster , it is clear that...current density distribution, and summarize findings from cold- and hot-flow pressure map data of our vacuum chamber for a number of Hall thruster mass flow rates.

High-density genetic mapping of a major QTL for resistance to multiple races of loose smut in a tetraploid wheat cross

PubMed Central

Kumar, Sachin; Knox, Ron E.; Singh, Asheesh K.; DePauw, Ron M.; Campbell, Heather L.; Isidro-Sanchez, Julio; Clarke, Fran R.; Pozniak, Curtis J.; N’Daye, Amidou; Meyer, Brad; Sharpe, Andrew; Ruan, Yuefeng; Cuthbert, Richard D.; Somers, Daryl; Fedak, George

2018-01-01

Loose smut, caused by Ustilago tritici (Pers.) Rostr., is a systemic disease of tetraploid durum wheat (Triticum turgidum L.). Loose smut can be economically controlled by growing resistant varieties, making it important to find and deploy new sources of resistance. Blackbird, a variety of T. turgidum L. subsp. carthlicum (Nevski) A. Love & D. Love, carries a high level of resistance to loose smut. Blackbird was crossed with the loose smut susceptible durum cultivar Strongfield to produce a doubled haploid (DH) mapping population. The parents and progenies were inoculated with U. tritici races T26, T32 and T33 individually and as a mixture at Swift Current, Canada in 2011 and 2012 and loose smut incidence (LSI) was assessed. Genotyping of the DH population and parents using an Infinium iSelect 90K single nucleotide polymorphism (SNP) array identified 12,952 polymorphic SNPs. The SNPs and 426 SSRs (previously genotyped in the same population) were mapped to 16 linkage groups spanning 3008.4 cM at an average inter-marker space of 0.2 cM in a high-density genetic map. Composite interval mapping analysis revealed three significant quantitative trait loci (QTL) for loose smut resistance on chromosomes 3A, 6B and 7A. The loose smut resistance QTL on 6B (QUt.spa-6B.2) and 7A (QUt.spa-7A.2) were derived from Blackbird. Strongfield contributed the minor QTL on 3A (QUt.spa-3A.2). The resistance on 6B was a stable major QTL effective against all individual races and the mixture of the three races; it explained up to 74% of the phenotypic variation. This study is the first attempt in durum wheat to identify and map loose smut resistance QTL using a high-density genetic map. The QTL QUt.spa-6B.2 would be an effective source for breeding resistance to multiple races of the loose smut pathogen because it provides near-complete broad resistance to the predominant virulence on the Canadian prairies. PMID:29485999

High-Density SNP Map Construction and QTL Identification for the Apetalous Character in Brassica napus L.

PubMed Central

Wang, Xiaodong; Yu, Kunjiang; Li, Hongge; Peng, Qi; Chen, Feng; Zhang, Wei; Chen, Song; Hu, Maolong; Zhang, Jiefu

2015-01-01

The apetalous genotype is a morphological ideotype for increasing seed yield and should be of considerable agricultural use; however, only a few studies have focused on the genetic control of this trait in Brassica napus. In the present study, a recombinant inbred line, the AH population, containing 189 individuals was derived from a cross between an apetalous line ‘APL01’ and a normally petalled variety ‘Holly’. The Brassica 60 K Infinium BeadChip Array harboring 52,157 single nucleotide polymorphism (SNP) markers was used to genotype the AH individuals. A high-density genetic linkage map was constructed based on 2,755 bins involving 11,458 SNPs and 57 simple sequence repeats, and was used to identify loci associated with petalous degree (PDgr). The linkage map covered 2,027.53 cM, with an average marker interval of 0.72 cM. The AH map had good collinearity with the B. napus reference genome, indicating its high quality and accuracy. After phenotypic analyses across five different experiments, a total of 19 identified quantitative trait loci (QTLs) distributed across chromosomes A3, A5, A6, A9 and C8 were obtained, and these QTLs were further integrated into nine consensus QTLs by a meta-analysis. Interestingly, the major QTL qPD.C8-2 was consistently detected in all five experiments, and qPD.A9-2 and qPD.C8-3 were stably expressed in four experiments. Comparative mapping between the AH map and the B. napus reference genome suggested that there were 328 genes underlying the confidence intervals of the three steady QTLs. Based on the Gene Ontology assignments of 52 genes to the regulation of floral development in published studies, 146 genes were considered as potential candidate genes for PDgr. The current study carried out a QTL analysis for PDgr using a high-density SNP map in B. napus, providing novel targets for improving seed yield. These results advanced our understanding of the genetic control of PDgr regulation in B. napus. PMID:26779193

High-Density SNP Map Construction and QTL Identification for the Apetalous Character in Brassica napus L.

PubMed

Wang, Xiaodong; Yu, Kunjiang; Li, Hongge; Peng, Qi; Chen, Feng; Zhang, Wei; Chen, Song; Hu, Maolong; Zhang, Jiefu

2015-01-01

The apetalous genotype is a morphological ideotype for increasing seed yield and should be of considerable agricultural use; however, only a few studies have focused on the genetic control of this trait in Brassica napus. In the present study, a recombinant inbred line, the AH population, containing 189 individuals was derived from a cross between an apetalous line 'APL01' and a normally petalled variety 'Holly'. The Brassica 60 K Infinium BeadChip Array harboring 52,157 single nucleotide polymorphism (SNP) markers was used to genotype the AH individuals. A high-density genetic linkage map was constructed based on 2,755 bins involving 11,458 SNPs and 57 simple sequence repeats, and was used to identify loci associated with petalous degree (PDgr). The linkage map covered 2,027.53 cM, with an average marker interval of 0.72 cM. The AH map had good collinearity with the B. napus reference genome, indicating its high quality and accuracy. After phenotypic analyses across five different experiments, a total of 19 identified quantitative trait loci (QTLs) distributed across chromosomes A3, A5, A6, A9 and C8 were obtained, and these QTLs were further integrated into nine consensus QTLs by a meta-analysis. Interestingly, the major QTL qPD.C8-2 was consistently detected in all five experiments, and qPD.A9-2 and qPD.C8-3 were stably expressed in four experiments. Comparative mapping between the AH map and the B. napus reference genome suggested that there were 328 genes underlying the confidence intervals of the three steady QTLs. Based on the Gene Ontology assignments of 52 genes to the regulation of floral development in published studies, 146 genes were considered as potential candidate genes for PDgr. The current study carried out a QTL analysis for PDgr using a high-density SNP map in B. napus, providing novel targets for improving seed yield. These results advanced our understanding of the genetic control of PDgr regulation in B. napus.

Elliptic-cylindrical analytical flux-rope model for ICMEs

NASA Astrophysics Data System (ADS)

Nieves-Chinchilla, T.; Linton, M.; Hidalgo, M. A. U.; Vourlidas, A.

2016-12-01

We present an analytical flux-rope model for realistic magnetic structures embedded in Interplanetary Coronal Mass Ejections. The framework of this model was established by Nieves-Chinchilla et al. (2016) with the circular-cylindrical analytical flux rope model and under the concept developed by Hidalgo et al. (2002). Elliptic-cylindrical geometry establishes the first-grade of complexity of a series of models. The model attempts to describe the magnetic flux rope topology with distorted cross-section as a possible consequence of the interaction with the solar wind. In this model, the flux rope is completely described in the non-euclidean geometry. The Maxwell equations are solved using tensor calculus consistently with the geometry chosen, invariance along the axial component, and with the only assumption of no radial current density. The model is generalized in terms of the radial dependence of the poloidal current density component and axial current density component. The misalignment between current density and magnetic field is studied in detail for the individual cases of different pairs of indexes for the axial and poloidal current density components. This theoretical analysis provides a map of the force distribution inside of the flux-rope. The reconstruction technique has been adapted to the model and compared with in situ ICME set of events with different in situ signatures. The successful result is limited to some cases with clear in-situ signatures of distortion. However, the model adds a piece in the puzzle of the physical-analytical representation of these magnetic structures. Other effects such as axial curvature, expansion and/or interaction could be incorporated in the future to fully understand the magnetic structure. Finally, the mathematical formulation of this model opens the door to the next model: toroidal flux rope analytical model.

Global terrestrial Human Footprint maps for 1993 and 2009

PubMed Central

Venter, Oscar; Sanderson, Eric W.; Magrach, Ainhoa; Allan, James R.; Beher, Jutta; Jones, Kendall R.; Possingham, Hugh P.; Laurance, William F.; Wood, Peter; Fekete, Balázs M.; Levy, Marc A.; Watson, James E.M.

2016-01-01

Remotely-sensed and bottom-up survey information were compiled on eight variables measuring the direct and indirect human pressures on the environment globally in 1993 and 2009. This represents not only the most current information of its type, but also the first temporally-consistent set of Human Footprint maps. Data on human pressures were acquired or developed for: 1) built environments, 2) population density, 3) electric infrastructure, 4) crop lands, 5) pasture lands, 6) roads, 7) railways, and 8) navigable waterways. Pressures were then overlaid to create the standardized Human Footprint maps for all non-Antarctic land areas. A validation analysis using scored pressures from 3114×1 km2 random sample plots revealed strong agreement with the Human Footprint maps. We anticipate that the Human Footprint maps will find a range of uses as proxies for human disturbance of natural systems. The updated maps should provide an increased understanding of the human pressures that drive macro-ecological patterns, as well as for tracking environmental change and informing conservation science and application. PMID:27552448

Imputing forest carbon stock estimates from inventory plots to a nationally continuous coverage

PubMed Central

2013-01-01

The U.S. has been providing national-scale estimates of forest carbon (C) stocks and stock change to meet United Nations Framework Convention on Climate Change (UNFCCC) reporting requirements for years. Although these currently are provided as national estimates by pool and year to meet greenhouse gas monitoring requirements, there is growing need to disaggregate these estimates to finer scales to enable strategic forest management and monitoring activities focused on various ecosystem services such as C storage enhancement. Through application of a nearest-neighbor imputation approach, spatially extant estimates of forest C density were developed for the conterminous U.S. using the U.S.’s annual forest inventory. Results suggest that an existing forest inventory plot imputation approach can be readily modified to provide raster maps of C density across a range of pools (e.g., live tree to soil organic carbon) and spatial scales (e.g., sub-county to biome). Comparisons among imputed maps indicate strong regional differences across C pools. The C density of pools closely related to detrital input (e.g., dead wood) is often highest in forests suffering from recent mortality events such as those in the northern Rocky Mountains (e.g., beetle infestations). In contrast, live tree carbon density is often highest on the highest quality forest sites such as those found in the Pacific Northwest. Validation results suggest strong agreement between the estimates produced from the forest inventory plots and those from the imputed maps, particularly when the C pool is closely associated with the imputation model (e.g., aboveground live biomass and live tree basal area), with weaker agreement for detrital pools (e.g., standing dead trees). Forest inventory imputed plot maps provide an efficient and flexible approach to monitoring diverse C pools at national (e.g., UNFCCC) and regional scales (e.g., Reducing Emissions from Deforestation and Forest Degradation projects) while allowing timely incorporation of empirical data (e.g., annual forest inventory). PMID:23305341

High-density genetic map using whole-genome re-sequencing for fine mapping and candidate gene discovery for disease resistance in peanut

USDA-ARS?s Scientific Manuscript database

High-density genetic linkage maps are essential for fine mapping QTLs controlling disease resistance traits, such as early leaf spot (ELS), late leaf spot (LLS), and Tomato spotted wilt virus (TSWV). With completion of the genome sequences of two diploid ancestors of cultivated peanut, we could use ...

Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

PubMed Central

2014-01-01

Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species. PMID:24581176

Local activation time sampling density for atrial tachycardia contact mapping: how much is enough?

PubMed

Williams, Steven E; Harrison, James L; Chubb, Henry; Whitaker, John; Kiedrowicz, Radek; Rinaldi, Christopher A; Cooklin, Michael; Wright, Matthew; Niederer, Steven; O'Neill, Mark D

2018-02-01

Local activation time (LAT) mapping forms the cornerstone of atrial tachycardia diagnosis. Although anatomic and positional accuracy of electroanatomic mapping (EAM) systems have been validated, the effect of electrode sampling density on LAT map reconstruction is not known. Here, we study the effect of chamber geometry and activation complexity on optimal LAT sampling density using a combined in silico and in vivo approach. In vivo 21 atrial tachycardia maps were studied in three groups: (1) focal activation, (2) macro-re-entry, and (3) localized re-entry. In silico activation was simulated on a 4×4cm atrial monolayer, sampled randomly at 0.25-10 points/cm2 and used to re-interpolate LAT maps. Activation patterns were studied in the geometrically simple porcine right atrium (RA) and complex human left atrium (LA). Activation complexity was introduced into the porcine RA by incomplete inter-caval linear ablation. In all cases, optimal sampling density was defined as the highest density resulting in minimal further error reduction in the re-interpolated maps. Optimal sampling densities for LA tachycardias were 0.67 ± 0.17 points/cm2 (focal activation), 1.05 ± 0.32 points/cm2 (macro-re-entry) and 1.23 ± 0.26 points/cm2 (localized re-entry), P = 0.0031. Increasing activation complexity was associated with increased optimal sampling density both in silico (focal activation 1.09 ± 0.14 points/cm2; re-entry 1.44 ± 0.49 points/cm2; spiral-wave 1.50 ± 0.34 points/cm2, P < 0.0001) and in vivo (porcine RA pre-ablation 0.45 ± 0.13 vs. post-ablation 0.78 ± 0.17 points/cm2, P = 0.0008). Increasing chamber geometry was also associated with increased optimal sampling density (0.61 ± 0.22 points/cm2 vs. 1.0 ± 0.34 points/cm2, P = 0.0015). Optimal sampling densities can be identified to maximize diagnostic yield of LAT maps. Greater sampling density is required to correctly reveal complex activation and represent activation across complex geometries. Overall, the optimal sampling density for LAT map interpolation defined in this study was ∼1.0-1.5 points/cm2. Published on behalf of the European Society of Cardiology

Likelihood-based modification of experimental crystal structure electron density maps

DOEpatents

Terwilliger, Thomas C [Sante Fe, NM

2005-04-16

A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

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

PubMed Central

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

2015-01-01

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

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

USDA-ARS?s Scientific Manuscript database

High-density linkage maps are fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, e.g., Upland cotton (Gossypium hirsutum L., 2n=52). Using 3 full-sib intra-specific mapping populations fr...

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis

PubMed Central

Mason, Annaliese S.; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E.; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A. P.; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N.

2016-01-01

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. PMID:26614742

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.

PubMed

Mason, Annaliese S; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A P; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N

2016-02-01

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. Copyright © 2016 by the Genetics Society of America.

Vision 20/20: Magnetic resonance imaging-guided attenuation correction in PET/MRI: Challenges, solutions, and opportunities

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

Mehranian, Abolfazl; Arabi, Hossein; Zaidi, Habib, E-mail: habib.zaidi@hcuge.ch

Attenuation correction is an essential component of the long chain of data correction techniques required to achieve the full potential of quantitative positron emission tomography (PET) imaging. The development of combined PET/magnetic resonance imaging (MRI) systems mandated the widespread interest in developing novel strategies for deriving accurate attenuation maps with the aim to improve the quantitative accuracy of these emerging hybrid imaging systems. The attenuation map in PET/MRI should ideally be derived from anatomical MR images; however, MRI intensities reflect proton density and relaxation time properties of biological tissues rather than their electron density and photon attenuation properties. Therefore, inmore » contrast to PET/computed tomography, there is a lack of standardized global mapping between the intensities of MRI signal and linear attenuation coefficients at 511 keV. Moreover, in standard MRI sequences, bones and lung tissues do not produce measurable signals owing to their low proton density and short transverse relaxation times. MR images are also inevitably subject to artifacts that degrade their quality, thus compromising their applicability for the task of attenuation correction in PET/MRI. MRI-guided attenuation correction strategies can be classified in three broad categories: (i) segmentation-based approaches, (ii) atlas-registration and machine learning methods, and (iii) emission/transmission-based approaches. This paper summarizes past and current state-of-the-art developments and latest advances in PET/MRI attenuation correction. The advantages and drawbacks of each approach for addressing the challenges of MR-based attenuation correction are comprehensively described. The opportunities brought by both MRI and PET imaging modalities for deriving accurate attenuation maps and improving PET quantification will be elaborated. Future prospects and potential clinical applications of these techniques and their integration in commercial systems will also be discussed.« less

Vision 20/20: Magnetic resonance imaging-guided attenuation correction in PET/MRI: Challenges, solutions, and opportunities.

PubMed

Mehranian, Abolfazl; Arabi, Hossein; Zaidi, Habib

2016-03-01

Attenuation correction is an essential component of the long chain of data correction techniques required to achieve the full potential of quantitative positron emission tomography (PET) imaging. The development of combined PET/magnetic resonance imaging (MRI) systems mandated the widespread interest in developing novel strategies for deriving accurate attenuation maps with the aim to improve the quantitative accuracy of these emerging hybrid imaging systems. The attenuation map in PET/MRI should ideally be derived from anatomical MR images; however, MRI intensities reflect proton density and relaxation time properties of biological tissues rather than their electron density and photon attenuation properties. Therefore, in contrast to PET/computed tomography, there is a lack of standardized global mapping between the intensities of MRI signal and linear attenuation coefficients at 511 keV. Moreover, in standard MRI sequences, bones and lung tissues do not produce measurable signals owing to their low proton density and short transverse relaxation times. MR images are also inevitably subject to artifacts that degrade their quality, thus compromising their applicability for the task of attenuation correction in PET/MRI. MRI-guided attenuation correction strategies can be classified in three broad categories: (i) segmentation-based approaches, (ii) atlas-registration and machine learning methods, and (iii) emission/transmission-based approaches. This paper summarizes past and current state-of-the-art developments and latest advances in PET/MRI attenuation correction. The advantages and drawbacks of each approach for addressing the challenges of MR-based attenuation correction are comprehensively described. The opportunities brought by both MRI and PET imaging modalities for deriving accurate attenuation maps and improving PET quantification will be elaborated. Future prospects and potential clinical applications of these techniques and their integration in commercial systems will also be discussed.

A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array

PubMed Central

Wen, Weie; He, Zhonghu; Gao, Fengmei; Liu, Jindong; Jin, Hui; Zhai, Shengnan; Qu, Yanying; Xia, Xianchun

2017-01-01

A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding. PMID:28848588

Reconstructing cortical current density by exploring sparseness in the transform domain

NASA Astrophysics Data System (ADS)

Ding, Lei

2009-05-01

In the present study, we have developed a novel electromagnetic source imaging approach to reconstruct extended cortical sources by means of cortical current density (CCD) modeling and a novel EEG imaging algorithm which explores sparseness in cortical source representations through the use of L1-norm in objective functions. The new sparse cortical current density (SCCD) imaging algorithm is unique since it reconstructs cortical sources by attaining sparseness in a transform domain (the variation map of cortical source distributions). While large variations are expected to occur along boundaries (sparseness) between active and inactive cortical regions, cortical sources can be reconstructed and their spatial extents can be estimated by locating these boundaries. We studied the SCCD algorithm using numerous simulations to investigate its capability in reconstructing cortical sources with different extents and in reconstructing multiple cortical sources with different extent contrasts. The SCCD algorithm was compared with two L2-norm solutions, i.e. weighted minimum norm estimate (wMNE) and cortical LORETA. Our simulation data from the comparison study show that the proposed sparse source imaging algorithm is able to accurately and efficiently recover extended cortical sources and is promising to provide high-accuracy estimation of cortical source extents.

Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata)

PubMed Central

2012-01-01

Background Brassica oleracea encompass a family of vegetables and cabbage that are among the most widely cultivated crops. In 2009, the B. oleracea Genome Sequencing Project was launched using next generation sequencing technology. None of the available maps were detailed enough to anchor the sequence scaffolds for the Genome Sequencing Project. This report describes the development of a large number of SSR and SNP markers from the whole genome shotgun sequence data of B. oleracea, and the construction of a high-density genetic linkage map using a double haploid mapping population. Results The B. oleracea high-density genetic linkage map that was constructed includes 1,227 markers in nine linkage groups spanning a total of 1197.9 cM with an average of 0.98 cM between adjacent loci. There were 602 SSR markers and 625 SNP markers on the map. The chromosome with the highest number of markers (186) was C03, and the chromosome with smallest number of markers (99) was C09. Conclusions This first high-density map allowed the assembled scaffolds to be anchored to pseudochromosomes. The map also provides useful information for positional cloning, molecular breeding, and integration of information of genes and traits in B. oleracea. All the markers on the map will be transferable and could be used for the construction of other genetic maps. PMID:23033896

Merging field mapping and numerical simulation to interpret the lithofacies variations from unsteady pyroclastic density currents on uneven terrain: The case of La Fossa di Vulcano (Aeolian Islands, Italy)

NASA Astrophysics Data System (ADS)

Doronzo, Domenico M.; Dellino, Pierfrancesco; Sulpizio, Roberto; Lucchi, Federico

2017-01-01

In order to obtain results from computer simulations of explosive volcanic eruptions, one either needs a statistical approach to test a wide range of initial and boundary conditions, or needs using a well-constrained field case study via stratigraphy. Here we followed the second approach, using data obtained from field mapping of the Grotta dei Palizzi 2 pyroclastic deposits (Vulcano Island, Italy) as input for numerical modeling. This case study deals with impulsive phreatomagmatic explosions of La Fossa Cone that generated ash-rich pyroclastic density currents, interacting with the topographic high of the La Fossa Caldera rim. One of the simplifications in dealing with well-sorted ash (one particle size in the model) is to highlight the topographic effects on the same pyroclastic material in an unsteady current. We demonstrate that by merging field data with 3D numerical simulation results it is possible to see key details of the dynamical current-terrain interaction, and to interpret the lithofacies variations of the associated deposits as a function of topography-induced sedimentation (settling) rate. Results suggest that a value of the sedimentation rate lower than 5 kg/m2 s at the bed load can still be sheared by the overlying current, producing tractional structures (laminae) in the deposits. Instead, a sedimentation rate higher than that threshold can preclude the formation of tractional structures, producing thicker massive deposits. We think that the approach used in this study could be applied to other case studies (both for active and ancient volcanoes) to confirm or refine such threshold value of the sedimentation rate, which is to be considered as an upper value as for the limitations of the numerical model.

Optimisation of air cooled, open-cathode fuel cells: Current of lowest resistance and electro-thermal performance mapping

NASA Astrophysics Data System (ADS)

Meyer, Quentin; Ronaszegi, Krisztian; Pei-June, Gan; Curnick, Oliver; Ashton, Sean; Reisch, Tobias; Adcock, Paul; Shearing, Paul R.; Brett, Daniel J. L.

2015-09-01

Selecting the ideal operating point for a fuel cell depends on the application and consequent trade-off between efficiency, power density and various operating considerations. A systematic methodology for determining the optimal operating point for fuel cells is lacking; there is also the need for a single-value metric to describe and compare fuel cell performance. This work shows how the 'current of lowest resistance' can be accurately measured using electrochemical impedance spectroscopy and used as a useful metric of fuel cell performance. This, along with other measures, is then used to generate an 'electro-thermal performance map' of fuel cell operation. A commercial air-cooled open-cathode fuel cell is used to demonstrate how the approach can be used; in this case leading to the identification of the optimum operating temperature of ∼45 °C.

The First Genetic Map in Sweet Osmanthus (Osmanthus fragrans Lour.) Using Specific Locus Amplified Fragment Sequencing

PubMed Central

He, Yanxia; Yuan, Wangjun; Dong, Meifang; Han, Yuanji; Shang, Fude

2017-01-01

Osmanthus fragrans is an ornamental plant of substantial commercial value, and no genetic linkage maps of this species have previously been reported. Specific-locus amplified fragment sequencing (SLAF-seq) is a recently developed technology that allows massive single nucleotide polymorphisms (SNPs) to be identified and high-resolution genotyping. In our current research, we generated the first genetic map of O. fragrans using SLAF-seq, which is composed with 206.92 M paired-end reads and 173,537 SLAF markers. Among total 90,715 polymorphic SLAF markers, 15,317 polymorphic SLAFs could be used for genetic map construction. The integrated map contained 14,189 high quality SLAFs that were grouped in 23 genetic linkage groups, with a total length of 2962.46 cM and an average distance of 0.21 cM between two adjacent markers. In addition, 23,664 SNPs were identified from the mapped markers. As far as we know, this is the first of the genetic map of O. fragrans. Our results are further demonstrate that SLAF-seq is a very effective method for developing markers and constructing high-density linkage maps. The SNP markers and the genetic map reported in this study should be valuable resource in future research. PMID:29018460

Hotspot detection in pancreatic neuroendocrine tumors: density approximation by α-shape maps

NASA Astrophysics Data System (ADS)

Niazi, M. K. K.; Hartman, Douglas J.; Pantanowitz, Liron; Gurcan, Metin N.

2016-03-01

The grading of neuroendocrine tumors of the digestive system is dependent on accurate and reproducible assessment of the proliferation with the tumor, either by counting mitotic figures or counting Ki-67 positive nuclei. At the moment, most pathologists manually identify the hotspots, a practice which is tedious and irreproducible. To better help pathologists, we present an automatic method to detect all potential hotspots in neuroendocrine tumors of the digestive system. The method starts by segmenting Ki-67 positive nuclei by entropy based thresholding, followed by detection of centroids for all Ki-67 positive nuclei. Based on geodesic distance, approximated by the nuclei centroids, we compute two maps: an amoeba map and a weighted amoeba map. These maps are later combined to generate the heat map, the segmentation of which results in the hotspots. The method was trained on three and tested on nine whole slide images of neuroendocrine tumors. When evaluated by two expert pathologists, the method reached an accuracy of 92.6%. The current method does not discriminate between tumor, stromal and inflammatory nuclei. The results show that α-shape maps may represent how hotspots are perceived.

Habitat analysis of North American sand flies near veterans returning from leishmania-endemic war zones.

PubMed

Claborn, David; Masuoka, Penny; Morrow, Meredith; Keep, Lisa

2008-12-18

Nearly 1300 cases of leishmaniasis have been identified in American military personnel deployed to Iraq and Afghanistan. The symptoms of this disease can range from a mild, self-limiting cutaneous infection to a deadly visceral infection and are not prevented by chemoprophylaxis or immunization. Effective treatments, however, are available. The disease-causing parasite is spread through the bite of the female sand fly. Although the disease occurs in both the Old World and the New World, the parasite species differ between the hemispheres. The large number of cases in military veterans has caused some concern that Old World, temperate-adapted parasite species could be introduced into the native sand fly populations of American military facilities where veterans of the current conflicts return following their deployments. This paper reports part of a larger study to analyze the risk of such an accidental importation. Four potential habitats on two large Army facilities in the Southeast United States were surveyed to determine relative sand fly density. The National Land Cover Map was used to provide sand fly density prediction maps by habitat. Sand fly density was significantly higher in deciduous forest and even higher at the interface between forest and open grassland. The evergreen forest and agricultural fields supported very low densities. On Fort Campbell, KY, the percentage of land covered by suitable habitat was very high. A sand fly density prediction map identified large tracts of land where infected individuals would be at higher risk of exposure to sand fly bites, resulting in an increased risk of introducing the parasite to a native insect population. On Fort Bragg, NC, however, commercial farming of long leaf pine reduced the percentage of the land covered in vegetation suitable for the support of sand flies. The risk of introducing an exotic Leishmania spp. on Fort Bragg, therefore, is considered to be much lower than on Fort Campbell. A readily available land cover product can be used at the regional level to identify areas of sand fly habitat where human populations may be at higher risk of exposure. The sand fly density prediction maps can be used to direct further surveillance, insect control, or additional patient monitoring of potentially infected soldiers.

Construction of a high-density genetic map and the X/Y sex-determining gene mapping in spinach based on large-scale markers developed by specific-locus amplified fragment sequencing (SLAF-seq).

PubMed

Qian, Wei; Fan, Guiyan; Liu, Dandan; Zhang, Helong; Wang, Xiaowu; Wu, Jian; Xu, Zhaosheng

2017-04-04

Cultivated spinach (Spinacia oleracea L.) is one of the most widely cultivated types of leafy vegetable in the world, and it has a high nutritional value. Spinach is also an ideal plant for investigating the mechanism of sex determination because it is a dioecious species with separate male and female plants. Some reports on the sex labeling and localization of spinach in the study of molecular markers have surfaced. However, there have only been two reports completed on the genetic map of spinach. The lack of rich and reliable molecular markers and the shortage of high-density linkage maps are important constraints in spinach research work. In this study, a high-density genetic map of spinach based on the Specific-locus Amplified Fragment Sequencing (SLAF-seq) technique was constructed; the sex-determining gene was also finely mapped. Through bio-information analysis, 50.75 Gb of data in total was obtained, including 207.58 million paired-end reads. Finally, 145,456 high-quality SLAF markers were obtained, with 27,800 polymorphic markers and 4080 SLAF markers were finally mapped onto the genetic map after linkage analysis. The map spanned 1,125.97 cM with an average distance of 0.31 cM between the adjacent marker loci. It was divided into 6 linkage groups corresponding to the number of spinach chromosomes. Besides, the combination of Bulked Segregation Analysis (BSA) with SLAF-seq technology(super-BSA) was employed to generate the linkage markers with the sex-determining gene. Combined with the high-density genetic map of spinach, the sex-determining gene X/Y was located at the position of the linkage group (LG) 4 (66.98 cM-69.72 cM and 75.48 cM-92.96 cM), which may be the ideal region for the sex-determining gene. A high-density genetic map of spinach based on the SLAF-seq technique was constructed with a backcross (BC 1 ) population (which is the highest density genetic map of spinach reported at present). At the same time, the sex-determining gene X/Y was mapped to LG4 with super-BSA. This map will offer a suitable basis for further study of spinach, such as gene mapping, map-based cloning of Specific genes, quantitative trait locus (QTL) mapping and marker-assisted selection (MAS). It will also provide an efficient reference for studies on the mechanism of sex determination in other dioecious plants.

A comparison of spatial analysis methods for the construction of topographic maps of retinal cell density.

PubMed

Garza-Gisholt, Eduardo; Hemmi, Jan M; Hart, Nathan S; Collin, Shaun P

2014-01-01

Topographic maps that illustrate variations in the density of different neuronal sub-types across the retina are valuable tools for understanding the adaptive significance of retinal specialisations in different species of vertebrates. To date, such maps have been created from raw count data that have been subjected to only limited analysis (linear interpolation) and, in many cases, have been presented as iso-density contour maps with contour lines that have been smoothed 'by eye'. With the use of stereological approach to count neuronal distribution, a more rigorous approach to analysing the count data is warranted and potentially provides a more accurate representation of the neuron distribution pattern. Moreover, a formal spatial analysis of retinal topography permits a more robust comparison of topographic maps within and between species. In this paper, we present a new R-script for analysing the topography of retinal neurons and compare methods of interpolating and smoothing count data for the construction of topographic maps. We compare four methods for spatial analysis of cell count data: Akima interpolation, thin plate spline interpolation, thin plate spline smoothing and Gaussian kernel smoothing. The use of interpolation 'respects' the observed data and simply calculates the intermediate values required to create iso-density contour maps. Interpolation preserves more of the data but, consequently includes outliers, sampling errors and/or other experimental artefacts. In contrast, smoothing the data reduces the 'noise' caused by artefacts and permits a clearer representation of the dominant, 'real' distribution. This is particularly useful where cell density gradients are shallow and small variations in local density may dramatically influence the perceived spatial pattern of neuronal topography. The thin plate spline and the Gaussian kernel methods both produce similar retinal topography maps but the smoothing parameters used may affect the outcome.

Dislocation related droop in InGaN/GaN light emitting diodes investigated via cathodoluminescence

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

Pozina, Galia; Ciechonski, Rafal; Bi, Zhaoxia

2015-12-21

Today's energy saving solutions for general illumination rely on efficient white light emitting diodes (LEDs). However, the output efficiency droop experienced in InGaN based LEDs with increasing current injection is a serious limitation factor for future development of bright white LEDs. We show using cathodoluminescence (CL) spatial mapping at different electron beam currents that threading dislocations are active as nonradiative recombination centers only at high injection conditions. At low current, the dislocations are inactive in carrier recombination due to local potentials, but these potentials are screened by carriers at higher injection levels. In CL images, this corresponds to the increasemore » of the dark contrast around dislocations with the injection (excitation) density and can be linked with droop related to the threading dislocations. Our data indicate that reduction of droop in the future efficient white LED can be achieved via a drastic reduction of the dislocation density by using, for example, bulk native substrates.« less

Support for the existence of invertible maps between electronic densities and non-analytic 1-body external potentials in non-relativistic time-dependent quantum mechanics

NASA Astrophysics Data System (ADS)

Mosquera, Martín A.

2017-10-01

Provided the initial state, the Runge-Gross theorem establishes that the time-dependent (TD) external potential of a system of non-relativistic electrons determines uniquely their TD electronic density, and vice versa (up to a constant in the potential). This theorem requires the TD external potential and density to be Taylor-expandable around the initial time of the propagation. This paper presents an extension without this restriction. Given the initial state of the system and evolution of the density due to some TD scalar potential, we show that a perturbative (not necessarily weak) TD potential that induces a non-zero divergence of the external force-density, inside a small spatial subset and immediately after the initial propagation time, will cause a change in the density within that subset, implying that the TD potential uniquely determines the TD density. In this proof, we assume unitary evolution of wavefunctions and first-order differentiability (which does not imply analyticity) in time of the internal and external force-densities, electronic density, current density, and their spatial derivatives over the small spatial subset and short time interval.

Isostatic gravity map with simplified geology of the Los Angeles 30 x 60 minute quadrangle

USGS Publications Warehouse

Wooley, R.J.; Yerkes, R.F.; Langenheim, V.E.; Chuang, F.C.

2003-01-01

This isostatic residual gravity map is part of the Southern California Areal Mapping Project (SCAMP) and is intended to promote further understanding of the geology in the Los Angeles 30 x 60 minute quadrangle, California, by serving as a basis for geophysical interpretations and by supporting both geological mapping and topical (especially earthquake) studies. Local spatial variations in the Earth's gravity field (after various corrections for elevation, terrain, and deep crustal structure explained below) reflect the lateral variation in density in the mid- to upper crust. Densities often can be related to rock type, and abrupt spatial changes in density commonly mark lithologic boundaries. The map shows contours of isostatic gravity overlain on a simplified geology including faults and rock types. The map is draped over shaded-relief topography to show landforms.

Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms.

PubMed

N'Diaye, Amidou; Haile, Jemanesh K; Fowler, D Brian; Ammar, Karim; Pozniak, Curtis J

2017-01-01

Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called 'large p, small n' problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly.

Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms

PubMed Central

N’Diaye, Amidou; Haile, Jemanesh K.; Fowler, D. Brian; Ammar, Karim; Pozniak, Curtis J.

2017-01-01

Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called ‘large p, small n’ problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly. PMID:28878789

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

USDA-ARS?s Scientific Manuscript database

Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 datasets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum...

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

PubMed Central

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

2015-01-01

The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species. PMID:26503227

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

PubMed Central

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

2012-01-01

Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization. PMID:22984541

Long-term multi-hazard assessment for El Misti volcano (Peru)

NASA Astrophysics Data System (ADS)

Sandri, Laura; Thouret, Jean-Claude; Constantinescu, Robert; Biass, Sébastien; Tonini, Roberto

2014-02-01

We propose a long-term probabilistic multi-hazard assessment for El Misti Volcano, a composite cone located <20 km from Arequipa. The second largest Peruvian city is a rapidly expanding economic centre and is classified by UNESCO as World Heritage. We apply the Bayesian Event Tree code for Volcanic Hazard (BET_VH) to produce probabilistic hazard maps for the predominant volcanic phenomena that may affect c.900,000 people living around the volcano. The methodology accounts for the natural variability displayed by volcanoes in their eruptive behaviour, such as different types/sizes of eruptions and possible vent locations. For this purpose, we treat probabilistically several model runs for some of the main hazardous phenomena (lahars, pyroclastic density currents (PDCs), tephra fall and ballistic ejecta) and data from past eruptions at El Misti (tephra fall, PDCs and lahars) and at other volcanoes (PDCs). The hazard maps, although neglecting possible interactions among phenomena or cascade effects, have been produced with a homogeneous method and refer to a common time window of 1 year. The probability maps reveal that only the north and east suburbs of Arequipa are exposed to all volcanic threats except for ballistic ejecta, which are limited to the uninhabited but touristic summit cone. The probability for pyroclastic density currents reaching recently expanding urban areas and the city along ravines is around 0.05 %/year, similar to the probability obtained for roof-critical tephra loading during the rainy season. Lahars represent by far the most probable threat (around 10 %/year) because at least four radial drainage channels can convey them approximately 20 km away from the volcano across the entire city area in heavy rain episodes, even without eruption. The Río Chili Valley represents the major concern to city safety owing to the probable cascading effect of combined threats: PDCs and rockslides, dammed lake break-outs and subsequent lahars or floods. Although this study does not intend to replace the current El Misti hazard map, the quantitative results of this probabilistic multi-hazard assessment can be incorporated into a multi-risk analysis, to support decision makers in any future improvement of the current hazard evaluation, such as further land-use planning and possible emergency management.

Assessment of the vegetation cover in a burned area 22-years ago using remote sensing techniques and GIS analysis (Sierra de las Nieves, South of Spain).

NASA Astrophysics Data System (ADS)

Martínez-Murillo, Juan F.; Remond, Ricardo; Ruiz-Sinoga, José D.

2015-04-01

The study aim was to characterize the vegetation cover in a burned area 22-years ago considering the previous situation to wildfire in 1991 and the current one in 2013. The objectives were to: (i) compare the current and previous vegetation cover to widlfire; (ii) evaluate whether the current vegetation has recovered the previous cover to wildfire; and (iii) determine the spatial variability of vegetation recovery after 22-years since the wildfire. The study area is located in Sierra de las Nieves, South of Spain. It corresponds to an area affected by a wildfire in August 8th, 1991. The burned area was equal to 8156 ha. The burn severity was spatially very high. The main geographic features of the burned area are: mountainous topography (altitudes ranging from 250 m to 1500 m; slope gradient >25%; exposure mainly southfacing); igneous (peridotites), metamorphic (gneiss) and calcareous rocks (limestones); and predominant forest land use (Pinus pinaster sp. woodlands, 10%; pinus opened forest + shrubland, 40%; shrubland, 35%; and bare soil + grassland, 15%). Remote sensing techniques and GIS analysis has been applied to achieve the objectives. Landsat 5 and Landsat 8 images were used: July 13th, 1991 and July 1st, 2013, for the previous wildfire situation and 22-years after, respectively. The 1990 CORINE land cover was also considered to map 1991 land uses prior the wildfire. Likewise, the Andalucía Regional Government wildfire historic records were used to select the burned area and its geographical limit. 1991 and 2013 land cover map were obtained by means of object-oriented classifications. Also, NDVI and PVI1 vegetation indexes were calculated and mapped for both years. Finally, some images transformations and kernel density images were applied to determine the most recovered areas and to map the spatial concentration of bare soil and pine cover areas in 1991 and 2013, respectively. According to the results, the combination of remote sensing and GIS analysis let map the most recovered areas affected by the wildfire in 1991. The vegetation indexes indicated that the vegetation cover in 2013 was still lower than that mapped just before the 1991 widlfire in most of the burned area after 22-years. This result was also confirmed by other techniques applied. Finally, the kernel density surface let identify and locate the most recovered areas of pine cover as well as those areas that still remain totally or partially uncovered (bare soil.

An Enhanced Linkage Map of the Sheep Genome Comprising More Than 1000 Loci

PubMed Central

Maddox, Jillian F.; Davies, Kizanne P.; Crawford, Allan M.; Hulme, Dennis J.; Vaiman, Daniel; Cribiu, Edmond P.; Freking, Bradley A.; Beh, Ken J.; Cockett, Noelle E.; Kang, Nina; Riffkin, Christopher D.; Drinkwater, Roger; Moore, Stephen S.; Dodds, Ken G.; Lumsden, Joanne M.; van Stijn, Tracey C.; Phua, Sin H.; Adelson, David L.; Burkin, Heather R.; Broom, Judith E.; Buitkamp, Johannes; Cambridge, Lisa; Cushwa, William T.; Gerard, Emily; Galloway, Susan M.; Harrison, Blair; Hawken, Rachel J.; Hiendleder, Stefan; Henry, Hannah M.; Medrano, Juan F.; Paterson, Korena A.; Schibler, Laurent; Stone, Roger T.; van Hest, Beryl

2001-01-01

A medium-density linkage map of the ovine genome has been developed. Marker data for 550 new loci were generated and merged with the previous sheep linkage map. The new map comprises 1093 markers representing 1062 unique loci (941 anonymous loci, 121 genes) and spans 3500 cM (sex-averaged) for the autosomes and 132 cM (female) on the X chromosome. There is an average spacing of 3.4 cM between autosomal loci and 8.3 cM between highly polymorphic [polymorphic information content (PIC) ≥ 0.7] autosomal loci. The largest gap between markers is 32.5 cM, and the number of gaps of >20 cM between loci, or regions where loci are missing from chromosome ends, has been reduced from 40 in the previous map to 6. Five hundred and seventy-three of the loci can be ordered on a framework map with odds of >1000 : 1. The sheep linkage map contains strong links to both the cattle and goat maps. Five hundred and seventy-two of the loci positioned on the sheep linkage map have also been mapped by linkage analysis in cattle, and 209 of the loci mapped on the sheep linkage map have also been placed on the goat linkage map. Inspection of ruminant linkage maps indicates that the genomic coverage by the current sheep linkage map is comparable to that of the available cattle maps. The sheep map provides a valuable resource to the international sheep, cattle, and goat gene mapping community. PMID:11435411

The role of disappeared disturbances in driving the North American prairie-forest boundary

NASA Astrophysics Data System (ADS)

Heilman, K.; McLachlan, J. S.; Staver, A. C.

2016-12-01

Globally, transitions from savanna to forest are often characterized by abrupt changes in tree density that cannot be fully explained by climate and edaphic factors. In the tropics, fire-vegetation feedbacks drive a bimodal distribution in tree cover that leads to alternative forest and savanna stable states within the same climate space. In temperate North America, the pre-European settlement prairie-forest transition has also been hypothesized to be influenced by widespread fires (anthropogenic or natural). However, large scale evidence for fire disturbance feedbacks on tree density in the temperate zone is currently lacking. We investigate both the pre-European and modern tree density along the North American prairie-forest boundary. We hypothesized that the pre-European distribution of tree density was distinctly bimodal due to intact vegetation-disturbance feedbacks along the prairie-forest boundary before settlement, but that fragmentation and fire suppression has produced a modern prairie-forest boundary that is less abrupt and less bimodal. We estimated tree density from aggregated Public Land Survey (PLS) data collected before the time of European agricultural settlement in Minnesota, Wisconsin, Michigan, Indiana, and Illinois and compared PLS density distributions to tree density estimated from modern USFS Forest Inventory Analysis (FIA) data. PLS tree density follows a bimodal distribution that abruptly shifts from savanna to forest at the boundary. Only 15% of the variance in pre-settlement tree density is explained by historical Mean Annual Precipitation (MAP), suggesting that the bimodality may be due to internal feedbacks in the vegetation-disturbance system, rather than to the past underlying environmental gradient. On the modern landscape, MAP explains 6% of FIA tree density variance, and tree density is not bimodal. Regions that had low tree density savannas in the PLS era have significantly increased in tree density, suggesting that the disappearance of disturbances that accompanied agricultural settlement resulted in closed forests where savannas were once an alternative stable state (p < 0.01). Additionally, the once high tree density forests in the PLS have significantly declined in density, suggesting that logging has contributed to land cover change in North America.

Improving snow density estimation for mapping SWE with Lidar snow depth: assessment of uncertainty in modeled density and field sampling strategies in NASA SnowEx

NASA Astrophysics Data System (ADS)

Raleigh, M. S.; Smyth, E.; Small, E. E.

2017-12-01

The spatial distribution of snow water equivalent (SWE) is not sufficiently monitored with either remotely sensed or ground-based observations for water resources management. Recent applications of airborne Lidar have yielded basin-wide mapping of SWE when combined with a snow density model. However, in the absence of snow density observations, the uncertainty in these SWE maps is dominated by uncertainty in modeled snow density rather than in Lidar measurement of snow depth. Available observations tend to have a bias in physiographic regime (e.g., flat open areas) and are often insufficient in number to support testing of models across a range of conditions. Thus, there is a need for targeted sampling strategies and controlled model experiments to understand where and why different snow density models diverge. This will enable identification of robust model structures that represent dominant processes controlling snow densification, in support of basin-scale estimation of SWE with remotely-sensed snow depth datasets. The NASA SnowEx mission is a unique opportunity to evaluate sampling strategies of snow density and to quantify and reduce uncertainty in modeled snow density. In this presentation, we present initial field data analyses and modeling results over the Colorado SnowEx domain in the 2016-2017 winter campaign. We detail a framework for spatially mapping the uncertainty in snowpack density, as represented across multiple models. Leveraging the modular SUMMA model, we construct a series of physically-based models to assess systematically the importance of specific process representations to snow density estimates. We will show how models and snow pit observations characterize snow density variations with forest cover in the SnowEx domains. Finally, we will use the spatial maps of density uncertainty to evaluate the selected locations of snow pits, thereby assessing the adequacy of the sampling strategy for targeting uncertainty in modeled snow density.

Prior-knowledge-based spectral mixture analysis for impervious surface mapping

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

Zhang, Jinshui; He, Chunyang; Zhou, Yuyu

2014-01-03

In this study, we developed a prior-knowledge-based spectral mixture analysis (PKSMA) to map impervious surfaces by using endmembers derived separately for high- and low-density urban regions. First, an urban area was categorized into high- and low-density urban areas, using a multi-step classification method. Next, in high-density urban areas that were assumed to have only vegetation and impervious surfaces (ISs), the Vegetation-Impervious model (V-I) was used in a spectral mixture analysis (SMA) with three endmembers: vegetation, high albedo, and low albedo. In low-density urban areas, the Vegetation-Impervious-Soil model (V-I-S) was used in an SMA analysis with four endmembers: high albedo, lowmore » albedo, soil, and vegetation. The fraction of IS with high and low albedo in each pixel was combined to produce the final IS map. The root mean-square error (RMSE) of the IS map produced using PKSMA was about 11.0%, compared to 14.52% using four-endmember SMA. Particularly in high-density urban areas, PKSMA (RMSE = 6.47%) showed better performance than four-endmember (15.91%). The results indicate that PKSMA can improve IS mapping compared to traditional SMA by using appropriately selected endmembers and is particularly strong in high-density urban areas.« less

Evolution of probability densities in stochastic coupled map lattices

NASA Astrophysics Data System (ADS)

Losson, Jérôme; Mackey, Michael C.

