Mapping Surface Cover Parameters Using Aggregation Rules and Remotely Sensed Cover Classes. Version 1.9

NASA Technical Reports Server (NTRS)

Arain, Altaf M.; Shuttleworth, W. James; Yang, Z-Liang; Michaud, Jene; Dolman, Johannes

1997-01-01

A coupled model, which combines the Biosphere-Atmosphere Transfer Scheme (BATS) with an advanced atmospheric boundary-layer model, was used to validate hypothetical aggregation rules for BATS-specific surface cover parameters. The model was initialized and tested with observations from the Anglo-Brazilian Amazonian Climate Observational Study and used to simulate surface fluxes for rain forest and pasture mixes at a site near Manaus in Brazil. The aggregation rules are shown to estimate parameters which give area-average surface fluxes similar to those calculated with explicit representation of forest and pasture patches for a range of meteorological and surface conditions relevant to this site, but the agreement deteriorates somewhat when there are large patch-to-patch differences in soil moisture. The aggregation rules, validated as above, were then applied to remotely sensed 1 km land cover data set to obtain grid-average values of BATS vegetation parameters for 2.8 deg x 2.8 deg and 1 deg x 1 deg grids within the conterminous United States. There are significant differences in key vegetation parameters (aerodynamic roughness length, albedo, leaf area index, and stomatal resistance) when aggregate parameters are compared to parameters for the single, dominant cover within the grid. However, the surface energy fluxes calculated by stand-alone BATS with the 2-year forcing, data from the International Satellite Land Surface Climatology Project (ISLSCP) CDROM were reasonably similar using aggregate-vegetation parameters and dominant-cover parameters, but there were some significant differences, particularly in the western USA.

Analysis of MAGSAT data of the Indian region

NASA Technical Reports Server (NTRS)

Agarwal, G. C.; Arur, M. G.

1982-01-01

Data tapes were decoded and 24 tracks over the Indian region were reduced to common elevation. Profiles of raw scalar and vector field data and the residuals along few passes were prepared. An anomaly data set was created from the Investigator-B tape. Data was sampled on an 0.5 deg by 0.5 deg grid.

Code Calibration Applied to the TCA High-Lift Model in the 14 x 22 Wind Tunnel (Simulation With and Without Model Post-Mount)

NASA Technical Reports Server (NTRS)

Lessard, Wendy B.

1999-01-01

The objective of this study is to calibrate a Navier-Stokes code for the TCA (30/10) baseline configuration (partial span leading edge flaps were deflected at 30 degs. and all the trailing edge flaps were deflected at 10 degs). The computational results for several angles of attack are compared with experimental force, moments, and surface pressures. The code used in this study is CFL3D; mesh sequencing and multi-grid were used to full advantage to accelerate convergence. A multi-grid approach was used similar to that used for the Reference H configuration allowing point-to-point matching across all the trailingedge block interfaces. From past experiences with the Reference H (ie, good force, moment, and pressure comparisons were obtained), it was assumed that the mounting system would produce small effects; hence, it was not initially modeled. However, comparisons of lower surface pressures indicated the post mount significantly influenced the lower surface pressures, so the post geometry was inserted into the existing grid using Chimera (overset grids).

GEOS-5 Seasonal Forecast System: ENSO Prediction Skill and Bias

NASA Technical Reports Server (NTRS)

Borovikov, Anna; Kovach, Robin; Marshak, Jelena

2018-01-01

The GEOS-5 AOGCM known as S2S-1.0 has been in service from June 2012 through January 2018 (Borovikov et al. 2017). The atmospheric component of S2S-1.0 is Fortuna-2.5, the same that was used for the Modern-Era Retrospective Analysis for Research and Applications (MERRA), but with adjusted parameterization of moist processes and turbulence. The ocean component is the Modular Ocean Model version 4 (MOM4). The sea ice component is the Community Ice CodE, version 4 (CICE). The land surface model is a catchment-based hydrological model coupled to the multi-layer snow model. The AGCM uses a Cartesian grid with a 1 deg × 1.25 deg horizontal resolution and 72 hybrid vertical levels with the upper most level at 0.01 hPa. OGCM nominal resolution of the tripolar grid is 1/2 deg, with a meridional equatorial refinement to 1/4 deg. In the coupled model initialization, selected atmospheric variables are constrained with MERRA. The Goddard Earth Observing System integrated Ocean Data Assimilation System (GEOS-iODAS) is used for both ocean state and sea ice initialization. SST, T and S profiles and sea ice concentration were assimilated.

Numerical simulation of three dimensional transonic flows

NASA Technical Reports Server (NTRS)

Sahu, Jubaraj; Steger, Joseph L.

1987-01-01

The three-dimensional flow over a projectile has been computed using an implicit, approximately factored, partially flux-split algorithm. A simple composite grid scheme has been developed in which a single grid is partitioned into a series of smaller grids for applications which require an external large memory device such as the SSD of the CRAY X-MP/48, or multitasking. The accuracy and stability of the composite grid scheme has been tested by numerically simulating the flow over an ellipsoid at angle of attack and comparing the solution with a single grid solution. The flowfield over a projectile at M = 0.96 and 4 deg angle-of-attack has been computed using a fine grid, and compared with experiment.

Distribution and Validation of CERES Irradiance Global Data Products Via Web Based Tools

NASA Technical Reports Server (NTRS)

Rutan, David; Mitrescu, Cristian; Doelling, David; Kato, Seiji

2016-01-01

The CERES SYN1deg product provides climate quality 3-hourly globally gridded and temporally complete maps of top of atmosphere, in atmosphere, and surface fluxes. This product requires efficient release to the public and validation to maintain quality assurance. The CERES team developed web-tools for the distribution of both the global gridded products and grid boxes that contain long term validation sites that maintain high quality flux observations at the Earth's surface. These are found at: http://ceres.larc.nasa.gov/order_data.php. In this poster we explore the various tools available to users to sub-set, download, and validate using surface observations the SYN1Deg and Surface-EBAF products. We also analyze differences found in long-term records from well-maintained land surface sites such as the ARM central facility and high quality buoy radiometers, which due to their isolated nature cannot be maintained in a similar manner to their land based counterparts.