1995-08-01

This paper describes the statistical properties of coupled map lattices subjected to the influence of stochastic perturbations. The stochastic analog of the Perron-Frobenius operator is derived for various types of noise. When the local dynamics satisfy rather mild conditions, this equation is shown to possess either stable, steady state solutions (i.e., a stable invariant density) or density limit cycles. Convergence of the phase space densities to these limit cycle solutions explains the nonstationary behavior of statistical quantifiers at equilibrium. Numerical experiments performed on various lattices of tent, logistic, and shift maps with diffusivelike interelement couplings are examined in light of these theoretical results.

Urban local climate zone mapping and apply in urban environment study

NASA Astrophysics Data System (ADS)

He, Shan; Zhang, Yunwei; Zhang, Jili

2018-02-01

The city’s local climate zone (LCZ) was considered to be a powerful tool for urban climate mapping. But for cities in different countries and regions, the LCZ division methods and results were different, thus targeted researches should be performed. In the current work, a LCZ mapping method was proposed, which is convenient in operation and city planning oriented. In this proposed method, the local climate zoning types were adjusted firstly, according to the characteristics of Chinese city, that more tall buildings and high density. Then the classification method proposed by WUDAPT based on remote sensing data was performed on Xi’an city, as an example, for LCZ mapping. Combined with the city road network, a reasonable expression of the dividing results was provided, to adapt to the characteristics in city planning that land parcels are usually recognized as the basic unit. The proposed method was validated against the actual land use and construction data that surveyed in Xi’an, with results indicating the feasibility of the proposed method for urban LCZ mapping in China.

Location of acoustic radiators and inversion for energy density using radio-frequency sources and thunder recordings

NASA Astrophysics Data System (ADS)

Anderson, J.; Johnson, J. B.; Arechiga, R. O.; Edens, H. E.; Thomas, R. J.

2011-12-01

We use radio frequency (VHF) pulse locations mapped with the New Mexico Tech Lightning Mapping Array (LMA) to study the distribution of thunder sources in lightning channels. A least squares inversion is used to fit channel acoustic energy radiation with broadband (0.01 to 500 Hz) acoustic recordings using microphones deployed local (< 10 km) to the lightning. We model the thunder (acoustic) source as a superposition of line segments connecting the LMA VHF pulses. An optimum branching algorithm is used to reconstruct conductive channels delineated by VHF sources, which we discretize as a superposition of finely-spaced (0.25 m) acoustic point sources. We consider total radiated thunder as a weighted superposition of acoustic waves from individual channels, each with a constant current along its length that is presumed to be proportional to acoustic energy density radiated per unit length. Merged channels are considered as a linear sum of current-carrying branches and radiate proportionally greater acoustic energy. Synthetic energy time series for a given microphone location are calculated for each independent channel. We then use a non-negative least squares inversion to solve for channel energy densities to match the energy time series determined from broadband acoustic recordings across a 4-station microphone network. Events analyzed by this method have so far included 300-1000 VHF sources, and correlations as high as 0.5 between synthetic and recorded thunder energy were obtained, despite the presence of wind noise and 10-30 m uncertainty in VHF source locations.

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

PubMed Central

2013-01-01

Background As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. Results Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. Conclusions Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing. PMID:23800011

High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut.

PubMed

Agarwal, Gaurav; Clevenger, Josh; Pandey, Manish K; Wang, Hui; Shasidhar, Yaduru; Chu, Ye; Fountain, Jake C; Choudhary, Divya; Culbreath, Albert K; Liu, Xin; Huang, Guodong; Wang, Xingjun; Deshmukh, Rupesh; Holbrook, C Corley; Bertioli, David J; Ozias-Akins, Peggy; Jackson, Scott A; Varshney, Rajeev K; Guo, Baozhu

2018-04-10

Whole-genome resequencing (WGRS) of mapping populations has facilitated development of high-density genetic maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases in peanut causing significant yield loss. We generated WGRS data on a recombinant inbred line population, developed a SNP-based high-density genetic map, and conducted fine mapping, candidate gene discovery and marker validation for ELS, LLS and TSWV. The first sequence-based high-density map was constructed with 8869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the 'T' population (Tifrunner × GT-C20) with a map length of 3120 cM and an average distance of 1.45 cM. The quantitative trait locus (QTL) analysis using high-density genetic map and multiple season phenotyping data identified 35 main-effect QTLs with phenotypic variation explained (PVE) from 6.32% to 47.63%. Among major-effect QTLs mapped, there were two QTLs for ELS on B05 with 47.42% PVE and B03 with 47.38% PVE, two QTLs for LLS on A05 with 47.63% and B03 with 34.03% PVE and one QTL for TSWV on B09 with 40.71% PVE. The epistasis and environment interaction analyses identified significant environmental effects on these traits. The identified QTL regions had disease resistance genes including R-genes and transcription factors. KASP markers were developed for major QTLs and validated in the population and are ready for further deployment in genomics-assisted breeding in peanut. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

The September 14, 2015 phreatomagmatic eruption of Nakadake first crater, Aso Volcano, Japan: Eruption sequence inferred from ballistic, pyroclastic density current and fallout deposits

NASA Astrophysics Data System (ADS)

Miyabuchi, Yasuo; Iizuka, Yoshiyuki; Hara, Chihoko; Yokoo, Akihiko; Ohkura, Takahiro

2018-02-01

An explosive eruption occurred at Nakadake first crater, Aso Volcano in central Kyushu, southwestern Japan, on September 14, 2015. The sequence and causes of the eruption were reconstructed from the distribution, textures, grain-size, component and chemical characteristics of the related deposits, and video record. The eruptive deposits are divided into ballistics, pyroclastic density current and ash-fall deposits. A large number of ballistic clasts (mostly < 10 cm in diameter; maximum size 1.6 m) are scattered within about 500 m from the center of the crater. Almost half of the ballistics appear as fresh and unaltered basaltic andesite rocks interpreted to be derived from a fresh batch of magma, while the rest is weakly to highly altered clasts. A relatively thin ash derived from pyroclastic density currents covered an area of 2.3 km2 with the SE-trending main axis and two minor axes to the NE and NW. The pyroclastic density current deposit (maximum thickness < 10 cm even at the crater rim) is wholly fine grained, containing no block-sized clasts. Based on the isopach map, the mass of the pyroclastic density current deposit was estimated at ca. 5.2 × 104 tons. The ash-fall deposit is finer grained and clearly distributed to about 8 km west of the source crater. The mass of the ash-fall deposit was calculated at about 2.7 × 104 tons. Adding the mass of the pyroclastic density current deposit, the total discharged mass of the September 14, 2015 eruption was 7.9 × 104 tons. The September 14 pyroclastic density current and ash-fall deposits consist of glass shards (ca. 30%), crystals (20-30%) and lithic (40-50%) grains. Most glass shards are unaltered poorly crystallized pale brown glasses which probably resulted from quenching of juvenile magma. This suggests that the September 14, 2015 event at the Nakadake first crater was a phreatomagmatic eruption. Similar phreatomagmatic eruptions occurred at the same crater on September 6, 1979 and April 20, 1990 whose eruptive masses were one order larger than that of the September 14, 2015 eruption. These events highlight the potential hazard from phreatic or phreatomagmatic eruptions at Nakadake first crater, and provide useful information that will assist in preventing or mitigating future disasters at other similar volcanoes worldwide.

Speech processing using conditional observable maximum likelihood continuity mapping

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

Hogden, John; Nix, David

A computer implemented method enables the recognition of speech and speech characteristics. Parameters are initialized of first probability density functions that map between the symbols in the vocabulary of one or more sequences of speech codes that represent speech sounds and a continuity map. Parameters are also initialized of second probability density functions that map between the elements in the vocabulary of one or more desired sequences of speech transcription symbols and the continuity map. The parameters of the probability density functions are then trained to maximize the probabilities of the desired sequences of speech-transcription symbols. A new sequence ofmore » speech codes is then input to the continuity map having the trained first and second probability function parameters. A smooth path is identified on the continuity map that has the maximum probability for the new sequence of speech codes. The probability of each speech transcription symbol for each input speech code can then be output.« less

U.S.A. National Surface Rock Density Map - Part 2

NASA Astrophysics Data System (ADS)

Winester, D.

2016-12-01

A map of surface rock densities over the USA has been developed by the NOAA-National Geodetic Survey (NGS) as part of its Gravity for the Redefinition of the American Vertical Datum (GRAV-D) Program. GRAV-D is part of an international effort to generate a North American gravimetric geoid for use as the vertical datum reference surface. As a part of modeling process, it is necessary to eliminate from the observed gravity data the topographic and density effects of all masses above the geoid. However, the long-standing tradition in geoid modeling, which is to use an average rock density (e.g. 2.67 g/cm3), does not adequately represent the variety of lithologies in the USA. The U.S. Geological Survey has assembled a downloadable set of surface geologic formation maps (typically 1:100,000 to 1:500, 000 scale in NAD27) in GIS format. The lithologies were assigned densities typical of their rock type (Part 1) and these variety of densities were then rasterized and averaged over one arc-minute areas. All were then transformed into WGS84 datum. Thin layers of alluvium and some water bodies (interpreted to be less than 40 m thick) have been ignored in deference to underlying rocks. Deep alluvial basins have not been removed, since they represent significant fraction of local mass. The initial assumption for modeling densities will be that the surface rock densities extend down to the geoid. If this results in poor modeling, variable lithologies with depth can be attempted. Initial modeling will use elevations from the SRTM DEM. A map of CONUS densities is presented (denser lithologies are shown brighter). While a visual map at this scale does show detailed features, digital versions are available upon request. Also presented are some pitfalls of using source GIS maps digitized from variable reference sources, including the infamous `state line faults.'

A tool for the estimation of the distribution of landslide area in R

NASA Astrophysics Data System (ADS)

Rossi, M.; Cardinali, M.; Fiorucci, F.; Marchesini, I.; Mondini, A. C.; Santangelo, M.; Ghosh, S.; Riguer, D. E. L.; Lahousse, T.; Chang, K. T.; Guzzetti, F.

2012-04-01

We have developed a tool in R (the free software environment for statistical computing, http://www.r-project.org/) to estimate the probability density and the frequency density of landslide area. The tool implements parametric and non-parametric approaches to the estimation of the probability density and the frequency density of landslide area, including: (i) Histogram Density Estimation (HDE), (ii) Kernel Density Estimation (KDE), and (iii) Maximum Likelihood Estimation (MLE). The tool is available as a standard Open Geospatial Consortium (OGC) Web Processing Service (WPS), and is accessible through the web using different GIS software clients. We tested the tool to compare Double Pareto and Inverse Gamma models for the probability density of landslide area in different geological, morphological and climatological settings, and to compare landslides shown in inventory maps prepared using different mapping techniques, including (i) field mapping, (ii) visual interpretation of monoscopic and stereoscopic aerial photographs, (iii) visual interpretation of monoscopic and stereoscopic VHR satellite images and (iv) semi-automatic detection and mapping from VHR satellite images. Results show that both models are applicable in different geomorphological settings. In most cases the two models provided very similar results. Non-parametric estimation methods (i.e., HDE and KDE) provided reasonable results for all the tested landslide datasets. For some of the datasets, MLE failed to provide a result, for convergence problems. The two tested models (Double Pareto and Inverse Gamma) resulted in very similar results for large and very large datasets (> 150 samples). Differences in the modeling results were observed for small datasets affected by systematic biases. A distinct rollover was observed in all analyzed landslide datasets, except for a few datasets obtained from landslide inventories prepared through field mapping or by semi-automatic mapping from VHR satellite imagery. The tool can also be used to evaluate the probability density and the frequency density of landslide volume.

Use of total electron content data to analyze ionosphere electron density gradients

NASA Astrophysics Data System (ADS)

Nava, B.; Radicella, S. M.; Leitinger, R.; Coïsson, P.

In the presence of electron density gradients the thin shell approximation for the ionosphere, used together with a simple mapping function to convert slant total electron content (TEC) to vertical TEC, could lead to TEC conversion errors. These "mapping function errors" can therefore be used to detect the electron density gradients in the ionosphere. In the present work GPS derived slant TEC data have been used to investigate the effects of the electron density gradients in the middle and low latitude ionosphere under geomagnetic quiet and disturbed conditions. In particular the data corresponding to the geographic area of the American Sector for the days 5-7 April 2000 have been used to perform a complete analysis of mapping function errors based on the "coinciding pierce point technique". The results clearly illustrate the electron density gradient effects according to the locations considered and to the actual levels of disturbance of the ionosphere. In addition, the possibility to assess an ionospheric shell height able to minimize the mapping function errors has been verified.

Birkeland currents during substorms: Statistical evidence for intensification of Regions 1 and 2 currents after onset and a localized signature of auroral dimming

NASA Astrophysics Data System (ADS)

Coxon, John C.; Rae, I. Jonathan; Forsyth, Colin; Jackman, Caitriona M.; Fear, Robert C.; Anderson, Brian J.

2017-06-01

We conduct a superposed epoch analysis of Birkeland current densities from AMPERE (Active Magnetosphere and Planetary Electrodynamics Response Experiment) using isolated substorm expansion phase onsets identified by an independently derived data set. In order to evaluate whether R1 and R2 currents contribute to the substorm current wedge, we rotate global maps of Birkeland currents into a common coordinate system centered on the magnetic local time of substorm onset. When the latitude of substorm is taken into account, it is clear that both R1 and R2 current systems play a role in substorm onset, contrary to previous studies which found that R2 current did not contribute. The latitude of substorm onset is colocated with the interface between R1 and R2 currents, allowing us to infer that R1 current closes just tailward and R2 current closes just earthward of the associated current disruption in the tail. AMPERE is the first data set to give near-instantaneous measurements of Birkeland current across the whole polar cap, and this study addresses apparent discrepancies in previous studies which have used AMPERE to examine the morphology of the substorm current wedge. Finally, we present evidence for an extremely localized reduction in current density immediately prior to substorm onset, and we interpret this as the first statistical signature of auroral dimming in Birkeland current.

An appraisal of Indonesia's immense peat carbon stock using national peatland maps: uncertainties and potential losses from conversion.

PubMed

Warren, Matthew; Hergoualc'h, Kristell; Kauffman, J Boone; Murdiyarso, Daniel; Kolka, Randall

2017-12-01

A large proportion of the world's tropical peatlands occur in Indonesia where rapid conversion and associated losses of carbon, biodiversity and ecosystem services have brought peatland management to the forefront of Indonesia's climate mitigation efforts. We evaluated peat volume from two commonly referenced maps of peat distribution and depth published by Wetlands International (WI) and the Indonesian Ministry of Agriculture (MoA), and used regionally specific values of carbon density to calculate carbon stocks. Peatland extent and volume published in the MoA maps are lower than those in the WI maps, resulting in lower estimates of carbon storage. We estimate Indonesia's total peat carbon store to be within 13.6 GtC (the low MoA map estimate) and 40.5 GtC (the high WI map estimate) with a best estimate of 28.1 GtC: the midpoint of medium carbon stock estimates derived from WI (30.8 GtC) and MoA (25.3 GtC) maps. This estimate is about half of previous assessments which used an assumed average value of peat thickness for all Indonesian peatlands, and revises the current global tropical peat carbon pool to 75 GtC. Yet, these results do not diminish the significance of Indonesia's peatlands, which store an estimated 30% more carbon than the biomass of all Indonesian forests. The largest discrepancy between maps is for the Papua province, which accounts for 62-71% of the overall differences in peat area, volume and carbon storage. According to the MoA map, 80% of Indonesian peatlands are <300 cm thick and thus vulnerable to conversion outside of protected areas according to environmental regulations. The carbon contained in these shallower peatlands is conservatively estimated to be 10.6 GtC, equivalent to 42% of Indonesia's total peat carbon and about 12 years of global emissions from land use change at current rates. Considering the high uncertainties in peatland extent, volume and carbon storage revealed in this assessment of current maps, a systematic revision of Indonesia's peat maps to produce a single geospatial reference that is universally accepted would improve national peat carbon storage estimates and greatly benefit carbon cycle research, land use management and spatial planning.

Polder maps: Improving OMIT maps by excluding bulk solvent

DOE PAGES

Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.; ...

2017-02-01

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factorsmore » and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX.« less

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

PubMed

Sekiguchi, Yuki; Oroguchi, Tomotaka; Nakasako, Masayoshi

2016-01-01

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

Beyond the double banana: improved recognition of temporal lobe seizures in long-term EEG.

PubMed

Rosenzweig, Ivana; Fogarasi, András; Johnsen, Birger; Alving, Jørgen; Fabricius, Martin Ejler; Scherg, Michael; Neufeld, Miri Y; Pressler, Ronit; Kjaer, Troels W; van Emde Boas, Walter; Beniczky, Sándor

2014-02-01

To investigate whether extending the 10-20 array with 6 electrodes in the inferior temporal chain and constructing computed montages increases the diagnostic value of ictal EEG activity originating in the temporal lobe. In addition, the accuracy of computer-assisted spectral source analysis was investigated. Forty EEG samples were reviewed by 7 EEG experts in various montages (longitudinal and transversal bipolar, common average, source derivation, source montage, current source density, and reference-free montages) using 2 electrode arrays (10-20 and the extended one). Spectral source analysis used source montage to calculate density spectral array, defining the earliest oscillatory onset. From this, phase maps were calculated for localization. The reference standard was the decision of the multidisciplinary epilepsy surgery team on the seizure onset zone. Clinical performance was compared with the double banana (longitudinal bipolar montage, 10-20 array). Adding the inferior temporal electrode chain, computed montages (reference free, common average, and source derivation), and voltage maps significantly increased the sensitivity. Phase maps had the highest sensitivity and identified ictal activity at earlier time-point than visual inspection. There was no significant difference concerning specificity. The findings advocate for the use of these digital EEG technology-derived analysis methods in clinical practice.

Improving experimental phases for strong reflections prior to density modification

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

Uervirojnangkoorn, Monarin; University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck; Hilgenfeld, Rolf, E-mail: hilgenfeld@biochem.uni-luebeck.de

A genetic algorithm has been developed to optimize the phases of the strongest reflections in SIR/SAD data. This is shown to facilitate density modification and model building in several test cases. Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the mapsmore » can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005 ▶), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. A computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

A Bayesian approach to tracking patients having changing pharmacokinetic parameters

NASA Technical Reports Server (NTRS)

Bayard, David S.; Jelliffe, Roger W.

2004-01-01

This paper considers the updating of Bayesian posterior densities for pharmacokinetic models associated with patients having changing parameter values. For estimation purposes it is proposed to use the Interacting Multiple Model (IMM) estimation algorithm, which is currently a popular algorithm in the aerospace community for tracking maneuvering targets. The IMM algorithm is described, and compared to the multiple model (MM) and Maximum A-Posteriori (MAP) Bayesian estimation methods, which are presently used for posterior updating when pharmacokinetic parameters do not change. Both the MM and MAP Bayesian estimation methods are used in their sequential forms, to facilitate tracking of changing parameters. Results indicate that the IMM algorithm is well suited for tracking time-varying pharmacokinetic parameters in acutely ill and unstable patients, incurring only about half of the integrated error compared to the sequential MM and MAP methods on the same example.

Spatiotemporal Built-up Land Density Mapping Using Various Spectral Indices in Landsat-7 ETM+ and Landsat-8 OLI/TIRS (Case Study: Surakarta City)

NASA Astrophysics Data System (ADS)

Risky, Yanuar S.; Aulia, Yogi H.; Widayani, Prima

2017-12-01

Spectral indices variations support for rapid and accurate extracting information such as built-up density. However, the exact determination of spectral waves for built-up density extraction is lacking. This study explains and compares the capabilities of 5 variations of spectral indices in spatiotemporal built-up density mapping using Landsat-7 ETM+ and Landsat-8 OLI/TIRS in Surakarta City on 2002 and 2015. The spectral indices variations used are 3 mid-infrared (MIR) based indices such as the Normalized Difference Built-up Index (NDBI), Urban Index (UI) and Built-up and 2 visible based indices such as VrNIR-BI (visible red) and VgNIR-BI (visible green). Linear regression statistics between ground value samples from Google Earth image in 2002 and 2015 and spectral indices for determining built-up land density. Ground value used amounted to 27 samples for model and 7 samples for accuracy test. The classification of built-up density mapping is divided into 9 classes: unclassified, 0-12.5%, 12.5-25%, 25-37.5%, 37.5-50%, 50-62.5%, 62.5-75%, 75-87.5% and 87.5-100 %. Accuracy of built-up land density mapping in 2002 and 2015 using VrNIR-BI (81,823% and 73.235%), VgNIR-BI (78.934% and 69.028%), NDBI (34.870% and 74.365%), UI (43.273% and 64.398%) and Built-up (59.755% and 72.664%). Based all spectral indices, Surakarta City on 2000-2015 has increased of built-up land density. VgNIR-BI has better capabilities for built-up land density mapping on Landsat-7 ETM + and Landsat-8 OLI/TIRS.

Visualization of Current and Mapping of Elements in Quantum Dot Solar Cells

DOE PAGES

Niezgoda, J. Scott; Ng, Amy; Poplawsky, Jonathan D.; ...

2015-12-17

The delicate influence of properties such as high surface state density and organic-inorganic boundaries on the individual quantum dot electronic structure complicates pursuits toward forming quantitative models of quantum dot thin films ab initio. Our report describes the application of electron beam-induced current (EBIC) microscopy to depleted-heterojunction colloidal quantum dot photovoltaics (DH-CQD PVs), a technique which affords one a map of current production within the active layer of a PV device. The effects of QD sample size polydispersity as well as layer thickness in CQD active layers as they pertain to current production within these PVs are imaged and explained.more » The results from these experiments compare well with previous estimations, and confirm the ability of EBIC to function as a valuable empirical tool for the design and betterment of DH-CQD PVs. Lastly, extensive and unexpected PbS QD penetration into the mesoporous TiO 2 layer is observed through imaging of device cross sections by energy-dispersive X-ray spectroscopy combined with scanning transmission electron microscopy. Finally, the effects of this finding are discussed and corroborated with the EBIC studies on similar devices.« less

Genome Mapping and Molecular Breeding of Tomato

PubMed Central

Foolad, Majid R.

2007-01-01

The cultivated tomato, Lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. It is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. The high-density molecular map, developed based on an L. esculentum × L. pennellii cross, includes more than 2200 markers with an average marker distance of less than 1 cM and an average of 750 kbp per cM. Different types of molecular markers such as RFLPs, AFLPs, SSRs, CAPS, RGAs, ESTs, and COSs have been developed and mapped onto the 12 tomato chromosomes. Markers have been used extensively for identification and mapping of genes and QTLs for many biologically and agriculturally important traits and occasionally for germplasm screening, fingerprinting, and marker-assisted breeding. The utility of MAS in tomato breeding has been restricted largely due to limited marker polymorphism within the cultivated species and economical reasons. Also, when used, MAS has been employed mainly for improving simply-inherited traits and not much for improving complex traits. The latter has been due to unavailability of reliable PCR-based markers and problems with linkage drag. Efforts are being made to develop high-throughput markers with greater resolution, including SNPs. The expanding tomato EST database, which currently includes ∼214 000 sequences, the new microarray DNA chips, and the ongoing sequencing project are expected to aid development of more practical markers. Several BAC libraries have been developed that facilitate map-based cloning of genes and QTLs. Sequencing of the euchromatic portions of the tomato genome is paving the way for comparative and functional analysis of important genes and QTLs. PMID:18364989

Breakdown Degradation Associated with Elementary Screw Dislocations in 4H-SiC P(+)N Junction Rectifiers

NASA Technical Reports Server (NTRS)

Neudeck, P. G.; Huang, W.; Dudley, M.

1998-01-01

It is well-known that SiC wafer quality deficiencies are delaying the realization of outstandingly superior 4H-SiC power electronics. While efforts to date have centered on eradicating micropipes (i.e., hollow core super-screw dislocations with Burgers vector greater than 2c), 4H-SiC wafers and epilayers also contain elementary screw dislocations (i.e., Burgers vector = lc with no hollow core) in densities on the order of thousands per sq cm, nearly 100-fold micropipe densities. This paper describes an initial study into the impact of elementary screw dislocations on the reverse-bias current-voltage (I-V) characteristics of 4H-SiC p(+)n diodes. First, Synchrotron White Beam X-ray Topography (SWBXT) was employed to map the exact locations of elementary screw dislocations within small-area 4H-SiC p(+)n mesa diodes. Then the high-field reverse leakage and breakdown properties of these diodes were subsequently characterized on a probing station outfitted with a dark box and video camera. Most devices without screw dislocations exhibited excellent characteristics, with no detectable leakage current prior to breakdown, a sharp breakdown I-V knee, and no visible concentration of breakdown current. In contrast devices that contained at least one elementary screw dislocation exhibited a 5% to 35% reduction in breakdown voltage, a softer breakdown I-V knee, and visible microplasmas in which highly localized breakdown current was concentrated. The locations of observed breakdown microplasmas corresponded exactly to the locations of elementary screw dislocations identified by SWBXT mapping. While not as detrimental to SiC device performance as micropipes, the undesirable breakdown characteristics of elementary screw dislocations could nevertheless adversely affect the performance and reliability of 4H-SiC power devices.

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

USDA-ARS?s Scientific Manuscript database

Fragaria iinumae is recognized as an ancestor of the octoploid strawberry species, including the cultivated strawberry, Fragaria ×ananassa. Here we report the construction of the first high density linkage map for F. iinumae. The map is based on two high-throughput techniques of single nucleotide p...

Demonstration of a Strategy to Perform Two-Dimensional Diode Laser Tomography

DTIC Science & Technology

2008-03-01

training set allows interpolation between beam paths resulting in temperature and density maps. Finally, the TDLAS temperature and density maps are... TDLAS and Tomography Results .................................................................. 38 Introduction...38 vii Page TDLAS Burner Setup

Biometric recognition via fixation density maps

NASA Astrophysics Data System (ADS)

Rigas, Ioannis; Komogortsev, Oleg V.

2014-05-01

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

Effects of allocryptopine on outward potassium current and slow delayed rectifier potassium current in rabbit myocardium.

PubMed

Fu, Yi-Cheng; Zhang, Yu; Tian, Liu-Yang; Li, Nan; Chen, Xi; Cai, Zhong-Qi; Zhu, Chao; Li, Yang

2016-05-01

Allocryptopine (ALL) is an effective alkaloid of Corydalis decumbens (Thunb.) Pers. Papaveraceae and has proved to be anti-arrhythmic. The purpose of our study is to investigate the effects of ALL on transmural repolarizing ionic ingredients of outward potassium current (I to) and slow delayed rectifier potassium current (I Ks). The monophasic action potential (MAP) technique was used to record the MAP duration of the epicardium (Epi), myocardium (M) and endocardium (Endo) of the rabbit heart and the whole cell patch clamp was used to record I to and I Ks in cardiomyocytes of Epi, M and Endo layers that were isolated from rabbit ventricles. The effects of ALL on MAP of Epi, M and Endo layers were disequilibrium. ALL could effectively reduce the transmural dispersion of repolarization (TDR) in rabbit transmural ventricular wall. ALL decreased the current densities of I to and I Ks in a voltage and concentration dependent way and narrowed the repolarizing differences among three layers. The analysis of gating kinetics showed ALL accelerated the channel activation of I to in M layers and partly inhibit the channel openings of I to in Epi, M and Endo cells. On the other hand, ALL mainly slowed channel deactivation of I Ks channel in Epi and Endo layers without affecting its activation. Our study gives partially explanation about the mechanisms of transmural inhibition of I to and I Ks channels by ALL in rabbit myocardium. These findings provide novel perspective regarding the anti-arrhythmogenesis application of ALL in clinical settings.

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

PubMed

Dominkovics, Pau; Granell, Carlos; Pérez-Navarro, Antoni; Casals, Martí; Orcau, Angels; Caylà, Joan A

2011-11-29

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

A Comparison of Spatial Analysis Methods for the Construction of Topographic Maps of Retinal Cell Density

PubMed Central

Garza-Gisholt, Eduardo; Hemmi, Jan M.; Hart, Nathan S.; Collin, Shaun P.

2014-01-01

Topographic maps that illustrate variations in the density of different neuronal sub-types across the retina are valuable tools for understanding the adaptive significance of retinal specialisations in different species of vertebrates. To date, such maps have been created from raw count data that have been subjected to only limited analysis (linear interpolation) and, in many cases, have been presented as iso-density contour maps with contour lines that have been smoothed ‘by eye’. With the use of stereological approach to count neuronal distribution, a more rigorous approach to analysing the count data is warranted and potentially provides a more accurate representation of the neuron distribution pattern. Moreover, a formal spatial analysis of retinal topography permits a more robust comparison of topographic maps within and between species. In this paper, we present a new R-script for analysing the topography of retinal neurons and compare methods of interpolating and smoothing count data for the construction of topographic maps. We compare four methods for spatial analysis of cell count data: Akima interpolation, thin plate spline interpolation, thin plate spline smoothing and Gaussian kernel smoothing. The use of interpolation ‘respects’ the observed data and simply calculates the intermediate values required to create iso-density contour maps. Interpolation preserves more of the data but, consequently includes outliers, sampling errors and/or other experimental artefacts. In contrast, smoothing the data reduces the ‘noise’ caused by artefacts and permits a clearer representation of the dominant, ‘real’ distribution. This is particularly useful where cell density gradients are shallow and small variations in local density may dramatically influence the perceived spatial pattern of neuronal topography. The thin plate spline and the Gaussian kernel methods both produce similar retinal topography maps but the smoothing parameters used may affect the outcome. PMID:24747568

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

PubMed Central

2011-01-01

Background Health professionals and authorities strive to cope with heterogeneous data, services, and statistical models to support decision making on public health. Sophisticated analysis and distributed processing capabilities over geocoded epidemiological data are seen as driving factors to speed up control and decision making in these health risk situations. In this context, recent Web technologies and standards-based web services deployed on geospatial information infrastructures have rapidly become an efficient way to access, share, process, and visualize geocoded health-related information. Methods Data used on this study is based on Tuberculosis (TB) cases registered in Barcelona city during 2009. Residential addresses are geocoded and loaded into a spatial database that acts as a backend database. The web-based application architecture and geoprocessing web services are designed according to the Representational State Transfer (REST) principles. These web processing services produce spatial density maps against the backend database. Results The results are focused on the use of the proposed web-based application to the analysis of TB cases in Barcelona. The application produces spatial density maps to ease the monitoring and decision making process by health professionals. We also include a discussion of how spatial density maps may be useful for health practitioners in such contexts. Conclusions In this paper, we developed web-based client application and a set of geoprocessing web services to support specific health-spatial requirements. Spatial density maps of TB incidence were generated to help health professionals in analysis and decision-making tasks. The combined use of geographic information tools, map viewers, and geoprocessing services leads to interesting possibilities in handling health data in a spatial manner. In particular, the use of spatial density maps has been effective to identify the most affected areas and its spatial impact. This study is an attempt to demonstrate how web processing services together with web-based mapping capabilities suit the needs of health practitioners in epidemiological analysis scenarios. PMID:22126392

Nanoscale Electronic Structure of Cuprate Superconductors Investigated with Scanning Tunneling Spectroscopy

NASA Astrophysics Data System (ADS)

Williams, Tess Lawanna

Despite 25 years of intense research activity, high-temperature superconductors remain poorly understood, with the underlying pairing mechanism still unidentified. Efforts are complicated by the remarkably complex phase diagram, rich in energy-dependent charge and spin orders. In this thesis I describe the use of a Scanning Tunneling Microscope (STM) to study energy-dependent charge orders in Bi2-- yPbySr2CuO6+delta , a cuprate high-temperature superconductor. STM, a surface-sensitive probe used to map electronic structure with sub-meV energy resolution and sub-A spatial resolution, has contributed greatly to our current understanding of the cuprate high-temperature superconductors. However, STM data is acquired with a constant-current normalization condition. The measured differential conductance, g(x, y, V), is often taken to be proportional to the density of states at energy eV (where V is the voltage applied between tip and sample). In fact, due to the normalization condition, the measured g(x, y, V) is actually the quotient of the density of states at energy eV and the integrated density of states from the Fermi energy to eV. This unavoidable quotient may fold electronic structure from its true energy range into other energies. I discuss a new method to correct STM differential conductance spectra to remove the constant-current normalization condition. Using local work function measurements and the constant-current topograph, I create a map which does not suffer from the setpoint effect and contains a mixture of topographic information and properly normalized spectroscopic information. I apply this method to the extraction of the incommensurate charge modulation at q⃗˜34 2pa0 . I also extend the study of electronic nematic order, an atomic-lattice-periodic C4 → C2 symmetry breaking, from highly underdoped Bi2 Sr2CaCu2O 8+delta [28] to overdoped Bi2--yPb ySr2CuO6+/-delta. I find that the electronic nematic order parameter is robust to change of scan angle. I define and contrast three different electronic nematic orders with different phases with respect to the crystal. I discuss the effect of the choice of normalization and possible alternate explanations for the source of the calculated nematic order. Finally, I discuss a drift-correction technique, which removes picometer scale drift that is introduced into a spectral map by experimental imperfections, and characterize the optimal algorithm and potential artifacts that drift-correction may introduce.

Construction of an ultrahigh-density genetic linkage map for Jatropha curcas L. and identification of QTL for fruit yield.

PubMed

Xia, Zhiqiang; Zhang, Shengkui; Wen, Mingfu; Lu, Cheng; Sun, Yufang; Zou, Meiling; Wang, Wenquan

2018-01-01

As an important biofuel plant, the demand for higher yield Jatropha curcas L. is rapidly increasing. However, genetic analysis of Jatropha and molecular breeding for higher yield have been hampered by the limited number of molecular markers available. An ultrahigh-density linkage map for a Jatropha mapping population of 153 individuals was constructed and covered 1380.58 cM of the Jatropha genome, with average marker density of 0.403 cM. The genetic linkage map consisted of 3422 SNP and indel markers, which clustered into 11 linkage groups. With this map, 13 repeatable QTLs (reQTLs) for fruit yield traits were identified. Ten reQTLs, qNF - 1 , qNF - 2a , qNF - 2b , qNF - 2c , qNF - 3 , qNF - 4 , qNF - 6 , qNF - 7a , qNF - 7b and qNF - 8, that control the number of fruits (NF) mapped to LGs 1, 2, 3, 4, 6, 7 and 8, whereas three reQTLs, qTWF - 1 , qTWF - 2 and qTWF - 3, that control the total weight of fruits (TWF) mapped to LGs 1, 2 and 3, respectively. It is interesting that there are two candidate critical genes, which may regulate Jatropha fruit yield. We also identified three pleiotropic reQTL pairs associated with both the NF and TWF traits. This study is the first to report an ultrahigh-density Jatropha genetic linkage map construction, and the markers used in this study showed great potential for QTL mapping. Thirteen fruit-yield reQTLs and two important candidate genes were identified based on this linkage map. This genetic linkage map will be a useful tool for the localization of other economically important QTLs and candidate genes for Jatropha .

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

PubMed Central

2012-01-01

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

Orientation-dependent imaging of electronically excited quantum dots

NASA Astrophysics Data System (ADS)

Nguyen, Duc; Goings, Joshua J.; Nguyen, Huy A.; Lyding, Joseph; Li, Xiaosong; Gruebele, Martin

2018-02-01

We previously demonstrated that we can image electronic excitations of quantum dots by single-molecule absorption scanning tunneling microscopy (SMA-STM). With this technique, a modulated laser beam periodically saturates an electronic transition of a single nanoparticle, and the resulting tunneling current modulation ΔI(x0, y0) maps out the SMA-STM image. In this paper, we first derive the basic theory to calculate ΔI(x0, y0) in the one-electron approximation. For near-resonant tunneling through an empty orbital "i" of the nanostructure, the SMA-STM signal is approximately proportional to the electron density |φi) (x0,y0)|

Orientation-dependent imaging of electronically excited quantum dots.

PubMed

Nguyen, Duc; Goings, Joshua J; Nguyen, Huy A; Lyding, Joseph; Li, Xiaosong; Gruebele, Martin

2018-02-14

We previously demonstrated that we can image electronic excitations of quantum dots by single-molecule absorption scanning tunneling microscopy (SMA-STM). With this technique, a modulated laser beam periodically saturates an electronic transition of a single nanoparticle, and the resulting tunneling current modulation ΔI(x 0 , y 0 ) maps out the SMA-STM image. In this paper, we first derive the basic theory to calculate ΔI(x 0 , y 0 ) in the one-electron approximation. For near-resonant tunneling through an empty orbital "i" of the nanostructure, the SMA-STM signal is approximately proportional to the electron density φ i x 0 ,y 0 2 of the excited orbital in the tunneling region. Thus, the SMA-STM signal is approximated by an orbital density map (ODM) of the resonantly excited orbital at energy E i . The situation is more complex for correlated electron motion, but either way a slice through the excited electronic state structure in the tunneling region is imaged. We then show experimentally that we can nudge quantum dots on the surface and roll them, thus imaging excited state electronic structure of a single quantum dot at different orientations. We use density functional theory to model ODMs at various orientations, for qualitative comparison with the SMA-STM experiment. The model demonstrates that our experimentally observed signal monitors excited states, localized by defects near the surface of an individual quantum dot. The sub-nanometer super-resolution imaging technique demonstrated here could become useful for mapping out the three-dimensional structure of excited states localized by defects within nanomaterials.

Radar observation of an along-front jet and transverse flow convergence associated with a North Sea front

NASA Astrophysics Data System (ADS)

Matthews, J. P.; Fox, A. D.; Prandle, D.

1993-01-01

This paper describes the first synoptic mapping of surface currents across a strong and stable tidal mixing front by HF radar. The radar deployment took place along the coast of northeast England during August and early September 1988 in parallel with extensive ship based CTD density and ADCP (Acoustic Doppler Current Profiler) measurements which provided data in the vertical plane to complement those of the HF radar. We describe two main results. Firstly, during a spring-tide period of strengthening inshore density gradients, an along-front jet with speeds of up to 14 cm s -1 was detected in the long term IIF radar residual field. The location and spatial form of this jet correspond with estimates of geostrophic currents derived from the measured density field. Secondly, a transverse "double-sided" surface flow convergence centred close to the frontal boundary and of net magnitude 4 cm s -1 accompanied the large along-front jet. Such a weaker cross-frontal component has been anticipated on theoretical grounds but never previously observed in this detailed fashion. The experiment underlines the power of a synergistic approach, based on HF remote sensing radar and ADCP, for the study of frontal circulation in coastal zones.

Assessing the quality of open spatial data for mobile location-based services research and applications

NASA Astrophysics Data System (ADS)

Ciepłuch, C.; Mooney, P.; Jacob, R.; Zheng, J.; Winstanely, A. C.

2011-12-01

New trends in GIS such as Volunteered Geographical Information (VGI), Citizen Science, and Urban Sensing, have changed the shape of the geoinformatics landscape. The OpenStreetMap (OSM) project provided us with an exciting, evolving, free and open solution as a base dataset for our geoserver and spatial data provider for our research. OSM is probably the best known and best supported example of VGI and user generated spatial content on the Internet. In this paper we will describe current results from the development of quality indicators for measures for OSM data. Initially we have analysed the Ireland OSM data in grid cells (5km) to gather statistical data about the completeness, accuracy, and fitness for purpose of the underlying spatial data. This analysis included: density of user contributions, spatial density of points and polygons, types of tags and metadata used, dominant contributors in a particular area or for a particular geographic feature type, etc. There greatest OSM activity and spatial data density is highly correlated with centres of large population. The ability to quantify and assess if VGI, such as OSM, is of sufficient quality for mobile mapping applications and Location-based services is critical to the future success of VGI as a spatial data source for these technologies.

StreamMap: Smooth Dynamic Visualization of High-Density Streaming Points.

PubMed

Li, Chenhui; Baciu, George; Han, Yu

2018-03-01

Interactive visualization of streaming points for real-time scatterplots and linear blending of correlation patterns is increasingly becoming the dominant mode of visual analytics for both big data and streaming data from active sensors and broadcasting media. To better visualize and interact with inter-stream patterns, it is generally necessary to smooth out gaps or distortions in the streaming data. Previous approaches either animate the points directly or present a sampled static heat-map. We propose a new approach, called StreamMap, to smoothly blend high-density streaming points and create a visual flow that emphasizes the density pattern distributions. In essence, we present three new contributions for the visualization of high-density streaming points. The first contribution is a density-based method called super kernel density estimation that aggregates streaming points using an adaptive kernel to solve the overlapping problem. The second contribution is a robust density morphing algorithm that generates several smooth intermediate frames for a given pair of frames. The third contribution is a trend representation design that can help convey the flow directions of the streaming points. The experimental results on three datasets demonstrate the effectiveness of StreamMap when dynamic visualization and visual analysis of trend patterns on streaming points are required.

Completing the Mapping of the W3 Giant Molecular Cloud; Testing Models and the Importance of Triggered Star Formation

NASA Astrophysics Data System (ADS)

Moore, Toby; Allsopp, James; Jones, Huw

2006-05-01

It is proposed to complete the R. Gehrz's mapping of W3 at both IRAC and MIPS 24um wavelengths. W3 is an outer galaxy Giant Molecular Cloud comprising of two regions; a quiescent, spontaneously star forming region and a region compressed by the W4 OB association containing the majority of star formation and all of the high mass star formation. Currently only the high-density region, Lada( put date) is mapped, but for a scientifically-valid comparision between the triggered and spontaneous modes we require the remainder of the cloud to be mapped. Triggered star formation is vitally important as it provides a mechanism for understanding the massive disparity between the low star formation efficiencies of galaxies such as our own andmore violent events such as galaxy mergers. Currently we have mapped the majority of the cloud at 850 um using SCUBA and the whole cloud using the CO(J=1-0) with the 12CO, 13CO and C18O isotomers. From these studies we have identified and measured the masses of 230 clumps. Without Spitzer data we have no way of determining which of these clumps have formed stars. This project forms the final crucial piece which when added to our current observations of the mass in the cloud will quantify the local star formation efficiency for each region. This is the first part of an ongoing much larger study into triggered star formation. We used Aztec (1.1mm continuum) on the JCMT in January 2006 to map two more clouds and Spitzer data on these from other observers has either been recently released or is about to be. In 2007, we will expand on the knowledge gained from this with the SCUBA2 JCMT Galactic Plane Survey (JPS) in which we are collaborators.

Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing

PubMed Central

Guo, Yinshan; Xing, Huiyang; Zhao, Yuhui; Liu, Zhendong; Li, Kun; Guo, Xiuwu

2017-01-01

Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, ‘Chardonnay’ and ‘Beibinghong’, and their 130 F1 plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for ‘Chardonnay’ (the female parent), 48.20 for ‘Beibinghong’ (the male parent), and 12.66 for the F1 offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape. PMID:28746364

Dog ownership, abundance and potential for bat-borne rabies spillover in Chile.

PubMed

Astorga, F; Escobar, L E; Poo-Muñoz, D A; Medina-Vogel, G

2015-03-01

Rabies is a viral infectious disease that affects all mammals, including humans. Factors associated with the incidence of rabies include the presence and density of susceptible hosts and potential reservoirs. Currently, Chile is declared free of canine-related rabies, but there is an overpopulation of dogs within the country and an emergence of rabies in bats. Our objectives are to determine potential areas for bat-borne rabies spillover into dog populations expressed as a risk map, and to explore some key features of dog ownership, abundance, and management in Chile. For the risk map, our variables included a dog density surface (dog/km(2)) and a distribution model of bat-borne rabies presence. From literature review, we obtained dog data from 112 municipalities, which represent 33% of the total municipalities (339). At country level, based on previous studies the median human per dog ratio was 4.8, with 64% of houses containing at least one dog, and a median of 0.9 dog per house. We estimate a national median of 5.3 dog/km(2), and a median of 3680 dogs by municipality, from which we estimate a total population of 3.5×10(6) owned dogs. The antirabies vaccination presented a median of 21% of dogs by municipality, and 29% are unrestricted to some degree. Human per dog ratio have a significant (but weak) negative association with human density. Unrestricted dogs have a negative association with human density and income, and a positive association with the number of dogs per house. Considering dog density by municipality, and areas of potential bat-borne rabies occurrence, we found that 163 (∼48%) of Chilean municipalities are at risk of rabies spillover from bats to dogs. Risk areas are concentrated in urban settlements, including Santiago, Chile's capital. To validate the risk map, we included cases of rabies in dogs from the last 27 years; all fell within high-risk areas of our map, confirming the assertive risk prediction. Our results suggest that the use of dog population parameters may be informative to determine risk areas for bat-rabies spillover events. In addition, we confirm that dog abundance is a neglected and emerging public health concern in Chile, particularly within urban areas, which deserves prompt intervention. Copyright © 2015. Published by Elsevier B.V.

Enhancing superconducting critical current by randomness

NASA Astrophysics Data System (ADS)

Wang, Y. L.; Thoutam, L. R.; Xiao, Z. L.; Shen, B.; Pearson, J. E.; Divan, R.; Ocola, L. E.; Crabtree, G. W.; Kwok, W. K.

2016-01-01

The key ingredient of high critical currents in a type-II superconductor is defect sites that pin vortices. Contrary to earlier understanding on nanopatterned artificial pinning, here we show unequivocally the advantages of a random pinscape over an ordered array in a wide magnetic field range. We reveal that the better performance of a random pinscape is due to the variation of its local density of pinning sites (LDOPS), which mitigates the motion of vortices. This is confirmed by achieving even higher enhancement of the critical current through a conformally mapped random pinscape, where the distribution of the LDOPS is further enlarged. The demonstrated key role of LDOPS in enhancing superconducting critical currents gets at the heart of random versus commensurate pinning. Our findings highlight the importance of random pinscapes in enhancing the superconducting critical currents of applied superconductors.

Shape information from a critical point analysis of calculated electron density maps: application to DNA-drug systems

NASA Astrophysics Data System (ADS)

Leherte, L.; Allen, F. H.; Vercauteren, D. P.

1995-04-01

A computational method is described for mapping the volume within the DNA double helix accessible to a groove-binding antibiotic, netropsin. Topological critical point analysis is used to locate maxima in electron density maps reconstructed from crystallographically determined atomic coordinates. The peaks obtained in this way are represented as ellipsoids with axes related to local curvature of the electron density function. Combining the ellipsoids produces a single electron density function which can be probed to estimate effective volumes of the interacting species. Close complementarity between host and ligand in this example shows the method to be a good representation of the electron density function at various resolutions; while at the atomic level the ellipsoid method gives results which are in close agreement with those from the conventional, spherical, van der Waals approach.

Shape information from a critical point analysis of calculated electron density maps: Application to DNA-drug systems

NASA Astrophysics Data System (ADS)

Leherte, Laurence; Allen, Frank H.

1994-06-01

A computational method is described for mapping the volume within the DNA double helix accessible to the groove-binding antibiotic netropsin. Topological critical point analysis is used to locate maxima in electron density maps reconstructed from crystallographically determined atomic coordinates. The peaks obtained in this way are represented as ellipsoids with axes related to local curvature of the electron density function. Combining the ellipsoids produces a single electron density function which can be probed to estimate effective volumes of the interacting species. Close complementarity between host and ligand in this example shows the method to give a good representation of the electron density function at various resolutions. At the atomic level, the ellipsoid method gives results which are in close agreement with those from the conventional spherical van der Waals approach.

Minutes of the Explosives Safety Seminar (25). Volume 4. Held in Anaheim, California on 18-20 Aug 1992

DTIC Science & Technology

1992-08-01

reaction process ; - sensitivity versus damage (vivacity, specific surface, porosity, density variation). So, most of the experimental tests need to...the later mapping process would form a better basis for compliance with published requirementsi I than the current approach. Seytion Summary It takes... Processing of Explosives, Propellants and Ingredients, AIIPA, San Diego, (’alif. April 1991. 49. W.11I. Andersen and N.A. Louie, " Projectile Impact Ignition

A journey from a SSR-based low density map to a SNP-based high density map for identification of disease resistance quantitative trait loci in peanut

USDA-ARS?s Scientific Manuscript database

Mapping and identification of quantitative trait loci (QTLs) are important for efficient marker-assisted breeding. Diseases such as leaf spots and Tomato spotted wilt virus (TSWV) cause significant loses to peanut growers. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to...

Assessing and modelling ecohydrologic processes at the agricultural field scale

NASA Astrophysics Data System (ADS)

Basso, Bruno

2015-04-01

One of the primary goals of agricultural management is to increase the amount of crop produced per unit of fertilizer and water used. World record corn yields demonstrated that water use efficiency can increase fourfold with improved agronomic management and cultivars able to tolerate high densities. Planting crops with higher plant density can lead to significant yield increases, and increase plant transpiration vs. soil water evaporation. Precision agriculture technologies have been adopted for the last twenty years but seldom have the data collected been converted to information that led farmers to different agronomic management. These methods are intuitively appealing, but yield maps and other spatial layers of data need to be properly analyzed and interpreted to truly become valuable. Current agro-mechanic and geospatial technologies allow us to implement a spatially variable plan for agronomic inputs including seeding rate, cultivars, pesticides, herbicides, fertilizers, and water. Crop models are valuable tools to evaluate the impact of management strategies (e.g., cover crops, tile drains, and genetically-improved cultivars) on yield, soil carbon sequestration, leaching and greenhouse gas emissions. They can help farmers identify adaptation strategies to current and future climate conditions. In this paper I illustrate the key role that precision agriculture technologies (yield mapping technologies, within season soil and crop sensing), crop modeling and weather can play in dealing with the impact of climate variability on soil ecohydrologic processes. Case studies are presented to illustrate this concept.

The ion population of the magnetotail during the 17 April 2002 magnetic storm: Large-scale kinetic simulations and IMAGE/HENA observations

NASA Astrophysics Data System (ADS)

Peroomian, Vahé; El-Alaoui, Mostafa; Brandt, Pontus C.:son

2011-05-01

The contribution of solar wind and ionospheric ions to the ion population of the magnetotail during the 17 April 2002 geomagnetic storm was investigated by using large-scale kinetic (LSK) particle tracing calculations. We began our investigation by carrying out a global magnetohydrodynamic simulation of the storm event by using upstream solar wind and interplanetary magnetic field data from the ACE spacecraft. We launched solar wind H+ ions and ionospheric O+ ions beginning at 0900 UT, ˜2 h prior to the sudden storm commencement (SSC), until 2000 UT. We found that during this Dst ˜ -98 nT storm, solar wind ions carried the bulk of the density and energy density in the nightside ring current and plasma sheet, with the notable exception of the 90 min immediately after the SSC when O+ densities in the ring current exceeded those of H+ ions. The LSK simulation did a very good job of reproducing ion densities observed by the Los Alamos National Laboratory spacecraft at geosynchronous orbit and reproduced the changes in the inner magnetosphere and the injection of ions observed by the IMAGE spacecraft during a substorm that occurred at 1900 UT. These comparisons with observations serve to validate our results throughout the magnetotail and allow us to obtain time-dependent maps of H+ and O+ density and energy density where IMAGE cannot make measurements. In essence, this work extends the viewing window of the IMAGE spacecraft far downtail.

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

PubMed Central

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

2013-01-01

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

PubMed

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W

2013-04-09

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F 7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. Copyright © 2013 Truco et al.

Geology, tectonics, and the 2002-2003 eruption of the Semeru volcano, Indonesia: Interpreted from high-spatial resolution satellite imagery

NASA Astrophysics Data System (ADS)

Solikhin, Akhmad; Thouret, Jean-Claude; Gupta, Avijit; Harris, Andy J. L.; Liew, Soo Chin

2012-02-01

The paper illustrates the application of high-spatial resolution satellite images in interpreting volcanic structures and eruption impacts in the Tengger-Semeru massif in east Java, Indonesia. We use high-spatial resolution images (IKONOS and SPOT 5) and aerial photos in order to analyze the structures of Semeru volcano and map the deposits. Geological and tectonic mapping is based on two DEMs and on the interpretation of aerial photos and four SPOT and IKONOS optical satellite images acquired between 1996 and 2002. We also compared two thermal Surface Kinetic Temperature ASTER images before and after the 2002-2003 eruption in order to delineate and evaluate the impacts of the pyroclastic density currents. Semeru's principal structural features are probably due to the tectonic setting of the volcano. A structural map of the Tengger-Semeru massif shows four groups of faults orientated N40, N160, N75, and N105 to N140. Conspicuous structures, such as the SE-trending horseshoe-shaped scar on Semeru's summit cone, coincide with the N160-trending faults. The direction of minor scars on the east flank parallels the first and second groups of faults. The Semeru composite cone hosts the currently active Jonggring-Seloko vent. This is located on, and buttressed against, the Mahameru edifice at the head of a large scar that may reflect a failure plane at shallow depth. Dipping 35° towards the SE, this failure plane may correspond to a weak basal layer of weathered volcaniclastic rocks of Tertiary age. We suggest that the deformation pattern of Semeru and its large scar may be induced by flank spreading over the weak basal layer of the volcano. It is therefore necessary to consider the potential for flank and summit collapse in the future. The last major eruption took place in December 2002-January 2003, and involved emplacement of block-and-ash flows. We have used the 2003 ASTER Surface Kinetic Temperature image to map the 2002-2003 pyroclastic density current deposits. We have also compared two 10 m-pixel images acquired before and after the event to describe the extent and impact of an estimated volume of 5.45 × 10 6 m 3 of block-and-ash flow deposits. An ash-rich pyroclastic surge escaped from one of the valley-confined block-and ash flows at 5 to 8 km distance from the crater and swept across the forest and tilled land on the SW side of the Bang River Valley. Downvalley, the temperature of the pyroclastic surge decreased and a mud-rich deposit coated the banks of the Bang River Valley. Thus, hazard mitigation at Semeru should combine: (1) continuous monitoring of the eruptive activity through an early-warning system, and (2) continuous remote sensing of the morphological changes in the drainage system due to the impact of frequent pyroclastic density currents and lahars.

A Cartographic Tool for Managing African Swine Fever in Eurasia: Mapping Wild Boar Distribution Based on the Quality of Available Habitats.

PubMed

Bosch, J; Iglesias, I; Muñoz, M J; de la Torre, A

2017-12-01

The current African swine fever (ASF) epidemic in Eurasia represents a risk for the swine industry with devastating socio-economic and political consequences. Wild boar appears to be a key factor in maintaining the disease in endemic areas (mainly the Russian Federation) and spreading the disease across borders, including within the European Union. To help predict and interpret the dynamics of ASF infection, we developed a standardized distribution map based on global land cover vegetation (GLOBCOVER) that quantifies the quality of available habitats (QAH) for wild boar across Eurasia as an indirect index for quantifying numbers of wild boar. QAHs were estimated using a seven-level scale based on expert opinion and found to correlate closely with georeferenced presence of wild boar (n = 22 362): the highest wild boar densities (74.47%) were found in areas at the two highest QAH levels, while the lowest densities (5.66%) were found in areas at the lowest QAH levels. Mapping notifications from 2007 to 2016 onto the QAH map showed that in endemic areas, 60% of ASF notifications occurred in domestic pigs, mostly in agricultural landscapes (QAHs 1.75 and 1) containing low-biosecurity domestic pig farms. In the EU, in contrast, 95% of ASF notifications occurred in wild boar, within natural landscapes (QAH 2). These results suggest that the QAH map can be a useful epi-tool for defining risk scenarios and identifying potential travel corridors for ASF. This tool will help inform resource allocation decisions and improve prevention, control and surveillance of ASF and potentially of other diseases affecting swine and wild boar in Eurasia. © 2016 Blackwell Verlag GmbH.

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

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

Britun, Nikolay, E-mail: nikolay.britun@umons.ac.be; Palmucci, Maria; Konstantinidis, Stephanos

2015-04-28

Time-resolved characterization of an Ar-Ti high-power impulse magnetron sputtering discharge has been performed. This paper deals with two-dimensional density mapping in the discharge volume obtained by laser-induced fluorescence imaging. The time-resolved density evolution of Ti neutrals, singly ionized Ti atoms (Ti{sup +}), and Ar metastable atoms (Ar{sup met}) in the area above the sputtered cathode is mapped for the first time in this type of discharges. The energetic characteristics of the discharge species are additionally studied by Doppler-shift laser-induced fluorescence imaging. The questions related to the propagation of both the neutral and ionized discharge particles, as well as to theirmore » spatial density distributions, are discussed.« less

Using Cloud-to-Ground Lightning Climatologies to Initialize Gridded Lightning Threat Forecasts for East Central Florida

NASA Technical Reports Server (NTRS)

Lambert, Winnie; Sharp, David; Spratt, Scott; Volkmer, Matthew

2005-01-01

Each morning, the forecasters at the National Weather Service in Melbourn, FL (NWS MLB) produce an experimental cloud-to-ground (CG) lightning threat index map for their county warning area (CWA) that is posted to their web site (http://www.srh.weather.gov/mlb/ghwo/lightning.shtml) . Given the hazardous nature of lightning in central Florida, especially during the warm season months of May-September, these maps help users factor the threat of lightning, relative to their location, into their daily plans. The maps are color-coded in five levels from Very Low to Extreme, with threat level definitions based on the probability of lightning occurrence and the expected amount of CG activity. On a day in which thunderstorms are expected, there are typically two or more threat levels depicted spatially across the CWA. The locations of relative lightning threat maxima and minima often depend on the position and orientation of the low-level ridge axis, forecast propagation and interaction of sea/lake/outflow boundaries, expected evolution of moisture and stability fields, and other factors that can influence the spatial distribution of thunderstorms over the CWA. The lightning threat index maps are issued for the 24-hour period beginning at 1200 UTC (0700 AM EST) each day with a grid resolution of 5 km x 5 km. Product preparation is performed on the AWIPS Graphical Forecast Editor (GFE), which is the standard NWS platform for graphical editing. Currently, the forecasters create each map manually, starting with a blank map. To improve efficiency of the forecast process, NWS MLB requested that the Applied Meteorology Unit (AMU) create gridded warm season lightning climatologies that could be used as first-guess inputs to initialize lightning threat index maps. The gridded values requested included CG strike densities and frequency of occurrence stratified by synoptic-scale flow regime. The intent is to increase consistency between forecasters while enabling them to focus on the mesoscale detail of the forecast, ultimately benefiting the end-users of the product. Several studies took place at the Florida State University (FSU) and NWS Tallahassee (TAE) for which they created daily flow regimes using Florida 1200 UTC synoptic soundings and CG strike densities from National Lightning Detection Network (NLDN) data. The densities were created on a 2.5 km x 2.5 km grid for every hour of every day during the warm seasons in the years 1989-2004. The grids encompass an area that includes the entire state of Florida and adjacent Atlantic and Gulf of Mexico waters. Personnel at the two organizations provided this data and supporting software for the work performed by the AMU. The densities were first stratified by flow regime, then by time in 1-, 3-, 6-, 12-, and 24-hour increments while maintaining the 2.5 km x 2.5 km grid resolution. A CG frequency of occurrence was calculated for each stratification and grid box by counting the number of days with lightning and dividing by the total number of days in the data set. New CG strike densities were calculated for each stratification and grid box by summing the strike number values over all warm seasons, then normalized by dividing the summed values by the number of lightning days. This makes the densities conditional on whether lightning occurred. The frequency climatology values will be used by forecasters as proxy inputs for lightning prObability, while the density climatology values will be used for CG amount. In addition to the benefits outlined above, these climatologies will provide improved temporal and spatial resolution, expansion of the lightning threat area to include adjacent coastal waters, and potential to extend the forecast to include the day-2 period. This presentation will describe the lightning threat index map, discuss the work done to create the maps initialized with climatological guidance, and show examples of the climatological CG lightning densities and frequencies of occurren based on flow regime.

High-Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge).

PubMed

Zhao, Yuhui; Su, Kai; Wang, Gang; Zhang, Liping; Zhang, Jijun; Li, Junpeng; Guo, Yinshan

2017-07-14

Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny. After quality trimming, 117,896 high-quality 2b-RAD tags were retained, of which 42,279 were polymorphic; of these, 12,951 markers were used for constructing the genetic linkage map. The map contained 17 linkage groups and 3,894 markers, with a total map length of 1,551.97 cM and an average marker interval of 0.40 cM. QTL mapping identified 21 QTLs associated with flavonoid content in 10 linkage groups, which explained 16.30-59.00% of the variance. This is the first high-density linkage map for hawthorn, which will serve as a basis for fine-scale QTL mapping and marker-assisted selection of important traits in hawthorn germplasm and will facilitate chromosome assignment for hawthorn whole-genome assemblies in the future.

High latitude currents in the 0600 to 0900 MLT sector - Observations from Viking and DMSP-F7

NASA Technical Reports Server (NTRS)

Bythrow, P. F.; Potemra, T. A.; Zanetti, L. J.; Erlandson, R. A.; Hardy, D. A.; Rich, F. J.; Acuna, M. H.

1987-01-01

High-resolution magnetic field and charged-particle data acquired on March 25, 1986 by the Viking and DMSP-F7 satellites, as they traversed the dawn sector auroral zone on nearly antiparallel trajectories within 40 min of each oher, are analyzed. Magnetic field measurements by Viking at 0850 MLT and by DMSP at 0630 MLT indicate the presence of a large-scale earthward-directed region 1 Birkeland current and an upward-flowing region 2 current. Both satellites also observed a third Birkeland current adjacent to and poleward of the region 1 system with opposite flow. This poleward system is about 0.5 deg invariant latitude wide and has a current density comparable to the region 1 and 2 systems. The highest-latitude current is identified as region 0. Its charged-particle signatures were used to infer field line mapping to the equatorial plane.

Fundamental quantum noise mapping with tunnelling microscopes tested at surface structures of subatomic lateral size.

PubMed

Herz, Markus; Bouvron, Samuel; Ćavar, Elizabeta; Fonin, Mikhail; Belzig, Wolfgang; Scheer, Elke

2013-10-21

We present a measurement scheme that enables quantitative detection of the shot noise in a scanning tunnelling microscope while scanning the sample. As test objects we study defect structures produced on an iridium single crystal at low temperatures. The defect structures appear in the constant current images as protrusions with curvature radii well below the atomic diameter. The measured power spectral density of the noise is very near to the quantum limit with Fano factor F = 1. While the constant current images show detailed structures expected for tunnelling involving d-atomic orbitals of Ir, we find the current noise to be without pronounced spatial variation as expected for shot noise arising from statistically independent events.

Vector MO magnetometry for mapping microwave currents

NASA Astrophysics Data System (ADS)

Višňovský, Š.; Lišková-Jakubisová, E.; Harward, I.; Celinski, Z.

2018-05-01

Magneto-optic (MO) effects in magnetic multilayers (MML) can be employed in non-invasive 2D mapping of microwave (mw) radiation on the surface of semiconductor chips. A typical sensor configuration consists of Fe nanolayers sandwiched with dielectrics on a thin Si substrate transparent to mw radiation. To extend the observation bandwidth, Δf, up to 100 GHz range the sensor works at ferromagnetic resonance (FMR) frequency in applied magnetic flux density, Bappl. The mw currents excite the precession of magnetization, M, in magnetic nanolayers proportional to their amplitude. The MO component reflected on the sensor surface is proportional to the amplitude of M component, M⊥. The laser source operates at the wavelength of 410 nm. Its plane of incidence is oriented perpendicular to the M⊥ plane. M⊥ oscillates between polar and transverse configurations. A substantial improvement of MO figure of merit takes place in aperiodic MML. More favorable Δf vs. Bappl dependence and MO response can potentially be achieved in MML imbedding hexagonal ferrite or Co nanolayers with in-plane magnetic anisotropy.

Spectral Dependence of Stratified Electrothermal Instability in Tamped Aluminum 6061 with Current in a Skin Layer

NASA Astrophysics Data System (ADS)

Bauer, Bruno; Hutchinson, Trevor; Awe, Thomas

2017-10-01

The stratified electrothermal instability (ETI) was recently observed on the surface of thick aluminum 6061 pulsed with rapidly rising lineal current density (3 ×1015 A m-1s-1) for 70 ns. A transparent 70- μm-thick Parylene-N coating tamped the aluminum expansion and suppressed surface plasma. The evolution of the aluminum surface emission pattern was recorded with time-resolved microscopy (3- μm resolution). The images were converted into a series of blackbody surface-temperature maps. Analysis of these temperature maps provides information on the evolution of temperature fluctuations, as a function of axial wavelength and azimuthal width. Perturbations with axial wavelength longer than 20 μm grow, while those with axial wavelength shorter than 10 μm decay. Comparing the spectral dependence of growth/decay rates with MHD simulations could test the modeling of ETI positive feedback and of damping by thermal conduction. Work supported by Sandia National Laboratories LDRD program, PO 1742766.

A New, Large-scale Map of Interstellar Reddening Derived from H I Emission

NASA Astrophysics Data System (ADS)

Lenz, Daniel; Hensley, Brandon S.; Doré, Olivier

2017-09-01

We present a new map of interstellar reddening, covering the 39% of the sky with low H I column densities ({N}{{H}{{I}}}< 4× {10}20 cm-2 or E(B-V)≈ 45 mmag) at 16\\buildrel{ \\prime}\\over{.} 1 resolution, based on all-sky observations of Galactic H I emission by the HI4PI Survey. In this low-column-density regime, we derive a characteristic value of {N}{{H}{{I}}}/E(B-V)=8.8 × {10}21 {{cm}}2 {{mag}}-1 for gas with | {v}{LSR}| < 90 km s-1 and find no significant reddening associated with gas at higher velocities. We compare our H I-based reddening map with the Schlegel et al. (SFD) reddening map and find them consistent to within a scatter of ≃ 5 mmag. Further, the differences between our map and the SFD map are in excellent agreement with the low-resolution (4\\buildrel{\\circ}\\over{.} 5) corrections to the SFD map derived by Peek and Graves based on observed reddening toward passive galaxies. We therefore argue that our H I-based map provides the most accurate interstellar reddening estimates in the low-column-density regime to date. Our reddening map is made publicly available at doi.org/10.7910/DVN/AFJNWJ.

Improving Weak Lensing Mass Map Reconstructions using Gaussian and Sparsity Priors: Application to DES SV

DOE PAGES

Jeffrey, N.; Abdalla, F. B.; Lahav, O.; ...

2018-05-15

Mapping the underlying density field, including non-visible dark matter, using weak gravitational lensing measurements is now a standard tool in cosmology. Due to its importance to the science results of current and upcoming surveys, the quality of the convergence reconstruction methods should be well understood. We compare three different mass map reconstruction methods: Kaiser-Squires (KS), Wiener filter, and GLIMPSE. KS is a direct inversion method, taking no account of survey masks or noise. The Wiener filter is well motivated for Gaussian density fields in a Bayesian framework. The GLIMPSE method uses sparsity, with the aim of reconstructing non-linearities in themore » density field. We compare these methods with a series of tests on the public Dark Energy Survey (DES) Science Verification (SV) data and on realistic DES simulations. The Wiener filter and GLIMPSE methods offer substantial improvement on the standard smoothed KS with a range of metrics. For both the Wiener filter and GLIMPSE convergence reconstructions we present a 12% improvement in Pearson correlation with the underlying truth from simulations. To compare the mapping methods' abilities to find mass peaks, we measure the difference between peak counts from simulated {\\Lambda}CDM shear catalogues and catalogues with no mass fluctuations. This is a standard data vector when inferring cosmology from peak statistics. The maximum signal-to-noise value of these peak statistic data vectors was increased by a factor of 3.5 for the Wiener filter and by a factor of 9 using GLIMPSE. With simulations we measure the reconstruction of the harmonic phases, showing that the concentration of the phase residuals is improved 17% by GLIMPSE and 18% by the Wiener filter. We show that the correlation between the reconstructions from data and the foreground redMaPPer clusters is increased 18% by the Wiener filter and 32% by GLIMPSE. [Abridged]« less

Improving Weak Lensing Mass Map Reconstructions using Gaussian and Sparsity Priors: Application to DES SV

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

Jeffrey, N.; et al.

2018-01-26

Mapping the underlying density field, including non-visible dark matter, using weak gravitational lensing measurements is now a standard tool in cosmology. Due to its importance to the science results of current and upcoming surveys, the quality of the convergence reconstruction methods should be well understood. We compare three different mass map reconstruction methods: Kaiser-Squires (KS), Wiener filter, and GLIMPSE. KS is a direct inversion method, taking no account of survey masks or noise. The Wiener filter is well motivated for Gaussian density fields in a Bayesian framework. The GLIMPSE method uses sparsity, with the aim of reconstructing non-linearities in themore » density field. We compare these methods with a series of tests on the public Dark Energy Survey (DES) Science Verification (SV) data and on realistic DES simulations. The Wiener filter and GLIMPSE methods offer substantial improvement on the standard smoothed KS with a range of metrics. For both the Wiener filter and GLIMPSE convergence reconstructions we present a 12% improvement in Pearson correlation with the underlying truth from simulations. To compare the mapping methods' abilities to find mass peaks, we measure the difference between peak counts from simulated {\\Lambda}CDM shear catalogues and catalogues with no mass fluctuations. This is a standard data vector when inferring cosmology from peak statistics. The maximum signal-to-noise value of these peak statistic data vectors was increased by a factor of 3.5 for the Wiener filter and by a factor of 9 using GLIMPSE. With simulations we measure the reconstruction of the harmonic phases, showing that the concentration of the phase residuals is improved 17% by GLIMPSE and 18% by the Wiener filter. We show that the correlation between the reconstructions from data and the foreground redMaPPer clusters is increased 18% by the Wiener filter and 32% by GLIMPSE. [Abridged]« less

Improving Weak Lensing Mass Map Reconstructions using Gaussian and Sparsity Priors: Application to DES SV

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

Jeffrey, N.; Abdalla, F. B.; Lahav, O.

Mapping the underlying density field, including non-visible dark matter, using weak gravitational lensing measurements is now a standard tool in cosmology. Due to its importance to the science results of current and upcoming surveys, the quality of the convergence reconstruction methods should be well understood. We compare three different mass map reconstruction methods: Kaiser-Squires (KS), Wiener filter, and GLIMPSE. KS is a direct inversion method, taking no account of survey masks or noise. The Wiener filter is well motivated for Gaussian density fields in a Bayesian framework. The GLIMPSE method uses sparsity, with the aim of reconstructing non-linearities in themore » density field. We compare these methods with a series of tests on the public Dark Energy Survey (DES) Science Verification (SV) data and on realistic DES simulations. The Wiener filter and GLIMPSE methods offer substantial improvement on the standard smoothed KS with a range of metrics. For both the Wiener filter and GLIMPSE convergence reconstructions we present a 12% improvement in Pearson correlation with the underlying truth from simulations. To compare the mapping methods' abilities to find mass peaks, we measure the difference between peak counts from simulated {\\Lambda}CDM shear catalogues and catalogues with no mass fluctuations. This is a standard data vector when inferring cosmology from peak statistics. The maximum signal-to-noise value of these peak statistic data vectors was increased by a factor of 3.5 for the Wiener filter and by a factor of 9 using GLIMPSE. With simulations we measure the reconstruction of the harmonic phases, showing that the concentration of the phase residuals is improved 17% by GLIMPSE and 18% by the Wiener filter. We show that the correlation between the reconstructions from data and the foreground redMaPPer clusters is increased 18% by the Wiener filter and 32% by GLIMPSE. [Abridged]« less

Mapping tree density at a global scale

NASA Astrophysics Data System (ADS)

Crowther, T. W.; Glick, H. B.; Covey, K. R.; Bettigole, C.; Maynard, D. S.; Thomas, S. M.; Smith, J. R.; Hintler, G.; Duguid, M. C.; Amatulli, G.; Tuanmu, M.-N.; Jetz, W.; Salas, C.; Stam, C.; Piotto, D.; Tavani, R.; Green, S.; Bruce, G.; Williams, S. J.; Wiser, S. K.; Huber, M. O.; Hengeveld, G. M.; Nabuurs, G.-J.; Tikhonova, E.; Borchardt, P.; Li, C.-F.; Powrie, L. W.; Fischer, M.; Hemp, A.; Homeier, J.; Cho, P.; Vibrans, A. C.; Umunay, P. M.; Piao, S. L.; Rowe, C. W.; Ashton, M. S.; Crane, P. R.; Bradford, M. A.

2015-09-01

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

Mapping tree density at a global scale.

PubMed

Crowther, T W; Glick, H B; Covey, K R; Bettigole, C; Maynard, D S; Thomas, S M; Smith, J R; Hintler, G; Duguid, M C; Amatulli, G; Tuanmu, M-N; Jetz, W; Salas, C; Stam, C; Piotto, D; Tavani, R; Green, S; Bruce, G; Williams, S J; Wiser, S K; Huber, M O; Hengeveld, G M; Nabuurs, G-J; Tikhonova, E; Borchardt, P; Li, C-F; Powrie, L W; Fischer, M; Hemp, A; Homeier, J; Cho, P; Vibrans, A C; Umunay, P M; Piao, S L; Rowe, C W; Ashton, M S; Crane, P R; Bradford, M A

2015-09-10

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

Use of Total Electron Content data to analyze ionosphere electron density gradients

NASA Astrophysics Data System (ADS)

Nava, B.; Radicella, S. M.; Leitinger, R.; Coisson, P.

In presence of electron density gradients the thin shell approximation for the ionosphere used together with a simple mapping function to convert slant Total Electron Content TEC to vertical TEC could lead to TEC conversion errors Therefore these mapping function errors can be used to identify the effects of the electron density gradients in the ionosphere In the present work high precision GPS derived slant TEC data have been used to investigate the effects of the electron density gradients in the middle and low latitude ionosphere under geomagnetic quiet and disturbed conditions In particular the data corresponding to the geographic area of the American sector for the days 5-7 April 2000 have been used to perform a complete analysis of mapping function errors based on the coinciding pierce point technique The results clearly illustrate the electron density gradient effects according to the locations considered and to the actual levels of disturbance of the ionosphere

Predicting Anthropogenic Noise Contributions to US Waters.

PubMed

Gedamke, Jason; Ferguson, Megan; Harrison, Jolie; Hatch, Leila; Henderson, Laurel; Porter, Michael B; Southall, Brandon L; Van Parijs, Sofie

2016-01-01

To increase understanding of the potential effects of chronic underwater noise in US waters, the National Oceanic and Atmospheric Administration (NOAA) organized two working groups in 2011, collectively called "CetSound," to develop tools to map the density and distribution of cetaceans (CetMap) and predict the contribution of human activities to underwater noise (SoundMap). The SoundMap effort utilized data on density, distribution, acoustic signatures of dominant noise sources, and environmental descriptors to map estimated temporal, spatial, and spectral contributions to background noise. These predicted soundscapes are an initial step toward assessing chronic anthropogenic noise impacts on the ocean's varied acoustic habitats and the animals utilizing them.

Computationally optimized ECoG stimulation with local safety constraints.

PubMed

Guler, Seyhmus; Dannhauer, Moritz; Roig-Solvas, Biel; Gkogkidis, Alexis; Macleod, Rob; Ball, Tonio; Ojemann, Jeffrey G; Brooks, Dana H

2018-06-01

Direct stimulation of the cortical surface is used clinically for cortical mapping and modulation of local activity. Future applications of cortical modulation and brain-computer interfaces may also use cortical stimulation methods. One common method to deliver current is through electrocorticography (ECoG) stimulation in which a dense array of electrodes are placed subdurally or epidurally to stimulate the cortex. However, proximity to cortical tissue limits the amount of current that can be delivered safely. It may be desirable to deliver higher current to a specific local region of interest (ROI) while limiting current to other local areas more stringently than is guaranteed by global safety limits. Two commonly used global safety constraints bound the total injected current and individual electrode currents. However, these two sets of constraints may not be sufficient to prevent high current density locally (hot-spots). In this work, we propose an efficient approach that prevents current density hot-spots in the entire brain while optimizing ECoG stimulus patterns for targeted stimulation. Specifically, we maximize the current along a particular desired directional field in the ROI while respecting three safety constraints: one on the total injected current, one on individual electrode currents, and the third on the local current density magnitude in the brain. This third set of constraints creates a computational barrier due to the huge number of constraints needed to bound the current density at every point in the entire brain. We overcome this barrier by adopting an efficient two-step approach. In the first step, the proposed method identifies the safe brain region, which cannot contain any hot-spots solely based on the global bounds on total injected current and individual electrode currents. In the second step, the proposed algorithm iteratively adjusts the stimulus pattern to arrive at a solution that exhibits no hot-spots in the remaining brain. We report on simulations on a realistic finite element (FE) head model with five anatomical ROIs and two desired directional fields. We also report on the effect of ROI depth and desired directional field on the focality of the stimulation. Finally, we provide an analysis of optimization runtime as a function of different safety and modeling parameters. Our results suggest that optimized stimulus patterns tend to differ from those used in clinical practice. Copyright © 2018 Elsevier Inc. All rights reserved.

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

PubMed

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

2017-01-01

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

Averaged kick maps: less noise, more signal…and probably less bias

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

Pražnikar, Jure; Afonine, Pavel V.; Gunčar, Gregor

2009-09-01

Averaged kick maps are the sum of a series of individual kick maps, where each map is calculated from atomic coordinates modified by random shifts. These maps offer the possibility of an improved and less model-biased map interpretation. Use of reliable density maps is crucial for rapid and successful crystal structure determination. Here, the averaged kick (AK) map approach is investigated, its application is generalized and it is compared with other map-calculation methods. AK maps are the sum of a series of kick maps, where each kick map is calculated from atomic coordinates modified by random shifts. As such, theymore » are a numerical analogue of maximum-likelihood maps. AK maps can be unweighted or maximum-likelihood (σ{sub A}) weighted. Analysis shows that they are comparable and correspond better to the final model than σ{sub A} and simulated-annealing maps. The AK maps were challenged by a difficult structure-validation case, in which they were able to clarify the problematic region in the density without the need for model rebuilding. The conclusion is that AK maps can be useful throughout the entire progress of crystal structure determination, offering the possibility of improved map interpretation.« less

LiDAR observations of an Earth magmatic plumbing system as an analog for Venus and Mars distributed volcanism

NASA Astrophysics Data System (ADS)

Richardson, Jacob; Connor, Charles; Malservisi, Rocco; Bleacher, Jacob; Connor, Laura

2014-05-01

Clusters of tens to thousands of small volcanoes (diameters generally <30 km) are common features on the surface of Mars, Venus, and the Earth. These clusters may be described as distributed-style volcanism. Better characterizing the magmatic plumbing system of these clusters can constrain magma ascent processes as well as the regional magma production budget and heat flux beneath each cluster. Unfortunately, directly observing the plumbing systems of volcano clusters on Mars and Venus eludes our current geologic abilities. Because erosion exposes such systems at the Earth's surface, a better understanding of magmatic processes and migration can be achieved via field analysis. The terrestrial plumbing system of an eroded volcanic field may be a valuable planetary analog for Venus and Mars clusters. The magmatic plumbing system of a Pliocene-aged monogenetic volcanic field, emplaced at 0.8 km depth, is currently exposed as a sill and dike swarm in the San Rafael Desert of Central Utah, USA. The mafic bodies in this region intruded into Mesozoic sedimentary units and now make up the most erosion resistant units as sills, dikes, and plug-like conduits. Light Detection and Ranging (LiDAR) can identify volcanic units (sills, dikes, and conduits) at high resolution, both geomorphologically and with near infrared return intensity values. Two Terrestrial LiDAR Surveys and an Airborne LiDAR Survey have been carried out over the San Rafael volcanic swarm, producing a three dimensional point cloud over approximately 36 sq. km. From the point clouds of these surveys, 1-meter DEMs are produced and volcanic intrusions have been mapped. Here we present reconstructions of the volcanic instrusions of the San Rafael Swarm. We create this reconstruction by extrapolating mapped intrustions from the LiDAR surveys into a 3D space around the current surface. We compare the estimated intrusive volume to the estimated conduit density and estimates of extrusive volume at volcano clusters of similar density. The extrapolated reconstruction and conduit mapping provide a first-order estimate of the final intrustive/extrusive volume ratio for the now eroded volcanic field. Earth, Venus and Mars clusters are compared using Kernel Density Estimation (KDE) , which objectively compares cluster area, complexity, and vent density per sq. km. We show that Martian clusters are less dense than Venus clusters, which in turn are less dense than those on Earth. KDE and previous models of intrusive morphology for Mars and Venus are here used to calibrate the San Rafael plumbing system model to clusters on the two planets. The results from the calibrated Mars and Venus plumbing system models can be compared to previous estimates of magma budget and intrusive/extrusive ratios on Venus and Mars.

Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix.

PubMed

Zeil, Stephanie; Kovacs, Julio; Wriggers, Willy; He, Jing

2017-01-01

Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4-7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map-model pairs.

Frequency spectra from current vs. magnetic flux density measurements for mobile phones and other electrical appliances.

PubMed

Straume, Aksel; Johnsson, Anders; Oftedal, Gunnhild; Wilén, Jonna

2007-10-01

The frequency spectra of electromagnetic fields have to be determined to evaluate human exposure in accordance to ICNIRP guidelines. In the literature, comparisons with magnetic field guidelines have been performed by using the frequency distribution of the current drawn from the battery. In the present study we compared the frequency spectrum in the range 217 Hz to 2.4 kHz of the magnetic flux density measured near the surface of a mobile phone with the frequency spectrum of the supply current. By using the multiple frequency rule, recommended in the ICNIRP guidelines, we estimated the magnetic field exposure in the two cases. Similar measurements and estimations were done for an electric drill, a hair dryer, and a fluorescent desk lamp. All the devices have a basic frequency of 50 Hz, and the frequency spectra were evaluated up to 550 Hz. We also mapped the magnetic field in 3D around three mobile phones. The frequency distributions obtained from the two measurement methods are not equal. The frequency content of the current leads to an overestimation of the magnetic field exposure by a factor up to 2.2 for the mobile phone. For the drill, the hair dryer, and the fluorescent lamp, the supply current signal underestimated the exposure by a factor up to 2.3. In conclusion, an accurate exposure evaluation requires the magnetic flux density spectrum of the device to be measured directly. There was no indication that the devices studied would exceed the reference levels at the working distances normally used.

Psychogenic seizures and frontal disconnection: EEG synchronisation study.

PubMed

Knyazeva, Maria G; Jalili, Mahdi; Frackowiak, Richard S; Rossetti, Andrea O

2011-05-01

Psychogenic non-epileptic seizures (PNES) are paroxysmal events that, in contrast to epileptic seizures, are related to psychological causes without the presence of epileptiform EEG changes. Recent models suggest a multifactorial basis for PNES. A potentially paramount, but currently poorly understood factor is the interplay between psychiatric features and a specific vulnerability of the brain leading to a clinical picture that resembles epilepsy. Hypothesising that functional cerebral network abnormalities may predispose to the clinical phenotype, the authors undertook a characterisation of the functional connectivity in PNES patients. The authors analysed the whole-head surface topography of multivariate phase synchronisation (MPS) in interictal high-density EEG of 13 PNES patients as compared with 13 age- and sex-matched controls. MPS mapping reduces the wealth of dynamic data obtained from high-density EEG to easily readable synchronisation maps, which provide an unbiased overview of any changes in functional connectivity associated with distributed cortical abnormalities. The authors computed MPS maps for both Laplacian and common-average-reference EEGs. In a between-group comparison, only patchy, non-uniform changes in MPS survived conservative statistical testing. However, against the background of these unimpressive group results, the authors found widespread inverse correlations between individual PNES frequency and MPS within the prefrontal and parietal cortices. PNES appears to be associated with decreased prefrontal and parietal synchronisation, possibly reflecting dysfunction of networks within these regions.

Surface Snow Density of East Antarctica Derived from In-Situ Observations

NASA Astrophysics Data System (ADS)

Tian, Y.; Zhang, S.; Du, W.; Chen, J.; Xie, H.; Tong, X.; Li, R.

2018-04-01

Models based on physical principles or semi-empirical parameterizations have used to compute the firn density, which is essential for the study of surface processes in the Antarctic ice sheet. However, parameterization of surface snow density is often challenged by the description of detailed local characterization. In this study we propose to generate a surface density map for East Antarctica from all the filed observations that are available. Considering that the observations are non-uniformly distributed around East Antarctica, obtained by different methods, and temporally inhomogeneous, the field observations are used to establish an initial density map with a grid size of 30 × 30 km2 in which the observations are averaged at a temporal scale of five years. We then construct an observation matrix with its columns as the map grids and rows as the temporal scale. If a site has an unknown density value for a period, we will set it to 0 in the matrix. In order to construct the main spatial and temple information of surface snow density matrix we adopt Empirical Orthogonal Function (EOF) method to decompose the observation matrix and only take first several lower-order modes, because these modes already contain most information of the observation matrix. However, there are a lot of zeros in the matrix and we solve it by using matrix completion algorithm, and then we derive the time series of surface snow density at each observation site. Finally, we can obtain the surface snow density by multiplying the modes interpolated by kriging with the corresponding amplitude of the modes. Comparative analysis have done between our surface snow density map and model results. The above details will be introduced in the paper.

The effect of respiratory induced density variations on non-TOF PET quantitation in the lung.

PubMed

Holman, Beverley F; Cuplov, Vesna; Hutton, Brian F; Groves, Ashley M; Thielemans, Kris

2016-04-21

Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant (18)F-FDG and (18)F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

The effect of respiratory induced density variations on non-TOF PET quantitation in the lung

NASA Astrophysics Data System (ADS)

Holman, Beverley F.; Cuplov, Vesna; Hutton, Brian F.; Groves, Ashley M.; Thielemans, Kris

2016-04-01

Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant 18F-FDG and 18F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

Critic: a new program for the topological analysis of solid-state electron densities

NASA Astrophysics Data System (ADS)

Otero-de-la-Roza, A.; Blanco, M. A.; Pendás, A. Martín; Luaña, Víctor

2009-01-01

In this paper we introduce CRITIC, a new program for the topological analysis of the electron densities of crystalline solids. Two different versions of the code are provided, one adapted to the LAPW (Linear Augmented Plane Wave) density calculated by the WIEN2K package and the other to the ab initio Perturbed Ion ( aiPI) density calculated with the PI7 code. Using the converged ground state densities, CRITIC can locate their critical points, determine atomic basins and integrate properties within them, and generate several graphical representations which include topological atomic basins and primary bundles, contour maps of ρ and ∇ρ, vector maps of ∇ρ, chemical graphs, etc. Program summaryProgram title: CRITIC Catalogue identifier: AECB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL, version 3 No. of lines in distributed program, including test data, etc.: 1 206 843 No. of bytes in distributed program, including test data, etc.: 12 648 065 Distribution format: tar.gz Programming language: FORTRAN 77 and 90 Computer: Any computer capable of compiling Fortran Operating system: Unix, GNU/Linux Classification: 7.3 Nature of problem: Topological analysis of the electron density in periodic solids. Solution method: The automatic localization of the electron density critical points is based on a recursive partitioning of the Wigner-Seitz cell into tetrahedra followed by a Newton search from significant points on each tetrahedra. Plotting of and integration on the atomic basins is currently based on a new implementation of Keith's promega algorithm. Running time: Variable, depending on the task. From seconds to a few minutes for the localization of critical points. Hours to days for the determination of the atomic basins shape and properties. Times correspond to a typical 2007 PC.

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

PubMed Central

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

2004-01-01

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

Improving Weak Lensing Mass Map Reconstructions using Gaussian and Sparsity Priors: Application to DES SV

NASA Astrophysics Data System (ADS)

Jeffrey, N.; Abdalla, F. B.; Lahav, O.; Lanusse, F.; Starck, J.-L.; Leonard, A.; Kirk, D.; Chang, C.; Baxter, E.; Kacprzak, T.; Seitz, S.; Vikram, V.; Whiteway, L.; Abbott, T. M. C.; Allam, S.; Avila, S.; Bertin, E.; Brooks, D.; Rosell, A. Carnero; Kind, M. Carrasco; Carretero, J.; Castander, F. J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; Davis, C.; De Vicente, J.; Desai, S.; Doel, P.; Eifler, T. F.; Evrard, A. E.; Flaugher, B.; Fosalba, P.; Frieman, J.; García-Bellido, J.; Gerdes, D. W.; Gruen, D.; Gruendl, R. A.; Gschwend, J.; Gutierrez, G.; Hartley, W. G.; Honscheid, K.; Hoyle, B.; James, D. J.; Jarvis, M.; Kuehn, K.; Lima, M.; Lin, H.; March, M.; Melchior, P.; Menanteau, F.; Miquel, R.; Plazas, A. A.; Reil, K.; Roodman, A.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, M.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Walker, A. R.

2018-05-01

Mapping the underlying density field, including non-visible dark matter, using weak gravitational lensing measurements is now a standard tool in cosmology. Due to its importance to the science results of current and upcoming surveys, the quality of the convergence reconstruction methods should be well understood. We compare three methods: Kaiser-Squires (KS), Wiener filter, and GLIMPSE. KS is a direct inversion, not accounting for survey masks or noise. The Wiener filter is well-motivated for Gaussian density fields in a Bayesian framework. GLIMPSE uses sparsity, aiming to reconstruct non-linearities in the density field. We compare these methods with several tests using public Dark Energy Survey (DES) Science Verification (SV) data and realistic DES simulations. The Wiener filter and GLIMPSE offer substantial improvements over smoothed KS with a range of metrics. Both the Wiener filter and GLIMPSE convergence reconstructions show a 12% improvement in Pearson correlation with the underlying truth from simulations. To compare the mapping methods' abilities to find mass peaks, we measure the difference between peak counts from simulated ΛCDM shear catalogues and catalogues with no mass fluctuations (a standard data vector when inferring cosmology from peak statistics); the maximum signal-to-noise of these peak statistics is increased by a factor of 3.5 for the Wiener filter and 9 for GLIMPSE. With simulations we measure the reconstruction of the harmonic phases; the phase residuals' concentration is improved 17% by GLIMPSE and 18% by the Wiener filter. The correlation between reconstructions from data and foreground redMaPPer clusters is increased 18% by the Wiener filter and 32% by GLIMPSE.

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

PubMed

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

2016-01-01

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

Mineral density volume gradients in normal and diseased human tissues

DOE PAGES

Djomehri, Sabra I.; Candell, Susan; Case, Thomas; ...

2015-04-09

Clinical computed tomography provides a single mineral density (MD) value for heterogeneous calcified tissues containing early and late stage pathologic formations. The novel aspect of this study is that, it extends current quantitative methods of mapping mineral density gradients to three dimensions, discretizes early and late mineralized stages, identifies elemental distribution in discretized volumes, and correlates measured MD with respective calcium (Ca) to phosphorus (P) and Ca to zinc (Zn) elemental ratios. To accomplish this, MD variations identified using polychromatic radiation from a high resolution micro-computed tomography (micro-CT) benchtop unit were correlated with elemental mapping obtained from a microprobe X-raymore » fluorescence (XRF) using synchrotron monochromatic radiation. Digital segmentation of tomograms from normal and diseased tissues (N=5 per group; 40-60 year old males) contained significant mineral density variations (enamel: 2820-3095mg/cc, bone: 570-1415mg/cc, cementum: 1240-1340mg/cc, dentin: 1480-1590mg/cc, cementum affected by periodontitis: 1100-1220mg/cc, hypomineralized carious dentin: 345-1450mg/cc, hypermineralized carious dentin: 1815-2740mg/cc, and dental calculus: 1290-1770mg/cc). A plausible linear correlation between segmented MD volumes and elemental ratios within these volumes was established, and Ca/P ratios for dentin (1.49), hypomineralized dentin (0.32-0.46), cementum (1.51), and bone (1.68) were observed. Furthermore, varying Ca/Zn ratios were distinguished in adapted compared to normal tissues, such as in bone (855-2765) and in cementum (595-990), highlighting Zn as an influential element in prompting observed adaptive properties. Hence, results provide insights on mineral density gradients with elemental concentrations and elemental footprints that in turn could aid in elucidating mechanistic processes for pathologic formations.« less

Mineral density volume gradients in normal and diseased human tissues

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

Djomehri, Sabra I.; Candell, Susan; Case, Thomas

Clinical computed tomography provides a single mineral density (MD) value for heterogeneous calcified tissues containing early and late stage pathologic formations. The novel aspect of this study is that, it extends current quantitative methods of mapping mineral density gradients to three dimensions, discretizes early and late mineralized stages, identifies elemental distribution in discretized volumes, and correlates measured MD with respective calcium (Ca) to phosphorus (P) and Ca to zinc (Zn) elemental ratios. To accomplish this, MD variations identified using polychromatic radiation from a high resolution micro-computed tomography (micro-CT) benchtop unit were correlated with elemental mapping obtained from a microprobe X-raymore » fluorescence (XRF) using synchrotron monochromatic radiation. Digital segmentation of tomograms from normal and diseased tissues (N=5 per group; 40-60 year old males) contained significant mineral density variations (enamel: 2820-3095mg/cc, bone: 570-1415mg/cc, cementum: 1240-1340mg/cc, dentin: 1480-1590mg/cc, cementum affected by periodontitis: 1100-1220mg/cc, hypomineralized carious dentin: 345-1450mg/cc, hypermineralized carious dentin: 1815-2740mg/cc, and dental calculus: 1290-1770mg/cc). A plausible linear correlation between segmented MD volumes and elemental ratios within these volumes was established, and Ca/P ratios for dentin (1.49), hypomineralized dentin (0.32-0.46), cementum (1.51), and bone (1.68) were observed. Furthermore, varying Ca/Zn ratios were distinguished in adapted compared to normal tissues, such as in bone (855-2765) and in cementum (595-990), highlighting Zn as an influential element in prompting observed adaptive properties. Hence, results provide insights on mineral density gradients with elemental concentrations and elemental footprints that in turn could aid in elucidating mechanistic processes for pathologic formations.« less

The Next Generation of Mars-GRAM and Its Role in the Autonomous Aerobraking Development Plan

NASA Technical Reports Server (NTRS)

Justh, Hilary L.; Justus, Carl G.; Ramey, Holly S.