Application of multiple grids topology to supersonic internal/external flow interactions

NASA Technical Reports Server (NTRS)

Kathong, M.; Tiwari, S. N.; Smith, R. E.

1988-01-01

For many aerodynamic applications, it is very difficult to construct a smooth body-fitted grid around complex configurations. An approach, called 'multiple grids' or 'zonal grids', which subdivides the entire physical domain into several subdomains, is used to overcome such difficulties. The approach is applied to obtain the solutions to the Euler equations for the supersonic internal/external flow around a fighter-aircraft configuration. Steady-state solutions are presented for Mach 2 at 0, 3.79, 7, and 10 deg angles-of-attack. The problem of conservative treatment at the zonal interfaces is also addressed.

An assessment of viscous effects in computational simulation of benign and burst vortex flows on generic fighter wind-tunnel models using TEAM code

NASA Technical Reports Server (NTRS)

Kinard, Tim A.; Harris, Brenda W.; Raj, Pradeep

1995-01-01

Vortex flows on a twin-tail and a single-tail modular transonic vortex interaction (MTVI) model, representative of a generic fighter configuration, are computationally simulated in this study using the Three-dimensional Euler/Navier-Stokes Aerodynamic Method (TEAM). The primary objective is to provide an assessment of viscous effects on benign (10 deg angle of attack) and burst (35 deg angle of attack) vortex flow solutions. This study was conducted in support of a NASA project aimed at assessing the viability of using Euler technology to predict aerodynamic characteristics of aircraft configurations at moderate-to-high angles of attack in a preliminary design environment. The TEAM code solves the Euler and Reynolds-average Navier-Stokes equations on patched multiblock structured grids. Its algorithm is based on a cell-centered finite-volume formulation with multistage time-stepping scheme. Viscous effects are assessed by comparing the computed inviscid and viscous solutions with each other and experimental data. Also, results of Euler solution sensitivity to grid density and numerical dissipation are presented for the twin-tail model. The results show that proper accounting of viscous effects is necessary for detailed design and optimization but Euler solutions can provide meaningful guidelines for preliminary design of flight vehicles which exhibit vortex flows in parts of their flight envelope.

Spectral photometry of extreme helium stars: Ultraviolet fluxes and effective temperature

NASA Technical Reports Server (NTRS)

Drilling, J. S.; Schoenberner, D.; Heber, U.; Lynas-Gray, A. E.

1982-01-01

Ultraviolet flux distributions are presented for the extremely helium rich stars BD +10 deg 2179, HD 124448, LSS 3378, BD -9 deg 4395, LSE 78, HD 160641, LSIV -1 deg 2, BD 1 deg 3438, HD 168476, MV Sgr, LS IV-14 deg 109 (CD -35 deg 11760), LSII +33 deg 5 and BD +1 deg 4381 (LSIV +2 deg 13) obtained with the International Ultraviolet Explorer (IUE). Broad band photometry and a newly computed grid of line blanketed model atmospheres were used to determine accurate angular diameters and total stellar fluxes. The resultant effective temperatures are in most cases in satisfactory agreement with those based on broad band photometry and/or high resolution spectroscopy in the visible. For two objects, LSII +33 deg 5 and LSE 78, disagreement was found between the IUE observations and broadband photometry: the colors predict temperatures around 20,000 K, whereas the UV spectra indicate much lower photospheric temperatures of 14,000 to 15,000 K. The new temperature scale for extreme helium stars extends to lower effective temperatures than that of Heber and Schoenberner (1981) and covers the range from 8,500 K to 32,000 K.

Navier-Stokes simulation of rotor-body flowfield in hover using overset grids

NASA Technical Reports Server (NTRS)

Srinivasan, G. R.; Ahmad, J. U.

1993-01-01

A free-wake Navier-Stokes numerical scheme and multiple Chimera overset grids have been utilized for calculating the quasi-steady hovering flowfield of a Boeing-360 rotor mounted on an axisymmetric whirl-tower. The entire geometry of this rotor-body configuration is gridded-up with eleven different overset grids. The composite grid has 1.3 million grid points for the entire flow domain. The numerical results, obtained using coarse grids and a rigid rotor assumption, show a thrust value that is within 5% of the experimental value at a flow condition of M(sub tip) = 0.63, Theta(sub c) = 8 deg, and Re = 2.5 x 10(exp 6). The numerical method thus demonstrates the feasibility of using a multi-block scheme for calculating the flowfields of complex configurations consisting of rotating and non-rotating components.

Thresholds for Shifting Visually Perceived Eye Level Due to Incremental Pitches

NASA Technical Reports Server (NTRS)

Scott, Donald M.; Welch, Robert; Cohen, M. M.; Hill, Cyndi

2001-01-01

Visually perceived eye level (VPEL) was judged by subjects as they viewed a luminous grid pattern that was pitched by 2 or 5 deg increments between -20 deg and +20 deg. Subjects were dark adapted for 20 min and indicated--VPEL by directing the beam of a laser pointer to the rear wall of a 1.25 m cubic pitch box that rotated about a horizontal axis midpoint on the rear wall. Data were analyzed by ANOVA and the Tukey HSD procedure. Results showed a 10.0 deg threshold for pitches P(sub i) above the reference pitch P(sub 0), and a -10.3 deg threshold for pitches P(sub i) below-the reference-pitch P(sub 0). Threshold data for pitches P(sub i) < P(sub 0) suggest an asymmetric threshold for VPEL below and above physical eye level.