2011-01-01

The Mars Global Reference Atmospheric Model (Mars-GRAM) is an engineering-level atmospheric model widely used for diverse mission applications. Mars-GRAM 2010 is currently being used to develop the onboard atmospheric density estimator that is part of the Autonomous Aerobraking Development Plan. In previous versions, Mars-GRAM was less than realistic when used for sensitivity studies for Thermal Emission Spectrometer (TES) MapYear=0 and large optical depth values, such as tau=3. A comparison analysis has been completed between Mars-GRAM, TES and data from the Planetary Data System (PDS) resulting in updated coefficients for the functions relating density, latitude, and longitude of the sun. The adjustment factors are expressed as a function of height (z), Latitude (Lat) and areocentric solar longitude (Ls). The latest release of Mars-GRAM 2010 includes these adjustment factors that alter the in-put data from MGCM and MTGCM for the Mapping Year 0 (user-controlled dust) case. The greatest adjustment occurs at large optical depths such as tau greater than 1. The addition of the adjustment factors has led to better correspondence to TES Limb data from 0-60 km as well as better agreement with MGS, ODY and MRO data at approximately 90-135 km. Improved simulations utilizing Mars-GRAM 2010 are vital to developing the onboard atmospheric density estimator for the Autonomous Aerobraking Development Plan. Mars-GRAM 2010 was not the only planetary GRAM utilized during phase 1 of this plan; Titan-GRAM and Venus-GRAM were used to generate density data sets for Aerobraking Design Reference Missions. These data sets included altitude profiles (both vertical and along a trajectory), GRAM perturbations (tides, gravity waves, etc.) and provided density and scale height values for analysis by other Autonomous Aero-braking team members.

Mineral density volume gradients in normal and diseased human tissues.

PubMed

Djomehri, Sabra I; Candell, Susan; Case, Thomas; Browning, Alyssa; Marshall, Grayson W; Yun, Wenbing; Lau, S H; Webb, Samuel; Ho, Sunita P

2015-01-01

Clinical computed tomography provides a single mineral density (MD) value for heterogeneous calcified tissues containing early and late stage pathologic formations. The novel aspect of this study is that, it extends current quantitative methods of mapping mineral density gradients to three dimensions, discretizes early and late mineralized stages, identifies elemental distribution in discretized volumes, and correlates measured MD with respective calcium (Ca) to phosphorus (P) and Ca to zinc (Zn) elemental ratios. To accomplish this, MD variations identified using polychromatic radiation from a high resolution micro-computed tomography (micro-CT) benchtop unit were correlated with elemental mapping obtained from a microprobe X-ray fluorescence (XRF) using synchrotron monochromatic radiation. Digital segmentation of tomograms from normal and diseased tissues (N=5 per group; 40-60 year old males) contained significant mineral density variations (enamel: 2820-3095 mg/cc, bone: 570-1415 mg/cc, cementum: 1240-1340 mg/cc, dentin: 1480-1590 mg/cc, cementum affected by periodontitis: 1100-1220 mg/cc, hypomineralized carious dentin: 345-1450 mg/cc, hypermineralized carious dentin: 1815-2740 mg/cc, and dental calculus: 1290-1770 mg/cc). A plausible linear correlation between segmented MD volumes and elemental ratios within these volumes was established, and Ca/P ratios for dentin (1.49), hypomineralized dentin (0.32-0.46), cementum (1.51), and bone (1.68) were observed. Furthermore, varying Ca/Zn ratios were distinguished in adapted compared to normal tissues, such as in bone (855-2765) and in cementum (595-990), highlighting Zn as an influential element in prompting observed adaptive properties. Hence, results provide insights on mineral density gradients with elemental concentrations and elemental footprints that in turn could aid in elucidating mechanistic processes for pathologic formations.

Extrapolating cetacean densities to quantitatively assess human impacts on populations in the high seas.

PubMed

Mannocci, Laura; Roberts, Jason J; Miller, David L; Halpin, Patrick N

2017-06-01

As human activities expand beyond national jurisdictions to the high seas, there is an increasing need to consider anthropogenic impacts to species inhabiting these waters. The current scarcity of scientific observations of cetaceans in the high seas impedes the assessment of population-level impacts of these activities. We developed plausible density estimates to facilitate a quantitative assessment of anthropogenic impacts on cetacean populations in these waters. Our study region extended from a well-surveyed region within the U.S. Exclusive Economic Zone into a large region of the western North Atlantic sparsely surveyed for cetaceans. We modeled densities of 15 cetacean taxa with available line transect survey data and habitat covariates and extrapolated predictions to sparsely surveyed regions. We formulated models to reduce the extent of extrapolation beyond covariate ranges, and constrained them to model simple and generalizable relationships. To evaluate confidence in the predictions, we mapped where predictions were made outside sampled covariate ranges, examined alternate models, and compared predicted densities with maps of sightings from sources that could not be integrated into our models. Confidence levels in model results depended on the taxon and geographic area and highlighted the need for additional surveying in environmentally distinct areas. With application of necessary caution, our density estimates can inform management needs in the high seas, such as the quantification of potential cetacean interactions with military training exercises, shipping, fisheries, and deep-sea mining and be used to delineate areas of special biological significance in international waters. Our approach is generally applicable to other marine taxa and geographic regions for which management will be implemented but data are sparse. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Mineral Density Volume Gradients in Normal and Diseased Human Tissues

PubMed Central

Djomehri, Sabra I.; Candell, Susan; Case, Thomas; Browning, Alyssa; Marshall, Grayson W.; Yun, Wenbing; Lau, S. H.; Webb, Samuel; Ho, Sunita P.

2015-01-01

Clinical computed tomography provides a single mineral density (MD) value for heterogeneous calcified tissues containing early and late stage pathologic formations. The novel aspect of this study is that, it extends current quantitative methods of mapping mineral density gradients to three dimensions, discretizes early and late mineralized stages, identifies elemental distribution in discretized volumes, and correlates measured MD with respective calcium (Ca) to phosphorus (P) and Ca to zinc (Zn) elemental ratios. To accomplish this, MD variations identified using polychromatic radiation from a high resolution micro-computed tomography (micro-CT) benchtop unit were correlated with elemental mapping obtained from a microprobe X-ray fluorescence (XRF) using synchrotron monochromatic radiation. Digital segmentation of tomograms from normal and diseased tissues (N=5 per group; 40-60 year old males) contained significant mineral density variations (enamel: 2820-3095mg/cc, bone: 570-1415mg/cc, cementum: 1240-1340mg/cc, dentin: 1480-1590mg/cc, cementum affected by periodontitis: 1100-1220mg/cc, hypomineralized carious dentin: 345-1450mg/cc, hypermineralized carious dentin: 1815-2740mg/cc, and dental calculus: 1290-1770mg/cc). A plausible linear correlation between segmented MD volumes and elemental ratios within these volumes was established, and Ca/P ratios for dentin (1.49), hypomineralized dentin (0.32-0.46), cementum (1.51), and bone (1.68) were observed. Furthermore, varying Ca/Zn ratios were distinguished in adapted compared to normal tissues, such as in bone (855-2765) and in cementum (595-990), highlighting Zn as an influential element in prompting observed adaptive properties. Hence, results provide insights on mineral density gradients with elemental concentrations and elemental footprints that in turn could aid in elucidating mechanistic processes for pathologic formations. PMID:25856386

Middle Atmosphere Program. Handbook for MAP, volume 19

NASA Technical Reports Server (NTRS)

Goldberg, R. A. (Editor)

1986-01-01

This MAP handbook is concerned with rocket techniques and instrumentation as they are currently employed in the middle atmosphere. It is composed of nine chapters, written by experts on rocket experiments. The emphasis is on measurement techniques rather than results, although results are incorporated wherever they provide examples which illustrate the measurement features. The chapters first cover techniques relating to measurements of neutral dynamics and chemistry, then measurements of the various intermittent and excessive radiation sources which effect the middle atmospheric environment, and finally measurements of the plasma environment including electric fields. The weighting toward plasma related parameters is not accidental, but reflects both the historical headstart given by early development of radio wave and probe techniques to measure electron density, and by the relatively limited number of techniques available for neutral atmospheric measurements.

Schlieren Cinematography of Current Driven Plasma Jet Dynamics

NASA Astrophysics Data System (ADS)

Loebner, Keith; Underwood, Thomas; Cappelli, Mark

2016-10-01

Schlieren cinematography of a pulsed plasma deflagration jet is presented and analyzed. An ultra-high frame rate CMOS camera coupled to a Z-type laser Schlieren apparatus is used to obtain flow-field refractometry data for the continuous flow Z-pinch formed within the plasma deflagration jet. The 10 MHz frame rate for 256 consecutive frames provides high temporal resolution, enabling turbulent fluctuations and plasma instabilities to be visualized over the course of a single pulse (20 μs). The Schlieren signal is radiometrically calibrated to obtain a two dimensional mapping of the refraction angle of the axisymmetric pinch plasma, and this mapping is then Abel inverted to derive the plasma density distribution as a function radius, axial coordinate, and time. Analyses of previously unknown discharge characteristics and comparisons with prior work are discussed.

Mapping the universe.

PubMed

Geller, M J; Huchra, J P

1989-11-17

Maps of the galaxy distribution in the nearby universe reveal large coherent structures. The extent of the largest features is limited only by the size of the survey. Voids with a density typically 20 percent of the mean and with diameters of 5000 km s(-1) are present in every survey large enough to contain them. Many galaxies lie in thin sheet-like structures. The largest sheet detected so far is the "Great Wall" with a minimum extent of 60 h(-1) Mpc x 170 h(-1) Mpc, where h is the Hubble constant in units of 100 km s(-1) Mpc(-1). The frequent occurrence of these structures is one of several serious challenges to our current understanding of the origin and evolution of the large-scale distribution of matter in the universe.

Utilizing field-aligned current profiles derived from Swarm to estimate the peak emission height of 630 nm auroral arcs: a comparison of methods and discussion of associated error estimates in the ASI data.

NASA Astrophysics Data System (ADS)

Gillies, D. M.; Knudsen, D. J.; Donovan, E.; Jackel, B. J.; Gillies, R.; Spanswick, E.

2017-12-01

We compare field-aligned currents (FACs) measured by the Swarm constellation of satellites with the location of red-line (630 nm) auroral arcs observed by all-sky imagers (ASIs) to derive a characteristic emission height for the optical emissions. In our 10 events we find that an altitude of 200 km applied to the ASI maps gives optimal agreement between the two observations. We also compare the new FAC method against the traditional triangulation method using pairs of all-sky imagers (ASIs), and against electron density profiles obtained from the Resolute Bay Incoherent Scatter Radar-Canadian radar (RISR-C), both of which are consistent with a characteristic emission height of 200 km. We also present the spatial error associated with georeferencing REdline Geospace Observatory (REGO) and THEMIS all-sky imagers (ASIs) and how it applies to altitude projections of the mapped image. Utilizing this error we validate the estimated altitude of redline aurora using two methods: triangulation between ASIs and field-aligned current profiles derived from magnetometers on-board the Swarm satellites.

Data services providing by the Ukrainian NODC (MHI NASU)

NASA Astrophysics Data System (ADS)

Eremeev, V.; Godin, E.; Khaliulin, A.; Ingerov, A.; Zhuk, E.

2009-04-01

At modern stage of the World Ocean study information support of investigation based on ad-vanced computer technologies becomes of particular importance. These abstracts are devoted to presentation of several data services developed in the Ukrainian NODC on the base of the Ma-rine Environmental and Information Technologies Department of MHI NASU. The Data Quality Control Service Using experience of international collaboration in the field of data collection and quality check we have developed the quality control (QC) software providing both preliminary(automatic) and expert(manual) data quality check procedures. The current version of the QC software works for the Mediterranean and Black seas and includes the climatic arrays for hydrological and few hydrochemical parameters based on such products as MEDAR/MEDATLAS II, Physical Oceanography of the Black Sea and Climatic Atlas of Oxygen and Hydrogen Sulfide in the Black sea. The data quality check procedure includes metadata control and hydrological and hydrochemical data control. Metadata control provides checking of duplicate cruises and pro-files, date and chronology, ship velocity, station location, sea depth and observation depth. Data QC procedure includes climatic (or range for parameters with small number of observations) data QC, density inversion check for hydrological data and searching for spikes. Using of cli-matic fields and profiles prepared by regional oceanography experts leads to more reliable results of data quality check procedure. The Data Access Services The Ukrainian NODC provides two products for data access - on-line software and data access module for the MHI NASU local net. This software allows select-ing data on rectangle area, on date, on months, on cruises. The result of query is metadata which are presented in the table and the visual presentation of stations on the map. It is possible to see both metadata and data. For this purpose it is necessary to select station in the table of metadata or on the map. There is also an opportunity to export data in ODV format. The product is avail-able on http://www.ocean.nodc.org.ua/DataAccess.php The local net version provides access to the oceanological database of the MHI NASU. The cur-rent version allows selecting data by spatial and temporal limits, depth, values of parameters, quality flags and works for the Mediterranean and Black seas. It provides visualization of meta-data and data, statistics of data selection, data export into several data formats. The Operational Data Management Services The collaborators of the MHI Experimental Branch developed a system of obtaining information on water pressure and temperature, as well as on atmospheric pressure. Sea level observations are also conducted. The obtained data are transferred online. The interface for operation data access was developed. It allows to select parameters (sea level, water temperature, atmospheric pressure, wind and wa-ter pressure) and time interval to see parameter graphics. The product is available on http://www.ocean.nodc.org.ua/Katsively.php . The Climatic products The current version of the Climatic Atlas includes maps on such pa-rameters as temperature, salinity, density, heat storage, dynamic heights, upper boundary of hy-drogen sulfide and lower boundary of oxygen for the Black sea basin. Maps for temperature, sa-linity, density were calculated on 19 standard depths and averaged monthly for depths 0 - 300 m and annually for lower depth values. The climatic maps of upper boundary of hydrogen sulfide and lower boundary of oxygen were averaged by decades from 20 till 90 of the XX century and by seasons. Two versions of climatic atlas viewer - on-line and desktop for presentation of the climatic maps were developed. They provide similar functions of selection and viewing maps by parameter, month and depth and saving maps in various formats. On-line version of atlas is available on http://www.ocean.nodc.org.ua/Main_Atlas.php .

Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

PubMed Central

Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

2014-01-01

For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information. PMID:25914583

Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench).

PubMed

Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

2014-12-01

For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information.

Global patterns of current and future road infrastructure

NASA Astrophysics Data System (ADS)

Meijer, Johan R.; Huijbregts, Mark A. J.; Schotten, Kees C. G. J.; Schipper, Aafke M.

2018-06-01

Georeferenced information on road infrastructure is essential for spatial planning, socio-economic assessments and environmental impact analyses. Yet current global road maps are typically outdated or characterized by spatial bias in coverage. In the Global Roads Inventory Project we gathered, harmonized and integrated nearly 60 geospatial datasets on road infrastructure into a global roads dataset. The resulting dataset covers 222 countries and includes over 21 million km of roads, which is two to three times the total length in the currently best available country-based global roads datasets. We then related total road length per country to country area, population density, GDP and OECD membership, resulting in a regression model with adjusted R 2 of 0.90, and found that that the highest road densities are associated with densely populated and wealthier countries. Applying our regression model to future population densities and GDP estimates from the Shared Socioeconomic Pathway (SSP) scenarios, we obtained a tentative estimate of 3.0–4.7 million km additional road length for the year 2050. Large increases in road length were projected for developing nations in some of the world’s last remaining wilderness areas, such as the Amazon, the Congo basin and New Guinea. This highlights the need for accurate spatial road datasets to underpin strategic spatial planning in order to reduce the impacts of roads in remaining pristine ecosystems.

Observation of sand waves in the Taiwan Banks using HJ-1A/1B sun glitter imagery

NASA Astrophysics Data System (ADS)

Zhang, Hua-guo; Lou, Xiu-lin; Shi, Ai-qin; He, Xie-kai; Guan, Wei-bing; Li, Dong-ling

2014-01-01

This study focuses on the large sand waves in the Taiwan Banks. Our goals are to observe the sand waves as completely as possible, to obtain their direction, wavelength, density, and ridge length, to analyze their spatial distributions, and to understand the effects of the current field and water depth on the sand waves. This study demonstrates the possibility of using HJ-1A/1B sun glitter imagery with a large swath width and rapid coverage in studying sand waves. Six cloud-free HJ-1A/1B optical images with sun glitter signals received during 2009 to 2011 were processed. The sand waves were mapped based on their features in the images; their direction, wavelength, density, and ridge length were measured and analyzed. We identified 4604 sand waves distributed in an area of 16,400 km2. The distributions of sand waves and their characteristics were analyzed, and the differences of sand waves between the northwestern subregion and the southeastern subregion are reported. Further analysis and discussion of the relationships between spatial distribution of the sand waves and both the tidal current field from a numerical simulation and water depth led to some interesting conclusions. The current field determines the orientation of the sand wave, while the hydrodynamic conditions and water depth influence the shape, size, and density of sand waves to a certain degree.

Mapping of trap densities and hotspots in pentacene thin-film transistors by frequency-resolved scanning photoresponse microscopy.

PubMed

Westermeier, Christian; Fiebig, Matthias; Nickel, Bert

2013-10-25

Frequency-resolved scanning photoresponse microscopy of pentacene thin-film transistors is reported. The photoresponse pattern maps the in-plane distribution of trap states which is superimposed by the level of trap filling adjusted by the gate voltage of the transistor. Local hotspots in the photoresponse map thus indicate areas of high trap densities within the pentacene thin film. © 2013 WILEY-VCH Verlag GmbH 8 Co. KGaA, Weinheim.

Genetic dissection of seed oil and protein content and identification of networks associated with oil content in Brassica napus.

PubMed

Chao, Hongbo; Wang, Hao; Wang, Xiaodong; Guo, Liangxing; Gu, Jianwei; Zhao, Weiguo; Li, Baojun; Chen, Dengyan; Raboanatahiry, Nadia; Li, Maoteng

2017-04-10

High-density linkage maps can improve the precision of QTL localization. A high-density SNP-based linkage map containing 3207 markers covering 3072.7 cM of the Brassica napus genome was constructed in the KenC-8 × N53-2 (KNDH) population. A total of 67 and 38 QTLs for seed oil and protein content were identified with an average confidence interval of 5.26 and 4.38 cM, which could explain up to 22.24% and 27.48% of the phenotypic variation, respectively. Thirty-eight associated genomic regions from BSA overlapped with and/or narrowed the SOC-QTLs, further confirming the QTL mapping results based on the high-density linkage map. Potential candidates related to acyl-lipid and seed storage underlying SOC and SPC, respectively, were identified and analyzed, among which six were checked and showed expression differences between the two parents during different embryonic developmental periods. A large primary carbohydrate pathway based on potential candidates underlying SOC- and SPC-QTLs, and interaction networks based on potential candidates underlying SOC-QTLs, was constructed to dissect the complex mechanism based on metabolic and gene regulatory features, respectively. Accurate QTL mapping and potential candidates identified based on high-density linkage map and BSA analyses provide new insights into the complex genetic mechanism of oil and protein accumulation in the seeds of rapeseed.

Electrophysiological mapping of the accessory olfactory bulb of the rabbit (Oryctolagus cuniculus).

PubMed

van Groen, T; Ruardy, L; da Silva, F H

1986-07-01

Field potentials elicited by electrical stimulation of the vomeronasal nerve were measured in the accessory olfactory bulb of the rabbit. Maps were made of the distribution of surface field potentials and of the corresponding depth profiles. The surface maps followed closely the contours of the accessory olfactory bulb: at the frontal border the field potential tended to zero and at the center of the structure the field potential attained a maximum. Depth profiles of the field potentials through the accessory olfactory bulb presented a surface-negative wave and, in depth, a positive wave. The polarity reversal occurred at the deep part of the granule cell layer. The zero equipotential line followed closely the curvature of the granule cell layer. Current source density analysis of the depth profiles revealed a main sink at the external plexiform and granule cell layers. This indicates that the main activity in the accessory olfactory bulb is generated by the synapses between the mitral cells and the granule cells as is found in the main olfactory bulb.

Some Comments on Topological Approaches to the π-Electron Currents in Conjugated Systems.

PubMed

Dickens, Timothy K; Gomes, José A N F; Mallion, Roger B

2011-11-08

Within the past two years, three sets of independent authors (Mandado, Ciesielski et al., and Randić) have proposed methods in which π-electron currents in conjugated systems are estimated by invoking the concept of circuits of conjugation. These methods are here compared with ostensibly similar approaches published more than 30 years ago by two of the present authors (Gomes and Mallion) and (likewise independently) by Gayoso. Patterns of bond currents and ring currents computed by these methods for the nonalternant isomer of coronene that was studied by Randić are also systematically compared with those calculated by the Hückel-London-Pople-McWeeny (HLPM) "topological" approach and with the ab initio, "ipso-centric" current-density maps of Balaban et al. These all agree that a substantial diamagnetic π-electron current flows around the periphery of the selected structure (which could be thought of as a "perturbed" [18]-annulene), and consideration is given to the differing trends predicted by these several methods for the π-electron currents around its central six-membered ring and in its internal bonds. It is observed that, for any method in which calculated π-electron currents respect Kirchhoff's Laws of current conservation at a junction, consideration of bond currents-as an alternative to the more-traditional ring currents-can give a different insight into the magnetic properties of conjugated systems. However, provided that charge/current conservation is guaranteed-or Kirchhoff's First Law holds for bond currents instead of the more-general current-densities-then ring currents represent a more efficient way of describing the molecular reaction to the external magnetic field: ring currents are independent quantities, while bond currents are not.

Remanent magnetization and three-dimensional density model of the Kentucky anomaly region

NASA Technical Reports Server (NTRS)

1982-01-01

Existing software was modified to handle 3-D density and magnetization models of the Kentucky body and is being tested. Gravity and magnetic anomaly data sets are ready for use. A preliminary block model is under construction using the 1:1,000,000 maps. An x-y grid to overlay the 1:2,500,000 Albers maps and keyed to the 1:1,000,000 scale block models was created. Software was developed to generate a smoothed MAGSAT data set over this grid; this is to be input to an inversion program for generating the regional magnetization map. The regional scale 1:2,500,000 map mosaic is being digitized using previous magnetization models, the U.S. magnetic anomaly map, and regional tectonic maps as a guide.

Earth GRAM-99 and Trace Constituents

NASA Technical Reports Server (NTRS)

Justus, C. G.; Duvall, Aleta; Keller, Vernon W.

2004-01-01

Global Reference Atmospheric Model (GRAM-99) is an engineering-level model of Earth's atmosphere. It provides both mean values and perturbations for density, temperature, pressure, and winds, as well as monthly- and geographically-varying trace constituent concentrations. From 0-27 km, GRAM thermodynamics and winds are based on National Oceanic and Atmospheric Administration Global Upper Air Climatic Atlas (GUACA) climatology. Above 120 km, GRAM is based on the NASA Marshall Engineering Thermosphere (MET) model. In the intervening altitude region, GRAM is based on Middle Atmosphere Program (MAP) climatology that also forms the basis of the 1986 COSPAR International Reference Atmosphere (CIRA). Atmospheric composition is represented in GRAM by concentrations of both major and minor species. Above 120 km, MET provides concentration values for N2, O2, Ar, O, He, and H. Below 120 km, species represented also include H2O, O3, N2O, CO, CH4, and CO2. At COSPAR 2002 a comparison was made between GRAM constituents below 120 km and those provided by Naval Research Laboratory (NRL) climatology. No current need to update GRAM constituent climatology in that height range was identified. This report examines GRAM (MET) constituents between 100 and 1000 km altitudes. Discrepancies are noted between GRAM (MET) constituent number densities and mass density or molecular weight. Near 110 km altitude, there is up to about 25% discrepancy between MET number density and mass density (with mass density being valid and number densities requiring adjustment). Near 700 km altitude there is also up to about 25% discrepancy between MET number density and mean molecular weight (with molecular weight requiring adjustment). In neither case are MET mass density estimates invalidated. These discrepancies have been traced to MET subroutines SLV (which affects 90-170 km height range) and SLVH (which affects helium above 440 km altitude). With these discrepancies corrected, results are presented to illustrate GRAM (MET) constituent mole fractions in terms of height-latitude cross sections from 100 to 1000 km altitude, and latitude-longitude 'maps' at 450 km (approximate height of International Space Station). Plans are discussed for an update of MET (and GRAM) to correct these constituent inconsistencies and to incorporate several new thermospheric model features.

Assessing the Age of an Asteroid's Surface with Data from the International Rosetta Mission

NASA Technical Reports Server (NTRS)

Lopez, Juan Carlos

2011-01-01

Rosetta is an international mission led by the European Space Agency (ESA) with key support and instrumentation from the National Aeronautics and Space Administration (NASA). Rosetta is currently on a ten-year mission to catch comet 67P/Churyumov-Gerasimenko (C-G); throughout its voyage, the spacecraft has performed flybys of two main belt asteroids (MBA): Steins and Lutetia. Data on the physical, chemical, and geological properties of these asteroids are currently being processed and analyzed. Accurate interpretation of such data is fundamental in the success of Rosetta's mission and overall objectives. Post-flyby data analyses strive to correlate the size, shape, volume, and rotational rate of Lutetia, in addition to interpreting its multi-color imagining, albedo, and spectral mapping. Although advancements in science have contributed to the examination of celestial bodies, methods to analyze asteroids remain largely empirical, not semi-empirical, nor ab initio. This study aims to interpret and document the scientific methods currently utilized in the characterization of asteroid (21) Lutetia in order to render these processes and methods accessible to the public. Examples include a standardized technique for assessing the age of an asteroid surface, complete with clickable reference maps, methodology of grouping surface characteristics together, and a standardized power law equation for the age. Other examples include determining the density of an object. Context for what both density and age mean is a bi-product of this study. Results of the study will aid in the development of pedagogical material on asteroids for public use, and in creation of an academic database for selected targets that might be used as a reference.

Charge generation layers for solution processed tandem organic light emitting diodes with regular device architecture.

PubMed

Höfle, Stefan; Bernhard, Christoph; Bruns, Michael; Kübel, Christian; Scherer, Torsten; Lemmer, Uli; Colsmann, Alexander

2015-04-22

Tandem organic light emitting diodes (OLEDs) utilizing fluorescent polymers in both sub-OLEDs and a regular device architecture were fabricated from solution, and their structure and performance characterized. The charge carrier generation layer comprised a zinc oxide layer, modified by a polyethylenimine interface dipole, for electron injection and either MoO3, WO3, or VOx for hole injection into the adjacent sub-OLEDs. ToF-SIMS investigations and STEM-EDX mapping verified the distinct functional layers throughout the layer stack. At a given device current density, the current efficiencies of both sub-OLEDs add up to a maximum of 25 cd/A, indicating a properly working tandem OLED.

Building a time series of water vapour maps: A first step towards assimilation of Interferometric SAR data in forecasting models

NASA Astrophysics Data System (ADS)

Nico, Giovanni; Mateus, Pedro; Catalão, João.

2010-05-01

The knowledge of water vapor spatial distribution in the Earth's atmosphere at a given time is an important information for numerical forecasting. In fact this is the most varying atmospheric constituent both in space and in time. The water vapor is basically concentrated in the troposphere, the atmosphere layer where the most important phenomena related to weather occur. This layer is destabilized by radiative heating and vertical wind shear near the surfce. The accuracy of quantitative precipitation forecasting over a given region strongly depends on the knowledge of the temporal and spatial variations in the water vapor spatial distribution. Currently, measurements based on ground-based and upper-air sounding networks furnish water vapor distribution only at a coarse scales. This could not be enough to capture variations of the local concentrations of water vapor. Spaceborne radiometer observations can observe atmospheric layers above 3 km due to absorption by water vapor and in any case maps of vater vapour density are too coarse. Availability of GPS measurements of on a routine basis is improving numerical forecasting. However, the density of meuserements which can be obtained by a GPS network is too low to capture spatial variations of local concentrations of water vapor. Synthetic Aperture Radar (SAR) interferometry provides maps of temporal variations of the vertically integrated water vapor density with a horizontal resolution as fine as 10-20 m depending on the radar wavelength and over a swath typically 100 km wide. In the past, the availability of the tandem ERS-1/2 interferometric SAR data allowed to get maps of the vertically-integrated with a temporal baseline of 1 day. In those maps it was possible to recognize signature of a precipitating cumulonimbus cloud, the effects of a cold front and the phenomenon of horizontal convective rolls. Current interferometric spaceborne missions use SAR sensors working at different frequency bands: L (ALOS-PALSAR), C (ENVISAT-ASAR, RADARSAT) and X (TerraSAR, Cosmo-Sky-Med) and with a repetition cycle ranging from 11 (TerraSAR-X) to 35 days (ENVISAT-ASAR). From each SAR sensor, it can be obtained a map of the temporal changes of the IPW occurred between the two subsequent acquisitions by interferometrically processing the SAR data. The accuracy of these maps depends on the radar wavelength and on spatial filtering. A procedure to properly merge all these maps could give information about the temporal evolution of the IPW spatial distribution with a sampling period shorter than the revisiting times of each of the SAR sensors. The main difficulty of this operation is related to the fact that the integration of temporal changes of IPW is not direct when maps are obtained by different SAR sensors. The aim of this work is to describe a methodologiy to merge IPW maps obtained by the different SAR sensor based on the availbality of GPS time series measuring the IPW over the same area. The Lisbon region, Portugal, was chosen as a study area. This region is monitored by a network of 12 GPS permanent stations covering an area of about squared kilometers. A set of SAR interferograms were processed using data acquired by ENVISAT-ASAR and TerraSAR-X mission over the Lisbon region during the period from 2009 to 2010. A time series with GPS measurement of IPW was processed to cover the time interval between the first and last SAR acquisition. This time series is then used to integrate all maps of temporal changes of IPW obtained by the different interferometric SAR couples. This results in a time series giving with the information about the spatial distribution of the IPW.

Local thermodynamic mapping for effective liquid density-functional theory

NASA Technical Reports Server (NTRS)

Kyrlidis, Agathagelos; Brown, Robert A.

1992-01-01

The structural-mapping approximation introduced by Lutsko and Baus (1990) in the generalized effective-liquid approximation is extended to include a local thermodynamic mapping based on a spatially dependent effective density for approximating the solid phase in terms of the uniform liquid. This latter approximation, called the local generalized effective-liquid approximation (LGELA) yields excellent predictions for the free energy of hard-sphere solids and for the conditions of coexistence of a hard-sphere fcc solid with a liquid. Moreover, the predicted free energy remains single valued for calculations with more loosely packed crystalline structures, such as the diamond lattice. The spatial dependence of the weighted density makes the LGELA useful in the study of inhomogeneous solids.

A protocol for searching the most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation.

PubMed

Sekiguchi, Yuki; Hashimoto, Saki; Kobayashi, Amane; Oroguchi, Tomotaka; Nakasako, Masayoshi

2017-09-01

Coherent X-ray diffraction imaging (CXDI) is a technique for visualizing the structures of non-crystalline particles with size in the submicrometer to micrometer range in material sciences and biology. In the structural analysis of CXDI, the electron density map of a specimen particle projected along the direction of the incident X-rays can be reconstructed only from the diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction, relying entirely on the computational procedure, sometimes fails because diffraction patterns miss the data in small-angle regions owing to the beam stop and saturation of the detector pixels, and are modified by Poisson noise in X-ray detection. To date, X-ray free-electron lasers have allowed us to collect a large number of diffraction patterns within a short period of time. Therefore, the reconstruction of correct electron density maps is the bottleneck for efficiently conducting structure analyses of non-crystalline particles. To automatically address the correctness of retrieved electron density maps, a data analysis protocol to extract the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a single diffraction pattern is proposed. Through monitoring the variations of the phase values during PR calculations, the tendency for the PR calculations to succeed when the retrieved phase sets converged on a certain value was found. On the other hand, if the phase set was in persistent variation, the PR calculation tended to fail to yield the correct electron density map. To quantify this tendency, here a figure of merit for the variation of the phase values during PR calculation is introduced. In addition, a PR protocol to evaluate the similarity between a map of the highest figure of merit and other independently reconstructed maps is proposed. The protocol is implemented and practically examined in the structure analyses for diffraction patterns from aggregates of gold colloidal particles. Furthermore, the feasibility of the protocol in the structure analysis of organelles from biological cells is examined.

Evaluation of a color-coded Landsat 5/6 ratio image for mapping lithologic differences in western South Dakota

USGS Publications Warehouse

Raines, Gary L.; Bretz, R.F.; Shurr, George W.

1979-01-01

From analysis of a color-coded Landsat 5/6 ratio, image, a map of the vegetation density distribution has been produced by Raines of 25,000 sq km of western South Dakota. This 5/6 ratio image is produced digitally calculating the ratios of the bands 5 and 6 of the Landsat data and then color coding these ratios in an image. Bretz and Shurr compared this vegetation density map with published and unpublished data primarily of the U.S. Geological Survey and the South Dakota Geological Survey; good correspondence is seen between this map and existing geologic maps, especially with the soils map. We believe that this Landsat ratio image can be used as a tool to refine existing maps of surficial geology and bedrock, where bedrock is exposed, and to improve mapping accuracy in areas of poor exposure common in South Dakota. In addition, this type of image could be a useful, additional tool in mapping areas that are unmapped.

Advances in the characterization of InAs/GaSb superlattice infrared photodetectors

NASA Astrophysics Data System (ADS)

Wörl, A.; Daumer, V.; Hugger, T.; Kohn, N.; Luppold, W.; Müller, R.; Niemasz, J.; Rehm, R.; Rutz, F.; Schmidt, J.; Schmitz, J.; Stadelmann, T.; Wauro, M.

2016-10-01

This paper reports on advances in the electro-optical characterization of InAs/GaSb short-period superlattice infrared photodetectors with cut-off wavelengths in the mid-wavelength and long-wavelength infrared ranges. To facilitate in-line monitoring of the electro-optical device performance at different processing stages we have integrated a semi-automated cryogenic wafer prober in our process line. The prober is configured for measuring current-voltage characteristics of individual photodiodes at 77 K. We employ it to compile a spatial map of the dark current density of a superlattice sample with a cut-off wavelength around 5 μm patterned into a regular array of 1760 quadratic mesa diodes with a pitch of 370 μm and side lengths varying from 60 to 350 μm. The different perimeter-to-area ratios make it possible to separate bulk current from sidewall current contributions. We find a sidewall contribution to the dark current of 1.2×10-11 A/cm and a corrected bulk dark current density of 1.1×10-7 A/cm2, both at 200 mV reverse bias voltage. An automated data analysis framework can extract bulk and sidewall current contributions for various subsets of the test device grid. With a suitable periodic arrangement of test diode sizes, the spatial distribution of the individual contributions can thus be investigated. We found a relatively homogeneous distribution of both bulk dark current density and sidewall current contribution across the sample. With the help of an improved capacitance-voltage measurement setup developed to complement this technique a residual carrier concentration of 1.3×1015 cm-3 is obtained. The work is motivated by research into high performance superlattice array sensors with demanding processing requirements. A novel long-wavelength infrared imager based on a heterojunction concept is presented as an example for this work. It achieves a noise equivalent temperature difference below 30 mK for realistic operating conditions.

Construction of a high-density genetic map and lint percentage and cottonseed nutrient trait QTL identification in upland cotton (Gossypium hirsutum L.).

PubMed

Liu, Dexin; Liu, Fang; Shan, Xiaoru; Zhang, Jian; Tang, Shiyi; Fang, Xiaomei; Liu, Xueying; Wang, Wenwen; Tan, Zhaoyun; Teng, Zhonghua; Zhang, Zhengsheng; Liu, Dajun

2015-10-01

Upland cotton plays a critical role not only in the textile industry, but also in the production of important secondary metabolites, such as oil and proteins. Construction of a high-density linkage map and identifying yield and seed trait quantitative trail loci (QTL) are prerequisites for molecular marker-assisted selective breeding projects. Here, we update a high-density upland cotton genetic map from recombinant inbred lines. A total of 25,313 SSR primer pairs were screened for polymorphism between Yumian 1 and T586, and 1712 SSR primer pairs were used to genotype the mapping population and construct a map. An additional 1166 loci have been added to our previously published map with 509 SSR markers. The updated genetic map spans a total recombinant length of 3338.2 cM and contains 1675 SSR loci and nine morphological markers, with an average interval of 1.98 cM between adjacent markers. Green lint (Lg) mapped on chromosome 15 in a previous report is mapped in an interval of 2.6 cM on chromosome 21. Based on the map and phenotypic data from multiple environments, 79 lint percentage and seed nutrient trait QTL are detected. These include 8 lint percentage, 13 crude protein, 15 crude oil, 8 linoleic, 10 oleic, 13 palmitic, and 12 stearic acid content QTL. They explain 3.5-62.7 % of the phenotypic variation observed. Four morphological markers identified have a major impact on lint percentage and cottonseed nutrients traits. In this study, our genetic map provides new sights into the tetraploid cotton genome. Furthermore, the stable QTL and morphological markers could be used for fine-mapping and map-based cloning.

Rapid model building of beta-sheets in electron-density maps.

PubMed

Terwilliger, Thomas C

2010-03-01

A method for rapidly building beta-sheets into electron-density maps is presented. beta-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and C(beta) atoms along the strand averaged over all repeats present in the strand. The beta-strands obtained are then assembled into a single atomic model of the beta-sheet regions. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 A. The beta-sheet regions were nearly completely built in all but two cases, the exceptions being one structure at 2.5 A resolution in which a third of the residues in beta-sheets were built and a structure at 3.8 A in which under 10% were built. The overall average r.m.s.d. of main-chain atoms in the residues built using this method compared with refined models of the structures was 1.5 A.

Using Flow Regime Lightning and Sounding Climatologies to Initialize Gridded Lightning Threat Forecasts for East Central Florida

NASA Technical Reports Server (NTRS)

Lambert, Winifred; Short, David; Wolkmer, Matthew; Sharp, David; Spratt, Scott

2006-01-01

Each morning, the forecasters at the National Weather Service in Melbourne, FL (NWS MLB) produce an experimental cloud-to-ground (CG) lightning threat index map for their county warning area (CWA) that is posted to their web site (http://www.srh.weather.gov/mlb/ghwo/lightning.shtml) . Given the hazardous nature of lightning in East Central Florida, especially during the warm season months of May September, these maps help users factor the threat of lightning, relative to their location, into their daily plans. The maps are color-coded in five levels from Very Low to Extreme, with threat level definitions based on the probability of lightning occurrence and the expected amount of CG activity. On a day in which thunderstorms are expected, there are typically two or more threat levels depicted spatially across the CWA. The locations of relative lightning threat maxima and minima often depend on the position and orientation of the low-level ridge axis, forecast propagation and interaction of sea/lake/outflow boundaries, expected evolution of moisture and stability fields, and other factors that can influence the spatial distribution of thunderstorms over the CWA. The lightning threat index maps are issued for the 24-hour period beginning at 1200 UTC each day with a grid resolution of 5 km x 5 km. Product preparation is performed on the AWIPS Graphical Forecast Editor (GFE), which is the standard NWS platform for graphical editing. Currently, the forecasters create each map manually, starting with a blank map. To improve efficiency of the forecast process, NWS MLB requested that the Applied Meteorology Unit (AMU) create gridded warm season lightning climatologies that could be used as first-guess inputs to initialize lightning threat index maps. The gridded values requested included CG strike densities and frequency of occurrence stratified by synoptic-scale flow regime. The intent is to improve consistency between forecasters while allowing them to focus on the mesoscale detail of the forecast, ultimately benefiting the end-users of the product. Several studies took place at the Florida State University (FSU) and NWS Tallahassee (TAE) in which they created daily flow regimes using Florida 1200 UTC synoptic soundings and CG strike densities, or number of strikes per specified area. The soundings used to determine the flow regimes were taken at Miami (MIA), Tampa (TBW), and Jacksonville (JAX), FL, and the lightning data for the strike densities came from the National Lightning Detection Network (NLDN). The densities were created on a 2.5 km x 2.5 km grid for every hour of every day during the warm seasons in the years 1989-2004. The grids encompass an area that includes the entire state of Florida and adjacent Atlantic and Gulf of Mexico waters. Personnel at FSU and NWS TAE provided this data and supporting software for the work performed by the AMU.

EnviroAtlas - New York, NY - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Paterson, NJ - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Fresno, CA - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Green Bay, WI - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Des Moines, IA - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Minneapolis/St. Paul, MN - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Woodbine, IA - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Phoenix, AZ - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Pittsburgh, PA - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - New Bedford, MA - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Milwaukee, WI - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Austin, TX - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Cleveland, OH - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Portland, ME - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Portland, OR - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Durham, NC - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Tampa, FL - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Memphis, TN - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

Single-Frame Terrain Mapping Software for Robotic Vehicles

NASA Technical Reports Server (NTRS)

Rankin, Arturo L.

2011-01-01

This software is a component in an unmanned ground vehicle (UGV) perception system that builds compact, single-frame terrain maps for distribution to other systems, such as a world model or an operator control unit, over a local area network (LAN). Each cell in the map encodes an elevation value, terrain classification, object classification, terrain traversability, terrain roughness, and a confidence value into four bytes of memory. The input to this software component is a range image (from a lidar or stereo vision system), and optionally a terrain classification image and an object classification image, both registered to the range image. The single-frame terrain map generates estimates of the support surface elevation, ground cover elevation, and minimum canopy elevation; generates terrain traversability cost; detects low overhangs and high-density obstacles; and can perform geometry-based terrain classification (ground, ground cover, unknown). A new origin is automatically selected for each single-frame terrain map in global coordinates such that it coincides with the corner of a world map cell. That way, single-frame terrain maps correctly line up with the world map, facilitating the merging of map data into the world map. Instead of using 32 bits to store the floating-point elevation for a map cell, the vehicle elevation is assigned to the map origin elevation and reports the change in elevation (from the origin elevation) in terms of the number of discrete steps. The single-frame terrain map elevation resolution is 2 cm. At that resolution, terrain elevation from 20.5 to 20.5 m (with respect to the vehicle's elevation) is encoded into 11 bits. For each four-byte map cell, bits are assigned to encode elevation, terrain roughness, terrain classification, object classification, terrain traversability cost, and a confidence value. The vehicle s current position and orientation, the map origin, and the map cell resolution are all included in a header for each map. The map is compressed into a vector prior to delivery to another system.

A High Density Consensus Genetic Map of Tetraploid Cotton That Integrates Multiple Component Maps through Molecular Marker Redundancy Check

PubMed Central

Blenda, Anna; Fang, David D.; Rami, Jean-François; Garsmeur, Olivier; Luo, Feng; Lacape, Jean-Marc

2012-01-01

A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton. PMID:23029214

A study on the carrying capacity of the available habitat for the Rhinopithecus bieti population at Mt. Laojun in Yunnan, China.

PubMed

Li, Li; Yu, Shixiao; Ren, Baoping; Li, Ming; Wu, Ruidong; Long, Yongcheng

2009-06-01

The Yunnan snub-nosed monkey is one of the most endangered primates in the world. It is experiencing a range of ongoing threats and the persisting effects of past disturbances. The prospects for this species are not very optimistic because habitat corridors are severely damaged by logging, grazing, and mining. Each group of the monkeys in different areas is facing a unique variety of threats. Based on genetic analysis, Rhinopithecus bieti should be separated into three management units for conservation, of which the Mt. Laojun management unit involves the most endangered primates. Despite the fact that the vegetation on Mt. Laojun is in a relatively pristine state, only two groups of monkeys, of a total of fewer than 300, survive in the area. With this paper, we aimed to address the capacity of the monkeys' habitat at the study site and the possible reasons for the small populations. Rapid ecological assessment based on a SPOT 5 image and field survey was used to simulate the vegetation of the whole area based on reference ecological factors of the GIS system. The vegetation map of the site was thus derived from this simulation. Based on the previous studies, the three vegetation types were identified as the suitable habitat of the monkeys. The confusion matrix-based field GPS points were applied to analyze the precision of the habitat map. Based on the map of suitable habitat of the monkeys, the utilization of the habitat and the carrying capacity were analyzed in the GIS. The confusion matrix-based field GPS points were applied to the habitat analysis process, and it was found that the habitat map was 81.3% precise. Then, with the current habitat map, we found that the mixed forest currently used by the monkeys is only a very small fraction (2.65%) of the overall potential habitat of the population, while the dark conifer forest is 4.09%. Poaching is the greatest short-term threat to this species, particularly in the southern range where local residents have a strong tradition of hunting. Quite a few individual monkeys are still trapped accidentally due to the high density of traps. These problems are hard to mitigate because it is difficult to enforce laws due to the extremely rugged terrain. The results show that there is a great ecological capacity of the area for the monkey's survival and a great potential for an expansion of the monkey population at the site. Based on the current population and its geographical range, it can be estimated that the suitable habitat area defined by this study can support more monkeys, about many times the current population. Thus, at least in the Mt. Laojun Area, poaching pressure is the main factor to be responsible for the low density of Yunnan snub-nosed monkeys instead of habitat alteration. Based on these results, some suggestions relating to conservation can be made: Focus conservation efforts on the current distribution area of the monkeys and create a 20 km buffer zone; design a long-term plan for the suitable habitat outside the buffer zone to set up a wildlife corridor in the long run; establish an association for the local hunters exploiting, their knowledge on the animals to promote monkey conservation and stop poaching. Also, the map derived from the study helps managers to allocate conservation resources more efficiently and enhances the overall outcomes of conservation measures.