Large-eddy simulation/Reynolds-averaged Navier-Stokes hybrid schemes for high speed flows

NASA Astrophysics Data System (ADS)

Xiao, Xudong

Three LES/RANS hybrid schemes have been proposed for the prediction of high speed separated flows. Each method couples the k-zeta (Enstrophy) BANS model with an LES subgrid scale one-equation model by using a blending function that is coordinate system independent. Two of these functions are based on turbulence dissipation length scale and grid size, while the third one has no explicit dependence on the grid. To implement the LES/RANS hybrid schemes, a new rescaling-reintroducing method is used to generate time-dependent turbulent inflow conditions. The hybrid schemes have been tested on a Mach 2.88 flow over 25 degree compression-expansion ramp and a Mach 2.79 flow over 20 degree compression ramp. A special computation procedure has been designed to prevent the separation zone from expanding upstream to the recycle-plane. The code is parallelized using Message Passing Interface (MPI) and is optimized for running on IBM-SP3 parallel machine. The scheme was validated first for a flat plate. It was shown that the blending function has to be monotonic to prevent the RANS region from appearing in the LES region. In the 25 deg ramp case, the hybrid schemes provided better agreement with experiment in the recovery region. Grid refinement studies demonstrated the importance of using a grid independent blend function and further improvement with experiment in the recovery region. In the 20 deg ramp case, with a relatively finer grid, the hybrid scheme characterized by grid independent blending function well predicted the flow field in both the separation region and the recovery region. Therefore, with "appropriately" fine grid, current hybrid schemes are promising for the simulation of shock wave/boundary layer interaction problems.

Artifacts Introduced in the Point Evaluation of Functions Expanded into a Degree 360 Spherical Harmonic Series

NASA Technical Reports Server (NTRS)

Rapp, R.

1999-01-01

An expansion of a function initially given in 1deg cells was carried out to degree 360 by using 30'cells whose value was initially assigned to be the value of the 1deg cell in which it fell. The evaluation of point values of the function from the degree 360 expansion revealed spurious patterns attributed to the coefficients from degree 181 to 360. Expansion of the original function in 1deg cells to degree 180 showed no problems in the point evaluation. Mean 1deg values computed from both degree 180 to 360 expansions showed close agreement with the original function. The artifacts could be removed if the 30' values were interpolated by spline procedures from adjacent I' cells. These results led to an examination of the gravity anomalies and geoid undulations from EGM96 in areas where I' values were "split up" to form 30'cells. The area considered was 75degS to 85degS, 100degE to 120degE where the split up cells were basically south of 81 degS. A small, latitude related, and possibly spurious effect might be detectable in anomaly variations in the region. These results suggest that point values of a function computed from a high degree expansion may have spurious signals unless the cell size is compatible with the maximum degree of expansion. The spurious signals could be eliminated by using a spline interpolation procedure to obtain the 30'values from the 1deg values.

Navier-Stokes Flowfield Simulation of Boeing 747-200 as Platform for SOFIA

NASA Technical Reports Server (NTRS)

Srinivasan, G.R.

1994-01-01

Steady and unsteady viscous, three-dimensional flowfields are calculated using a thin layer approximation of Navier-Stokes equations in conjunction with Chimera overset grids. The finite-difference numerical scheme uses structured grids and a pentadiagonal flow solver called "OVERFLOW". The configuration of Boeing 747-200 has been chosen as one of configurations to be used as a platform for the SOFIA (Stratospheric Observatory For Infrared Astronomy). Initially, the steady flowfield of the full aircraft is calculated for the clean configuration (without a cavity to house telescope). This solution is then used to start the unsteady flowfield of a configuration containing cavity housing the observation telescope and its peripheral units. Analysis of unsteady flowfield in the cavity and its influence on the tail empennage, as well as the noise due to turbulence and optical quality of the flow are the main focus of this study. For the configuration considered here, the telescope housing cavity is located slightly downstream of the portwing. The entire flow-field is carefully constructed using 45 overset grids and consists of nearly 4 million grid points. All the computations axe done at one freestream flow condition of M(sub infinity) = 0.85, alpha = 2.5deg, and a Reynolds of Re = 1.85x10deg

Dynamics of the transition zone in coastal zone color scanner-sensed ocean color in the North Pacific during oceanographic spring

NASA Technical Reports Server (NTRS)

Glover, David M.; Wroblewski, J. S.; Mcclain, Charles R.

1994-01-01

A transition zone in phytoplankton concentration running across the North Pacific basin at 30 deg to 40 deg north latitude corresponds to a basin-wide front in surface chlorophyll observed in a composite of coastal zone color scanner (CZCS) images for May, June, and July 1979-1986. This transition zone with low chlorophyll to the south and higher chlorophyll to the north can be simulated by a simple model of the concentration of phytoplankton, zooplankton, and dissolved nutrient (nitrate) in the surface mixed layer of the ocean applied to the North Pacific basin for the climatological conditions during oceanographic springtime (May, June, and July). The model is initialized with a 1 deg x 1 deg gridded estimate of wintertime (February, March, and April) mixed layer nitrate concentrations calculated from an extensive nutrient database and a similarly gridded mixed layer depth data set. Comparison of model predictions with CZCS data provides a means of evaluating the dynamics of the transition zone. We conclude that in the North Pacific, away from major boundary currents and coastal upwelling zones, wintertime vertical mixing determines the total nutrient available to the plankton ecosystem in the spring. The transition zone seen in basin-scale CZCS images is a reflection of the geographic variation in the wintertime mixed layer depth and the nitracline, leading to a latitudinal gradient in phytoplankton chlorophyll.

Calculation of unsteady airfoil loads with and without flap deflection at -90 degrees incidence

NASA Technical Reports Server (NTRS)

Stremel, Paul M.

1991-01-01

A method has been developed for calculating the viscous flow about airfoils with and without deflected flaps at -90 deg incidence. This unique method provides for the direct solution of the incompressible Navier-Stokes equations by means of a fully coupled implicit technique. The solution is calculated on a body-fitted computational mesh incorporating a staggered grid method. The vorticity is determined at the node points, and the velocity components are defined at the mesh-cell sides. The staggered-grid orientation provides for accurate representation of vorticity at the node points and for the conservation of mass at the mesh-cell centers. The method provides for the direct solution of the flow field and satisfies the conservation of mass to machine zero at each time-step. The results of the present analysis and experimental results obtained for a XV-15 airfoil are compared. The comparisons indicate that the calculated drag reduction caused by flap deflection and the calculated average surface pressure are in excellent agreement with the measured results. Comparisons of the numerical results of the present method for several airfoils demonstrate the significant influence of airfoil curvature and flap deflection on the predicted download.

A statistical evaluation and comparison of VISSR Atmospheric Sounder (VAS) data and corresponding rawinsonde measurements

NASA Technical Reports Server (NTRS)

1984-01-01

Three mesoscale sounding data sets from the VISSR Atmospheric Sounder (VAS) produced using different retrieval techniques were evaluated of corresponding ground truth rawinsonde data for 6-7 March 1982. Mean, standard deviations, and RMS differences between the satellite and rawinsonde parameters were calculated over gridded fields in central Texas and Oklahoma. Large differences exist between each satellite data set and the ground truth data. Biases in the satellite temperature and moisture profiles seem extremely dependent upon the three dimensional structure of the atmosphere and range from 1 deg to 3 deg C for temperature and 3 deg to 6 deg C for dewpoint temperature. Atmospheric gradients of basic and derived parameters determined from the VAS data sets produced an adequate representation of the mesoscale environment but their magnitudes were often reduced by 30 to 50%.

Numerical simulation of incidence and sweep effects on delta wing vortex breakdown

NASA Technical Reports Server (NTRS)

Ekaterinaris, J. A.; Schiff, Lewis B.

1994-01-01

The structure of the vortical flowfield over delta wings at high angles of attack was investigated. Three-dimensional Navier-Stokes numerical simulations were carried out to predict the complex leeward-side flowfield characteristics, including leading-edge separation, secondary separation, and vortex breakdown. Flows over a 75- and a 63-deg sweep delta wing with sharp leading edges were investigated and compared with available experimental data. The effect of variation of circumferential grid resolution grid resolution in the vicinity of the wing leading edge on the accuracy of the solutions was addressed. Furthermore, the effect of turbulence modeling on the solutions was investigated. The effects of variation of angle of attack on the computed vortical flow structure for the 75-deg sweep delta wing were examined. At moderate angles of attack no vortex breakdown was observed. When a critical angle of attack was reached, bubble-type vortex breakdown was found. With further increase in angle of attack, a change from bubble-type breakdown to spiral-type vortex breakdown was predicted by the numerical solution. The effects of variation of sweep angle and freestream Mach number were addressed with the solutions on a 63-deg sweep delta wing.

Downscaling Reanalysis over Continental Africa with a Regional Model: NCEP Versus ERA Interim Forcing

NASA Technical Reports Server (NTRS)

Druyan, Leonard M.; Fulakeza, Matthew B.

2013-01-01

Five annual climate cycles (1998-2002) are simulated for continental Africa and adjacent oceans by a regional atmospheric model (RM3). RM3 horizontal grid spacing is 0.44deg at 28 vertical levels. Each of 2 simulation ensembles is driven by lateral boundary conditions from each of 2 alternative reanalysis data sets. One simulation downs cales National Center for Environmental Prediction reanalysis 2 (NCPR2) and the other the European Centre for Medium Range Weather Forecasts Interim reanalysis (ERA-I). NCPR2 data are archived at 2.5deg grid spacing, while a recent version of ERA-I provides data at 0.75deg spacing. ERA-I-forced simulations are recomrp. ended by the Coordinated Regional Downscaling Experiment (CORDEX). Comparisons of the 2 sets of simulations with each other and with observational evidence assess the relative performance of each downscaling system. A third simulation also uses ERA-I forcing, but degraded to the same horizontal resolution as NCPR2. RM3-simulated pentad and monthly mean precipitation data are compared to Tropical Rainfall Measuring Mission (TRMM) data, gridded at 0.5deg, and RM3-simulated circulation is compared to both reanalyses. Results suggest that each downscaling system provides advantages and disadvantages relative to the other. The RM3/NCPR2 achieves a more realistic northward advance of summer monsoon rains over West Africa, but RM3/ERA-I creates the more realistic monsoon circulation. Both systems recreate some features of JulySeptember 1999 minus 2002 precipitation differences. Degrading the resolution of ERA-I driving data unrealistically slows the monsoon circulation and considerably diminishes summer rainfall rates over West Africa. The high resolution of ERA-I data, therefore, contributes to the quality of the downscaling, but NCPR2laterai boundary conditions nevertheless produce better simulations of some features.

A 1400 MHz sky survey. II - Confusion-limited maps covering ascension between 19 H 30 M and 7 H 30 m, declination between -5 deg and +82 deg

NASA Astrophysics Data System (ADS)

Condon, J. J.; Broderick, J. J.

1986-05-01

The NRAO 91 m transit telescope and rebuilt four-feed receiver were used to make a 1400 MHz continuum survey with 12.7 arcmin x 11.1 arcmin resolution. New maps covering ascension between 19 h 30 m and 7 h 30 m supplement those in the right ascension range between 7 h 30 m and 19 h 30 m (Condon and Broderick, 1985) to complete the roughly 6.8 sr declination band between -5 deg and +82 deg. Both sets of maps are confusion-limited and contain roughly 3000 sources per sr stronger than 0.15 Jy. They are available on FITS tapes and can be displayed and analyzed with standard AIPS programs. A procedure for making radio 'identifications' automatically from the map tapes is given. A 1400 MHz radio sky atlas of contour plots and coordinate-grid overlays covering declination between -5 deg and +82 deg with a roughly 200 arcsec/mm scale was also produced.