Two-dimensional Coupled Petrological-tectonic Modelling of Extensional Basins

NASA Astrophysics Data System (ADS)

Kaus, B. J. P.; Podladchikov, Y. Y.; Connolly, J. A. D.

Most numerical codes that simulate the deformation of a lithosphere assume the den- sity of the lithosphere to be either constant or depend only on temperature and pres- sure. It is, however, well known that rocks undergo phase transformations in response to changes in pressure and temperature. Such phase transformations may substantially alter the bulk properties of the rock (i.e., density, thermal conductivity, thermal ex- pansivity and elastic moduli). Several previous studies demonstrated that the density effects due to phase transitions are indeed large enough to have an impact on the litho- sphere dynamics. These studies were however oversimplified in that they accounted for only one or two schematic discontinuous phase transitions. The current study there- fore takes into account all the reactions that occur for a realistic lithospheric composi- tion. Calculation of the phase diagram and bulk physical properties of the stable phase assemblages for the crust and mantle within the continental lithosphere was done ac- counting for mineral solution behaviour using a free energy minimization program for natural rock compositions. The results of these calculations provide maps of the varia- tions in rock properties as a function of pressure and temperature that are easily incor- porated in any dynamic model computations. In this contribution we implemented a density map in the two-dimensional basin code TECMOD2D. We compare the results of the model with metamorphic reactions with a model without reactions and define some effective parameters that allow the use of a simpler model that still mimics most of the density effects of the metamorphic reactions.

One-step solvothermal synthesis of carnation flower-like SnS2 as superior electrodes for supercapacitor applications

NASA Astrophysics Data System (ADS)

Mishra, Rajneesh Kumar; Baek, Geun Woo; Kim, Kyuwon; Kwon, Hyuck-In; Jin, Sung Hun

2017-12-01

We report the synthesis of carnation flower-like SnS2 (CF-SnS2) via a one-step solvothermal method for potential application as supercapacitor electrodes in energy storage devices. The structural and morphological properties of CF-SnS2 were characterized by X-ray diffraction, Raman analysis, and field-emission scanning and transmission electron microscopies. X-ray photoelectron spectroscopy and scanning tunneling electron microscopy with color mapping verified the distribution of Sn and S, and depicted the successful formation of SnS2. Electrochemical studies were performed to explore the supercapacitive nature of CF-SnS2. Supercapacitors with CF-SnS2 electrodes delivered excellent cyclic voltammetry performances, superior gravimetric specific capacitances, and high power densities. The evaluated specific capacitance and power density reached ∼524.5 F/g and 12.3 W/kg, respectively, at a current density of 0.08 A/g, and ∼215.9 F/g and 61.4 W/kg, respectively, at a current density of 0.38 A/g. These values are at least two times higher than those previously reported. The long-term cyclic stability was also tested to demonstrate the endurance of the CF-SnS2-based supercapacitor, with a 66% rate retention and galvanostatic charge/discharge reversibility. These electrochemical findings indicate that CF-SnS2 is a promising candidate for electrode materials in supercapacitor applications.

Suicide Among Military Personnel and Veterans Aged 18-35 Years by County-16 States.

PubMed

Logan, Joseph E; Fowler, Katherine A; Patel, Nimeshkumar P; Holland, Kristin M

2016-11-01

Suicide among military personnel and young Veterans remains a health concern. This study examined stateside distribution of suicides by U.S. county to help focus prevention efforts. Using 2005-2012 National Violent Death Reporting System data from 16 states (963 counties, or county-equivalent entities), this study mapped the county-level distribution of suicides among current military and Veteran decedents aged 18-35 years. This study also compared incident circumstances of death between decedents in high-density counties (i.e., counties with the highest proportion of deaths) versus those in medium/low-density counties to better understand the precipitators of suicide in counties most affected. Last, this study identified potential military and Veteran Health Administration intervention sites. All analyses were conducted in 2015. Within the National Violent Death Reporting System participating states, an estimated 262 (33%) current military suicides occurred in just ten (1.0%) counties, and 391 (33%) Veteran suicides occurred in 33 (3.4%) counties. Mental health and intimate partner problems were common precipitating circumstances, and some circumstances differed between cases in high- versus those in medium/low-density counties. Multiple potential intervention sites were identified in high-density counties. These findings suggest that military and Veteran suicides are concentrated in a small number of counties. Increased efforts at these locales might be beneficial. Published by Elsevier Inc.

A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome

PubMed Central

Li, Xuehui; Wei, Yanling; Acharya, Ananta; Jiang, Qingzhen; Kang, Junmei; Brummer, E. Charles

2014-01-01

A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map for alfalfa that greatly improved genome coverage relative to previous maps and that will facilitate investigation of genome structure. GBS could be used in breeding populations to accelerate molecular breeding in alfalfa. PMID:25147192

A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome.

PubMed

Li, Xuehui; Wei, Yanling; Acharya, Ananta; Jiang, Qingzhen; Kang, Junmei; Brummer, E Charles

2014-08-21

A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map for alfalfa that greatly improved genome coverage relative to previous maps and that will facilitate investigation of genome structure. GBS could be used in breeding populations to accelerate molecular breeding in alfalfa. Copyright © 2014 Li et al.

Assessment and Mapping of Forest Parcel Sizes

Treesearch

Brett J. Butler; Susan L. King

2005-01-01

A method for analyzing and mapping forest parcel sizes in the Northeastern United States is presented. A decision tree model was created that predicts forest parcel size from spatially explicit predictor variables: population density, State, percentage forest land cover, and road density. The model correctly predicted parcel size for 60 percent of the observations in a...

A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication

PubMed Central

2014-01-01

Background Recent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication. Results We generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication. Conclusions The ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel. PMID:24669946

A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication.

PubMed

Kai, Wataru; Nomura, Kazuharu; Fujiwara, Atushi; Nakamura, Yoji; Yasuike, Motoshige; Ojima, Nobuhiko; Masaoka, Tetsuji; Ozaki, Akiyuki; Kazeto, Yukinori; Gen, Koichiro; Nagao, Jiro; Tanaka, Hideki; Kobayashi, Takanori; Ototake, Mitsuru

2014-03-26

Recent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication. We generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication. The ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel.

FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps.

PubMed

Tiemann, Johanna K S; Rose, Alexander S; Ismer, Jochen; Darvish, Mitra D; Hilal, Tarek; Spahn, Christian M T; Hildebrand, Peter W

2018-05-21

Cryo-electron microscopy (cryo-EM) is a standard method to determine the three-dimensional structures of molecular complexes. However, easy to use tools for modeling of protein segments into cryo-EM maps are sparse. Here, we present the FragFit web-application, a web server for interactive modeling of segments of up to 35 amino acids length into cryo-EM density maps. The fragments are provided by a regularly updated database containing at the moment about 1 billion entries extracted from PDB structures and can be readily integrated into a protein structure. Fragments are selected based on geometric criteria, sequence similarity and fit into a given cryo-EM density map. Web-based molecular visualization with the NGL Viewer allows interactive selection of fragments. The FragFit web-application, accessible at http://proteinformatics.de/FragFit, is free and open to all users, without any login requirements.

A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv].

PubMed

Fang, Xiaomei; Dong, Kongjun; Wang, Xiaoqin; Liu, Tianpeng; He, Jihong; Ren, Ruiyu; Zhang, Lei; Liu, Rui; Liu, Xueying; Li, Man; Huang, Mengzhu; Zhang, Zhengsheng; Yang, Tianyu

2016-05-04

Foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundation for marker-assisted selection for agronomic traits and yield improvement. A total of 10598 SSR markers were developed according to the reference genome sequence of foxtail millet cultivar 'Yugu1'. A total of 1013 SSR markers showing polymorphism between Yugu1 and Longgu7 were used to genotype 167 individuals from a Yugu1 × Longgu7 F2 population, and a high density genetic map was constructed. The genetic map contained 1035 loci and spanned 1318.8 cM with an average distance of 1.27 cM between adjacent markers. Based on agronomic and yield traits identified in 2 years, 29 QTL were identified for 11 traits with combined analysis and single environment analysis. These QTL explained from 7.0 to 14.3 % of phenotypic variation. Favorable QTL alleles for peduncle length originated from Longgu7 whereas favorable alleles for the other traits originated from Yugu1 except for qLMS6.1. New SSR markers, a high density genetic map and QTL identified for agronomic and yield traits lay the ground work for functional gene mapping, map-based cloning and marker-assisted selection in foxtail millet.

Potential Stream Density in Mid-Atlantic U.S. Watersheds

PubMed Central

Elmore, Andrew J.; Julian, Jason P.; Guinn, Steven M.; Fitzpatrick, Matthew C.

2013-01-01

Stream network density exerts a strong influence on ecohydrologic processes in watersheds, yet existing stream maps fail to capture most headwater streams and therefore underestimate stream density. Furthermore, discrepancies between mapped and actual stream length vary between watersheds, confounding efforts to understand the impacts of land use on stream ecosystems. Here we report on research that predicts stream presence from coupled field observations of headwater stream channels and terrain variables that were calculated both locally and as an average across the watershed upstream of any location on the landscape. Our approach used maximum entropy modeling (MaxEnt), a robust method commonly implemented to model species distributions that requires information only on the presence of the entity of interest. In validation, the method correctly predicts the presence of 86% of all 10-m stream segments and errors are low (<1%) for catchments larger than 10 ha. We apply this model to the entire Potomac River watershed (37,800 km2) and several adjacent watersheds to map stream density and compare our results with the National Hydrography Dataset (NHD). We find that NHD underestimates stream density by up to 250%, with errors being greatest in the densely urbanized cities of Washington, DC and Baltimore, MD and in regions where the NHD has never been updated from its original, coarse-grain mapping. This work is the most ambitious attempt yet to map stream networks over a large region and will have lasting implications for modeling and conservation efforts. PMID:24023704

Distinguishability notion based on Wootters statistical distance: Application to discrete maps

NASA Astrophysics Data System (ADS)

Gomez, Ignacio S.; Portesi, M.; Lamberti, P. W.

2017-08-01

We study the distinguishability notion given by Wootters for states represented by probability density functions. This presents the particularity that it can also be used for defining a statistical distance in chaotic unidimensional maps. Based on that definition, we provide a metric d ¯ for an arbitrary discrete map. Moreover, from d ¯ , we associate a metric space with each invariant density of a given map, which results to be the set of all distinguished points when the number of iterations of the map tends to infinity. Also, we give a characterization of the wandering set of a map in terms of the metric d ¯ , which allows us to identify the dissipative regions in the phase space. We illustrate the results in the case of the logistic and the circle maps numerically and analytically, and we obtain d ¯ and the wandering set for some characteristic values of their parameters. Finally, an extension of the metric space associated for arbitrary probability distributions (not necessarily invariant densities) is given along with some consequences. The statistical properties of distributions given by histograms are characterized in terms of the cardinal of the associated metric space. For two conjugate variables, the uncertainty principle is expressed in terms of the diameters of the associated metric space with those variables.

Deriving Continuous Fields of Tree Cover at 1-m over the Continental United States From the National Agriculture Imagery Program (NAIP) Imagery to Reduce Uncertainties in Forest Carbon Stock Estimation

NASA Astrophysics Data System (ADS)

Ganguly, S.; Basu, S.; Mukhopadhyay, S.; Michaelis, A.; Milesi, C.; Votava, P.; Nemani, R. R.

2013-12-01

An unresolved issue with coarse-to-medium resolution satellite-based forest carbon mapping over regional to continental scales is the high level of uncertainty in above ground biomass (AGB) estimates caused by the absence of forest cover information at a high enough spatial resolution (current spatial resolution is limited to 30-m). To put confidence in existing satellite-derived AGB density estimates, it is imperative to create continuous fields of tree cover at a sufficiently high resolution (e.g. 1-m) such that large uncertainties in forested area are reduced. The proposed work will provide means to reduce uncertainty in present satellite-derived AGB maps and Forest Inventory and Analysis (FIA) based regional estimates. Our primary objective will be to create Very High Resolution (VHR) estimates of tree cover at a spatial resolution of 1-m for the Continental United States using all available National Agriculture Imaging Program (NAIP) color-infrared imagery from 2010 till 2012. We will leverage the existing capabilities of the NASA Earth Exchange (NEX) high performance computing and storage facilities. The proposed 1-m tree cover map can be further aggregated to provide percent tree cover at any medium-to-coarse resolution spatial grid, which will aid in reducing uncertainties in AGB density estimation at the respective grid and overcome current limitations imposed by medium-to-coarse resolution land cover maps. We have implemented a scalable and computationally-efficient parallelized framework for tree-cover delineation - the core components of the algorithm [that] include a feature extraction process, a Statistical Region Merging image segmentation algorithm and a classification algorithm based on Deep Belief Network and a Feedforward Backpropagation Neural Network algorithm. An initial pilot exercise has been performed over the state of California (~11,000 scenes) to create a wall-to-wall 1-m tree cover map and the classification accuracy has been assessed. Results show an improvement in accuracy of tree-cover delineation as compared to existing forest cover maps from NLCD, especially over fragmented, heterogeneous and urban landscapes. Estimates of VHR tree cover will complement and enhance the accuracy of present remote-sensing based AGB modeling approaches and forest inventory based estimates at both national and local scales. A requisite step will be to characterize the inherent uncertainties in tree cover estimates and propagate them to estimate AGB.

Redwing: A MOOSE application for coupling MPACT and BISON

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

Frederick N. Gleicher; Michael Rose; Tom Downar

Fuel performance and whole core neutron transport programs are often used to analyze fuel behavior as it is depleted in a reactor. For fuel performance programs, internal models provide the local intra-pin power density, fast neutron flux, burnup, and fission rate density, which are needed for a fuel performance analysis. The fuel performance internal models have a number of limitations. These include effects on the intra-pin power distribution by nearby assembly elements, such as water channels and control rods, and the further limitation of applicability to a specified fuel type such as low enriched UO2. In addition, whole core neutronmore » transport codes need an accurate intra-pin temperature distribution in order to calculate neutron cross sections. Fuel performance simulations are able to model the intra-pin fuel displacement as the fuel expands and densifies. These displacements must be accurately modeled in order to capture the eventual mechanical contact of the fuel and the clad; the correct radial gap width is needed for an accurate calculation of the temperature distribution of the fuel rod. Redwing is a MOOSE-based application that enables coupling between MPACT and BISON for transport and fuel performance coupling. MPACT is a 3D neutron transport and reactor core simulator based on the method of characteristics (MOC). The development of MPACT began at the University of Michigan (UM) and now is under the joint development of ORNL and UM as part of the DOE CASL Simulation Hub. MPACT is able to model the effects of local assembly elements and is able calculate intra-pin quantities such as the local power density on a volumetric mesh for any fuel type. BISON is a fuel performance application of Multi-physics Object Oriented Simulation Environment (MOOSE), which is under development at Idaho National Laboratory. BISON is able to solve the nonlinearly coupled mechanical deformation and heat transfer finite element equations that model a fuel element as it is depleted in a nuclear reactor. Redwing couples BISON and MPACT in a single application. Redwing maps and transfers the individual intra-pin quantities such as fission rate density, power density, and fast neutron flux from the MPACT volumetric mesh to the individual BISON finite element meshes. For a two-way coupling Redwing maps and transfers the individual pin temperature field and axially dependent coolant densities from the BISON mesh to the MPACT volumetric mesh. Details of the mapping are given. Redwing advances the simulation with the MPACT solution for each depletion time step and then advances the multiple BISON simulations for fuel performance calculations. Sub-cycle advancement can be applied to the individual BISON simulations and allows multiple time steps to be applied to the fuel performance simulations. Currently, only loose coupling where data from a previous time step is applied to the current time step is performed.« less

NASA Redox cell stack shunt current, pumping power, and cell performance tradeoffs

NASA Technical Reports Server (NTRS)

Hagedorn, N.; Hoberecht, M. A.; Thaller, L. H.

1982-01-01

The NASA Redox energy storage system is under active technology development. The hardware undergoing laboratory testing is either 310 sq. cm. or 929 sq. cm. (0.33 sq. ft. or 1.0 sq. ft. per cell active area with up to 40 individual cells connected to make up a modular cell stack. This size of hardware allows rather accurate projections to be made of the shunt power/pump power tradeoffs. The modeling studies that were completed on the system concept are reviewed along with the approach of mapping the performance of Redox cells over a wide range of flow rates and depths of discharge of the Redox solutions. Methods are outlined for estimating the pumping and shunt current losses for any type of cell and stack combination. These methods are applicable to a variety of pumping options that are present with Redox systems. The results show that a fully developed Redox system has acceptable parasitic losses when using a fixed flow rate adequate to meet the worst conditions of current density and depth of discharge. These losses are reduced by about 65 percent if variable flow schedules are used. The exact value of the overall parasitics will depend on the specific system requirements of current density, voltage limits, charge, discharge time, etc.

InGaN based micro light emitting diodes featuring a buried GaN tunnel junction

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

Malinverni, M., E-mail: marco.malinverni@epfl.ch; Martin, D.; Grandjean, N.

GaN tunnel junctions (TJs) are grown by ammonia molecular beam epitaxy. High doping levels are achieved with a net acceptor concentration close to ∼10{sup 20 }cm{sup −3}, thanks to the low growth temperature. This allows for the realization of p-n junctions with ultrathin depletion width enabling efficient interband tunneling. n-p-n structures featuring such a TJ exhibit low leakage current densities, e.g., <5 × 10{sup −5} A cm{sup −2} at reverse bias of 10 V. Under forward bias, the voltage is 3.3 V and 4.8 V for current densities of 20 A cm{sup −2} and 2000 A cm{sup −2}, respectively. The specific series resistance of the whole device ismore » 3.7 × 10{sup −4} Ω cm{sup 2}. Then micro-light emitting diodes (μ-LEDs) featuring buried TJs are fabricated. Excellent current confinement is demonstrated together with homogeneous electrical injection, as seen on electroluminescence mapping. Finally, the I-V characteristics of μ-LEDs with various diameters point out the role of the access resistance at the current aperture edge.« less

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

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

Mashouf, S; University of Toronto, Dept of Radiation Oncology, Toronto, Ontario; Fatemi-Ardekani, A

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

Simulation-Based Validation for Four-Dimensional Multi-Channel Ultrasound Current Source Density Imaging

PubMed Central

Wang, Zhaohui; Witte, Russell S.

2015-01-01

Ultrasound current source density imaging (UCSDI), which has application to the heart and brain, exploits the acoustoelectric (AE) effect and Ohm's law to detect and map an electrical current distribution. In this study, we describe 4-D UCSDI simulations of a dipole field for comparison and validation with bench-top experiments. The simulations consider the properties of the ultrasound pulse as it passes through a conductive medium, the electric field of the injected dipole, and the lead field of the detectors. In the simulation, the lead fields of detectors and electric field of the dipole were calculated by the finite element (FE) method, and the convolution and correlation in the computation of the detected AE voltage signal were accelerated using 3-D fast Fourier transforms. In the bench-top experiment, an electric dipole was produced in a bath of 0.9% NaCl solution containing two electrodes, which injected an ac pulse (200 Hz, 3 cycles) ranging from 0 to 140 mA. Stimulating and recording electrodes were placed in a custom electrode chamber made on a rapid prototype printer. Each electrode could be positioned anywhere on an x-y grid (5 mm spacing) and individually adjusted in the depth direction for precise control of the geometry of the current sources and detecting electrodes. A 1-MHz ultrasound beam was pulsed and focused through a plastic film to modulate the current distribution inside the saline-filled tank. AE signals were simultaneously detected at a sampling frequency of 15 MHz on multiple recording electrodes. A single recording electrode is sufficient to form volume images of the current flow and electric potentials. The AE potential is sensitive to the distance from the dipole, but is less sensitive to the angle between the detector and the dipole. Multi-channel UCSDI potentially improves 4-D mapping of bioelectric sources in the body at high spatial resolution, which is especially important for diagnosing and guiding treatment of cardiac and neurologic disorders, including arrhythmia and epilepsy. PMID:24569247

Leveraging field and remotely sensed data to reduce uncertainty in national inventories of coastal wetland carbon fluxes: Year 2 findings from the NASA "Blue" Carbon Monitoring System

NASA Astrophysics Data System (ADS)

Windham-Myers, L.; Holmquist, J. R.; Woo, I.; Bergamaschi, B. A.; Byrd, K. B.; Crooks, S.; Drexler, J. Z.; Feagin, R. A.; Ferner, M. C.; Gonneea, M. E.; Kroeger, K. D.; Megonigal, P.; Morris, J. T.; Schile, L. M.; Simard, M.; Sutton-Grier, A.; Takekawa, J.; Troxler, T.; Weller, D.; Callaway, J.; Herold, N.

2016-12-01

In Year 2, the NASA Blue Carbon Monitoring Systems group leveraged USDA, USFWS and NOAA datasets, extensive field datasets, and targeted remote-sensing products to address basic questions regarding the size of carbon (C) stocks, and the directions and magnitudes of C fluxes in the US coastal zone since 1996. We review the uncertainty associated with 5 major terms in our Land Use-Land Cover Change (LULCC)-based accounting, both nationally and within sentinel sites (Cape Cod, Chesapeake Bay, Everglades, Louisiana, San Francisco Bay, Puget Sound). 1) To make distinctions between tidal and non-tidal wetlands we have relied on a combination of wetland and LiDAR-derived elevation maps. Existing products appear sufficient for saline wetlands, however many freshwater wetlands (1M ha) may be tidal despite current hydrologic mapcodes. 2) We are currently estimating methane emissions using salinity regime as a proxy. Methane emissions are variable across intermediate salinities, though not captured by the current binary classification of wetlands as either fresh or saline. 3) We are currently using a combination of USDA's SSURGO and independent core data to map soil C stocks. Soil C density varies little and is consistent across depth, salinity regime, and dominant plant cover type. 4) To model soil C fluxes, with C accumulating as sea level rises and C released with erosion or oxidation, we have applied IPCC default emission factors for the 2% of tidal wetland acreage lost to water (the dominant conversion), but have modeled C gain in wetlands-remaining-wetlands (98% of CONUS tidal wetlands) based on correlations between sea-level rise and sediment accretion, with the equation - Δ soil organic C stock = Δ elevation x soil C density. 5) To quantify biomass change through time, we developed a robust (R2 > 0.6) hybrid mapping approach including object-based image analysis, multispectral data, and RADAR. Overall, soil and biomass C stocks appear readily estimated and improved from Tier 1 default values. To further reduce uncertainty in the US GHG inventory for coastal wetlands, we propose efforts to confirm the extent of tidal inundation, develop default values for methane emissions associated with intermediate salinities, and model soil C accretion, the dominant "blue carbon" sink, across continental and local gradients.

Eulerian Mapping Closure Approach for Probability Density Function of Concentration in Shear Flows

NASA Technical Reports Server (NTRS)

He, Guowei; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

The Eulerian mapping closure approach is developed for uncertainty propagation in computational fluid mechanics. The approach is used to study the Probability Density Function (PDF) for the concentration of species advected by a random shear flow. An analytical argument shows that fluctuation of the concentration field at one point in space is non-Gaussian and exhibits stretched exponential form. An Eulerian mapping approach provides an appropriate approximation to both convection and diffusion terms and leads to a closed mapping equation. The results obtained describe the evolution of the initial Gaussian field, which is in agreement with direct numerical simulations.

Application of LiDAR Date to Assess the Landslide Susceptibility Map Using Weights of Evidence Method - AN Example from Podhale Region (southern Poland)

NASA Astrophysics Data System (ADS)

Kamiński, Mirosław

2016-06-01

Podhale is a region in southern Poland, which is the northernmost part of the Central Carpathian Mountains. It is characterized by the presence of a large number of landslides that threaten the local infrastructure. In an article presents application of LiDAR data and geostatistical methods to assess landslides susceptibility map. Landslide inventory map were performed using LiDAR data and field work. The Weights of Evidence method was applied to assess landslides susceptibility map. Used factors for modeling: slope gradient, slope aspect, elevation, drainage density, faults density, lithology and curvature. All maps were subdivided into different classes. Then were converted to grid format in the ArcGIS 10.0. The conditional independence test was carried out to determine factors that are conditionally independent of each other with landslides. As a result, chi-square test for further GIS analysis used only five factors: slope gradient, slope aspect, elevation, drainage density and lithology. The final prediction results, it is concluded that the susceptibility map gives useful information both on present instability of the area and its possible future evolution in agreement with the morphological evolution of the area.

Novel and lost forests in the Upper Midwestern United States, from new estimates of settlement-era composition, stem density, and biomass

USGS Publications Warehouse

Goring, Simon; Mladenoff, David J.; Cogbill, Charles; Record, Sydne; Paciorek, Christopher J.; Dietze, Michael C.; Dawson, Andria; Matthes, Jaclyn; McLachlan, Jason S.; Williams, John W.

2016-01-01

EuroAmerican land-use and its legacies have transformed forest structure and composition across the United States (US). More accurate reconstructions of historical states are critical to understanding the processes governing past, current, and future forest dynamics. Here we present new gridded (8x8km) reconstructions of pre-settlement (1800s) forest composition and structure from the upper Midwestern US (Minnesota, Wisconsin, and most of Michigan), using 19th Century Public Land Survey System (PLSS), with estimates of relative composition, above-ground biomass, stem density, and basal area for 28 tree types. This mapping is more robust than past efforts, using spatially varying correction factors to accommodate sampling design, azimuthal censoring, and biases in tree selection.

Characterization of YBa2Cu3O7, including critical current density Jc, by trapped magnetic field

NASA Technical Reports Server (NTRS)

Chen, In-Gann; Liu, Jianxiong; Weinstein, Roy; Lau, Kwong

1992-01-01

Spatial distributions of persistent magnetic field trapped by sintered and melt-textured ceramic-type high-temperature superconductor (HTS) samples have been studied. The trapped field can be reproduced by a model of the current consisting of two components: (1) a surface current Js and (2) a uniform volume current Jv. This Js + Jv model gives a satisfactory account of the spatial distribution of the magnetic field trapped by different types of HTS samples. The magnetic moment can be calculated, based on the Js + Jv model, and the result agrees well with that measured by standard vibrating sample magnetometer (VSM). As a consequence, Jc predicted by VSM methods agrees with Jc predicted from the Js + Jv model. The field mapping method described is also useful to reveal the granular structure of large HTS samples and regions of weak links.

Mars-GRAM: Increasing the Precision of Sensitivity Studies at Large Optical Depths

NASA Technical Reports Server (NTRS)

Justh, Hilary L.; Justus, C. G.; Badger, Andrew M.

2010-01-01

The Mars Global Reference Atmospheric Model (Mars-GRAM) is an engineering-level atmospheric model widely used for diverse mission applications. Mars-GRAM's perturbation modeling capability is commonly used, in a Monte-Carlo mode, to perform high fidelity engineering end-to-end simulations for entry, descent, and landing (EDL). It has been discovered during the Mars Science Laboratory (MSL) site selection process that Mars-GRAM, when used for sensitivity studies for MapYear=0 and large optical depth values such as tau=3, is less than realistic. A comparison study between Mars atmospheric density estimates from Mars-GRAM and measurements by Mars Global Surveyor (MGS) has been undertaken for locations of varying latitudes, Ls, and LTST on Mars. The preliminary results from this study have validated the Thermal Emission Spectrometer (TES) limb data. From the surface to 80 km altitude, Mars-GRAM is based on the NASA Ames Mars General Circulation Model (MGCM). MGCM results that were used for Mars-GRAM with MapYear=0 were from a MGCM run with a fixed value of tau=3 for the entire year at all locations. This has resulted in an imprecise atmospheric density at all altitudes. To solve this pressure-density problem, density factor values were determined for tau=.3, 1 and 3 that will adjust the input values of MGCM MapYear 0 pressure and density to achieve a better match of Mars-GRAM MapYear 0 with TES observations for MapYears 1 and 2 at comparable dust loading. The addition of these density factors to Mars-GRAM will improve the results of the sensitivity studies done for large optical depths.

Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.).

PubMed

Zhang, Zhen; Shang, Haihong; Shi, Yuzhen; Huang, Long; Li, Junwen; Ge, Qun; Gong, Juwu; Liu, Aiying; Chen, Tingting; Wang, Dan; Wang, Yanling; Palanga, Koffi Kibalou; Muhammad, Jamshed; Li, Weijie; Lu, Quanwei; Deng, Xiaoying; Tan, Yunna; Song, Weiwu; Cai, Juan; Li, Pengtao; Rashid, Harun or; Gong, Wankui; Yuan, Youlu

2016-04-11

Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.

Preliminary Correlations of Gravity and Topography from Mars Global Surveyor

NASA Technical Reports Server (NTRS)

Zuber, M. T.; Tyler, G. L.; Smith, D. E.; Balmino, G. S.; Johnson, G. L.; Lemoine, F. G.; Neumann, G. A.; Phillips, R. J.; Sjogren, W. L.; Solomon, S. C.

1999-01-01

The Mars Global Surveyor (MGS) spacecraft is currently in a 400-km altitude polar mapping orbit and scheduled to begin global mapping of Mars in March of 1999. Doppler tracking data collected in this Gravity Calibration Orbit prior to the nominal mapping mission combined with observations from the MGS Science Phasing Orbit in Spring - Summer 1999 and the Viking and mariner 9 orbiters has led to preliminary high resolution gravity fields. Spherical harmonic expansions have been performed to degree and order 70 and are characterized by the first high spatial resolution coverage of high latitudes. Topographic mapping by the Mars Orbiter Laser Altimeter on MGS is providing measurements of the height of the martian surface with sub-meter vertical resolution and 5-30 m absolute accuracy. Data obtained during the circular mapping phase are expected to provide the first high resolution measurements of surface heights in the southern hemisphere. The combination of gravity and topography measurements provides information on the structure of the planetary interior, i.e. the rigidity and distribution of internal density. The observations can also be used to address the mechanisms of support of surface topography. Preliminary results of correlations of gravity and topography at long planetary wavelengths will be presented and the implications for internal structure will be addressed.

Genetic dissection of seed oil and protein content and identification of networks associated with oil content in Brassica napus

PubMed Central

Chao, Hongbo; Wang, Hao; Wang, Xiaodong; Guo, Liangxing; Gu, Jianwei; Zhao, Weiguo; Li, Baojun; Chen, Dengyan; Raboanatahiry, Nadia; Li, Maoteng

2017-01-01

High-density linkage maps can improve the precision of QTL localization. A high-density SNP-based linkage map containing 3207 markers covering 3072.7 cM of the Brassica napus genome was constructed in the KenC-8 × N53-2 (KNDH) population. A total of 67 and 38 QTLs for seed oil and protein content were identified with an average confidence interval of 5.26 and 4.38 cM, which could explain up to 22.24% and 27.48% of the phenotypic variation, respectively. Thirty-eight associated genomic regions from BSA overlapped with and/or narrowed the SOC-QTLs, further confirming the QTL mapping results based on the high-density linkage map. Potential candidates related to acyl-lipid and seed storage underlying SOC and SPC, respectively, were identified and analyzed, among which six were checked and showed expression differences between the two parents during different embryonic developmental periods. A large primary carbohydrate pathway based on potential candidates underlying SOC- and SPC-QTLs, and interaction networks based on potential candidates underlying SOC-QTLs, was constructed to dissect the complex mechanism based on metabolic and gene regulatory features, respectively. Accurate QTL mapping and potential candidates identified based on high-density linkage map and BSA analyses provide new insights into the complex genetic mechanism of oil and protein accumulation in the seeds of rapeseed. PMID:28393910

Digital mapping of soil properties in Canadian managed forests at 250 m of resolution using the k-nearest neighbor method

NASA Astrophysics Data System (ADS)

Mansuy, N. R.; Paré, D.; Thiffault, E.

2015-12-01

Large-scale mapping of soil properties is increasingly important for environmental resource management. Whileforested areas play critical environmental roles at local and global scales, forest soil maps are typically at lowresolution.The objective of this study was to generate continuous national maps of selected soil variables (C, N andsoil texture) for the Canadian managed forest landbase at 250 m resolution. We produced these maps using thekNN method with a training dataset of 538 ground-plots fromthe National Forest Inventory (NFI) across Canada,and 18 environmental predictor variables. The best predictor variables were selected (7 topographic and 5 climaticvariables) using the Least Absolute Shrinkage and Selection Operator method. On average, for all soil variables,topographic predictors explained 37% of the total variance versus 64% for the climatic predictors. Therelative root mean square error (RMSE%) calculated with the leave-one-out cross-validation method gave valuesranging between 22% and 99%, depending on the soil variables tested. RMSE values b 40% can be considered agood imputation in light of the low density of points used in this study. The study demonstrates strong capabilitiesfor mapping forest soil properties at 250m resolution, compared with the current Soil Landscape of CanadaSystem, which is largely oriented towards the agricultural landbase. The methodology used here can potentiallycontribute to the national and international need for spatially explicit soil information in resource managementscience.

Changes of cerebral current source by audiovisual erotic stimuli in premature ejaculation patients.

PubMed

Hyun, Jae-Seog; Kam, Sung-Chul; Kwon, Oh-Young

2008-06-01

Premature ejaculation (PE) is one of the most common forms of male sexual dysfunction. The mechanisms of PE remain poorly understood, despite its high prevalence. To investigate the pathophysiology and causes of PE in the central nervous system, we tried to observe the changes in brain current source distribution by audiovisual induction of sexual arousal. Electroencephalograpies were recorded in patients with PE (45.0 +/- 10.3 years old, N = 18) and in controls (45.6 +/- 9.8 years old, N = 18) during four 10-minute segments of resting, watching a music video excerpt, resting, and watching an erotic video excerpt. Five artifact-free 5-second segments were used to obtain cross-spectral low-resolution brain electromagnetic tomography (LORETA) images. Statistical nonparametric maps (SnPM) were obtained to detect the current density changes of six frequency bands between the erotic video session and the music video session in each group. Comparisons were also made between the two groups in the erotic video session. In the SnPM of each spectrum in patients with PE, the current source density of the alpha band was significantly reduced in the right precentral gyrus, the right insula, and both superior parietal lobules (P < 0.01). Comparing the two groups in the erotic video session, the current densities of the beta-2 and -3 bands in the PE group were significantly decreased in the right parahippocampal gyrus and left middle temporal gyrus (P < 0.01). Neuronal activity in the right precental gyrus, the right insula, both the superior parietal lobule, the right parahippocampal gyrus, and the left middle temporal gyrus may be decreased in PE patients upon sexual arousal. Further studies are needed to evaluate the meaning of decreased neuronal activities in PE patients.

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

PubMed Central

2012-01-01

Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps

PubMed Central

Gosselin, Thierry; Normandeau, Eric; Lamothe, Manuel; Isabel, Nathalie; Audet, Céline; Bernatchez, Louis

2016-01-01

Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/ PMID:28173098

A high-density intraspecific SNP linkage map of pigeonpea (Cajanas cajan L. Millsp.)

PubMed Central

Mandal, Paritra; Bhutani, Shefali; Dutta, Sutapa; Kumawat, Giriraj; Singh, Bikram Pratap; Chaudhary, A. K.; Yadav, Rekha; Gaikwad, K.; Sevanthi, Amitha Mithra; Datta, Subhojit; Raje, Ranjeet S.; Sharma, Tilak R.; Singh, Nagendra Kumar

2017-01-01

Pigeonpea (Cajanus cajan (L.) Millsp.) is a major food legume cultivated in semi-arid tropical regions including the Indian subcontinent, Africa, and Southeast Asia. It is an important source of protein, minerals, and vitamins for nearly 20% of the world population. Due to high carbon sequestration and drought tolerance, pigeonpea is an important crop for the development of climate resilient agriculture and nutritional security. However, pigeonpea productivity has remained low for decades because of limited genetic and genomic resources, and sparse utilization of landraces and wild pigeonpea germplasm. Here, we present a dense intraspecific linkage map of pigeonpea comprising 932 markers that span a total adjusted map length of 1,411.83 cM. The consensus map is based on three different linkage maps that incorporate a large number of single nucleotide polymorphism (SNP) markers derived from next generation sequencing data, using Illumina GoldenGate bead arrays, and genotyping with restriction site associated DNA (RAD) sequencing. The genotyping-by-sequencing enhanced the marker density but was met with limited success due to lack of common markers across the genotypes of mapping population. The integrated map has 547 bead-array SNP, 319 RAD-SNP, and 65 simple sequence repeat (SSR) marker loci. We also show here correspondence between our linkage map and published genome pseudomolecules of pigeonpea. The availability of a high-density linkage map will help improve the anchoring of the pigeonpea genome to its chromosomes and the mapping of genes and quantitative trait loci associated with useful agronomic traits. PMID:28654689

Initial Experience With Ultra High-Density Mapping of Human Right Atria.

PubMed

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

2016-02-01

Recently, an automatic, high-resolution mapping system has been presented to accurately and quickly identify right atrial geometry and activation patterns in animals, but human data are lacking. This study aims to assess the clinical feasibility and accuracy of high-density electroanatomical mapping of various RA arrhythmias. Electroanatomical maps of the RA (35 partial and 24 complete) were created in 23 patients using a novel mini-basket catheter with 64 electrodes and automatic electrogram annotation. Median acquisition time was 6:43 minutes (0:39-23:05 minutes) with shorter times for partial (4.03 ± 4.13 minutes) than for complete maps (9.41 ± 4.92 minutes). During mapping 3,236 (710-16,306) data points were automatically annotated without manual correction. Maps obtained during sinus rhythm created geometry consistent with CT imaging and demonstrated activation originating at the middle to superior crista terminalis, while maps during CS pacing showed right atrial activation beginning at the infero-septal region. Activation patterns were consistent with cavotricuspid isthmus-dependent atrial flutter (n = 4), complex reentry tachycardia (n = 1), or ectopic atrial tachycardia (n = 2). His bundle and fractionated potentials in the slow pathway region were automatically detected in all patients. Ablation of the cavotricuspid isthmus (n = 9), the atrio-ventricular node (n = 2), atrial ectopy (n = 2), and the slow pathway (n = 3) was successfully and safely performed. RA mapping with this automatic high-density mapping system is fast, feasible, and safe. It is possible to reproducibly identify propagation of atrial activation during sinus rhythm, various tachycardias, and also complex reentrant arrhythmias. © 2015 Wiley Periodicals, Inc.

Navigation Challenges in the MAVEN Science Phase

NASA Technical Reports Server (NTRS)

Demcak, Stuart; Young, Brian; Lam, Try; Trawny, Nikolas; Lee, Clifford; Anderson, Rodney; Broschart, Stephen; Ballard, Christopher; Folta, David C.

2012-01-01

The MAVEN spacecraft will explore Mars' upper atmosphere. The primary science phase will last one (Earth) year, during which the spacecraft will be in an elliptical 4.5 hour orbit at an inclination of 75 degrees. The 75 degree inclination results in the orbit periapsis oscillating between +/-75 degrees latitude, thus naturally covering most Mars latitudes during the primary mission. The orbit will be controlled via maneuvers so that the maximum orbit density remains in a density corridor. This results in the MAVEN science phase being in a light aerobraking type orbit of around 160 km for an extended period. In addition, the mission has significantly less tracking data than aerobraking phases of other missions, and even less than other NASA Mars orbiter primary phases. This results in significant challenges for the Navigation Team. They can be summarized as a difficulty in determining the current density profile, which maps into degraded trajectory predictions and less accurate control over the spacecraft location in the targeted density corridor via maneuvers. This paper describes these challenges and the Navigation Team's plans to meet them.

Standard cell electrical and physical variability analysis based on automatic physical measurement for design-for-manufacturing purposes

NASA Astrophysics Data System (ADS)

Shauly, Eitan; Parag, Allon; Khmaisy, Hafez; Krispil, Uri; Adan, Ofer; Levi, Shimon; Latinski, Sergey; Schwarzband, Ishai; Rotstein, Israel

2011-04-01

A fully automated system for process variability analysis of high density standard cell was developed. The system consists of layout analysis with device mapping: device type, location, configuration and more. The mapping step was created by a simple DRC run-set. This database was then used as an input for choosing locations for SEM images and for specific layout parameter extraction, used by SPICE simulation. This method was used to analyze large arrays of standard cell blocks, manufactured using Tower TS013LV (Low Voltage for high-speed applications) Platforms. Variability of different physical parameters like and like Lgate, Line-width-roughness and more as well as of electrical parameters like drive current (Ion), off current (Ioff) were calculated and statistically analyzed, in order to understand the variability root cause. Comparison between transistors having the same W/L but with different layout configurations and different layout environments (around the transistor) was made in terms of performances as well as process variability. We successfully defined "robust" and "less-robust" transistors configurations, and updated guidelines for Design-for-Manufacturing (DfM).

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

USDA-ARS?s Scientific Manuscript database

High-throughput genotyping arrays provide a standardized resource for crop research communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), candidate marker and quantitative trait loci (QTL) ide...

High and low density development in Puerto Rico

Treesearch

William A. Gould; Sebastian Martinuzzi; Olga M. Ramos Gonzalez

2008-01-01

This map shows the distribution of high and low density developed lands in Puerto Rico (Martinuzzi et al. 2007). The map was created using a mosaic of Landsat ETM+ images that range from the years 2000 to 2003. The developed land cover was classified using the Iterative Self-Organizing Data Analysis Technique (ISODATA) unsupervised classification (ERDAS 2003)....

Maps and models of density and stiffness within individual Douglas-fir trees

Treesearch

Christine L. Todoroki; Eini C. Lowell; Dennis P. Dykstra; David G. Briggs

2012-01-01

Spatial maps of density and stiffness patterns within individual trees were developed using two methods: (1) measured wood properties of veneer sheets; and (2) mixed effects models, to test the hypothesis that within-tree patterns could be predicted from easily measurable tree variables (height, taper, breast-height diameter, and acoustic velocity). Sample trees...

A River Runs Under It: Modeling the Distribution of Streams and Stream Burial in Large River Basins

NASA Astrophysics Data System (ADS)

Elmore, A. J.; Julian, J.; Guinn, S.; Weitzell, R.; Fitzpatrick, M.

2011-12-01

Stream network density exerts a strong control on hydrologic processes in watersheds. Over land and through soil and bedrock substrate, water moves slowly and is subject to chemical transformations unique to conditions of continuous contact with geologic materials. In contrast, once water enters stream channels it is efficiently transported out of watersheds, reducing the amount of time for biological uptake and stream nutrient processing. Therefore, stream network density dictates both the relative importance of terrestrial and aquatic influences to stream chemistry and the residence time of water in watersheds, and is critical to modeling and empirical studies aimed at understanding the impact of land use on stream water quantity and quality. Stream network density is largely a function of the number and length of the smallest streams. Methods for mapping and measuring these headwater streams range from simple measurement of stream length from existing maps, to detailed field mapping efforts, which are difficult to implement over large areas. Confounding the simplest approaches, many headwater stream reaches are not included in hydrographical maps, such as the U.S. National Hydrography Dataset (NHD), either because they were buried during the course of urban development or because they were seen as smaller than the minimum mapping size at the time of map generation. These "missing streams" severely limit the effective analyses of stream network density based on the NHD, constituting a major problem for many efforts to understand land-use impacts on streams. Here we report on research that predicts stream presence and absence by coupling field observations of headwater stream channels with maximum entropy models (MaxEnt) commonly implemented in biogeographical studies to model species distributions. The model utilizes terrain variables that are continuously accumulated along hydrologic flowpaths derived from a 10-m digital elevation model. In validation, the model correctly predicts the presence of 91% of all 10-m stream segments, and rarely miscalculates tributary numbers. We apply this model to the entire Potomac River Basin (37,800 km2) and several adjacent basins to map stream channel density and compare our results with NHD flowline data. We find that NHD underestimates stream channel density by a factor of two in most sub watersheds and this effect is strongest in the densely urbanized cities of Washington, DC and Baltimore, MD. We then apply a second predictive model based on impervious surface area data to map the extent of stream burial. Results demonstrate that the extent of stream burial increases with decreasing stream catchment area. When applied at four time steps (1975, 1990, 2001, and 2006), we find that although stream burial rates have slowed in the recent decade, streams that are not mapped in NHD flowline data continue to be buried during development. This work is the most ambitious attempt yet to map stream network density over a large region and will have lasting implications for modeling and conservation efforts.

Development of an Asset Value Map for Disaster Risk Assessment in China by Spatial Disaggregation Using Ancillary Remote Sensing Data.

PubMed

Wu, Jidong; Li, Ying; Li, Ning; Shi, Peijun

2018-01-01

The extent of economic losses due to a natural hazard and disaster depends largely on the spatial distribution of asset values in relation to the hazard intensity distribution within the affected area. Given that statistical data on asset value are collected by administrative units in China, generating spatially explicit asset exposure maps remains a key challenge for rapid postdisaster economic loss assessment. The goal of this study is to introduce a top-down (or downscaling) approach to disaggregate administrative-unit level asset value to grid-cell level. To do so, finding the highly correlated "surrogate" indicators is the key. A combination of three data sets-nighttime light grid, LandScan population grid, and road density grid, is used as ancillary asset density distribution information for spatializing the asset value. As a result, a high spatial resolution asset value map of China for 2015 is generated. The spatial data set contains aggregated economic value at risk at 30 arc-second spatial resolution. Accuracy of the spatial disaggregation reflects redistribution errors introduced by the disaggregation process as well as errors from the original ancillary data sets. The overall accuracy of the results proves to be promising. The example of using the developed disaggregated asset value map in exposure assessment of watersheds demonstrates that the data set offers immense analytical flexibility for overlay analysis according to the hazard extent. This product will help current efforts to analyze spatial characteristics of exposure and to uncover the contributions of both physical and social drivers of natural hazard and disaster across space and time. © 2017 Society for Risk Analysis.