Global Precipitation at One-Degree Daily Resolution From Multi-Satellite Observations

NASA Technical Reports Server (NTRS)

Huffman, George J.; Adler, Robert F.; Morrissey, Mark M.; Curtis, Scott; Joyce, Robert; McGavock, Brad; Susskind, Joel

2000-01-01

The One-Degree Daily (1DD) technique is described for producing globally complete daily estimates of precipitation on a 1 deg x 1 deg lat/long grid from currently available observational data. Where possible (40 deg N-40 deg S), the Threshold-Matched Precipitation Index (TMPI) provides precipitation estimates in which the 3-hourly infrared brightness temperatures (IR T(sub b)) are thresholded and all "cold" pixels are given a single precipitation rate. This approach is an adaptation of the Geostationary Operational Environmental Satellite (GOES) Precipitation Index (GPI), but for the TMPI the IR Tb threshold and conditional rain rate are set locally by month from Special Sensor Microwave/Imager (SSM/I)-based precipitation frequency and the Global Precipitation Climatology Project (GPCP) satellite-gauge (SG) combined monthly precipitation estimate, respectively. At higher latitudes the 1DD features a rescaled daily Television Infrared Observation Satellite (TIROS) Operational Vertical Sounder (TOVS) precipitation. The frequency of rain days in the TOVS is scaled down to match that in the TMPI at the data boundaries, and the resulting non-zero TOVS values are scaled locally to sum to the SG (which is a globally complete monthly product). The time series of the daily 1DD global images shows good continuity in time and across the data boundaries. Various examples are shown to illustrate uses. Validation for individual grid -box values shows a very high root-mean-square error but, it improves quickly when users perform time/space averaging according to their own requirements.

Tidal estimation in the Atlantic and Indian Oceans, 3 deg x 3 deg solution

NASA Technical Reports Server (NTRS)

Sanchez, Braulio V.; Rao, Desiraju B.; Steenrod, Stephen D.

1987-01-01

An estimation technique was developed to extrapolate tidal amplitudes and phases over entire ocean basins using existing gauge data and the altimetric measurements provided by satellite oceanography. The technique was previously tested. Some results obtained by using a 3 deg by 3 deg grid are presented. The functions used in the interpolation are the eigenfunctions of the velocity (Proudman functions) which are computed numerically from a knowledge of the basin's bottom topography, the horizontal plan form and the necessary boundary conditions. These functions are characteristic of the particular basin. The gravitational normal modes of the basin are computed as part of the investigation; they are used to obtain the theoretical forced solutions for the tidal constituents. The latter can provide the simulated data for the testing of the method and serve as a guide in choosing the most energetic functions for the interpolation.

The aerodynamic performance of several flow control devices for internal flow systems

NASA Technical Reports Server (NTRS)

Eckert, W. T.; Wettlaufer, B. M.; Mort, K. W.

1982-01-01

An experimental reseach and development program was undertaken to develop and document new flow-control devices for use in the major modifications to the 40 by 80 Foot wind tunnel at Ames Research Center. These devices, which are applicable to other facilities as well, included grid-type and quasi-two-dimensional flow straighteners, louver panels for valving, and turning-vane cascades with net turning angles from 0 deg to 90 deg. The tests were conducted at model scale over a Reynolds number range from 2 x 100,000 to 17 x 100,000, based on chord. The results showed quantitatively the performance benefits of faired, low-blockage, smooth-surface straightener systems, and the advantages of curved turning-vanes with hinge-line gaps sealed and a preferred chord-to-gap ratio between 2.5 and 3.0 for 45 deg or 90 deg turns.

Procedure for locating 10 km UTM grid on Alabama County general highway maps

NASA Technical Reports Server (NTRS)

Paludan, C. T. N.

1975-01-01

Each county highway map has a geographic grid of degrees and tens of minutes in both longitude and latitude in the margins and within the map as intersection crosses. These will be used to locate the universal transverse mercator (UTM) grid at 10 km intervals. Since the maps used may have stretched or shrunk in height and/or width, interpolation should be done between the 10 min intersections when possible. A table of UTM coordinates of 10 min intersections is required and included. In Alabama, all eastings are referred to a false easting of 500,000 m at 87 deg W longitude (central meridian, CM).

Three dimensional inventories of aircraft emissions

NASA Technical Reports Server (NTRS)

Baughcum, Steven L.; Henderson, Stephen C.; Hertel, Peter S.

1994-01-01

Three dimensional inventories of fuel burned and emissions (NO(x), CO, and hydrocarbons) have been developed on a 1 deg latitude by 1 deg longitude by 1 km altitude grid for scheduled commercial air traffic (passenger jet, cargo, and turboprop aircraft) for 1990 and projected to the year 2015. Emission scenarios have also been calculated for projected fleets of Mach 2 and Mach 2.4 high speed civil transports. The methodology and results are discussed. These emission inventories are now in use in the assessment of aircraft emissions impact by NASA.

Global map of lithosphere thermal thickness on a 1 deg x 1 deg grid - digitally available

NASA Astrophysics Data System (ADS)

Artemieva, Irina

2014-05-01

This presentation reports a 1 deg ×1 deg global thermal model for the continental lithosphere (TC1). The model is digitally available from the author's web-site: www.lithosphere.info. Geotherms for continental terranes of different ages (early Archean to present) are constrained by reliable data on borehole heat flow measurements (Artemieva and Mooney, 2001), checked with the original publications for data quality, and corrected for paleo-temperature effects where needed. These data are supplemented by cratonic geotherms based on xenolith data. Since heat flow measurements cover not more than half of the continents, the remaining areas (ca. 60% of the continents) are filled by the statistical numbers derived from the thermal model constrained by borehole data. Continental geotherms are statistically analyzed as a function of age and are used to estimate lithospheric temperatures in continental regions with no or low quality heat flow data. This analysis requires knowledge of lithosphere age globally. A compilation of tectono-thermal ages of lithospheric terranes on a 1 deg × 1 deg grid forms the basis for the statistical analysis. It shows that, statistically, lithospheric thermal thickness z (in km) depends on tectono-thermal age t (in Ma) as: z=0.04t+93.6. This relationship formed the basis for a global thermal model of the continental lithosphere (TC1). Statistical analysis of continental geotherms also reveals that this relationship holds for the Archean cratons in general, but not in detail. Particularly, thick (more than 250 km) lithosphere is restricted solely to young Archean terranes (3.0-2.6 Ga), while in old Archean cratons (3.6-3.0 Ga) lithospheric roots do not extend deeper than 200-220 km. The TC1 model is presented by a set of maps, which show significant thermal heterogeneity within continental upper mantle. The strongest lateral temperature variations (as large as 800 deg C) are typical of the shallow mantle (depth less than 100 km). A map of the depth to a 600 deg C isotherm in continental upper mantle is presented as a proxy to the elastic thickness of the cratonic lithosphere, in which flexural rigidity is dominated by olivine rheology of the mantle. The TC1 model of the lithosphere thickness is used to calculate the growth and preservation rates of the lithosphere since the Archean.