Digital mine claim density map for Federal lands in Montana, 1996

USGS Publications Warehouse

Campbell, Harry W.; Hyndman, Paul C.

1998-01-01

This report describes a digital map and data files generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim information for Federal lands in Montana as of March, 1997. Statewide, 159,704 claims had been recorded with the Bureau of Land Management since 1975. Of those claims, 21,055 (13%) are still actively held while 138,649 (87%) are closed and are no longer held. Montana contains 147,704 sections (usually 1 section equals 1 square mile) in the Public Land Survey System, with 8,569 sections (6%) containing claim data. Of the sections with claim data, 2,192 (26%) contain actively held claims. Only 1.5% of Montana’s sections contains actively held mining claims. The four types of mining claim are lode, placer, mill, and tunnel. A mill claim may be as much as 5 acres or 1/128th (0.78125%) of a square mile. A lode claim, about 20 acres, would cover 1/32nd (3.125%) of a square mile. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. The digital map and data files that are available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller. Campbell (1996) summarized the methodology and GIS techniques that were used to produce the mining claim density map of the Pacific Northwest. Campbell and Hyndman (1997) displayed mining claim information for the Pacific Northwest that used data acquired in 1994. Appendix A of this report lists the attribute data for the digital data files. Appendix B contains the GIS metadata.

Preliminary isostatic gravity map of the Sonoma volcanic field and vicinity, Sonoma and Napa Counties, California

USGS Publications Warehouse

Langenheim, V.E.; Roberts, C.W.; McCabe, C.A.; McPhee, D.K.; Tilden, J.E.; Jachens, R.C.

2006-01-01

This isostatic residual gravity map is part of a three-dimensional mapping effort focused on the subsurface distribution of rocks of the Sonoma volcanic field in Napa and Sonoma counties, northern California. This map will serve as a basis for modeling the shapes of basins beneath the Santa Rosa Plain and Napa and Sonoma Valleys, and for determining the location and geometry of faults within the area. Local spatial variations in the Earth's gravity field (after accounting for variations caused by elevation, terrain, and deep crustal structure explained below) reflect the distribution of densities in the mid to upper crust. Densities often can be related to rock type, and abrupt spatial changes in density commonly mark lithologic boundaries. High-density basement rocks exposed within the northern San Francisco Bay area include those of the Mesozoic Franciscan Complex and Great Valley Sequence present in the mountainous areas of the quadrangle. Alluvial sediment and Tertiary sedimentary rocks are characterized by low densities. However, with increasing depth of burial and age, the densities of these rocks may become indistinguishable from those of basement rocks. Tertiary volcanic rocks are characterized by a wide range in densities, but, on average, are less dense than the Mesozoic basement rocks. Isostatic residual gravity values within the map area range from about -41 mGal over San Pablo Bay to about 11 mGal near Greeg Mountain 10 km east of St. Helena. Steep linear gravity gradients are coincident with the traces of several Quaternary strike-slip faults, most notably along the West Napa fault bounding the west side of Napa Valley, the projection of the Hayward fault in San Pablo Bay, the Maacama Fault, and the Rodgers Creek fault in the vicinity of Santa Rosa. These gradients result from juxtaposing dense basement rocks against thick Tertiary volcanic and sedimentary rocks.

Prediction of AL and Dst Indices from ACE Measurements Using Hybrid Physics/Black-Box Techniques

NASA Astrophysics Data System (ADS)

Spencer, E.; Rao, A.; Horton, W.; Mays, L.

2008-12-01

ACE measurements of the solar wind velocity, IMF and proton density is used to drive a hybrid Physics/Black- Box model of the nightside magnetosphere. The core physics is contained in a low order nonlinear dynamical model of the nightside magnetosphere called WINDMI. The model is augmented by wavelet based nonlinear mappings between the solar wind quantities and the input into the physics model, followed by further wavelet based mappings of the model output field aligned currents onto the ground based magnetometer measurements of the AL index and Dst index. The black box mappings are introduced at the input stage to account for uncertainties in the way the solar wind quantities are transported from the ACE spacecraft at L1 to the magnetopause. Similar mappings are introduced at the output stage to account for a spatially and temporally varying westward auroral electrojet geometry. The parameters of the model are tuned using a genetic algorithm, and trained using the large geomagnetic storm dataset of October 3-7 2000. It's predictive performance is then evaluated on subsequent storm datasets, in particular the April 15-24 2002 storm. This work is supported by grant NSF 7020201

Semiautomated model building for RNA crystallography using a directed rotameric approach.

PubMed

Keating, Kevin S; Pyle, Anna Marie

2010-05-04

Structured RNA molecules play essential roles in a variety of cellular processes; however, crystallographic studies of such RNA molecules present a large number of challenges. One notable complication arises from the low resolutions typical of RNA crystallography, which results in electron density maps that are imprecise and difficult to interpret. This problem is exacerbated by the lack of computational tools for RNA modeling, as many of the techniques commonly used in protein crystallography have no equivalents for RNA structure. This leads to difficulty and errors in the model building process, particularly in modeling of the RNA backbone, which is highly error prone due to the large number of variable torsion angles per nucleotide. To address this, we have developed a method for accurately building the RNA backbone into maps of intermediate or low resolution. This method is semiautomated, as it requires a crystallographer to first locate phosphates and bases in the electron density map. After this initial trace of the molecule, however, an accurate backbone structure can be built without further user intervention. To accomplish this, backbone conformers are first predicted using RNA pseudotorsions and the base-phosphate perpendicular distance. Detailed backbone coordinates are then calculated to conform both to the predicted conformer and to the previously located phosphates and bases. This technique is shown to produce accurate backbone structure even when starting from imprecise phosphate and base coordinates. A program implementing this methodology is currently available, and a plugin for the Coot model building program is under development.

The recombination landscape around forensic STRs: Accurate measurement of genetic distances between syntenic STR pairs using HapMap high density SNP data.

PubMed

Phillips, C; Ballard, D; Gill, P; Court, D Syndercombe; Carracedo, A; Lareu, M V

2012-05-01

Family studies can be used to measure the genetic distance between same-chromosome (syntenic) STRs in order to detect physical linkage or linkage disequilibrium. However, family studies are expensive and time consuming, in many cases uninformative, and lack a reliable means to infer the phase of the diplotypes obtained. HapMap provides a more comprehensive and fine-scale estimation of recombination rates using high density multi-point SNP data (average inter-SNP distance: 900 nucleotides). Data at this fine scale detects sub-kilobase genetic distances across the whole recombining human genome. We have used the most recent HapMap SNP data release 22 to measure and compare genetic distances, and by inference fine-scale recombination rates, between 29 syntenic STR pairs identified from 39 validated STRs currently available for forensic use. The 39 STRs comprise 23 core loci: SE33, Penta D & E, 13 CODIS and 7 non-CODIS European Standard Set STRs, plus supplementary STRs in the recently released Promega CS-7™ and Qiagen Investigator HDplex™ kits. Also included were D9S1120, a marker we developed for forensic use unique to chromosome 9, and the novel D6S1043 component STR of SinoFiler™ (Applied Biosystems). The data collated provides reliable estimates of recombination rates between each STR pair, that can then be placed into haplotype frequency calculators for short pedigrees with multiple meiotic inputs and which just requires the addition of allele frequencies. This allows all current STR sets or their combinations to be used in supplemented paternity analyses without the need for further adjustment for physical linkage. The detailed analysis of recombination rates made for autosomal forensic STRs was extended to the more than 50 X chromosome STRs established or in development for complex kinship analyses. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.

PubMed

Sanchez Sorzano, Carlos Oscar; Alvarez-Cabrera, Ana Lucia; Kazemi, Mohsen; Carazo, Jose María; Jonić, Slavica

2016-04-26

Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Sparse-grid, reduced-basis Bayesian inversion: Nonaffine-parametric nonlinear equations

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

Chen, Peng, E-mail: peng@ices.utexas.edu; Schwab, Christoph, E-mail: christoph.schwab@sam.math.ethz.ch

2016-07-01

We extend the reduced basis (RB) accelerated Bayesian inversion methods for affine-parametric, linear operator equations which are considered in [16,17] to non-affine, nonlinear parametric operator equations. We generalize the analysis of sparsity of parametric forward solution maps in [20] and of Bayesian inversion in [48,49] to the fully discrete setting, including Petrov–Galerkin high-fidelity (“HiFi”) discretization of the forward maps. We develop adaptive, stochastic collocation based reduction methods for the efficient computation of reduced bases on the parametric solution manifold. The nonaffinity and nonlinearity with respect to (w.r.t.) the distributed, uncertain parameters and the unknown solution is collocated; specifically, by themore » so-called Empirical Interpolation Method (EIM). For the corresponding Bayesian inversion problems, computational efficiency is enhanced in two ways: first, expectations w.r.t. the posterior are computed by adaptive quadratures with dimension-independent convergence rates proposed in [49]; the present work generalizes [49] to account for the impact of the PG discretization in the forward maps on the convergence rates of the Quantities of Interest (QoI for short). Second, we propose to perform the Bayesian estimation only w.r.t. a parsimonious, RB approximation of the posterior density. Based on the approximation results in [49], the infinite-dimensional parametric, deterministic forward map and operator admit N-term RB and EIM approximations which converge at rates which depend only on the sparsity of the parametric forward map. In several numerical experiments, the proposed algorithms exhibit dimension-independent convergence rates which equal, at least, the currently known rate estimates for N-term approximation. We propose to accelerate Bayesian estimation by first offline construction of reduced basis surrogates of the Bayesian posterior density. The parsimonious surrogates can then be employed for online data assimilation and for Bayesian estimation. They also open a perspective for optimal experimental design.« less

Preliminary isostatic residual gravity anomaly map of Paso Robles 30 x 60 minute quadrangle, California

USGS Publications Warehouse

McPhee, D.K.; Langenheim, V.E.; Watt, J.T.

2011-01-01

This isostatic residual gravity map is part of an effort to map the three-dimensional distribution of rocks in the central California Coast Ranges and will serve as a basis for modeling the shape of basins and for determining the location and geometry of faults within the Paso Robles quadrangle. Local spatial variations in the Earth\\'s gravity field, after accounting for variations caused by elevation, terrain, and deep crustal structure reflect the distribution of densities in the mid- to upper crust. Densities often can be related to rock type, and abrupt spatial changes in density commonly mark lithological or structural boundaries. High-density rocks exposed within the central Coast Ranges include Mesozoic granitic rocks (exposed northwest of Paso Robles), Jurassic to Cretaceous marine strata of the Great Valley Sequence (exposed primarily northeast of the San Andreas fault), and Mesozoic sedimentary and volcanic rocks of the Franciscan Complex [exposed in the Santa Lucia Range and northeast of the San Andreas fault (SAF) near Parkfield, California]. Alluvial sediments and Tertiary sedimentary rocks are characterized by low densities; however, with increasing depth of burial and age, the densities of these rocks may become indistinguishable from those of older basement rocks.

Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico

NASA Astrophysics Data System (ADS)

Roberts, Jason J.; Best, Benjamin D.; Mannocci, Laura; Fujioka, Ei; Halpin, Patrick N.; Palka, Debra L.; Garrison, Lance P.; Mullin, Keith D.; Cole, Timothy V. N.; Khan, Christin B.; McLellan, William A.; Pabst, D. Ann; Lockhart, Gwen G.

2016-03-01

Cetaceans are protected worldwide but vulnerable to incidental harm from an expanding array of human activities at sea. Managing potential hazards to these highly-mobile populations increasingly requires a detailed understanding of their seasonal distributions and habitats. Pursuant to the urgent need for this knowledge for the U.S. Atlantic and Gulf of Mexico, we integrated 23 years of aerial and shipboard cetacean surveys, linked them to environmental covariates obtained from remote sensing and ocean models, and built habitat-based density models for 26 species and 3 multi-species guilds using distance sampling methodology. In the Atlantic, for 11 well-known species, model predictions resembled seasonal movement patterns previously suggested in the literature. For these we produced monthly mean density maps. For lesser-known taxa, and in the Gulf of Mexico, where seasonal movements were less well described, we produced year-round mean density maps. The results revealed high regional differences in small delphinoid densities, confirmed the importance of the continental slope to large delphinoids and of canyons and seamounts to beaked and sperm whales, and quantified seasonal shifts in the densities of migratory baleen whales. The density maps, freely available online, are the first for these regions to be published in the peer-reviewed literature.

Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico

PubMed Central

Roberts, Jason J.; Best, Benjamin D.; Mannocci, Laura; Fujioka, Ei; Halpin, Patrick N.; Palka, Debra L.; Garrison, Lance P.; Mullin, Keith D.; Cole, Timothy V. N.; Khan, Christin B.; McLellan, William A.; Pabst, D. Ann; Lockhart, Gwen G.

2016-01-01

Cetaceans are protected worldwide but vulnerable to incidental harm from an expanding array of human activities at sea. Managing potential hazards to these highly-mobile populations increasingly requires a detailed understanding of their seasonal distributions and habitats. Pursuant to the urgent need for this knowledge for the U.S. Atlantic and Gulf of Mexico, we integrated 23 years of aerial and shipboard cetacean surveys, linked them to environmental covariates obtained from remote sensing and ocean models, and built habitat-based density models for 26 species and 3 multi-species guilds using distance sampling methodology. In the Atlantic, for 11 well-known species, model predictions resembled seasonal movement patterns previously suggested in the literature. For these we produced monthly mean density maps. For lesser-known taxa, and in the Gulf of Mexico, where seasonal movements were less well described, we produced year-round mean density maps. The results revealed high regional differences in small delphinoid densities, confirmed the importance of the continental slope to large delphinoids and of canyons and seamounts to beaked and sperm whales, and quantified seasonal shifts in the densities of migratory baleen whales. The density maps, freely available online, are the first for these regions to be published in the peer-reviewed literature. PMID:26936335

Oregon Cascades Play Fairway Analysis: Faults and Heat Flow maps

DOE Data Explorer

Adam Brandt

2015-11-15

This submission includes a fault map of the Oregon Cascades and backarc, a probability map of heat flow, and a fault density probability layer. More extensive metadata can be found within each zip file.

An improved consensus linkage map of barley based on flow-sorted chromosomes and SNP markers

USDA-ARS?s Scientific Manuscript database

Recent advances in high-throughput genotyping have made it easier to combine information from different mapping populations into consensus genetic maps, which provide increased marker density and genome coverage compared to individual maps. Previously, a SNP-based genotyping platform was developed a...

Snake states and their symmetries in graphene

NASA Astrophysics Data System (ADS)

Tiwari, Rakesh; Liu, Yang; Brada, Matej; Bruder, C.; Kusmartsev, F. V.; Mele, E. J.

Snake states are open trajectories for charged particles moving in two dimensions under the influence of a spatially varying perpendicular magnetic field. They can also occur in a constant perpendicular magnetic field when the particle density is made nonuniform as realized at a pn junction in a semiconductor, or in graphene. We examine the correspondence of such trajectories in monolayer graphene in the quantum limit for two families of domain walls: (a) a uniform doped carrier density in an antisymmetric perpendicular magnetic field and (b) antisymmetric carrier density distribution in a uniform perpendicular magnetic field. Although, these families support different internal symmetries, the pattern of the boundary and interface currents is the same in both cases. We demonstrate that these two physically different situations are gauge equivalent when rewritten in a Nambu doubled formulation of the two limiting problems. Using gauge transformations in particle-hole space to connect these two problems, we map the protected interfacial modes to the Bogoliubov quasiparticles of an interfacial one-dimensional p-wave paired state.

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

NASA Technical Reports Server (NTRS)

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

1980-01-01

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

Very High Quality Crystals of Wide-Gap II-VI Semiconductors: What for?

DTIC Science & Technology

2001-01-01

the reciprocal space mapping , by the etch pit density (EPD) measurements (to determine the density of dislocations) and by the measurement of the width...crystals. The EPD was in the range 5 x 1 + 104 cmn2 for Cdl.,ZnxTe crystals and about 104 cmz for ZnTe. The reciprocal space mapping of the crystals

Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix

PubMed Central

Zeil, Stephanie; Kovacs, Julio; Wriggers, Willy

2017-01-01

Abstract Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4–7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map–model pairs. PMID:27936925

Spectroscopic infrared extinction mapping as a probe of grain growth in IRDCs

NASA Astrophysics Data System (ADS)

Lim, Wanggi; Carey, Sean J.

2014-07-01

We present photometric and spectroscopic tests of MIR to FIR extinction laws toward IRDC G028.36+00.07, a potential site of massive star formation. Lim & Tan (2014, hereafter LT14) developed methods of FIR extinction mapping of this source using Spitzer-MIPS 24 micron and Herschel-PACS 70 micron images, and extending the MIR 8 micron mapping methods of (Butler & Tan 2012, hereafter BT12), finding evidence for grain growth in the highest mass surface density regions. Here we present initial results of spectroscopic infrared extinction (SIREX) mapping using Spitzer-IRS (14 to 38 micron) data of the same IRDC. These methods allow us to measure the SED of the diffuse Galactic ISM, which we compare to theoretical models of Draine & Li (2007), as well as to search for opacity law variations with mass surface density within the IRDC. By comparison with theoretical dust models, e.g., Ossenkopf & Henning (1994) and Ormel et al. (2011), we are able to search for compositional signatures of the grain ices, such as water and methanol. We find evidence for generally flatter MIR to FIR extinction laws as mass surface density increases, strengthening the evidence for grain and ice mantle growth in higher density regions.

A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity

PubMed Central

Leitwein, Maeva; Guinand, Bruno; Pouzadoux, Juliette; Desmarais, Erick; Berrebi, Patrick; Gagnaire, Pierre-Alexandre

2017-01-01

High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout. PMID:28235829

Comprehensive Characterization a Tidal Energy Site (Invited)

NASA Astrophysics Data System (ADS)

Polagye, B. L.; Thomson, J. M.; Bassett, C. S.; Epler, J.; Northwest National Marine Renewable Energy Center

2010-12-01

Northern Admiralty Inlet, Puget Sound, Washington is the proposed location of a pilot tidal energy project. Site-specific characterization of the physical and biological environment is required for device engineering and environmental analysis. However, the deep water and strong currents which make the site attractive for tidal energy development also pose unique challenges to collecting comprehensive information. This talk focuses on efforts to optimally site hydrokinetic turbines and estimate their acoustic impact, based on 18 months of field data collected to date. Additional characterization efforts being undertaken by the University of Washington branch of the Northwest National Marine Renewable Energy Center and its partners include marine mammal presence and behavior, water quality, seabed geology, and biofouling potential. Because kinetic power density varies with the cube of horizontal current velocity, an accurate map of spatial current variations is required to optimally site hydrokinetic turbines. Acoustic Doppler profilers deployed on the seabed show operationally meaningful variations in flow characteristics (e.g., power density, directionality, vertical shear) and tidal harmonic constituents over length scales of less than 100m. This is, in part, attributed to the proximity of this site to a headland. Because of these variations, interpolation between stationary measurement locations introduces potentially high uncertainty. The use of shipboard acoustic Doppler profilers is shown to be an effective tool for mapping peak currents and, combined with information from seabed profilers, may be able to resolve power density variations in the project area. Because noise levels from operating turbines are expected to exceed regulatory thresholds for incidental harassment of marine mammals known to be present in the project area, an estimate of the acoustic footprint is required to permit the pilot project. This requires site-specific descriptions of pre-existing ambient noise levels and the transmission loss (or practical spreading) at frequencies of interest. Recording hydrophones deployed on the seabed are used to quantify ambient noise, but are contaminated by self-noise during periods of strong currents. An empirical estimate of transmission loss is obtained from a source of opportunity - a passenger ferry which operates for more than twelve hours each day. By comparing recorded sound pressure levels against the location of the passenger ferry and other vessels (logged by an AIS receiver), the empirical transmission loss and source level for the ferry are obtained. Measurements of current velocity and underwater noise can apply routine oceanographic instruments and techniques. More unique measurements will be more challenging, such as high resolution sampling of current structure upstream and downstream of an operating device tens of meters off the seabed. Innovative approaches are required for cost effective characterization of tidal energy sites and monitoring of operating projects.

High critical currents in heavily doped (Gd,Y)Ba 2Cu 3O x superconductor tapes

DOE PAGES

Selvamanickam, V.; Gharahcheshmeh, M. Heydari; Xu, A.; ...

2015-01-20

REBa 2Cu 3O x superconductor tapes with moderate levels of dopants have been optimized for high critical current density in low magnetic fields at 77 K, but they do not exhibit exemplary performance in conditions of interest for practical applications, i.e., temperatures less than 50 K and fields of 2–30 T. Heavy doping of REBCO tapes has been avoided by researchers thus far due to deterioration in properties. Here, we report achievement of critical current densities (J c) above 20 MA/cm 2 at 30 K, 3 T in heavily doped (25 mol. % Zr-added) (Gd,Y)Ba 2Cu 3O x superconductor tapes,more » which is more than three times higher than the J c typically obtained in moderately doped tapes. Pinning force levels above 1000 GN/m 3 have also been attained at 20 K. A composition map of lift factor in J c (ratio of J c at 30 K, 3 T to the J c at 77 K, 0 T) has been developed which reveals the optimum film composition to obtain lift factors above six, which is thrice the typical value. A highly c-axis aligned BaZrO 3 (BZO) nanocolumn defect density of nearly 7 × 10 11 cm –2 as well as 2–3nm sized particles rich in Cu and Zr have been found in the high J c films.« less

Adaptive treatment-length optimization in spatiobiologically integrated radiotherapy

NASA Astrophysics Data System (ADS)

Ajdari, Ali; Ghate, Archis; Kim, Minsun

2018-04-01

Recent theoretical research on spatiobiologically integrated radiotherapy has focused on optimization models that adapt fluence-maps to the evolution of tumor state, for example, cell densities, as observed in quantitative functional images acquired over the treatment course. We propose an optimization model that adapts the length of the treatment course as well as the fluence-maps to such imaged tumor state. Specifically, after observing the tumor cell densities at the beginning of a session, the treatment planner solves a group of convex optimization problems to determine an optimal number of remaining treatment sessions, and a corresponding optimal fluence-map for each of these sessions. The objective is to minimize the total number of tumor cells remaining (TNTCR) at the end of this proposed treatment course, subject to upper limits on the biologically effective dose delivered to the organs-at-risk. This fluence-map is administered in future sessions until the next image is available, and then the number of sessions and the fluence-map are re-optimized based on the latest cell density information. We demonstrate via computer simulations on five head-and-neck test cases that such adaptive treatment-length and fluence-map planning reduces the TNTCR and increases the biological effect on the tumor while employing shorter treatment courses, as compared to only adapting fluence-maps and using a pre-determined treatment course length based on one-size-fits-all guidelines.

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

PubMed Central

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

2014-01-01

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

A high-density genetic map with array-based markers facilitates structural and quantitative trait locus analyses of the common wheat genome.

PubMed

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

2014-10-01

The large genome and allohexaploidy of common wheat have complicated construction of a high-density genetic map. Although improvements in the throughput of next-generation sequencing (NGS) technologies have made it possible to obtain a large amount of genotyping data for an entire mapping population by direct sequencing, including hexaploid wheat, a significant number of missing data points are often apparent due to the low coverage of sequencing. In the present study, a microarray-based polymorphism detection system was developed using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring (CS) and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808. On average, 2.49 missing data points per marker were observed in the 201 recombinant inbred lines, with a maximum of 42. Around 40% of the new markers were derived from genic regions and 11% from repetitive regions. The low number of retroelements indicated that the new polymorphic markers were mainly derived from the less repetitive region of the wheat genome. Around 25% of the mapped sequences were useful for alignment with the physical map of barley. Quantitative trait locus (QTL) analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Three-dimensional quantification of vorticity and helicity from 3D cine PC-MRI using finite-element interpolations.

PubMed

Sotelo, Julio; Urbina, Jesús; Valverde, Israel; Mura, Joaquín; Tejos, Cristián; Irarrazaval, Pablo; Andia, Marcelo E; Hurtado, Daniel E; Uribe, Sergio

2018-01-01

We propose a 3D finite-element method for the quantification of vorticity and helicity density from 3D cine phase-contrast (PC) MRI. By using a 3D finite-element method, we seamlessly estimate velocity gradients in 3D. The robustness and convergence were analyzed using a combined Poiseuille and Lamb-Ossen equation. A computational fluid dynamics simulation was used to compared our method with others available in the literature. Additionally, we computed 3D maps for different 3D cine PC-MRI data sets: phantom without and with coarctation (18 healthy volunteers and 3 patients). We found a good agreement between our method and both the analytical solution of the combined Poiseuille and Lamb-Ossen. The computational fluid dynamics results showed that our method outperforms current approaches to estimate vorticity and helicity values. In the in silico model, we observed that for a tetrahedral element of 2 mm of characteristic length, we underestimated the vorticity in less than 5% with respect to the analytical solution. In patients, we found higher values of helicity density in comparison to healthy volunteers, associated with vortices in the lumen of the vessels. We proposed a novel method that provides entire 3D vorticity and helicity density maps, avoiding the used of reformatted 2D planes from 3D cine PC-MRI. Magn Reson Med 79:541-553, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Mapping Mangrove Density from Rapideye Data in Central America

NASA Astrophysics Data System (ADS)

Son, Nguyen-Thanh; Chen, Chi-Farn; Chen, Cheng-Ru

2017-06-01

Mangrove forests provide a wide range of socioeconomic and ecological services for coastal communities. Extensive aquaculture development of mangrove waters in many developing countries has constantly ignored services of mangrove ecosystems, leading to unintended environmental consequences. Monitoring the current status and distribution of mangrove forests is deemed important for evaluating forest management strategies. This study aims to delineate the density distribution of mangrove forests in the Gulf of Fonseca, Central America with Rapideye data using the support vector machines (SVM). The data collected in 2012 for density classification of mangrove forests were processed based on four different band combination schemes: scheme-1 (bands 1-3, 5 excluding the red-edge band 4), scheme-2 (bands 1-5), scheme-3 (bands 1-3, 5 incorporating with the normalized difference vegetation index, NDVI), and scheme-4 (bands 1-3, 5 incorporating with the normalized difference red-edge index, NDRI). We also hypothesized if the obvious contribution of Rapideye red-edge band could improve the classification results. Three main steps of data processing were employed: (1), data pre-processing, (2) image classification, and (3) accuracy assessment to evaluate the contribution of red-edge band in terms of the accuracy of classification results across these four schemes. The classification maps compared with the ground reference data indicated the slightly higher accuracy level observed for schemes 2 and 4. The overall accuracies and Kappa coefficients were 97% and 0.95 for scheme-2 and 96.9% and 0.95 for scheme-4, respectively.

ERTS-1 image enhancement by optically combining density slices

NASA Technical Reports Server (NTRS)

Tapper, G. O.; Pease, R. W.

1973-01-01

The technique of density slicing using a photographic film and its application to enhancement of ERTS-1 imagery has proved to be useful for mapping varigated areal phenomena and provides a useful supplement ot the I2S MiniAddcol viewing system. The intial experiments conducted with this film were encouraging, and indicated that this technique of density slicing using readily accessible darkroom facilities and simple darkroom procedures allows rapid, accurate, and facile interpretation of certain areal phenomena to be made from the imagery. The distribution of the tree yucca, Yucca brevifolia Jaegeriana, in the eastern Mojave Desert of Southern California and southern Nevada was used as an example to test the accuracy of the technique for mapping purposes. The distribution was mapped at a relatively high level of accuracy.

Complex mountain terrain and disturbance history drive variation in forest aboveground live carbon density in the western Oregon Cascades, USA

PubMed Central

Zald, Harold S.J.; Spies, Thomas A.; Seidl, Rupert; Pabst, Robert J.; Olsen, Keith A.; Steel, E. Ashley

2016-01-01

Forest carbon (C) density varies tremendously across space due to the inherent heterogeneity of forest ecosystems. Variation of forest C density is especially pronounced in mountainous terrain, where environmental gradients are compressed and vary at multiple spatial scales. Additionally, the influence of environmental gradients may vary with forest age and developmental stage, an important consideration as forest landscapes often have a diversity of stand ages from past management and other disturbance agents. Quantifying forest C density and its underlying environmental determinants in mountain terrain has remained challenging because many available data sources lack the spatial grain and ecological resolution needed at both stand and landscape scales. The objective of this study was to determine if environmental factors influencing aboveground live carbon (ALC) density differed between young versus old forests. We integrated aerial light detection and ranging (lidar) data with 702 field plots to map forest ALC density at a grain of 25 m across the H.J. Andrews Experimental Forest, a 6369 ha watershed in the Cascade Mountains of Oregon, USA. We used linear regressions, random forest ensemble learning (RF) and sequential autoregressive modeling (SAR) to reveal how mapped forest ALC density was related to climate, topography, soils, and past disturbance history (timber harvesting and wildfires). ALC increased with stand age in young managed forests, with much greater variation of ALC in relation to years since wildfire in old unmanaged forests. Timber harvesting was the most important driver of ALC across the entire watershed, despite occurring on only 23% of the landscape. More variation in forest ALC density was explained in models of young managed forests than in models of old unmanaged forests. Besides stand age, ALC density in young managed forests was driven by factors influencing site productivity, whereas variation in ALC density in old unmanaged forests was also affected by finer scale topographic conditions associated with sheltered sites. Past wildfires only had a small influence on current ALC density, which may be a result of long times since fire and/or prevalence of non-stand replacing fire. Our results indicate that forest ALC density depends on a suite of multi-scale environmental drivers mediated by complex mountain topography, and that these relationships are dependent on stand age. The high and context-dependent spatial variability of forest ALC density has implications for quantifying forest carbon stores, establishing upper bounds of potential carbon sequestration, and scaling field data to landscape and regional scales. PMID:27041818

A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

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

Shirasawa, Kenta; Tanaka, Masaru; Takahata, Yasuhiro

Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we usedmore » an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.« less

A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

DOE PAGES

Shirasawa, Kenta; Tanaka, Masaru; Takahata, Yasuhiro; ...

2017-03-10

Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we usedmore » an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.« less

The relation of ground-water quality to housing density, Cape Cod, Massachusetts

USGS Publications Warehouse

Persky, J.H.

1986-01-01

Correlation of median nitrate concentration in groundwater with housing density for 18 sample areas on Cape Cod yields a Pearson correlation coefficient of 0.802, which is significant at the 95 % confidence level. In five of nine sample areas where housing density is greater than one unit/acre, nitrate concentrations exceed 5 mg of nitrate/L (the Barnstable County planning goal for nitrate) in 25% of wells. Nitrate concentrations exceed 5 mg of nitrogen/L in 25% of wells in only one of nine sample areas where housing density is less than one unit/acre. Median concentrations of sodium and iron, and median levels of pH and specific conductance, are not significantly correlated with housing density. A computer generated map of nitrate shows a positive relation between nitrate concentration and housing density on Cape Cod. However, the presence of septage- or sewage-disposal sites and fertilizer use are also important factors that affect the nitrate concentration. A map of specific conductance also shows a positive relation to housing density, but little or no relation between housing density and sodium, ammonia, pH, or iron is apparent on the maps. Chemical analyses of samples collected from 3,468 private- and public-supply wells between January 1980 and June 1984 were used to examine the extent to which housing density determines water quality on Cape Cod, an area largely unsewered and underlain by a sole source aquifer. (Author 's abstract)

Mapping the Recent US Hurricanes Triggered Flood Events in Near Real Time

NASA Astrophysics Data System (ADS)

Shen, X.; Lazin, R.; Anagnostou, E. N.; Wanik, D. W.; Brakenridge, G. R.

2017-12-01

Synthetic Aperture Radar (SAR) observations is the only reliable remote sensing data source to map flood inundation during severe weather events. Unfortunately, since state-of-art data processing algorithms cannot meet the automation and quality standard of a near-real-time (NRT) system, quality controlled inundation mapping by SAR currently depends heavily on manual processing, which limits our capability to quickly issue flood inundation maps at global scale. Specifically, most SAR-based inundation mapping algorithms are not fully automated, while those that are automated exhibit severe over- and/or under-detection errors that limit their potential. These detection errors are primarily caused by the strong overlap among the SAR backscattering probability density functions (PDF) of different land cover types. In this study, we tested a newly developed NRT SAR-based inundation mapping system, named Radar Produced Inundation Diary (RAPID), using Sentinel-1 dual polarized SAR data over recent flood events caused by Hurricanes Harvey, Irma, and Maria (2017). The system consists of 1) self-optimized multi-threshold classification, 2) over-detection removal using land-cover information and change detection, 3) under-detection compensation, and 4) machine-learning based correction. Algorithm details are introduced in another poster, H53J-1603. Good agreements were obtained by comparing the result from RAPID with visual interpretation of SAR images and manual processing from Dartmouth Flood Observatory (DFO) (See Figure 1). Specifically, the over- and under-detections that is typically noted in automated methods is significantly reduced to negligible levels. This performance indicates that RAPID can address the automation and accuracy issues of current state-of-art algorithms and has the potential to apply operationally on a number of satellite SAR missions, such as SWOT, ALOS, Sentinel etc. RAPID data can support many applications such as rapid assessment of damage losses and disaster alleviation/rescue at global scale.

High-density genetic map construction and comparative genome analysis in asparagus bean.

PubMed

Huang, Haitao; Tan, Huaqiang; Xu, Dongmei; Tang, Yi; Niu, Yisong; Lai, Yunsong; Tie, Manman; Li, Huanxiu

2018-03-19

Genetic maps are a prerequisite for quantitative trait locus (QTL) analysis, marker-assisted selection (MAS), fine gene mapping, and assembly of genome sequences. So far, several asparagus bean linkage maps have been established using various kinds of molecular markers. However, these maps were all constructed by gel- or array-based markers. No maps based on sequencing method have been reported. In this study, an NGS-based strategy, SLAF-seq, was applied to create a high-density genetic map for asparagus bean. Through SLAF library construction and Illumina sequencing of two parents and 100 F2 individuals, a total of 55,437 polymorphic SLAF markers were developed and mined for SNP markers. The map consisted of 5,225 SNP markers in 11 LGs, spanning a total distance of 1,850.81 cM, with an average distance between markers of 0.35 cM. Comparative genome analysis with four other legume species, soybean, common bean, mung bean and adzuki bean showed that asparagus bean is genetically more related to adzuki bean. The results will provide a foundation for future genomic research, such as QTL fine mapping, comparative mapping in pulses, and offer support for assembling asparagus bean genome sequence.

Optimization of magnetic flux density for fast MREIT conductivity imaging using multi-echo interleaved partial fourier acquisitions.

PubMed

Chauhan, Munish; Jeong, Woo Chul; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

2013-08-27

Magnetic resonance electrical impedance tomography (MREIT) has been introduced as a non-invasive method for visualizing the internal conductivity and/or current density of an electrically conductive object by externally injected currents. The injected current through a pair of surface electrodes induces a magnetic flux density distribution inside the imaging object, which results in additional magnetic flux density. To measure the magnetic flux density signal in MREIT, the phase difference approach in an interleaved encoding scheme cancels out the systematic artifacts accumulated in phase signals and also reduces the random noise effect by doubling the measured magnetic flux density signal. For practical applications of in vivo MREIT, it is essential to reduce the scan duration maintaining spatial-resolution and sufficient contrast. In this paper, we optimize the magnetic flux density by using a fast gradient multi-echo MR pulse sequence. To recover the one component of magnetic flux density Bz, we use a coupled partial Fourier acquisitions in the interleaved sense. To prove the proposed algorithm, we performed numerical simulations using a two-dimensional finite-element model. For a real experiment, we designed a phantom filled with a calibrated saline solution and located a rubber balloon inside the phantom. The rubber balloon was inflated by injecting the same saline solution during the MREIT imaging. We used the multi-echo fast low angle shot (FLASH) MR pulse sequence for MRI scan, which allows the reduction of measuring time without a substantial loss in image quality. Under the assumption of a priori phase artifact map from a reference scan, we rigorously investigated the convergence ratio of the proposed method, which was closely related with the number of measured phase encode set and the frequency range of the background field inhomogeneity. In the phantom experiment with a partial Fourier acquisition, the total scan time was less than 6 seconds to measure the magnetic flux density Bz data with 128×128 spacial matrix size, where it required 10.24 seconds to fill the complete k-space region. Numerical simulation and experimental results demonstrated that the proposed method reduces the scanning time and provides the recovered Bz data comparable to what we obtained by measuring complete k-space data.

Density-Aware Clustering Based on Aggregated Heat Kernel and Its Transformation

DOE PAGES

Huang, Hao; Yoo, Shinjae; Yu, Dantong; ...

2015-06-01

Current spectral clustering algorithms suffer from the sensitivity to existing noise, and parameter scaling, and may not be aware of different density distributions across clusters. If these problems are left untreated, the consequent clustering results cannot accurately represent true data patterns, in particular, for complex real world datasets with heterogeneous densities. This paper aims to solve these problems by proposing a diffusion-based Aggregated Heat Kernel (AHK) to improve the clustering stability, and a Local Density Affinity Transformation (LDAT) to correct the bias originating from different cluster densities. AHK statistically\\ models the heat diffusion traces along the entire time scale, somore » it ensures robustness during clustering process, while LDAT probabilistically reveals local density of each instance and suppresses the local density bias in the affinity matrix. Our proposed framework integrates these two techniques systematically. As a result, not only does it provide an advanced noise-resisting and density-aware spectral mapping to the original dataset, but also demonstrates the stability during the processing of tuning the scaling parameter (which usually controls the range of neighborhood). Furthermore, our framework works well with the majority of similarity kernels, which ensures its applicability to many types of data and problem domains. The systematic experiments on different applications show that our proposed algorithms outperform state-of-the-art clustering algorithms for the data with heterogeneous density distributions, and achieve robust clustering performance with respect to tuning the scaling parameter and handling various levels and types of noise.« less

The Effect of Arc Proximity on Hydrothermal Activity Along Spreading Centers: New Evidence From the Mariana Back Arc (12.7°N-18.3°N)

NASA Astrophysics Data System (ADS)

Baker, Edward T.; Walker, Sharon L.; Resing, Joseph A.; Chadwick, William W.; Merle, Susan G.; Anderson, Melissa O.; Butterfield, David A.; Buck, Nathan J.; Michael, Susanna

2017-11-01

Back-arc spreading centers (BASCs) form a distinct class of ocean spreading ridges distinguished by steep along-axis gradients in spreading rate and by additional magma supplied through subduction. These characteristics can affect the population and distribution of hydrothermal activity on BASCs compared to mid-ocean ridges (MORs). To investigate this hypothesis, we comprehensively explored 600 km of the southern half of the Mariana BASC. We used water column mapping and seafloor imaging to identify 19 active vent sites, an increase of 13 over the current listing in the InterRidge Database (IRDB), on the bathymetric highs of 7 of the 11 segments. We identified both high and low (i.e., characterized by a weak or negligible particle plume) temperature discharge occurring on segment types spanning dominantly magmatic to dominantly tectonic. Active sites are concentrated on the two southernmost segments, where distance to the adjacent arc is shortest (<40 km), spreading rate is highest (>48 mm/yr), and tectonic extension is pervasive. Re-examination of hydrothermal data from other BASCs supports the generalization that hydrothermal site density increases on segments <90 km from an adjacent arc. Although exploration quality varies greatly among BASCs, present data suggest that, for a given spreading rate, the mean spatial density of hydrothermal activity varies little between MORs and BASCs. The present global database, however, may be misleading. On both BASCs and MORs, the spatial density of hydrothermal sites mapped by high-quality water-column surveys is 2-7 times greater than predicted by the existing IRDB trend of site density versus spreading rate.

Kinematic state estimation and motion planning for stochastic nonholonomic systems using the exponential map.

PubMed

Park, Wooram; Liu, Yan; Zhou, Yu; Moses, Matthew; Chirikjian, Gregory S

2008-04-11

A nonholonomic system subjected to external noise from the environment, or internal noise in its own actuators, will evolve in a stochastic manner described by an ensemble of trajectories. This ensemble of trajectories is equivalent to the solution of a Fokker-Planck equation that typically evolves on a Lie group. If the most likely state of such a system is to be estimated, and plans for subsequent motions from the current state are to be made so as to move the system to a desired state with high probability, then modeling how the probability density of the system evolves is critical. Methods for solving Fokker-Planck equations that evolve on Lie groups then become important. Such equations can be solved using the operational properties of group Fourier transforms in which irreducible unitary representation (IUR) matrices play a critical role. Therefore, we develop a simple approach for the numerical approximation of all the IUR matrices for two of the groups of most interest in robotics: the rotation group in three-dimensional space, SO(3), and the Euclidean motion group of the plane, SE(2). This approach uses the exponential mapping from the Lie algebras of these groups, and takes advantage of the sparse nature of the Lie algebra representation matrices. Other techniques for density estimation on groups are also explored. The computed densities are applied in the context of probabilistic path planning for kinematic cart in the plane and flexible needle steering in three-dimensional space. In these examples the injection of artificial noise into the computational models (rather than noise in the actual physical systems) serves as a tool to search the configuration spaces and plan paths. Finally, we illustrate how density estimation problems arise in the characterization of physical noise in orientational sensors such as gyroscopes.

An updated Lagrangian discontinuous Galerkin hydrodynamic method for gas dynamics

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

Wu, Tong; Shashkov, Mikhail Jurievich; Morgan, Nathaniel Ray

Here, we present a new Lagrangian discontinuous Galerkin (DG) hydrodynamic method for gas dynamics. The new method evolves conserved unknowns in the current configuration, which obviates the Jacobi matrix that maps the element in a reference coordinate system or the initial coordinate system to the current configuration. The density, momentum, and total energy (ρ, ρu, E) are approximated with conservative higher-order Taylor expansions over the element and are limited toward a piecewise constant field near discontinuities using a limiter. Two new limiting methods are presented for enforcing the bounds on the primitive variables of density, velocity, and specific internal energymore » (ρ, u, e). The nodal velocity, and the corresponding forces, are calculated by solving an approximate Riemann problem at the element nodes. An explicit second-order method is used to temporally advance the solution. This new Lagrangian DG hydrodynamic method conserves mass, momentum, and total energy. 1D Cartesian coordinates test problem results are presented to demonstrate the accuracy and convergence order of the new DG method with the new limiters.« less

An updated Lagrangian discontinuous Galerkin hydrodynamic method for gas dynamics

DOE PAGES

Wu, Tong; Shashkov, Mikhail Jurievich; Morgan, Nathaniel Ray; ...

2018-04-09

Here, we present a new Lagrangian discontinuous Galerkin (DG) hydrodynamic method for gas dynamics. The new method evolves conserved unknowns in the current configuration, which obviates the Jacobi matrix that maps the element in a reference coordinate system or the initial coordinate system to the current configuration. The density, momentum, and total energy (ρ, ρu, E) are approximated with conservative higher-order Taylor expansions over the element and are limited toward a piecewise constant field near discontinuities using a limiter. Two new limiting methods are presented for enforcing the bounds on the primitive variables of density, velocity, and specific internal energymore » (ρ, u, e). The nodal velocity, and the corresponding forces, are calculated by solving an approximate Riemann problem at the element nodes. An explicit second-order method is used to temporally advance the solution. This new Lagrangian DG hydrodynamic method conserves mass, momentum, and total energy. 1D Cartesian coordinates test problem results are presented to demonstrate the accuracy and convergence order of the new DG method with the new limiters.« less

Operational specification and forecasting advances for Dst, LEO thermospheric densities, and aviation radiation dose and dose rate

NASA Astrophysics Data System (ADS)

Tobiska, W.; Knipp, D. J.; Burke, W. J.; Bouwer, D.; Bailey, J. J.; Hagan, M. P.; Didkovsky, L. V.; Garrett, H. B.; Bowman, B. R.; Gannon, J. L.; Atwell, W.; Blake, J. B.; Crain, W.; Rice, D.; Schunk, R. W.; Fulgham, J.; Bell, D.; Gersey, B.; Wilkins, R.; Fuschino, R.; Flynn, C.; Cecil, K.; Mertens, C. J.; Xu, X.; Crowley, G.; Reynolds, A.; Azeem, S. I.; Wiley, S.; Holland, M.; Malone, K.

2013-12-01

Space weather's effects upon the near-Earth environment are due to dynamic changes in the energy transfer processes from the Sun's photons, particles, and fields. Of the space environment domains that are affected by space weather, the magnetosphere, thermosphere, and even troposphere are key regions that are affected. Space Environment Technologies (SET) has developed and is producing innovative space weather applications. Key operational systems for providing timely information about the effects of space weather on these domains are SET's Magnetosphere Alert and Prediction System (MAPS), LEO Alert and Prediction System (LAPS), and Automated Radiation Measurements for Aviation Safety (ARMAS) system. MAPS provides a forecast Dst index out to 6 days through the data-driven, redundant data stream Anemomilos algorithm. Anemomilos uses observational proxies for the magnitude, location, and velocity of solar ejecta events. This forecast index is used by satellite operations to characterize upcoming geomagnetic storms, for example. LAPS is the SET fully redundant operational system providing recent history, current epoch, and forecast solar and geomagnetic indices for use in operational versions of the JB2008 thermospheric density model. The thermospheric densities produced by that system, driven by the LAPS data, are forecast to 72-hours to provide the global mass densities for satellite operators. ARMAS is a project that has successfully demonstrated the operation of a micro dosimeter on aircraft to capture the real-time radiation environment due to Galactic Cosmic Rays and Solar Energetic Particles. The dose and dose-rates are captured on aircraft, downlinked in real-time via the Iridium satellites, processed on the ground, incorporated into the most recent NAIRAS global radiation climatology data runs, and made available to end users via the web and smart phone apps. ARMAS provides the 'weather' of the radiation environment to improve air-crew and passenger safety. Many of the data products from MAPS, LAPS, and ARMAS are available on the SpaceWx smartphone app for iPhone, iPad, iPod, and Android professional users and public space weather education. We describe recent forecasting advances for moving the space weather information from these automated systems into operational, derivative products for communications, aviation, and satellite operations uses.

SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications

PubMed Central

Iquebal, Mir Asif; Jaiswal, Sarika; Angadi, U.B.; Sablok, Gaurav; Arora, Vasu; Kumar, Sunil; Rai, Anil; Kumar, Dinesh

2015-01-01

DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world’s first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of ‘mono’ repeat (76.82%) over ‘di’ repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of bioethanol and biogas production along with reaping advantage of crop efficiency in terms of low water and carbon footprint especially in era of climate change. Database URL: http://webapp.cabgrid.res.in/sbmdb/ PMID:26647370

SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.

PubMed

Iquebal, Mir Asif; Jaiswal, Sarika; Angadi, U B; Sablok, Gaurav; Arora, Vasu; Kumar, Sunil; Rai, Anil; Kumar, Dinesh

2015-01-01

DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world's first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of 'mono' repeat (76.82%) over 'di' repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of bioethanol and biogas production along with reaping advantage of crop efficiency in terms of low water and carbon footprint especially in era of climate change. Database URL: http://webapp.cabgrid.res.in/sbmdb/. © The Author(s) 2015. Published by Oxford University Press.

Mapping the spatial distribution of star formation in cluster galaxies at z ~0.5 with the Grism Lens-Amplified Survey from Space (GLASS)

NASA Astrophysics Data System (ADS)

Vulcani, B.; Treu, T.; Schmidt, K. B.; Poggianti, B. M.; Dressler, A.; Fontana, A.; Bradač, M.; Brammer, G. B.; Hoag, A.; Huang, K.; Malkan, M.; Pentericci, L.; Trenti, M.; von der Linden, A.; Abramson, L.; He, J.; Morris, G.

2016-06-01

What physical processes regulate star formation in dense environments? Understanding why galaxy evolution is environment dependent is one of the key questions of current astrophysics. I will present the first characterization of the spatial distribution of star formation in cluster galaxies at z~0.5, and compare to a field control sample, in order to quantify the role of different physical processes that are believed to be responsible for shutting down star formation (Vulcani et al. 2015, Vulcani et al. in prep). The analysis makes use of data from the Grism Lens-Amplified Survey from Space (GLASS), a large HST cycle-21 program targeting 10 massive galaxy clusters with extensive HST imaging from CLASH and the Frontier Field Initiative. The program consists of 140 primary and 140 parallel orbits of near-infrared WCF3 and optical ACS slitless grism observations, which result in 3D spectroscopy of hundreds of galaxies. The grism data are used to produce spatially resolved maps of the star formation density, while the stellar mass density and optical surface brightness are obtained from multiband imaging. I will describe quantitative measures of the spatial location and extent of the star formation rate. I will show that both in clusters and in the field, Hα is more extended than the rest-frame UV continuum in 60% of the cases, consistent with diffuse star formation and inside out growth. The Hα emission appears more extended in cluster galaxies than in the field, pointing perhaps to ionized gas being stripped and/or star formation being enhanced at large radii. The peak of the Hα emission and that of the continuum are offset by less than 1 kpc. I will also correlate the properties of the Hα maps to the cluster global properties, such as the hot gas density, and the surface mass density. The characterization of the spatial distribution of Halpha provides a new window, yet poorly exploited, on the mechanisms that regulate star formation and morphological transformation in dense environments.

Anomalous Transport Properties of Dense QCD in a Magnetic Field

NASA Astrophysics Data System (ADS)

de la Incera, Vivian

2017-06-01

Despite recent advancements in the study and understanding of the phase diagram of strongly interacting matter, the region of high baryonic densities and low temperatures has remained difficult to reach in the lab. Things are expected to change with the planned HIC experiments at FAIR in Germany and NICA in Russia, which will open a window to the high-density-low-temperature segment of the QCD phase map, providing a unique opportunity to test the validity of model calculations that have predicted the formation of spatially inhomogeneous phases with broken chiral symmetry at intermediate-to-high densities. Such a density region is also especially relevant for the physics of neutron stars, as they have cores that can have several times the nuclear saturation density. On the other hand, strong magnetic fields, whose presence is fairly common in HIC and in neutron stars, can affect the properties of these exotic phases and lead to signatures potentially observable in these two settings. In this paper, I examine the anomalous transport properties produced by the spectral asymmetry of the lowest Landau level (LLL) in a QCD-inspired NJL model with a background magnetic field that exhibits chiral symmetry breaking at high density via the formation of a Dual Chiral Density Wave (DCDW) condensate. It turns out that in this model the electromagnetic interactions are described by the axion electrodynamics equations and there is a dissipationless Hall current.

The use of current source density as electrophysiological correlates in neuropsychiatric disorders: a review of human studies

PubMed Central

Kamarajan, Chella; Pandey, Ashwini K.; Chorlian, David B.; Porjesz, Bernice

2014-01-01

The use of current source density (CSD), the Laplacian of the scalp surface voltage, to map the electrical activity of the brain is a powerful method in studies of cognitive and affective phenomena. During the last few decades, mapping of CSD has been successfully applied to characterize several neuropsychiatric conditions such as alcoholism, schizophrenia, depression, anxiety disorders, childhood/developmental disorders, and neurological conditions (i.e., epilepsy and brain lesions) using electrophysiological data from resting state and during cognitive performance. Use of CSD and Laplacian measures has proven effective in elucidating topographic and activation differences between groups: i) patients with a specific diagnosis vs. healthy controls, ii) subjects at high risk for a specific diagnosis vs. low risk or normal controls, and iii) patients with specific symptom(s) vs. patients without these symptom(s). The present review outlines and summarizes the studies that have employed CSD measures in investigating several neuropsychiatric conditions. The advantages and potential of CSD-based methods in clinical and research applications along with some of the limitations inherent in the CSD-based methods are discussed in the review, as well as future directions to expand the implementation of CSD to other potential clinical applications. As CSD methods have proved to be more advantageous than using scalp potential data to understand topographic and source activations, its clinical applications offer promising potential, not only for a better understanding of a range of psychiatric conditions, but also for a variety of focal neurological disorders, including epilepsy and other conditions involving brain lesions and surgical interventions. PMID:25448264

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

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

Dalcanton, Julianne J.; Fouesneau, Morgan; Weisz, Daniel R.

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 ofmore » ≳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.« less

Preliminary Mapping of the Western Corn Rootworm (Diabrotica virgifera virgifera) Genome and Quantitative Trait Locus (QTL) Interval Mapping for Growth

USDA-ARS?s Scientific Manuscript database

Preliminary investigations into the organization of the western corn rootworm (Diabrotica virgifera virgifera; WCR) genome have resulted in low to moderate density gender-specific maps constructed from progeny of a backcrossed, short-diapause WCR family. Maps were based upon variation at microsatel...

The North American upper mantle: density, composition, and evolution

USGS Publications Warehouse

Mooney, Walter D.; Kaban, Mikhail K.

2010-01-01

The upper mantle of North America has been well studied using various seismic methods. Here we investigate the density structure of the North American (NA) upper mantle based on the integrative use of the gravity field and seismic data. The basis of our study is the removal of the gravitational effect of the crust to determine the mantle gravity anomalies. The effect of the crust is removed in three steps by subtracting the gravitational contributions of (1) topography and bathymetry, (2) low-density sedimentary accumulations, and (3) the three-dimensional density structure of the crystalline crust as determined by seismic observations. Information regarding sedimentary accumulations, including thickness and density, are taken from published maps and summaries of borehole measurements of densities; the seismic structure of the crust is based on a recent compilation, with layer densities estimated from P-wave velocities. The resultant mantle gravity anomaly map shows a pronounced negative anomaly (−50 to −400 mGal) beneath western North America and the adjacent oceanic region and positive anomalies (+50 to +350 mGal) east of the NA Cordillera. This pattern reflects the well-known division of North America into the stable eastern region and the tectonically active western region. The close correlation of large-scale features of the mantle anomaly map with those of the topographic map indicates that a significant amount of the topographic uplift in western NA is due to buoyancy in the hot upper mantle, a conclusion supported by previous investigations. To separate the contributions of mantle temperature anomalies from mantle compositional anomalies, we apply an additional correction to the mantle anomaly map for the thermal structure of the uppermost mantle. The thermal model is based on the conversion of seismic shear-wave velocities to temperature and is consistent with mantle temperatures that are independently estimated from heat flow and heat production data. The thermally corrected mantle density map reveals density anomalies that are chiefly due to compositional variations. These compositional density anomalies cause gravitational anomalies that reach ~250 mGal. A pronounced negative anomaly (−50 to −200 mGal) is found over the Canadian shield, which is consistent with chemical depletion and a corresponding low density of the lithospheric mantle, also referred to as the mantle tectosphere. The strongest positive anomaly is coincident with the Gulf of Mexico and indicates a positive density anomaly in the upper mantle, possibly an eclogite layer that has caused subsidence in the Gulf. Two linear positive anomalies are also seen south of 40°N: one with a NE-SW trend in the eastern United States, roughly coincident with the Grenville-Appalachians, and a second with a NW-SE trend beneath the states of Texas, New Mexico, and Colorado. These anomalies are interpreted as being due to (1) the presence of remnants of an oceanic slab in the upper mantle beneath the Grenville-Appalachian suture and (2) mantle thickening caused by a period of shallow, flat subduction during the Laramie orogeny, respectively. Based on these geophysical results, the evolution of the NA upper mantle is depicted in a series of maps and cartoons that display the primary processes that have formed and modified the NA crust and lithospheric upper mantle.

Shadows and Dust: Mid-Infrared Extinction Mapping of the Initial Conditions of Massive Star and Star Cluster Formation

NASA Astrophysics Data System (ADS)

Tan, Jonathan

We describe a research plan to develop and extend the mid-infrared (MIR) extinction mapping technique presented by Butler & Tan (2009), who studied Infrared Dark Clouds (IRDCs) using Spitzer Space Telescope Infrared Array Camera (IRAC) 8 micron images. This method has the ability to probe the detailed spatial structure of very high column density regions, i.e. the gas clouds thought to represent the initial conditions for massive star and star cluster formation. We will analyze the data Spitzer obtained at other wavelengths, i.e. the IRAC bands at 3.6, 4.5 and 5.8 microns, and the Multiband Imaging Photometer (MIPS) bands, especially at 24 microns. This will allow us to measure the dust extinction law across the MIR and search for evidence of dust grain evolution, e.g. grain growth and ice mantle formation, as a function of gas density and column density. We will also study the detailed structure of the extinction features, including individual cores that may form single stars or close binaries, especially focusing on those cores that may form massive stars. By studying independent dark cores in a given IRDC, we will be able to test if they have a common minimum observed intensity, which we will then attribute to the foreground. This is a new method that should allow us to more accurately map distant, high column density IRDCs, probing more extreme regimes of star formation. We will combine MIR extinction mapping, which works best at high column densities, with near- IR mapping based on 2MASS images of star fields, which is most useful at lower columns that probe the extended giant molecular cloud structure. This information is crucial to help understand the formation process of IRDCs, which may be the rate limiting step for global galactic star formation rates. We will use our new extinction mapping methods to analyze large samples of IRDCs and thus search the Galaxy for the most extreme examples of high column density cores and assess the global star formation efficiency in dense gas. We will estimate the ability of future NASA missions, such as JWST, to carry out MIR extinction mapping science. We will develop the results of this research into an E/PO presentation to be included in the various public outreach events organized and courses taught by the PI.

Modeling Earth's surface topography: decomposition of the static and dynamic components

NASA Astrophysics Data System (ADS)

Guerri, M.; Cammarano, F.; Tackley, P. J.

2017-12-01

Isolating the portion of topography supported by mantle convection, the so-called dynamic topography, would give us precious information on vigor and style of the convection itself. Contrasting results on the estimate of dynamic topography motivate us to analyse the sources of uncertainties affecting its modeling. We obtain models of mantle and crust density, leveraging on seismic and mineral physics constraints. We use the models to compute isostatic topography and residual topography maps. Estimates of dynamic topography and associated synthetic geoid are obtained by instantaneous mantle flow modeling. We test various viscosity profiles and 3D viscosity distributions accounting for inferred lateral variations in temperature. We find that the patterns of residual and dynamic topography are robust, with an average correlation coefficient of 0.74 and 0.71, respectively. The amplitudes are however poorly constrained. For the static component, the considered lithospheric mantle density models result in topographies that differ, on average, 720 m, with peaks reaching 1.7 km. The crustal density models produce variations in isostatic topography averaging 350 m, with peaks of 1 km. For the dynamic component, we obtain peak-to-peak topography amplitude exceeding 3 km for all the tested mantle density and viscosity models. Such values of dynamic topography produce geoid undulations that are not in agreement with observations. Assuming chemical heterogeneities in the lower mantle, in correspondence with the LLSVPs (Large Low Shear wave Velocity Provinces), helps to decrease the amplitudes of dynamic topography and geoid, but reduces the correlation between synthetic and observed geoid. The correlation coefficients between the residual and dynamic topography maps is always less than 0.55. In general, our results indicate that, i) current knowledge of crust density, mantle density and mantle viscosity is still limited, ii) it is important to account for all the various sources of uncertainties when computing static and dynamic topography. In conclusion, a multidisciplinary approach, which involves multiple geophysics observations and constraints from mineral physics, is necessary for obtaining robust density models and, consequently, for properly estimating the dynamic topography.

Spatial mapping of humeral head bone density.

PubMed

Alidousti, Hamidreza; Giles, Joshua W; Emery, Roger J H; Jeffers, Jonathan

2017-09-01

Short-stem humeral replacements achieve fixation by anchoring to the metaphyseal trabecular bone. Fixing the implant in high-density bone can provide strong fixation and reduce the risk of loosening. However, there is a lack of data mapping the bone density distribution in the proximal humerus. The aim of the study was to investigate the bone density in proximal humerus. Eight computed tomography scans of healthy cadaveric humeri were used to map bone density distribution in the humeral head. The proximal humeral head was divided into 12 slices parallel to the humeral anatomic neck. Each slice was then divided into 4 concentric circles. The slices below the anatomic neck, where short-stem implants have their fixation features, were further divided into radial sectors. The average bone density for each of these regions was calculated, and regions of interest were compared using a repeated-measures analysis of variance with significance set at P < .05. Average apparent bone density was found to decrease from proximal to distal regions, with the majority of higher bone density proximal to the anatomic neck of the humerus (P < .05). Below the anatomic neck, bone density increases from central to peripheral regions, where cortical bone eventually occupies the space (P < .05). In distal slices below the anatomic neck, a higher bone density distribution in the medial calcar region was also observed. This study indicates that it is advantageous with respect to implant fixation to preserve some bone above the anatomic neck and epiphyseal plate and to use the denser bone at the periphery. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Regression modeling and mapping of coniferous forest basal area and tree density from discrete-return lidar and multispectral data

Treesearch

Andrew T. Hudak; Nicholas L. Crookston; Jeffrey S. Evans; Michael K. Falkowski; Alistair M. S. Smith; Paul E. Gessler; Penelope Morgan

2006-01-01

We compared the utility of discrete-return light detection and ranging (lidar) data and multispectral satellite imagery, and their integration, for modeling and mapping basal area and tree density across two diverse coniferous forest landscapes in north-central Idaho. We applied multiple linear regression models subset from a suite of 26 predictor variables derived...

Distribution of electric currents in sunspots from photosphere to corona

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

Gosain, Sanjay; Démoulin, Pascal; López Fuentes, Marcelo

2014-09-20

We present a study of two regular sunspots that exhibit nearly uniform twist from the photosphere to the corona. We derive the twist parameter in the corona and in the chromosphere by minimizing the difference between the extrapolated linear force-free field model field lines and the observed intensity structures in the extreme-ultraviolet images of the Sun. The chromospheric structures appear more twisted than the coronal structures by a factor of two. Further, we derive the vertical component of electric current density, j{sub z} , using vector magnetograms from the Hinode Solar Optical Telescope (SOT). The spatial distribution of j{sub z}more » has a zebra pattern of strong positive and negative values owing to the penumbral fibril structure resolved by Hinode/SOT. This zebra pattern is due to the derivative of the horizontal magnetic field across the thin fibrils; therefore, it is strong and masks weaker currents that might be present, for example, as a result of the twist of the sunspot. We decompose j{sub z} into the contribution due to the derivatives along and across the direction of the horizontal field, which follows the fibril orientation closely. The map of the tangential component has more distributed currents that are coherent with the chromospheric and coronal twisted structures. Moreover, it allows us to map and identify the direct and return currents in the sunspots. Finally, this decomposition of j{sub z} is general and can be applied to any vector magnetogram in order to better identify the weaker large-scale currents that are associated with coronal twisted/sheared structures.« less

Intracranial current density (LORETA) differences in QEEG frequency bands between depressed and non-depressed alcoholic patients.

PubMed

Coutin-Churchman, Pedro; Moreno, Rocío

2008-04-01

To assess possible differences in intracranial source distribution of surface QEEG power between depressed and non-depressed alcoholic patients in order to find any symptom-related topographic features of physiopathologic relevance. Low-Resolution Electromagnetic Tomography (LORETA) for the delta, theta, alpha and beta bands of EEG spectra was estimated from 38 alcoholic patients, 20 with and 18 without clinical depression, in which QEEG showed decreased slow and increased beta activity diffusely. Statistical non-parametric mapping was used to compare depressed and non-depressed groups. Measures of intracranial current density in individual patients at areas of significant differences were correlated with BDI scores. Patients with clinical depression showed areas of significantly lower current density than non-depressed patients in delta band at left anterior temporal, left midtemporal (including amygdala and hippocampus), and both frontopolar cortices mostly on the right; and in theta band at bilateral parietal lobe, anterior cingulate and medial frontal cortex. No differences were found at alpha and beta band. Intracranial current density in delta band at left parahippocampal, left midfrontal cortex and right frontopolar cortex was negatively correlated with BDI score. Theta band also showed negative correlations with BDI at sites of significant differences. Diffusely decreased delta and theta activity in the surface QEEG of alcoholic patients has a different intracranial distribution linked to the presence or not of clinical depression that seems to reveal a dysfunctional neuronal state at several specific limbic and other cortical locations that have been related to a specific clinical disorder such as depression. These results provided further evidence on the effects of depression in the context of alcohol dependence, in this case decreased slow activity as a possible marker of neuronal damage secondary to alcohol toxicity, clinically expressed as depressive symptoms when present in structures that are known to be related to clinical depression.

On Schrödinger's bridge problem

NASA Astrophysics Data System (ADS)

Friedland, S.

2017-11-01

In the first part of this paper we generalize Georgiou-Pavon's result that a positive square matrix can be scaled uniquely to a column stochastic matrix which maps a given positive probability vector to another given positive probability vector. In the second part we prove that a positive quantum channel can be scaled to another positive quantum channel which maps a given positive definite density matrix to another given positive definite density matrix using Brouwer's fixed point theorem. This result proves the Georgiou-Pavon conjecture for two positive definite density matrices, made in their recent paper. We show that the fixed points are unique for certain pairs of positive definite density matrices. Bibliography: 15 titles.

Effective absorption correction for energy dispersive X-ray mapping in a scanning transmission electron microscope: analysing the local indium distribution in rough samples of InGaN alloy layers.

PubMed

Wang, X; Chauvat, M-P; Ruterana, P; Walther, T

2017-12-01

We have applied our previous method of self-consistent k*-factors for absorption correction in energy-dispersive X-ray spectroscopy to quantify the indium content in X-ray maps of thick compound InGaN layers. The method allows us to quantify the indium concentration without measuring the sample thickness, density or beam current, and works even if there is a drastic local thickness change due to sample roughness or preferential thinning. The method is shown to select, point-by-point in a two-dimensional spectrum image or map, the k*-factor from the local Ga K/L intensity ratio that is most appropriate for the corresponding sample geometry, demonstrating it is not the sample thickness measured along the electron beam direction but the optical path length the X-rays have to travel through the sample that is relevant for the absorption correction. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

PubMed Central

2012-01-01

Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource for tetraploid cotton genome assembly, for cloning genes related to superior agronomic traits, and for further comparative genomic analyses in Gossypium. PMID:23046547

Evaluation of Techniques Used to Estimate Cortical Feature Maps

PubMed Central

Katta, Nalin; Chen, Thomas L.; Watkins, Paul V.; Barbour, Dennis L.

2011-01-01

Functional properties of neurons are often distributed nonrandomly within a cortical area and form topographic maps that reveal insights into neuronal organization and interconnection. Some functional maps, such as in visual cortex, are fairly straightforward to discern with a variety of techniques, while other maps, such as in auditory cortex, have resisted easy characterization. In order to determine appropriate protocols for establishing accurate functional maps in auditory cortex, artificial topographic maps were probed under various conditions, and the accuracy of estimates formed from the actual maps was quantified. Under these conditions, low-complexity maps such as sound frequency can be estimated accurately with as few as 25 total samples (e.g., electrode penetrations or imaging pixels) if neural responses are averaged together. More samples are required to achieve the highest estimation accuracy for higher complexity maps, and averaging improves map estimate accuracy even more than increasing sampling density. Undersampling without averaging can result in misleading map estimates, while undersampling with averaging can lead to the false conclusion of no map when one actually exists. Uniform sample spacing only slightly improves map estimation over nonuniform sample spacing typical of serial electrode penetrations. Tessellation plots commonly used to visualize maps estimated using nonuniform sampling are always inferior to linearly interpolated estimates, although differences are slight at higher sampling densities. Within primary auditory cortex, then, multiunit sampling with at least 100 samples would likely result in reasonable feature map estimates for all but the highest complexity maps and the highest variability that might be expected. PMID:21889537

An overview on genome organization of marine organisms.

PubMed

Costantini, Maria

2015-12-01

In this review we will concentrate on some general genome features of marine organisms and their evolution, ranging from vertebrate to invertebrates until unicellular organisms. Before genome sequencing, the ultracentrifugation in CsCl led to high resolution of mammalian DNA (without seeing at the sequence). The analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong in a small number of families characterized by different GC levels. The recent availability of a number of fully sequenced genomes allowed mapping very precisely the isochores, based on DNA sequences. Since isochores are tightly linked to biological properties such as gene density, replication timing and recombination, the new level of detail provided by the isochore map helped the understanding of genome structure, function and evolution. This led the current level of knowledge and to further insights. Copyright © 2015. Published by Elsevier B.V.

Assessment of groundwater recharge potential zone using GIS approach in Purworejo regency, Central Java province, Indonesia

NASA Astrophysics Data System (ADS)

Aryanto, Daniel Eko; Hardiman, Gagoek

2018-02-01

Floods and droughts in Purworejo regency are an indication of problems in groundwater management. The current development progress has led to land conversion which has an impact on the problem of water infiltration in Purworejo regency. This study aims to determine the distribution of groundwater recharge potential zones by using geographic information system as the basis for ground water management. The groundwater recharge potential zone is obtained by overlaying all the thematic maps that affect the groundwater infiltration. Each thematic map is weighted according to its effect on groundwater infiltration such as land-use - 25%, rainfall - 20%, litology - 20%, soil - 15%, slope - 10%, lineament - 5%, and river density - 5% to find groundwater recharge potential zones. The groundwater recharge potential zones thus obtained were divided into five categories, viz., very high, high, medium, low and very low zones. The results of this study may be useful for better groundwater planning and management.

Mapping brain activity with flexible graphene micro-transistors

NASA Astrophysics Data System (ADS)

Blaschke, Benno M.; Tort-Colet, Núria; Guimerà-Brunet, Anton; Weinert, Julia; Rousseau, Lionel; Heimann, Axel; Drieschner, Simon; Kempski, Oliver; Villa, Rosa; Sanchez-Vives, Maria V.; Garrido, Jose A.

2017-06-01

Establishing a reliable communication interface between the brain and electronic devices is of paramount importance for exploiting the full potential of neural prostheses. Current microelectrode technologies for recording electrical activity, however, evidence important shortcomings, e.g. challenging high density integration. Solution-gated field-effect transistors (SGFETs), on the other hand, could overcome these shortcomings if a suitable transistor material were available. Graphene is particularly attractive due to its biocompatibility, chemical stability, flexibility, low intrinsic electronic noise and high charge carrier mobilities. Here, we report on the use of an array of flexible graphene SGFETs for recording spontaneous slow waves, as well as visually evoked and also pre-epileptic activity in vivo in rats. The flexible array of graphene SGFETs allows mapping brain electrical activity with excellent signal-to-noise ratio (SNR), suggesting that this technology could lay the foundation for a future generation of in vivo recording implants.

Resonant coupling through a slot to a loaded cylindrical cavity: Experimental results

NASA Astrophysics Data System (ADS)

Norgard, John D.; Sega, Ronald M.

1990-03-01

The effect of cavity geometry on the energy coupled through a slot aperture is investigated through the use of planar mappings of the internal cavity field. A copper cylinder, closed at both ends, is constructed with copper mesh sections incorporated at the ends of the cylinder and in the cylinder wall opposite a thin slot aperture placed in the wall. The frequencies used for testing are 2 to 4 GHz. Internal field mapping is accomplished by placing thin carbon-loaded sheets in the plane of interest and recording the digitized temperature distribution using an infrared scanning system. The sheets are calibrated such that the temperature data is transformed to current densities or electric field strengths. Using several positions for the detection material, a three-dimensional field profile is obtained. The onset of the internal cavity resonance is studied as it is related to the energy coupled through small apertures.

A sequencing-based linkage map of cucumber

USDA-ARS?s Scientific Manuscript database

Genetic maps are important tools for molecular breeding, gene cloning, and study of meiotic recombination. In cucumber (Cucumis sativus L.), the marker density, resolution and genome coverage of previously developed genetic maps using PCR-based molecular markers are relatively low. In this study we ...

Snake River Plain Geothermal Play Fairway Analysis - Phase 1 Raster Files

DOE Data Explorer

John Shervais

2015-10-09

Snake River Plain Play Fairway Analysis - Phase 1 CRS Raster Files. This dataset contains raster files created in ArcGIS. These raster images depict Common Risk Segment (CRS) maps for HEAT, PERMEABILITY, AND SEAL, as well as selected maps of Evidence Layers. These evidence layers consist of either Bayesian krige functions or kernel density functions, and include: (1) HEAT: Heat flow (Bayesian krige map), Heat flow standard error on the krige function (data confidence), volcanic vent distribution as function of age and size, groundwater temperature (equivalue interval and natural breaks bins), and groundwater T standard error. (2) PERMEABILTY: Fault and lineament maps, both as mapped and as kernel density functions, processed for both dilational tendency (TD) and slip tendency (ST), along with data confidence maps for each data type. Data types include mapped surface faults from USGS and Idaho Geological Survey data bases, as well as unpublished mapping; lineations derived from maximum gradients in magnetic, deep gravity, and intermediate depth gravity anomalies. (3) SEAL: Seal maps based on presence and thickness of lacustrine sediments and base of SRP aquifer. Raster size is 2 km. All files generated in ArcGIS.

Human and Robotic Mission to Small Bodies: Mapping, Planning and Exploration

NASA Technical Reports Server (NTRS)

Neffian, Ara V.; Bellerose, Julie; Beyer, Ross A.; Archinal, Brent; Edwards, Laurence; Lee, Pascal; Colaprete, Anthony; Fong, Terry

2013-01-01

This study investigates the requirements, performs a gap analysis and makes a set of recommendations for mapping products and exploration tools required to support operations and scientific discovery for near- term and future NASA missions to small bodies. The mapping products and their requirements are based on the analysis of current mission scenarios (rendezvous, docking, and sample return) and recommendations made by the NEA Users Team (NUT) in the framework of human exploration. The mapping products that sat- isfy operational, scienti c, and public outreach goals include topography, images, albedo, gravity, mass, density, subsurface radar, mineralogical and thermal maps. The gap analysis points to a need for incremental generation of mapping products from low (flyby) to high-resolution data needed for anchoring and docking, real-time spatial data processing for hazard avoidance and astronaut or robot localization in low gravity, high dynamic environments, and motivates a standard for coordinate reference systems capable of describing irregular body shapes. Another aspect investigated in this study is the set of requirements and the gap analysis for exploration tools that support visualization and simulation of operational conditions including soil interactions, environment dynamics, and communications coverage. Building robust, usable data sets and visualisation/simulation tools is the best way for mission designers and simulators to make correct decisions for future missions. In the near term, it is the most useful way to begin building capabilities for small body exploration without needing to commit to specific mission architectures.

Mapping invasive Phragmites australis in the coastal Great Lakes with ALOS PALSAR satellite imagery for decision support

USGS Publications Warehouse

Bourgeau-Chavez, Laura L.; Kowalski, Kurt P.; Carlson Mazur, Martha L.; Scarbrough, Kirk A.; Powell, Richard B.; Brooks, Colin N.; Huberty, Brian; Jenkins, Liza K.; Banda, Elizabeth C.; Galbraith, David M.; Laubach, Zachary M.; Riordan, Kevin

2013-01-01

The invasive variety of Phragmites australis (common reed) forms dense stands that can cause negative impacts on coastal Great Lakes wetlands including habitat degradation and reduced biological diversity. Early treatment is key to controlling Phragmites, therefore a map of the current distribution is needed. ALOS PALSAR imagery was used to produce the first basin-wide distribution map showing the extent of large, dense invasive Phragmites-dominated habitats in wetlands and other coastal ecosystems along the U.S. shore of the Great Lakes. PALSAR is a satellite imaging radar sensor that is sensitive to differences in plant biomass and inundation patterns, allowing for the detection and delineation of these tall (up to 5 m), high density, high biomass invasive Phragmites stands. Classification was based on multi-season ALOS PALSAR L-band (23 cm wavelength) HH and HV polarization data. Seasonal (spring, summer, and fall) datasets were used to improve discrimination of Phragmites by taking advantage of phenological changes in vegetation and inundation patterns over the seasons. Extensive field collections of training and randomly selected validation data were conducted in 2010–2011 to aid in mapping and for accuracy assessments. Overall basin-wide map accuracy was 87%, with 86% producer's accuracy and 43% user's accuracy for invasive Phragmites. The invasive Phragmites maps are being used to identify major environmental drivers of this invader's distribution, to assess areas vulnerable to new invasion, and to provide information to regional stakeholders through a decision support tool.

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

PubMed Central

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

2013-01-01

Monitoring changes in the distribution and density of plant species often requires accurate and high-resolution baseline maps of those species. Detecting such change at the landscape scale is often problematic, particularly in remote areas. We examine a new technique to improve accuracy and objectivity in mapping vegetation, combining species distribution modelling and satellite image classification on a remote sub-Antarctic island. In this study, we combine spectral data from very high resolution WorldView-2 satellite imagery and terrain variables from a high resolution digital elevation model to improve mapping accuracy, in both pixel- and object-based classifications. Random forest classification was used to explore the effectiveness of these approaches on mapping the distribution of the critically endangered cushion plant 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. PMID:23940805

Geology of the Cape Mendocino, Eureka, Garberville, and Southwestern Part of the Hayfork 30 x 60 Minute Quadrangles and Adjacent Offshore Area, Northern California

USGS Publications Warehouse

McLaughlin, Robert J.; Ellen, S.D.; Blake, M.C.; Jayko, Angela S.; Irwin, W.P.; Aalto, K.R.; Carver, G.A.; Clarke, S.H.; Barnes, J.B.; Cecil, J.D.; Cyr, K.A.

2000-01-01

Introduction These geologic maps and accompanying structure sections depict the geology and structure of much of northwestern California and the adjacent continental margin. The map area includes the Mendocino triple junction, which is the juncture of the North American continental plate with two plates of the Pacific ocean basin. The map area also encompasses major geographic and geologic provinces of northwestern California. The maps incorporate much previously unpublished geologic mapping done between 1980 and 1995, as well as published mapping done between about 1950 and 1978. To construct structure sections to mid-crustal depths, we integrate the surface geology with interpretations of crustal structure based on seismicity, gravity and aeromagnetic data, offshore structure, and seismic reflection and refraction data. In addition to describing major geologic and structural features of northwestern California, the geologic maps have the potential to address a number of societally relevant issues, including hazards from earthquakes, landslides, and floods and problems related to timber harvest, wildlife habitat, and changing land use. All of these topics will continue to be of interest in the region, as changing land uses and population density interact with natural conditions. In these interactions, it is critical that the policies and practices affecting man and the environment integrate an adequate understanding of the geology. This digital map database, compiled from previously published and unpublished data, and new mapping by the authors, represents the general distribution of bedrock and surficial deposits in the mapped area. Together with the accompanying text file (ceghmf.ps, ceghmf.pdf, ceghmf.txt), it provides current information on the geologic structure and stratigraphy of the area covered. The database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U.S. Geological Survey. The scale of the source maps limits the spatial resolution (scale) of the database to 1:100,000 or smaller.

Formation of a spatter-rich pyroclastic density current deposit in a Neogene sequence of trachytic-mafic igneous rocks at Mason Spur, Erebus volcanic province, Antarctica

NASA Astrophysics Data System (ADS)

Martin, A. P.; Smellie, J. L.; Cooper, A. F.; Townsend, D. B.

2018-01-01

Erosion has revealed a remarkable section through the heart of a volcanic island, Mason Spur, in the southwestern Ross Sea, Antarctica, including an unusually well-exposed section of caldera fill. The near-continuous exposure, 10 km laterally and > 1 km vertically, cuts through Cenozoic alkalic volcanic rocks of the Erebus volcanic province (McMurdo Volcanic Group) and permits the study of an ancient volcanic succession that is rarely available due to subsequent burial or erosion. The caldera filling sequence includes an unusual trachytic spatter-rich lapilli tuff (ignimbrite) facies that is particularly striking because of the presence of abundant black fluidal, dense juvenile spatter clasts of trachytic obsidian up to 2 m long supported in a pale cream-coloured pumiceous lapilli tuff matrix. Field mapping indicates that the deposit is an ignimbrite and, together with petrological considerations, it is suggested that mixing of dense spatter and pumiceous lapilli tuff in the investigated deposit occurred during emplacement, not necessarily in the same vent, with the mixed fragmental material emplaced as a pyroclastic density current. Liquid water was not initially present but a steam phase was probably generated during transport and may represent water ingested during passage of the current as it passed over either wet ground, stream, shallow lake or (possibly) snow. Well-exposed caldera interiors are uncommon and that at Mason Spur is helping understand eruption dynamics associated with a complex large island volcano. The results of our study should help to elucidate interpretations of other, less well exposed, pyroclastic density current deposits elsewhere in Antarctica and globally.

Study on the mapping of dark matter clustering from real space to redshift space

NASA Astrophysics Data System (ADS)

Zheng, Yi; Song, Yong-Seon

2016-08-01

The mapping of dark matter clustering from real space to redshift space introduces the anisotropic property to the measured density power spectrum in redshift space, known as the redshift space distortion effect. The mapping formula is intrinsically non-linear, which is complicated by the higher order polynomials due to indefinite cross correlations between the density and velocity fields, and the Finger-of-God effect due to the randomness of the peculiar velocity field. Whilst the full higher order polynomials remain unknown, the other systematics can be controlled consistently within the same order truncation in the expansion of the mapping formula, as shown in this paper. The systematic due to the unknown non-linear density and velocity fields is removed by separately measuring all terms in the expansion directly using simulations. The uncertainty caused by the velocity randomness is controlled by splitting the FoG term into two pieces, 1) the ``one-point" FoG term being independent of the separation vector between two different points, and 2) the ``correlated" FoG term appearing as an indefinite polynomials which is expanded in the same order as all other perturbative polynomials. Using 100 realizations of simulations, we find that the Gaussian FoG function with only one scale-independent free parameter works quite well, and that our new mapping formulation accurately reproduces the observed 2-dimensional density power spectrum in redshift space at the smallest scales by far, up to k~ 0.2 Mpc-1, considering the resolution of future experiments.

Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes

PubMed Central

Anderson, Lorinda K.; Lai, Ann; Stack, Stephen M.; Rizzon, Carene; Gaut, Brandon S.

2006-01-01

Examining the relationships among DNA sequence, meiotic recombination, and chromosome structure at a genome-wide scale has been difficult because only a few markers connect genetic linkage maps with physical maps. Here, we have positioned 1195 genetically mapped expressed sequence tag (EST) markers onto the 10 pachytene chromosomes of maize by using a newly developed resource, the RN-cM map. The RN-cM map charts the distribution of crossing over in the form of recombination nodules (RNs) along synaptonemal complexes (SCs, pachytene chromosomes) and allows genetic cM distances to be converted into physical micrometer distances on chromosomes. When this conversion is made, most of the EST markers used in the study are located distally on the chromosomes in euchromatin. ESTs are significantly clustered on chromosomes, even when only euchromatic chromosomal segments are considered. Gene density and recombination rate (as measured by EST and RN frequencies, respectively) are strongly correlated. However, crossover frequencies for telomeric intervals are much higher than was expected from their EST frequencies. For pachytene chromosomes, EST density is about fourfold higher in euchromatin compared with heterochromatin, while DNA density is 1.4 times higher in heterochromatin than in euchromatin. Based on DNA density values and the fraction of pachytene chromosome length that is euchromatic, we estimate that ∼1500 Mbp of the maize genome is in euchromatin. This overview of the organization of the maize genome will be useful in examining genome and chromosome evolution in plants. PMID:16339046

A fully traits-based approach to modeling global vegetation distribution.

PubMed

van Bodegom, Peter M; Douma, Jacob C; Verheijen, Lieneke M

2014-09-23

Dynamic Global Vegetation Models (DGVMs) are indispensable for our understanding of climate change impacts. The application of traits in DGVMs is increasingly refined. However, a comprehensive analysis of the direct impacts of trait variation on global vegetation distribution does not yet exist. Here, we present such analysis as proof of principle. We run regressions of trait observations for leaf mass per area, stem-specific density, and seed mass from a global database against multiple environmental drivers, making use of findings of global trait convergence. This analysis explained up to 52% of the global variation of traits. Global trait maps, generated by coupling the regression equations to gridded soil and climate maps, showed up to orders of magnitude variation in trait values. Subsequently, nine vegetation types were characterized by the trait combinations that they possess using Gaussian mixture density functions. The trait maps were input to these functions to determine global occurrence probabilities for each vegetation type. We prepared vegetation maps, assuming that the most probable (and thus, most suited) vegetation type at each location will be realized. This fully traits-based vegetation map predicted 42% of the observed vegetation distribution correctly. Our results indicate that a major proportion of the predictive ability of DGVMs with respect to vegetation distribution can be attained by three traits alone if traits like stem-specific density and seed mass are included. We envision that our traits-based approach, our observation-driven trait maps, and our vegetation maps may inspire a new generation of powerful traits-based DGVMs.

[CT pulmonary density mapping: surgical utility].

PubMed

Gavezzoli, D; Caputo, P; Manelli, A; Zuccon, W; Faccini, M; Bonandrini, L

2002-04-01

The present paper considers the technique of CT scan maps of pulmonary isodensity, examining lung density differences as a function of the type of disease and considering their significance for the purposes of refined, useful diagnosis in a surgical context. METHODS. The method is used to examine 3 groups of subjects selected on a clinical/anamnestic basis and a further group already admitted for surgery. For each patient we obtained 2 thoracic density scans during the phase of maximum inspiration and expiration. On each scan we constructed 50 isodensity maps, the equivalent of more than 2500 measurements: the preliminary standard was represented by 100 wide windows to produce total "illumination" of the pulmonary fields. The isodensity windows were then codified differently. Subsequently, the density scans were analysed with the technique of scalar decomposition. The CT scan maps of lung isodensity proved useful for certain lung diseases in which early diagnosis, topographic extent of the pathology and the refined definition of the pathological picture provide important solutions as regards the indication and planning of surgical treatment and for the evaluation of the operative risk and prognosis. We consider that the technique is rapidly performed, not complex and inexpensive and is able to supply detailed information on the lung parenchyma such as to be used not only as a routine technique but also in emergencies.

Long-range hazard assessment of volcanic ash dispersal for a Plinian eruptive scenario at Popocatépetl volcano (Mexico): implications for civil aviation safety

USGS Publications Warehouse

Bonasia, Rosanna; Scaini, Chirara; Capra, Lucia; Nathenson, Manuel; Siebe, Claus; Arana-Salinas, Lilia; Folch, Arnau

2013-01-01

Popocatépetl is one of Mexico’s most active volcanoes threatening a densely populated area that includes Mexico City with more than 20 million inhabitants. The destructive potential of this volcano is demonstrated by its Late Pleistocene–Holocene eruptive activity, which has been characterized by recurrent Plinian eruptions of large magnitude, the last two of which destroyed human settlements in pre-Hispanic times. Popocatépetl’s reawakening in 1994 produced a crisis that culminated with the evacuation of two villages on the northeastern flank of the volcano. Shortly after, a monitoring system and a civil protection contingency plan based on a hazard zone map were implemented. The current volcanic hazards map considers the potential occurrence of different volcanic phenomena, including pyroclastic density currents and lahars. However, no quantitative assessment of the tephra hazard, especially related to atmospheric dispersal, has been performed. The presence of airborne volcanic ash at low and jet-cruise atmospheric levels compromises the safety of aircraft operations and forces re-routing of aircraft to prevent encounters with volcanic ash clouds. Given the high number of important airports in the surroundings of Popocatépetl volcano and considering the potential threat posed to civil aviation in Mexico and adjacent regions in case of a Plinian eruption, a hazard assessment for tephra dispersal is required. In this work, we present the first probabilistic tephra dispersal hazard assessment for Popocatépetl volcano. We compute probabilistic hazard maps for critical thresholds of airborne ash concentrations at different flight levels, corresponding to the situation defined in Europe during 2010, and still under discussion. Tephra dispersal mode is performed using the FALL3D numerical model. Probabilistic hazard maps are built for a Plinian eruptive scenario defined on the basis of geological field data for the “Ochre Pumice” Plinian eruption (4965 14C yr BP). FALL3D model input eruptive parameters are constrained through an inversion method carried out with the semi-analytical HAZMAP model and are varied by sampling them using probability density functions. We analyze the influence of seasonal variations on ash dispersal and estimate the average persistence of critical ash concentrations at relevant locations and airports. This study assesses the impact that a Plinian eruption similar to the Ochre Pumice eruption would have on the main airports of Mexico and adjacent areas. The hazard maps presented here can support long-term planning that would help minimize the impacts of such an eruption on civil aviation.

Long-range hazard assessment of volcanic ash dispersal for a Plinian eruptive scenario at Popocatépetl volcano (Mexico): implications for civil aviation safety

NASA Astrophysics Data System (ADS)

Bonasia, Rosanna; Scaini, Chiara; Capra, Lucia; Nathenson, Manuel; Siebe, Claus; Arana-Salinas, Lilia; Folch, Arnau

2014-01-01

Popocatépetl is one of Mexico's most active volcanoes threatening a densely populated area that includes Mexico City with more than 20 million inhabitants. The destructive potential of this volcano is demonstrated by its Late Pleistocene-Holocene eruptive activity, which has been characterized by recurrent Plinian eruptions of large magnitude, the last two of which destroyed human settlements in pre-Hispanic times. Popocatépetl's reawakening in 1994 produced a crisis that culminated with the evacuation of two villages on the northeastern flank of the volcano. Shortly after, a monitoring system and a civil protection contingency plan based on a hazard zone map were implemented. The current volcanic hazards map considers the potential occurrence of different volcanic phenomena, including pyroclastic density currents and lahars. However, no quantitative assessment of the tephra hazard, especially related to atmospheric dispersal, has been performed. The presence of airborne volcanic ash at low and jet-cruise atmospheric levels compromises the safety of aircraft operations and forces re-routing of aircraft to prevent encounters with volcanic ash clouds. Given the high number of important airports in the surroundings of Popocatépetl volcano and considering the potential threat posed to civil aviation in Mexico and adjacent regions in case of a Plinian eruption, a hazard assessment for tephra dispersal is required. In this work, we present the first probabilistic tephra dispersal hazard assessment for Popocatépetl volcano. We compute probabilistic hazard maps for critical thresholds of airborne ash concentrations at different flight levels, corresponding to the situation defined in Europe during 2010, and still under discussion. Tephra dispersal mode is performed using the FALL3D numerical model. Probabilistic hazard maps are built for a Plinian eruptive scenario defined on the basis of geological field data for the "Ochre Pumice" Plinian eruption (4965 14C yr BP). FALL3D model input eruptive parameters are constrained through an inversion method carried out with the semi-analytical HAZMAP model and are varied by sampling them using probability density functions. We analyze the influence of seasonal variations on ash dispersal and estimate the average persistence of critical ash concentrations at relevant locations and airports. This study assesses the impact that a Plinian eruption similar to the Ochre Pumice eruption would have on the main airports of Mexico and adjacent areas. The hazard maps presented here can support long-term planning that would help minimize the impacts of such an eruption on civil aviation.

Preliminary Isostatic Gravity Map of Joshua Tree National Park and Vicinity, Southern California

USGS Publications Warehouse

Langenheim, V.E.; Biehler, Shawn; McPhee, D.K.; McCabe, C.A.; Watt, J.T.; Anderson, M.L.; Chuchel, B.A.; Stoffer, P.

2007-01-01

This isostatic residual gravity map is part of an effort to map the three-dimensional distribution of rocks in Joshua Tree National Park, southern California. This map will serve as a basis for modeling the shape of basins beneath the Park and in adjacent valleys and also for determining the location and geometry of faults within the area. Local spatial variations in the Earth's gravity field, after accounting for variations caused by elevation, terrain, and deep crustal structure, reflect the distribution of densities in the mid- to upper crust. Densities often can be related to rock type, and abrupt spatial changes in density commonly mark lithologic or structural boundaries. High-density basement rocks exposed within the Eastern Transverse Ranges include crystalline rocks that range in age from Proterozoic to Mesozoic and these rocks are generally present in the mountainous areas of the quadrangle. Alluvial sediments, usually located in the valleys, and Tertiary sedimentary rocks are characterized by low densities. However, with increasing depth of burial and age, the densities of these rocks may become indistinguishable from those of basement rocks. Tertiary volcanic rocks are characterized by a wide range of densities, but, on average, are less dense than the pre-Cenozoic basement rocks. Basalt within the Park is as dense as crystalline basement, but is generally thin (less than 100 m thick; e.g., Powell, 2003). Isostatic residual gravity values within the map area range from about 44 mGal over Coachella Valley to about 8 mGal between the Mecca Hills and the Orocopia Mountains. Steep linear gravity gradients are coincident with the traces of several Quaternary strike-slip faults, most notably along the San Andreas Fault bounding the east side of Coachella Valley and east-west-striking, left-lateral faults, such as the Pinto Mountain, Blue Cut, and Chiriaco Faults (Fig. 1). Gravity gradients also define concealed basin-bounding faults, such as those beneath the Chuckwalla Valley (e.g. Rotstein and others, 1976). These gradients result from juxtaposing dense basement rocks against thick Cenozoic sedimentary rocks.

Appliation of rad-sequencing to linkage mapping in citrus

USDA-ARS?s Scientific Manuscript database

High density linkage maps can be developed for modest cost using high-throughput DNA sequencing to genotype a defined fraction (representation) of the genome. We developed linkage maps in two citrus populations using the RAD (Restriction site Associated DNA) genotyping method which involves restrict...