A 3-Year Climatology of Cloud and Radiative Properties Derived from GOES-8 Data Over the Southern Great Plains

NASA Technical Reports Server (NTRS)

Khaiyer, M. M.; Rapp, A. D.; Doelling, D. R.; Nordeen, M. L.; Minnis, P.; Smith, W. L., Jr.; Nguyen, L.

2001-01-01

While the various instruments maintained at the Atmospheric Radiation Measurement (ARM) Program Southern Great Plains (SGP) Central Facility (CF) provide detailed cloud and radiation measurements for a small area, satellite cloud property retrievals provide a means of examining the large-scale properties of the surrounding region over an extended period of time. Seasonal and inter-annual climatological trends can be analyzed with such a dataset. For this purpose, monthly datasets of cloud and radiative properties from December 1996 through November 1999 over the SGP region have been derived using the layered bispectral threshold method (LBTM). The properties derived include cloud optical depths (ODs), temperatures and albedos, and are produced on two grids of lower (0.5 deg) and higher resolution (0.3 deg) centered on the ARM SGP CF. The extensive time period and high-resolution of the inner grid of this dataset allows for comparison with the suite of instruments located at the ARM CF. In particular, Whole-Sky Imager (WSI) and the Active Remote Sensing of Clouds (ARSCL) cloud products can be compared to the cloud amounts and heights of the LBTM 0.3 deg grid box encompassing the CF site. The WSI provides cloud fraction and the ARSCL computes cloud fraction, base, and top heights using the algorithms by Clothiaux et al. (2001) with a combination of Belfort Laser Ceilometer (BLC), Millimeter Wave Cloud Radar (MMCR), and Micropulse Lidar (MPL) data. This paper summarizes the results of the LBTM analysis for 3 years of GOES-8 data over the SGP and examines the differences between surface and satellite-based estimates of cloud fraction.

Regional and seasonal estimates of fractional storm coverage based on station precipitation observations

NASA Technical Reports Server (NTRS)

Gong, Gavin; Entekhabi, Dara; Salvucci, Guido D.

1994-01-01

Simulated climates using numerical atmospheric general circulation models (GCMs) have been shown to be highly sensitive to the fraction of GCM grid area assumed to be wetted during rain events. The model hydrologic cycle and land-surface water and energy balance are influenced by the parameter bar-kappa, which is the dimensionless fractional wetted area for GCM grids. Hourly precipitation records for over 1700 precipitation stations within the contiguous United States are used to obtain observation-based estimates of fractional wetting that exhibit regional and seasonal variations. The spatial parameter bar-kappa is estimated from the temporal raingauge data using conditional probability relations. Monthly bar-kappa values are estimated for rectangular grid areas over the contiguous United States as defined by the Goddard Institute for Space Studies 4 deg x 5 deg GCM. A bias in the estimates is evident due to the unavoidably sparse raingauge network density, which causes some storms to go undetected by the network. This bias is corrected by deriving the probability of a storm escaping detection by the network. A Monte Carlo simulation study is also conducted that consists of synthetically generated storm arrivals over an artificial grid area. It is used to confirm the bar-kappa estimation procedure and to test the nature of the bias and its correction. These monthly fractional wetting estimates, based on the analysis of station precipitation data, provide an observational basis for assigning the influential parameter bar-kappa in GCM land-surface hydrology parameterizations.

Using an electronic compass to determine telemetry azimuths

USGS Publications Warehouse

Cox, R.R.; Scalf, J.D.; Jamison, B.E.; Lutz, R.S.

2002-01-01

Researchers typically collect azimuths from known locations to estimate locations of radiomarked animals. Mobile, vehicle-mounted telemetry receiving systems frequently are used to gather azimuth data. Use of mobile systems typically involves estimating the vehicle's orientation to grid north (vehicle azimuth), recording an azimuth to the transmitter relative to the vehicle azimuth from a fixed rosette around the antenna mast (relative azimuth), and subsequently calculating an azimuth to the transmitter (animal azimuth). We incorporated electronic compasses into standard null-peak antenna systems by mounting the compass sensors atop the antenna masts and evaluated the precision of this configuration. This system increased efficiency by eliminating vehicle orientation and calculations to determine animal azimuths and produced estimates of precision (azimuth SD=2.6 deg., SE=0.16 deg.) similar to systems that required orienting the mobile system to grid north. Using an electronic compass increased efficiency without sacrificing precision and should produce more accurate estimates of locations when marked animals are moving or when vehicle orientation is problematic.

Satellite-derived ice data sets no. 2: Arctic monthly average microwave brightness temperatures and sea ice concentrations, 1973-1976

NASA Technical Reports Server (NTRS)

Parkinson, C. L.; Comiso, J. C.; Zwally, H. J.

1987-01-01

A summary data set for four years (mid 70's) of Arctic sea ice conditions is available on magnetic tape. The data include monthly and yearly averaged Nimbus 5 electrically scanning microwave radiometer (ESMR) brightness temperatures, an ice concentration parameter derived from the brightness temperatures, monthly climatological surface air temperatures, and monthly climatological sea level pressures. All data matrices are applied to 293 by 293 grids that cover a polar stereographic map enclosing the 50 deg N latitude circle. The grid size varies from about 32 X 32 km at the poles to about 28 X 28 km at 50 deg N. The ice concentration parameter is calculated assuming that the field of view contains only open water and first-year ice with an ice emissivity of 0.92. To account for the presence of multiyear ice, a nomogram is provided relating the ice concentration parameter, the total ice concentration, and the fraction of the ice cover which is multiyear ice.