A new all-sky map of Galactic high-velocity clouds from the 21-cm HI4PI survey

NASA Astrophysics Data System (ADS)

Westmeier, Tobias

2018-02-01

High-velocity clouds (HVCs) are neutral or ionized gas clouds in the vicinity of the Milky Way that are characterized by high radial velocities inconsistent with participation in the regular rotation of the Galactic disc. Previous attempts to create a homogeneous all-sky H I map of HVCs have been hampered by a combination of poor angular resolution, limited surface brightness sensitivity and suboptimal sampling. Here, a new and improved H I map of Galactic HVCs based on the all-sky HI4PI survey is presented. The new map is fully sampled and provides significantly better angular resolution (16.2 versus 36 arcmin) and column density sensitivity (2.3 versus 3.7 × 1018 cm-2 at the native resolution) than the previously available LAB survey. The new HVC map resolves many of the major HVC complexes in the sky into an intricate network of narrow H I filaments and clumps that were not previously resolved by the LAB survey. The resulting sky coverage fraction of high-velocity H I emission above a column density level of 2 × 1018 cm-2 is approximately 15 per cent, which reduces to about 13 per cent when the Magellanic Clouds and other non-HVC emission are removed. The differential sky coverage fraction as a function of column density obeys a truncated power law with an exponent of -0.93 and a turnover point at about 5 × 1019 cm-2. H I column density and velocity maps of the HVC sky are made publicly available as FITS images for scientific use by the community.

Mapping erosion susceptibility by a multivariate statistical method: A case study from the Ayvalık region, NW Turkey

NASA Astrophysics Data System (ADS)

Akgün, Aykut; Türk, Necdet

2011-09-01

Erosion is one of the most important natural hazard phenomena in the world, and it poses a significant threat to Turkey in terms of land degredation and desertification. To cope with this problem, we must determine which areas are erosion-prone. Many studies have been carried out and different models and methods have been used to this end. In this study, we used a logistic regression to prepare an erosion susceptibility map for the Ayvalık region in Balıkesir (NW Turkey). The following were our assessment parameters: weathering grades of rocks, slope gradient, structural lineament density, drainage density, land cover, stream power index (SPI) and profile curvature. These were processed by Idrisi Kilimanjaro GIS software. We used logistic regression analysis to relate predictor variables to the occurrence or non-occurrence of gully erosion sites within geographic cells, and then we used this relationship to produce a probability map for future erosion sites. The results indicate that lineament density, weathering grades of rocks and drainage density are the most important variables governing erosion susceptibility. Other variables, such as land cover and slope gradient, were revealed as secondary important variables. Highly weathered basalt, andesite, basaltic andesite and lacustrine sediments were the units most susceptible to erosion. In order to calculate the prediction accuracy of the erosion susceptibility map generated, we compared it with the map showing the gully erosion areas. On the basis of this comparison, the area under curvature (AUC) value was found to be 0.81. This result suggests that the erosion susceptibility map we generated is accurate.

Mapping the distribution of specific antibody interaction forces on individual red blood cells

NASA Astrophysics Data System (ADS)

Yeow, Natasha; Tabor, Rico F.; Garnier, Gil

2017-02-01

Current blood typing methods rely on the agglutination of red blood cells (RBCs) to macroscopically indicate a positive result. An indirect agglutination mechanism is required when blood typing with IgG forms of antibodies. To date, the interaction forces between anti-IgG and IgG antibodies have been poorly quantified, and blood group related antigens have never been quantified with the atomic force microscope (AFM). Instead, the total intensity resulting from fluorescent-tagged antibodies adsorbed on RBC has been measured to calculate an average antigen density on a series of RBCs. In this study we mapped specific antibody interaction forces on the RBC surface. AFM cantilever tips functionalized with anti-IgG were used to probe RBCs incubated with specific IgG antibodies. This work provides unique insight into antibody-antigen interactions in their native cell-bound location, and crucially, on a per-cell basis rather than an ensemble average set of properties. Force profiles obtained from the AFM directly provide not only the anti-IgG - IgG antibody interaction force, but also the spatial distribution and density of antigens over a single cell. This new understanding might be translated into the development of very selective and quantitative interactions that underpin the action of drugs in the treatment of frontier illnesses.

Detection of an electron beam in a high density plasma via an electrostatic probe

NASA Astrophysics Data System (ADS)

Majeski, Stephen; Yoo, Jongsoo; Zweben, Stewart; Yamada, Masaaki; Ji, Hantao

2017-10-01

The perturbation in floating potential by an electron beam is detected by a 1D floating potential probe array to evaluate the use of an electron beam for magnetic field line mapping in the Magnetic Reconnection Experiment (MRX) plasma. The MRX plasma is relatively high density (1013 cm-3) and low temperature (5 eV). Beam electrons are emitted from a tungsten filament and are accelerated by a 200 V potential across the sheath. They stream along the magnetic field lines towards the probe array. The spatial electron beam density profile is assumed to be a Gaussian along the radial axis of MRX and the effective beam width is determined from the radial profile of the floating potential. The magnitude of the perturbation is in agreement with theoretical predictions and the location of the perturbation is also in agreement with field line mapping. In addition, no significant broadening of the electron beam is observed after propagation for tens of centimeters through the high density plasma. These results demonstrate that this method of field line mapping is, in principle, feasible in high density plasmas. This work is supported by the DOE Contract No. DE-AC0209CH11466.

Bouguer gravity anomaly and isostatic residual gravity maps of the Tonopah 1 degree by 2 degrees Quadrangle, central Nevada

USGS Publications Warehouse

Plouff, Donald

1992-01-01

A residual isostatic gravity map (sheet 2) was prepared so that the regional effect of isostatic compensation present on the Bouguer gravity anomaly map (sheet 1) would be minimized. Isostatic corrections based on the Airy-Heiskanen system (Heiskanen and Vening Meinesz, 1958, p. 135-137) were estimated by using 3-minute topographic digitization and applying the method of Jachens and Roberts (1981). Parameters selected for the isostatic model were 25 km for the normal crustal thickness at sea level, 2.67 g/cm3 for the density of the crust, and 0.4 g/cm3 for the contrast in density between the crust and the upper mantle. These parameters were selected so that the isostatic residual gravity map would be consistent with isostatic residual gravity maps of the adjacent Walker Lake quadrangle (Plouff, 1987) and the state of Nevada (Saltus, 1988c).

Construction of High-Density Genetic Linkage Maps and Mapping of Growth-Related Quantitative Trail Loci in the Japanese Flounder (Paralichthys olivaceus)

PubMed Central

Niu, Yuze; Gao, Fengtao; Zhao, Yongwei; Zhang, Jing; Sun, Jian; Shao, Changwei; Liao, Xiaolin; Wang, Lei; Tian, Yongsheng; Chen, Songlin

2012-01-01

High-density genetic linkage maps were constructed for the Japanese flounder (Paralichthys olivaceus). A total of 1624 microsatellite markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 resulted in the mapping of 1487 markers to 24 linkage groups, a result which was consistent with the 24 chromosomes seen in chromosome spreads. The female map was composed of 1257 markers, covering a total of 1663.8 cM with an average interval 1.35 cM between markers. The male map consisted of 1224 markers, spanning 1726.5 cM, with an average interval of 1.44 cM. The genome length in the Japanese flounder was estimated to be 1730.3 cM for the females and 1798.0 cM for the males, a coverage of 96.2% for the female and 96.0% for the male map. The mean recombination at common intervals throughout the genome revealed a slight difference between sexes, i.e. 1.07 times higher in the male than female. High-density genetic linkage maps are very useful for marker-assisted selection (MAS) programs for economically valuable traits in this species and for further evolutionary studies in flatfish and vertebrate species. Furthermore, four quantiative trait loci (QTL) associated with growth traits were mapped on the genetic map. One QTL was identified for body weight on LG 14 f, which explained 14.85% of the total variation of the body weight. Three QTL were identified for body width on LG14f and LG14m, accounting for 16.75%, 13.62% and 13.65% of the total variation in body width, respectively. The additive effects were evident as negative values. There were four QTL for growth traits clustered on LG14, which should prove to be very useful for improving growth traits using molecular MAS. PMID:23209734

Diagnostic evaluations of a beam-shielded 8-cm mercury ion thruster

NASA Technical Reports Server (NTRS)

Nakanishi, S.

1978-01-01

An engineering model thruster fitted with a remotely actuated graphite fiber polyimide composite beam shield was tested in a 3- by 6.5-meter vacuum facility for in-situ assessment of beam shield effects on thruster performance. Accelerator drain current neutralizer floating potential and ion beam floating potential increased slightly when the shield was moved into position. A target exposed to the low density regions of the ion beam was used to map the boundaries of energetic fringe ions capable of sputtering. The particle efflux was evaluated by measurement of film deposits on cold, heated, bare, and enclosed glass slides.

High-excitation lines of molecular hydrogen: A discriminant between shock models

NASA Technical Reports Server (NTRS)

Burton, M.; Brand, P.; Moorhouse, A.; Geballe, T.

1989-01-01

The results of column densities of molecular hydrogen, calculated from nineteen infrared line intensities, are discussed. They were measured at peak 1 of the outflow of the Orion molecular cloud OMC-1. The 1-0 O(7) and 0-0 S(13) lines of H2, at 3.8 microns, are mapped over the source. Their intensity ratio is found to be independent of position in the outflow. These observations are well fitted by a simple cooling-flow model of the line emitting region, but seem to be at variance with predictions of C-shocks current in the literature.

Using global maps to predict the risk of dengue in Europe.

PubMed

Rogers, David J; Suk, Jonathan E; Semenza, Jan C

2014-01-01

This article attempts to quantify the risk to Europe of dengue, following the arrival and spread there of one of dengue's vector species Aedes (Stegomyia) albopictus. A global risk map for dengue is presented, based on a global database of the occurrence of this disease, derived from electronic literature searches. Remotely sensed satellite data (from NASA's MODIS series), interpolated meteorological data, predicted distribution maps of dengue's two main vector species, Aedes aegypti and Aedes albopictus, a digital elevation surface and human population density data were all used as potential predictor variables in a non-linear discriminant analysis modelling framework. One hundred bootstrap models were produced by randomly sub-sampling three different training sets for dengue fever, severe dengue (i.e. dengue haemorrhagic fever, DHF) and all-dengue, and output predictions were averaged to produce a single global risk map for each type of dengue. This paper concentrates on the all-dengue models. Key predictor variables were various thermal data layers, including both day- and night-time Land Surface Temperature, human population density, and a variety of rainfall variables. The relative importance of each may be shown visually using rainbow files and quantitatively using a ranking system. Vegetation Index variables (a common proxy for humidity or saturation deficit) were rarely chosen in the models. The kappa index of agreement indicated an excellent (dengue haemorrhagic fever, Cohen's kappa=0.79 ± 0.028, AUC=0.96 ± 0.007) or good fit of the top ten models in each series to the data (Cohen's kappa=0.73 ± 0.018, AUC=0.94 ± 0.007 for dengue fever and 0.74 ± 0.017, AUC=0.95 ± 0.005 for all dengue). The global risk map predicts widespread dengue risk in SE Asia and India, in Central America and parts of coastal South America, but in relatively few regions of Africa. In many cases these are less extensive predictions than those of other published dengue risk maps and arise because of the key importance of high human population density for the all-dengue risk maps produced here. Three published dengue risk maps are compared using the Fleiss kappa index, and are shown to have only fair agreement globally (Fleiss kappa=0.377). Regionally the maps show greater (but still only moderate) agreement in SE Asia (Fleiss kappa=0.566), fair agreement in the Americas (Fleiss kappa=0.325) and only slight agreement in Africa (Fleiss kappa=0.095). The global dengue risk maps show that very few areas of rural Europe are presently suitable for dengue, but several major cities appear to be at some degree of risk, probably due to a combination of thermal conditions and high human population density, the top two variables in many models. Mahalanobis distance images were produced of Europe and the southern United States showing the distance in environmental rather than geographical space of each site from any site where dengue currently occurs. Parts of Europe are quite similar in Mahalanobis distance terms to parts of the southern United States, where dengue occurred in the recent past and which remain environmentally suitable for it. High standards of living rather than a changed environmental suitability keep dengue out of the USA. The threat of dengue to Europe at present is considered to be low but sufficiently uncertain to warrant monitoring in those areas of greatest predicted environmental suitability, especially in northern Italy and parts of Austria, Slovenia and Croatia, Bosnia and Herzegovina, Serbia and Montenegro, Albania, Greece, south-eastern France, Germany and Switzerland, and in smaller regions elsewhere. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.).

PubMed

Guo, Yinshan; Shi, Guangli; Liu, Zhendong; Zhao, Yuhui; Yang, Xiaoxu; Zhu, Junchi; Li, Kun; Guo, Xiuwu

2015-01-01

In this study, 149 F1 plants from the interspecific cross between 'Red Globe' (Vitis vinifera L.) and 'Shuangyou' (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for 'Red Globe,' 63.65 for 'Shuangyou,' and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape.

Investigating Star-Gas Correlation and Evolution in the 100pc Cygnus X Complex

NASA Astrophysics Data System (ADS)

Gutermuth, Robert

We request support to pursue a substantial refinement of the ongoing characterizations of star and gas surface density in nearby star forming regions by engaging in a focused study of the Cygnus X star forming complex. The substantial physical size of the region and high spatial dynamic range of its surveys enables us to achieve the following science goals: - Characterize the distributions of gas and stellar column densities in a large, nearby starforming complex and integrate those values over successively larger physical scales in order to gauge the effect of varying physical resolution on the measured star-gas correlation. - Validate integrated 24 ¼m luminosity as a method of estimating star formation rate surface density using a region in which the substantial number of known forming members should ensure that the IMF is statistically well-sampled. - Validate 12CO luminosity as a method of estimating molecular gas column density against 13CO column density. tegrated 24 micron and radio continuum luminosity. To achieve these goals, we will perform substantial improvement and expansion of the Cygnus X Spitzer (and 2MASS) Legacy Survey point source catalog using UKIRT Infrared Deep Sky Survey (UKIDSS) near-IR data and WISE mid-IR data. From this catalog, we will produce a comprehensive census of young stellar objects (YSOs) with IR-excess emission over the numerical bulk of the stellar mass function (0.2 2 M ). This YSO catalog is expected to be considerably larger than the entire YSO census of the nearest kiloparsec. Both the point source and YSO catalogs will be contributed to the Infrared Science Archive (IRSA) to facilitate community access to these improved data products. In addition, we will provide a star formation surface density map derived from the MIPS 24 micron map of Cygnus X from the Spitzer Legacy Survey and gas column density maps derived from 12CO and 13CO data from the Exeter-Five College Radio Astronomy Observatory Cygnus Survey. The proposed program will bring to maturity a major new scientific result from the combination of data from several NASA program investments (Spitzer Legacy, WISE, & 2MASS) and some external archives (UKIDSS GPS, Exeter-FCRAO XGRS) that we have shown above add considerable value to the scientific interpretation of the data from the NASA archive. The improvement in effective sensitivity to low mass YSOs from the Cygnus X Legacy Survey source catalog and our targeted science investigation to examine the star-gas correlation (and any deviation that may correlate with local YSO evolutionary age) are relevant to the NASA Astrophysics Theme, Cosmic Origins, which aspires to unveil how the universe developed to the current day configuration of galaxies, stars and planets and the conditions necessary for life.

Influence of Particle Morphology on 3D Kinematic Behavior and Strain Localization of Sheared Sand

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

Alshibli, Khalid A.; Jarrar, Maha F.; Druckrey, Andrew M.

The constitutive behavior of sheared sand is highly influenced by particle morphology, gradation, mineralogy, specimen density, loading condition, stress path, and boundary conditions. The current literature lacks a three-dimensional (3D) systematic experimental study that investigates the influence of particle morphology, confining pressure, and specimen density on the failure mode of sheared sand. In this paper, surface texture, roundness, and sphericity of three uniform sands and glass beads with similar grain size were quantified by using 3D images of particles. In situ nondestructive 3D synchrotron microcomputed tomography (SMT) was used to monitor the deformation of medium-dense and very dense dry sandmore » specimens that were tested under axisymmetric triaxial loading condition at 15 and 400 kPa confining pressures. The particles were identified and tracked in 3D as shearing progressed within the specimens, and maps of incremental particle translation and rotation were developed and used to uncover the relationship between particle morphology, specimen density, and confining pressure on the deformation and failure mode of sheared sand. This paper discusses the relationship between the failure mode and particle morphology, specimen density, and confining pressure.« less

Reply to "Comment on 'Fractional quantum mechanics' and 'Fractional Schrödinger equation' ".

PubMed

Laskin, Nick

2016-06-01

The fractional uncertainty relation is a mathematical formulation of Heisenberg's uncertainty principle in the framework of fractional quantum mechanics. Two mistaken statements presented in the Comment have been revealed. The origin of each mistaken statement has been clarified and corrected statements have been made. A map between standard quantum mechanics and fractional quantum mechanics has been presented to emphasize the features of fractional quantum mechanics and to avoid misinterpretations of the fractional uncertainty relation. It has been shown that the fractional probability current equation is correct in the area of its applicability. Further studies have to be done to find meaningful quantum physics problems with involvement of the fractional probability current density vector and the extra term emerging in the framework of fractional quantum mechanics.

Occupancy change detection system and method

DOEpatents

Bruemmer, David J [Idaho Falls, ID; Few, Douglas A [Idaho Falls, ID

2009-09-01

A robot platform includes perceptors, locomotors, and a system controller. The system controller executes instructions for producing an occupancy grid map of an environment around the robot, scanning the environment to generate a current obstacle map relative to a current robot position, and converting the current obstacle map to a current occupancy grid map. The instructions also include processing each grid cell in the occupancy grid map. Within the processing of each grid cell, the instructions include comparing each grid cell in the occupancy grid map to a corresponding grid cell in the current occupancy grid map. For grid cells with a difference, the instructions include defining a change vector for each changed grid cell, wherein the change vector includes a direction from the robot to the changed grid cell and a range from the robot to the changed grid cell.

Spatial patterns of distribution, abundance, and species diversity of small odontocetes estimated using density surface modeling with line transect sampling

NASA Astrophysics Data System (ADS)

Kanaji, Yu; Okazaki, Makoto; Miyashita, Tomio

2017-06-01

Spatial patterns of distribution, abundance, and species diversity of small odontocetes including species in the Delphinidae and Phocoenidae families were investigated using long-term dedicated sighting survey data collected between 1983 and 2006 in the North Pacific. Species diversity indices were calculated from abundance estimated using density surface modeling of line-transect data. The estimated abundance ranged from 19,521 individuals in killer whale to 1,886,022 in pantropical spotted dolphin. The predicted density maps showed that the habitats of small odontocetes corresponded well with distinct oceanic domains. Species richness was estimated to be highest between 30 and 40°N where warm- and cold-water currents converge. Simpson's Diversity Index showed latitudinal diversity gradients of decreasing species numbers toward the poles. Higher diversity was also estimated in the coastal areas and the zonal areas around 35-42°N. Coastal-offshore gradients and latitudinal gradients are known for many taxa. The zonal areas around 35°N and 40°N coincide with the Kuroshio Current and its extension and the subarctic boundary, respectively. These results suggest that the species diversity of small odontocetes primarily follows general patterns of latitudinal and longitudinal gradients, while the confluence of faunas originating in distinct water masses increases species diversify in frontal waters around 30-40°N. Population densities tended to be higher for the species inhabiting higher latitudes, but were highest for intermediate latitudes at approximately 35-40°N. According to latitudinal gradients in water temperature and biological productivity, the costs for thermoregulation will decrease in warmer low latitudes, while feeding efficiency will increase in colder high latitudes. These trade-offs could optimize population density in intermediate latitudes.

Relationship between Hard X-Ray Footpoint Sources and Photospheric Electric Currents in Solar Flares: a Statistical Study

NASA Astrophysics Data System (ADS)

Zimovets, I. V.; Sharykin, I. N.; Wang, R.; Liu, Y. D.; Kosovichev, A. G.

2017-12-01

It is believed that solar flares are a result of release of free magnetic energy contained in electric currents (ECs) flowing in active regions (ARs). However, there are still debates whether the primary energy release and acceleration of electrons take place in coronal current sheets or in chromospheric footpoints of current-carrying magnetic flux tubes (loops). We present results of an observational statistical study of spatial relationship between hard X-ray (HXR; EHXR≥50keV) footpoint sources detected by RHESSI and vertical photospheric ECs calculated using vector magnetograms obtained from the SDO/HMI data. We found that for a sample of 47 flares (from C3.0 to X3.1 class) observed on the solar disk by both instruments in 2010-2016, at least one HXR source was in a region of strong (within 20% of the maximum EC density in the corresponding ARs) vertical ECs having the form of a ribbon (79%) or an island (21%). The total vertical ECs in such HXR sources are in the range of 1010-1013 A. The EC density is in the range of 0.01-1.0 A/m2. We found no correlation between intensity of the HXR sources and the EC density. By comparing pre-flare and post-flare EC maps we did not find evidences of significant dissipation of vertical ECs in the regions corresponding to the HXR sources. In some cases, we found amplification of ECs during flares. We discuss effects of sensitivity and angular resolution of RHESSI and SDO/HMI. In general, the results indicate that there is a link between the flare HXR footpoint sources and enhanced vertical ECs in the photosphere. However, the results do not support a concept of electron acceleration by the electric field excited in footpoints of current-carrying loops due to some (e.g. Rayleigh-Taylor) instabilities (Zaitsev et al., 2016), since strong correlation between the HXR intensity and the EC density is expected in such concept.

Evidence of Cross-correlation between the CMB Lensing and the γ-Ray Sky

NASA Astrophysics Data System (ADS)

Fornengo, Nicolao; Perotto, Laurence; Regis, Marco; Camera, Stefano

2015-03-01

We report the measurement of the angular power spectrum of cross-correlation between the unresolved component of the Fermi-LAT γ-ray sky maps and the cosmic microwave background lensing potential map reconstructed by the Planck satellite. The matter distribution in the universe determines the bending of light coming from the last scattering surface. At the same time, the matter density drives the growth history of astrophysical objects, including their capability at generating non-thermal phenomena, which in turn give rise to γ-ray emissions. The Planck lensing map provides information on the integrated distribution of matter, while the integrated history of γ-ray emitters is imprinted in the Fermi-LAT sky maps. We report here the first evidence of their correlation. We find that the multipole dependence of the cross-correlation measurement is in agreement with current models of the γ-ray luminosity function for active galactic nuclei and star-forming galaxies, with a statistical evidence of 3.0σ. Moreover, its amplitude can in general be matched only assuming that these extragalactic emitters are also the bulk contribution of the measured isotopic γ-ray background (IGRB) intensity. This leaves little room for a big contribution from galactic sources to the IGRB measured by Fermi-LAT, pointing toward direct evidence of the extragalactic origin of the IGRB.

Investigating the Capability of IRS-P6-LISS IV Satellite Image for Pistachio Forests Density Mapping (case Study: Northeast of Iran)

NASA Astrophysics Data System (ADS)

Hoseini, F.; Darvishsefat, A. A.; Zargham, N.

2012-07-01

In order to investigate the capability of satellite images for Pistachio forests density mapping, IRS-P6-LISS IV data were analyzed in an area of 500 ha in Iran. After geometric correction, suitable training areas were determined based on fieldwork. Suitable spectral transformations like NDVI, PVI and PCA were performed. A ground truth map included of 34 plots (each plot 1 ha) were prepared. Hard and soft supervised classifications were performed with 5 density classes (0-5%, 5-10%, 10-15%, 15-20% and > 20%). Because of low separability of classes, some classes were merged and classifications were repeated with 3 classes. Finally, the highest overall accuracy and kappa coefficient of 70% and 0.44, respectively, were obtained with three classes (0-5%, 5-20%, and > 20%) by fuzzy classifier. Considering the low kappa value obtained, it could be concluded that the result of the classification was not desirable. Therefore, this approach is not appropriate for operational mapping of these valuable Pistachio forests.

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

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

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

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

Charge Density Dependent Hole Mobility and Density of States Throughout the Entire Finite Potential Window of Conductivity in Ionic Liquid Gated Poly(3-hexylthiophene)

NASA Astrophysics Data System (ADS)

Paulsen, Bryan D.; Frisbie, C. Daniel

2012-02-01

Ionic liquids, used in place of traditional gate dielectric materials, allow for the accumulation of very high 2D and 3D charge densities (>10^14 #/cm^2 and >10^21 #/cm^3 respectively) at low voltage (<5 V). Here we study the electrochemical gating of the benchmark semiconducting polymer poly(3-hexylthiophene) (P3HT) with the ionic liquid 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([EMI][FAP]). The electrochemical stability of [EMI][FAP] allowed the reproducible accumulation of 2 x 10^21 hole/cm^3, or one hole (and stabilizing anion dopant) per every two thiophene rings. A finite potential/charge density window of high electrical conductivity was observed with hole mobility reaching a maximum of 0.86 cm^2/V s at 0.12 holes per thiophene ring. Displacement current measurements, collected versus a calibrated reference electrode, allowed the mapping of the highly structured and extremely broad density of states of the P3HT/[EMI][FAP] doped composite. Variable temperature and charge density hole transport measurements revealed hole transport to be thermally activated and non-monotonic, displaying a activation energy minimum of ˜20 meV in the region of maximum conductivity and hole mobility. To show the generality of this result, the study was extended to an additional four ionic liquids and three semiconducting polymers.

SU-G-JeP2-02: A Unifying Multi-Atlas Approach to Electron Density Mapping Using Multi-Parametric MRI for Radiation Treatment Planning

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

Ren, S; Tianjin University, Tianjin; Hara, W

Purpose: MRI has a number of advantages over CT as a primary modality for radiation treatment planning (RTP). However, one key bottleneck problem still remains, which is the lack of electron density information in MRI. In the work, a reliable method to map electron density is developed by leveraging the differential contrast of multi-parametric MRI. Methods: We propose a probabilistic Bayesian approach for electron density mapping based on T1 and T2-weighted MRI, using multiple patients as atlases. For each voxel, we compute two conditional probabilities: (1) electron density given its image intensity on T1 and T2-weighted MR images, and (2)more » electron density given its geometric location in a reference anatomy. The two sources of information (image intensity and spatial location) are combined into a unifying posterior probability density function using the Bayesian formalism. The mean value of the posterior probability density function provides the estimated electron density. Results: We evaluated the method on 10 head and neck patients and performed leave-one-out cross validation (9 patients as atlases and remaining 1 as test). The proposed method significantly reduced the errors in electron density estimation, with a mean absolute HU error of 138, compared with 193 for the T1-weighted intensity approach and 261 without density correction. For bone detection (HU>200), the proposed method had an accuracy of 84% and a sensitivity of 73% at specificity of 90% (AUC = 87%). In comparison, the AUC for bone detection is 73% and 50% using the intensity approach and without density correction, respectively. Conclusion: The proposed unifying method provides accurate electron density estimation and bone detection based on multi-parametric MRI of the head with highly heterogeneous anatomy. This could allow for accurate dose calculation and reference image generation for patient setup in MRI-based radiation treatment planning.« less

Improving the Accuracy of Mapping Urban Vegetation Carbon Density by Combining Shadow Remove, Spectral Unmixing Analysis and Spatial Modeling

NASA Astrophysics Data System (ADS)

Qie, G.; Wang, G.; Wang, M.

2016-12-01

Mixed pixels and shadows due to buildings in urban areas impede accurate estimation and mapping of city vegetation carbon density. In most of previous studies, these factors are often ignored, which thus result in underestimation of city vegetation carbon density. In this study we presented an integrated methodology to improve the accuracy of mapping city vegetation carbon density. Firstly, we applied a linear shadow remove analysis (LSRA) on remotely sensed Landsat 8 images to reduce the shadow effects on carbon estimation. Secondly, we integrated a linear spectral unmixing analysis (LSUA) with a linear stepwise regression (LSR), a logistic model-based stepwise regression (LMSR) and k-Nearest Neighbors (kNN), and utilized and compared the integrated models on shadow-removed images to map vegetation carbon density. This methodology was examined in Shenzhen City of Southeast China. A data set from a total of 175 sample plots measured in 2013 and 2014 was used to train the models. The independent variables statistically significantly contributing to improving the fit of the models to the data and reducing the sum of squared errors were selected from a total of 608 variables derived from different image band combinations and transformations. The vegetation fraction from LSUA was then added into the models as an important independent variable. The estimates obtained were evaluated using a cross-validation method. Our results showed that higher accuracies were obtained from the integrated models compared with the ones using traditional methods which ignore the effects of mixed pixels and shadows. This study indicates that the integrated method has great potential on improving the accuracy of urban vegetation carbon density estimation. Key words: Urban vegetation carbon, shadow, spectral unmixing, spatial modeling, Landsat 8 images

Spatially associated clump populations in Rosette from CO and dust maps

NASA Astrophysics Data System (ADS)

Veltchev, Todor V.; Ossenkopf-Okada, Volker; Stanchev, Orlin; Schneider, Nicola; Donkov, Sava; Klessen, Ralf S.

2018-04-01

Spatial association of clumps from different tracers turns out to be a valuable tool to determine the physical properties of molecular clouds. It provides a reliable estimate for the X-factors, serves to trace the density of clumps seen in column densities only, and allows one to measure the velocity dispersion of clumps identified in dust emission. We study the spatial association between clump populations, extracted by use of the GAUSSCLUMPS technique from 12CO (1-0), 13CO (1-0) line maps and Herschel dust-emission maps of the star-forming region Rosette, and analyse their physical properties. All CO clumps that overlap with another CO or dust counterpart are found to be gravitationally bound and located in the massive star-forming filaments of the molecular cloud. They obey a single mass-size relation M_cl∝ R_cl^γ with γ ≃ 3 (implying constant mean density) and display virtually no velocity-size relation. We interpret their population as low-density structures formed through compression by converging flows and still not evolved under the influence of self-gravity. The high-mass parts of their clump mass functions are fitted by a power law dN_cl/d log M_cl∝ M_cl^{Γ } and display a nearly Salpeter slope Γ ˜ -1.3. On the other hand, clumps extracted from the dust-emission map exhibit a shallower mass-size relation with γ = 2.5 and mass functions with very steep slopes Γ ˜ -2.3 even if associated with CO clumps. They trace density peaks of the associated CO clumps at scales of a few tenths of pc where no single density scaling law should be expected.

Models of regional habitat quality and connectivity for pumas (Puma concolor) in the southwestern United States.

PubMed

Dickson, Brett G; Roemer, Gary W; McRae, Brad H; Rundall, Jill M

2013-01-01

The impact of landscape changes on the quality and connectivity of habitats for multiple wildlife species is of global conservation concern. In the southwestern United States, pumas (Puma concolor) are a well distributed and wide-ranging large carnivore that are sensitive to loss of habitat and to the disruption of pathways that connect their populations. We used an expert-based approach to define and derive variables hypothesized to influence the quality, location, and permeability of habitat for pumas within an area encompassing the entire states of Arizona and New Mexico. Survey results indicated that the presence of woodland and forest cover types, rugged terrain, and canyon bottom and ridgeline topography were expected to be important predictors of both high quality habitat and heightened permeability. As road density, distance to water, or human population density increased, the quality and permeability of habitats were predicted to decline. Using these results, we identified 67 high quality patches across the study area, and applied concepts from electronic circuit theory to estimate regional patterns of connectivity among these patches. Maps of current flow among individual pairs of patches highlighted possible pinch points along two major interstate highways. Current flow summed across all pairs of patches highlighted areas important for keeping the entire network connected, regardless of patch size. Cumulative current flow was highest in Arizona north of the Colorado River and around Grand Canyon National Park, and in the Sky Islands region owing to the many small habitat patches present. Our outputs present a first approximation of habitat quality and connectivity for dispersing pumas in the southwestern United States. Map results can be used to help target finer-scaled analyses in support of planning efforts concerned with the maintenance of puma metapopulation structure, as well as the protection of landscape features that facilitate the dispersal process.

Models of Regional Habitat Quality and Connectivity for Pumas (Puma concolor) in the Southwestern United States

PubMed Central

Dickson, Brett G.; Roemer, Gary W.; McRae, Brad H.; Rundall, Jill M.

2013-01-01

The impact of landscape changes on the quality and connectivity of habitats for multiple wildlife species is of global conservation concern. In the southwestern United States, pumas (Puma concolor) are a well distributed and wide-ranging large carnivore that are sensitive to loss of habitat and to the disruption of pathways that connect their populations. We used an expert-based approach to define and derive variables hypothesized to influence the quality, location, and permeability of habitat for pumas within an area encompassing the entire states of Arizona and New Mexico. Survey results indicated that the presence of woodland and forest cover types, rugged terrain, and canyon bottom and ridgeline topography were expected to be important predictors of both high quality habitat and heightened permeability. As road density, distance to water, or human population density increased, the quality and permeability of habitats were predicted to decline. Using these results, we identified 67 high quality patches across the study area, and applied concepts from electronic circuit theory to estimate regional patterns of connectivity among these patches. Maps of current flow among individual pairs of patches highlighted possible pinch points along two major interstate highways. Current flow summed across all pairs of patches highlighted areas important for keeping the entire network connected, regardless of patch size. Cumulative current flow was highest in Arizona north of the Colorado River and around Grand Canyon National Park, and in the Sky Islands region owing to the many small habitat patches present. Our outputs present a first approximation of habitat quality and connectivity for dispersing pumas in the southwestern United States. Map results can be used to help target finer-scaled analyses in support of planning efforts concerned with the maintenance of puma metapopulation structure, as well as the protection of landscape features that facilitate the dispersal process. PMID:24367495

Utilizing NASA Earth Observations to Model Volcanic Hazard Risk Levels in Areas Surrounding the Copahue Volcano in the Andes Mountains

NASA Astrophysics Data System (ADS)

Keith, A. M.; Weigel, A. M.; Rivas, J.

2014-12-01

Copahue is a stratovolcano located along the rim of the Caviahue Caldera near the Chile-Argentina border in the Andes Mountain Range. There are several small towns located in proximity of the volcano with the two largest being Banos Copahue and Caviahue. During its eruptive history, it has produced numerous lava flows, pyroclastic flows, ash deposits, and lahars. This isolated region has steep topography and little vegetation, rendering it poorly monitored. The need to model volcanic hazard risk has been reinforced by recent volcanic activity that intermittently released several ash plumes from December 2012 through May 2013. Exposure to volcanic ash is currently the main threat for the surrounding populations as the volcano becomes more active. The goal of this project was to study Copahue and determine areas that have the highest potential of being affected in the event of an eruption. Remote sensing techniques were used to examine and identify volcanic activity and areas vulnerable to experiencing volcanic hazards including volcanic ash, SO2 gas, lava flow, pyroclastic density currents and lahars. Landsat 7 Enhanced Thematic Mapper Plus (ETM+), Landsat 8 Operational Land Imager (OLI), EO-1 Advanced Land Imager (ALI), Terra Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), Shuttle Radar Topography Mission (SRTM), ISS ISERV Pathfinder, and Aura Ozone Monitoring Instrument (OMI) products were used to analyze volcanic hazards. These datasets were used to create a historic lava flow map of the Copahue volcano by identifying historic lava flows, tephra, and lahars both visually and spectrally. Additionally, a volcanic risk and hazard map for the surrounding area was created by modeling the possible extent of ash fallout, lahars, lava flow, and pyroclastic density currents (PDC) for future eruptions. These model results were then used to identify areas that should be prioritized for disaster relief and evacuation orders.

Agriculture/forestry hydrology

NASA Technical Reports Server (NTRS)

Vanderoord, W. J. (Principal Investigator)

1977-01-01

The author has identified the following significant results. The main vegetation units of the lower Mekong basin and the land development conditions were mapped by interpretation of LANDSAT 1 data. By interpretation of various shades of gray on satellite images, it was possible to map the density of the vegetation cover. Study of seasonal variations makes it possible to distinguish between mainly deciduous forests. In the Mekong basin area, these are generally related to the vegetation cover density.

Nanoscale temperature mapping in operating microelectronic devices

DOE PAGES

Mecklenburg, Matthew; Hubbard, William A.; White, E. R.; ...

2015-02-05

We report that modern microelectronic devices have nanoscale features that dissipate power nonuniformly, but fundamental physical limits frustrate efforts to detect the resulting temperature gradients. Contact thermometers disturb the temperature of a small system, while radiation thermometers struggle to beat the diffraction limit. Exploiting the same physics as Fahrenheit’s glass-bulb thermometer, we mapped the thermal expansion of Joule-heated, 80-nanometer-thick aluminum wires by precisely measuring changes in density. With a scanning transmission electron microscope (STEM) and electron energy loss spectroscopy (EELS), we quantified the local density via the energy of aluminum’s bulk plasmon. Rescaling density to temperature yields maps with amore » statistical precision of 3 kelvin/hertz ₋1/2, an accuracy of 10%, and nanometer-scale resolution. Lastly, many common metals and semiconductors have sufficiently sharp plasmon resonances to serve as their own thermometers.« less

Vision 20/20: Mammographic breast density and its clinical applications

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

Ng, Kwan-Hoong, E-mail: ngkh@ummc.edu.my; Lau, Susie

2015-12-15

Breast density is a strong predictor of the failure of mammography screening to detect breast cancer and is a strong predictor of the risk of developing breast cancer. The many imaging options that are now available for imaging dense breasts show great promise, but there is still the question of determining which women are “dense” and what imaging modality is suitable for individual women. To date, mammographic breast density has been classified according to the Breast Imaging-Reporting and Data System (BI-RADS) categories from visual assessment, but this is known to be very subjective. Despite many research reports, the authors believemore » there has been a lack of physics-led and evidence-based arguments about what breast density actually is, how it should be measured, and how it should be used. In this paper, the authors attempt to start correcting this situation by reviewing the history of breast density research and the debates generated by the advocacy movement. The authors review the development of breast density estimation from pattern analysis to area-based analysis, and the current automated volumetric breast density (VBD) analysis. This is followed by a discussion on seeking the ground truth of VBD and mapping volumetric methods to BI-RADS density categories. The authors expect great improvement in VBD measurements that will satisfy the needs of radiologists, epidemiologists, surgeons, and physicists. The authors believe that they are now witnessing a paradigm shift toward personalized breast screening, which is going to see many more cancers being detected early, with the use of automated density measurement tools as an important component.« less

ShelXle: a Qt graphical user interface for SHELXL.

PubMed

Hübschle, Christian B; Sheldrick, George M; Dittrich, Birger

2011-12-01

ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (F(o)) and difference density (F(o)-F(c)) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

Identifying the 630 nm auroral arc emission height: A comparison of the triangulation, FAC profile, and electron density methods

NASA Astrophysics Data System (ADS)

Megan Gillies, D.; Knudsen, D.; Donovan, E.; Jackel, B.; Gillies, R.; Spanswick, E.

2017-08-01

We present a comprehensive survey of 630 nm (red-line) emission discrete auroral arcs using the newly deployed Redline Emission Geospace Observatory. In this study we discuss the need for observations of 630 nm aurora and issues with the large-altitude range of the red-line aurora. We compare field-aligned currents (FACs) measured by the Swarm constellation of satellites with the location of 10 red-line (630 nm) auroral arcs observed by all-sky imagers (ASIs) and find that a characteristic emission height of 200 km applied to the ASI maps gives optimal agreement between the two observations. We also compare the new FAC method against the traditional triangulation method using pairs of all-sky imagers (ASIs), and against electron density profiles obtained from the Resolute Bay Incoherent Scatter Radar-Canadian radar, both of which are consistent with a characteristic emission height of 200 km.

Muographic mapping of the subsurface density structures in Miura, Boso and Izu peninsulas, Japan

NASA Astrophysics Data System (ADS)

Tanaka, Hiroyuki K. M.

2015-02-01

While the benefits of determining the bulk density distribution of a landmass are evident, established experimental techniques reliant on gravity measurements cannot uniquely determine the underground density distribution. We address this problem by taking advantage of traffic tunnels densely distributed throughout the country. Cosmic ray muon flux is measured in the tunnels to determine the average density of each rock overburden. After analyzing the data collected from 146 observation points in Miura, South-Boso and South-Izu Peninsula, Japan as an example, we mapped out the shallow density distribution of an area of 1340 km2. We find a good agreement between muographically determined density distribution and geologic features as described in existing geological studies. The average shallow density distribution below each peninsula was determined with a great accuracy (less than +/-0.8%). We also observed a significant reduction in density along fault lines and interpreted that as due to the presence of multiple cracks caused by mechanical stress during recurrent seismic events. We show that this new type of muography technique can be applied to estimate the terrain density and porosity distribution, thus determining more precise Bouguer reduction densities.

Muographic mapping of the subsurface density structures in Miura, Boso and Izu peninsulas, Japan

PubMed Central

Tanaka, Hiroyuki K. M.

2015-01-01

While the benefits of determining the bulk density distribution of a landmass are evident, established experimental techniques reliant on gravity measurements cannot uniquely determine the underground density distribution. We address this problem by taking advantage of traffic tunnels densely distributed throughout the country. Cosmic ray muon flux is measured in the tunnels to determine the average density of each rock overburden. After analyzing the data collected from 146 observation points in Miura, South-Boso and South-Izu Peninsula, Japan as an example, we mapped out the shallow density distribution of an area of 1340 km2. We find a good agreement between muographically determined density distribution and geologic features as described in existing geological studies. The average shallow density distribution below each peninsula was determined with a great accuracy (less than ±0.8%). We also observed a significant reduction in density along fault lines and interpreted that as due to the presence of multiple cracks caused by mechanical stress during recurrent seismic events. We show that this new type of muography technique can be applied to estimate the terrain density and porosity distribution, thus determining more precise Bouguer reduction densities. PMID:25660352

Muographic mapping of the subsurface density structures in Miura, Boso and Izu peninsulas, Japan.

PubMed

Tanaka, Hiroyuki K M

2015-02-09

While the benefits of determining the bulk density distribution of a landmass are evident, established experimental techniques reliant on gravity measurements cannot uniquely determine the underground density distribution. We address this problem by taking advantage of traffic tunnels densely distributed throughout the country. Cosmic ray muon flux is measured in the tunnels to determine the average density of each rock overburden. After analyzing the data collected from 146 observation points in Miura, South-Boso and South-Izu Peninsula, Japan as an example, we mapped out the shallow density distribution of an area of 1340 km(2). We find a good agreement between muographically determined density distribution and geologic features as described in existing geological studies. The average shallow density distribution below each peninsula was determined with a great accuracy (less than ±0.8%). We also observed a significant reduction in density along fault lines and interpreted that as due to the presence of multiple cracks caused by mechanical stress during recurrent seismic events. We show that this new type of muography technique can be applied to estimate the terrain density and porosity distribution, thus determining more precise Bouguer reduction densities.

Density and Reproductive Success of California Towhees

Treesearch

Kathryn L. Purcell; Jared Verner

1998-01-01

Models of habitat selection commonly asume that higher-quality source habitats will be occupied at higher densities than sink habitats. We examined an apparent sink habitat for California Towhees (Pipilo crissalis) in which densities are greater than in nearby source habitats. We estimated territory density using spot-mapping and monitored nests of towhees in grazed...

Empirical Succession Mapping and Data Assimilation to Constrain Demographic Processes in an Ecosystem Model

NASA Astrophysics Data System (ADS)

Kelly, R.; Andrews, T.; Dietze, M.

2015-12-01

Shifts in ecological communities in response to environmental change have implications for biodiversity, ecosystem function, and feedbacks to global climate change. Community composition is fundamentally the product of demography, but demographic processes are simplified or missing altogether in many ecosystem, Earth system, and species distribution models. This limitation arises in part because demographic data are noisy and difficult to synthesize. As a consequence, demographic processes are challenging to formulate in models in the first place, and to verify and constrain with data thereafter. Here, we used a novel analysis of the USFS Forest Inventory Analysis to improve the representation of demography in an ecosystem model. First, we created an Empirical Succession Mapping (ESM) based on ~1 million individual tree observations from the eastern U.S. to identify broad demographic patterns related to forest succession and disturbance. We used results from this analysis to guide reformulation of the Ecosystem Demography model (ED), an existing forest simulator with explicit tree demography. Results from the ESM reveal a coherent, cyclic pattern of change in temperate forest tree size and density over the eastern U.S. The ESM captures key ecological processes including succession, self-thinning, and gap-filling, and quantifies the typical trajectory of these processes as a function of tree size and stand density. Recruitment is most rapid in early-successional stands with low density and mean diameter, but slows as stand density increases; mean diameter increases until thinning promotes recruitment of small-diameter trees. Strikingly, the upper bound of size-density space that emerges in the ESM conforms closely to the self-thinning power law often observed in ecology. The ED model obeys this same overall size-density boundary, but overestimates plot-level growth, mortality, and fecundity rates, leading to unrealistic emergent demographic patterns. In particular, the current ED formulation cannot capture steady state dynamics evident in the ESM. Ongoing efforts are aimed at reformulating ED to more closely approach overall forest dynamics evident in the ESM, and then assimilating inventory data to constrain model parameters and initial conditions.

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

PubMed Central

Hulse-Kemp, Amanda M.; Lemm, Jana; Plieske, Joerg; Ashrafi, Hamid; Buyyarapu, Ramesh; Fang, David D.; Frelichowski, James; Giband, Marc; Hague, Steve; Hinze, Lori L.; Kochan, Kelli J.; Riggs, Penny K.; Scheffler, Jodi A.; Udall, Joshua A.; Ulloa, Mauricio; Wang, Shirley S.; Zhu, Qian-Hao; Bag, Sumit K.; Bhardwaj, Archana; Burke, John J.; Byers, Robert L.; Claverie, Michel; Gore, Michael A.; Harker, David B.; Islam, Md S.; Jenkins, Johnie N.; Jones, Don C.; Lacape, Jean-Marc; Llewellyn, Danny J.; Percy, Richard G.; Pepper, Alan E.; Poland, Jesse A.; Mohan Rai, Krishan; Sawant, Samir V.; Singh, Sunil Kumar; Spriggs, Andrew; Taylor, Jen M.; Wang, Fei; Yourstone, Scott M.; Zheng, Xiuting; Lawley, Cindy T.; Ganal, Martin W.; Van Deynze, Allen; Wilson, Iain W.; Stelly, David M.

2015-01-01

High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community. PMID:25908569