Development of a Distributed Parallel Computing Framework to Facilitate Regional/Global Gridded Crop Modeling with Various Scenarios

NASA Astrophysics Data System (ADS)

Jang, W.; Engda, T. A.; Neff, J. C.; Herrick, J.

2017-12-01

Many crop models are increasingly used to evaluate crop yields at regional and global scales. However, implementation of these models across large areas using fine-scale grids is limited by computational time requirements. In order to facilitate global gridded crop modeling with various scenarios (i.e., different crop, management schedule, fertilizer, and irrigation) using the Environmental Policy Integrated Climate (EPIC) model, we developed a distributed parallel computing framework in Python. Our local desktop with 14 cores (28 threads) was used to test the distributed parallel computing framework in Iringa, Tanzania which has 406,839 grid cells. High-resolution soil data, SoilGrids (250 x 250 m), and climate data, AgMERRA (0.25 x 0.25 deg) were also used as input data for the gridded EPIC model. The framework includes a master file for parallel computing, input database, input data formatters, EPIC model execution, and output analyzers. Through the master file for parallel computing, the user-defined number of threads of CPU divides the EPIC simulation into jobs. Then, Using EPIC input data formatters, the raw database is formatted for EPIC input data and the formatted data moves into EPIC simulation jobs. Then, 28 EPIC jobs run simultaneously and only interesting results files are parsed and moved into output analyzers. We applied various scenarios with seven different slopes and twenty-four fertilizer ranges. Parallelized input generators create different scenarios as a list for distributed parallel computing. After all simulations are completed, parallelized output analyzers are used to analyze all outputs according to the different scenarios. This saves significant computing time and resources, making it possible to conduct gridded modeling at regional to global scales with high-resolution data. For example, serial processing for the Iringa test case would require 113 hours, while using the framework developed in this study requires only approximately 6 hours, a nearly 95% reduction in computing time.

Influence of numerical dissipation in computing supersonic vortex-dominated flows

NASA Technical Reports Server (NTRS)

Kandil, O. A.; Chuang, A.

1986-01-01

Steady supersonic vortex-dominated flows are solved using the unsteady Euler equations for conical and three-dimensional flows around sharp- and round-edged delta wings. The computational method is a finite-volume scheme which uses a four-stage Runge-Kutta time stepping with explicit second- and fourth-order dissipation terms. The grid is generated by a modified Joukowski transformation. The steady flow solution is obtained through time-stepping with initial conditions corresponding to the freestream conditions, and the bow shock is captured as a part of the solution. The scheme is applied to flat-plate and elliptic-section wings with a leading edge sweep of 70 deg at an angle of attack of 10 deg and a freestream Mach number of 2.0. Three grid sizes of 29 x 39, 65 x 65 and 100 x 100 have been used. The results for sharp-edged wings show that they are consistent with all grid sizes and variation of the artificial viscosity coefficients. The results for round-edged wings show that separated and attached flow solutions can be obtained by varying the artificial viscosity coefficients. They also show that the solutions are independent of the way time stepping is done. Local time-stepping and global minimum time-steeping produce same solutions.

Conical Euler analysis and active roll suppression for unsteady vortical flows about rolling delta wings

NASA Technical Reports Server (NTRS)

Lee-Rausch, Elizabeth M.; Batina, John T.

1993-01-01

A conical Euler code was developed to study unsteady vortex-dominated flows about rolling, highly swept delta wings undergoing either forced motions or free-to-roll motions that include active roll suppression. The flow solver of the code involves a multistage, Runge-Kutta time-stepping scheme that uses a cell-centered, finite-volume, spatial discretization of the Euler equations on an unstructured grid of triangles. The code allows for the additional analysis of the free to-roll case by simultaneously integrating in time the rigid-body equation of motion with the governing flow equations. Results are presented for a delta wing with a 75 deg swept, sharp leading edge at a free-stream Mach number of 1.2 and at 10 deg, 20 deg, and 30 deg angle of attack alpha. At the lower angles of attack (10 and 20 deg), forced-harmonic analyses indicate that the rolling-moment coefficients provide a positive damping, which is verified by free-to-roll calculations. In contrast, at the higher angle of attack (30 deg), a forced-harmonic analysis indicates that the rolling-moment coefficient provides negative damping at the small roll amplitudes. A free-to-roll calculation for this case produces an initially divergent response, but as the amplitude of motion grows with time, the response transitions to a wing-rock type of limit cycle oscillation, which is characteristic of highly swept delta wings. This limit cycle oscillation may be actively suppressed through the use of a rate-feedback control law and antisymmetrically deflected leading-edge flaps. Descriptions of the conical Euler flow solver and the free-to roll analysis are included in this report. Results are presented that demonstrate how the systematic analysis of the forced response of the delta wing can be used to predict the stable, neutrally stable, and unstable free response of the delta wing. These results also give insight into the flow physics associated with unsteady vortical flows about delta wings undergoing forced motions and free-to-roll motions, including the active suppression of the wing-rock type phenomenon. The conical Euler methodology developed is directly extend able to three-dimensional calculations.

Extending the Precipitation Map Offshore Using Daily and 3-Hourly Combined Precipitation Estimates

NASA Technical Reports Server (NTRS)

Huffman, George J.; Adler, Robert F.; Bolvin, David T.; Curtis, Scott; Einaudi, Franco (Technical Monitor)

2001-01-01

One of the difficulties in studying landfalling extratropical cyclones along the Pacific Coast is the lack of antecedent data over the ocean, including precipitation. Recent research on combining various satellite-based precipitation estimates opens the possibility of realistic precipitation estimates on a global 1 deg. x 1 deg. latitude-longitude grid at the daily or even 3-hourly interval. The goal in this work is to provide quantitative precipitation estimates that correctly represent the precipitation- related variables in the hydrological cycle: surface accumulations (fresh-water flux into oceans), frequency and duration statistics, net latent heating, etc.

Effect of high latitude filtering on NWP skill

NASA Technical Reports Server (NTRS)

Kalnay, E.; Takacs, L. L.; Hoffman, R. N.

1984-01-01

The high latitude filtering techniques commonly employed in global grid point models to eliminate the high frequency waves associated with the convergence of meridians, can introduce serious distortions which ultimately affect the solution at all latitudes. Experiments completed so far with the 4 deg x 5 deg, 9-level GLAS Fourth Order Model indicate that the high latitude filter currently in operation affects only minimally its forecasting skill. In one case, however, the use of pressure gradient filter significantly improved the forecast. Three day forecasts with the pressure gradient and operational filters are compared as are 5-day forecasts with no filter.

Ocean Circulation Modeling for Aquatic Dispersion of Liquid Radioactive Effluents from Nuclear Power Plants

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

Chung, Y.G.; Lee, G.B.; Bang, S.Y.

2006-07-01

Recently, three-dimensional models have been used for aquatic dispersion of radioactive effluents in relation to nuclear power plant siting based on the Notice No. 2003-12 'Guideline for investigating and assessing hydrological and aquatic characteristics of nuclear facility site' of the Ministry of Science and Technology (MOST) in Korea. Several nuclear power plants have been under construction or planed, which are Shin-Kori Unit 1 and 2, Shin-Wolsong Unit 1 and 2, and Shin-Ulchin Unit 1 and 2. For assessing the aquatic dispersion of radionuclides released from the above nuclear power plants, it is necessary to know the coastal currents around sitesmore » which are affected by circulation of East Sea. In this study, a three dimensional hydrodynamic model for the circulation of the East Sea of Korea has been developed as the first phase, which is based on the RIAMOM (Research Institute of Applied Mechanics' Ocean Model, Kyushu University, Japan). The model uses the primitive equation with hydrostatic approximation, and uses Arakawa-B grid system horizontally and Z coordinate vertically. Model domain is 126.5 deg. E to 142.5 deg. E of east longitude and 33 deg. N and 52 deg. N of the north latitude. The space of the horizontal grid was 1/12 deg. to longitude and latitude direction and vertical level was divided to 20. This model uses Generalized Arakawa Scheme, Slant Advection, and Mode-Splitting Method. The input data were from JODC (Japan Oceanographic Data Center), KNFRDI (Korea National Fisheries Research and Development Institute), and ECMWF (European Center for Medium-Range Weather Forecasts). The modeling results are in fairly good agreement with schematic patterns of the surface circulation in the East Sea/Japan Sea. The local current model and aquatic dispersion model of the coastal region will be developed as the second phase. The oceanic dispersion experiments will be also carried out by using ARGO Drifter around a nuclear power plant site. (authors)« less

Numerical simulation of the flow about the F-18 HARV at high angle of attack

NASA Technical Reports Server (NTRS)

Murman, Scott M.

1994-01-01

This report summarizes research done over the past two years as part of NASA Grant NCC 2-729. This research has been aimed at validating numerical methods for computing the flow about the complete F-18 HARV at alpha = 30 deg and alpha = 45 deg. At 30 deg angle of attack, the flow about the F-18 is dominated by the formation, and subsequent breakdown, of strong vortices over the wing leading-edge extensions (LEX). As the angle of attack is increased to alpha = 45 deg, the fuselage forebody of the F-18 contains significant laminar and transitional regions which are not present at alpha = 30 deg. Further, the flow over the LEX at alpha = 45 deg is dominated by an unsteady shedding in time, rather than strong coherent vortices. This complex physics, combined with the complex geometry of a full aircraft configuration, provides a challenge for current computational fluid dynamics (CFD) techniques. The following sections present the numerical method and grid generation scheme that was used, a review of prior research done to numerically model the F-18 HARV, and a discussion of the current research. The current research is broken into two main topics: the effect of engine-inlet mass-flow rate on the F-18 vortex breakdown position, and the results using a refined F-18 computational model to compute the flow at alpha = 30 deg and alpha = 45 deg.

Numerical simulation of the flow about the F-18 HARV at high angle of attack

NASA Technical Reports Server (NTRS)

Murman, Scott M.

1995-01-01

This research has been aimed at validating numerical methods for computing the flow about the complete F-18 HARV at alpha = 30 deg and alpha = 45 deg. At 30 deg angle of attack, the flow about the F-18 is dominated by the formation, and subsequent breakdown, of strong vortices over the wing leading-edge extensions (LEX). As the angle of attack is increased to alpha = 45 deg, the fuselage forebody of the F-18 contains significant laminar and transitional regions which are not present at alpha = 30 deg. Further, the flow over the LEX at alpha = 45 deg is dominated by an unsteady shedding in time, rather than strong coherent vortices. This complex physics, combined with the complex geometry of a full-aircraft configuration, provides a challenge for current computational fluid dynamics (CFD) techniques. The following sections present the numerical method and grid generation scheme that was used, a review of prior research done to numerically model the F-18 HARV, and a discussion of the current research. The current research is broken into three main topics; the effect of engine-inlet mass-flow rate on the F-18 vortex breakdown position, the results using a refined F-18 computational model to compute the flow at alpha = 30 deg and alpha = 45 deg, and research done using the simplified geometry of an ogive-cylinder configuration to investigate the physics of unsteady shear-layer shedding. The last section briefly summarizes the discussion.

Estimates of Lightning NOx Production Based on OMI NO2 Observations Over the Gulf of Mexico

NASA Technical Reports Server (NTRS)

Pickering, Kenneth E.; Bucsela, Eric; Allen, Dale; Ring, Allison; Holzworth, Robert; Krotkov, Nickolay

2016-01-01

We evaluate nitrogen oxide (NO(sub x) NO + NO2) production from lightning over the Gulf of Mexico region using data from the Ozone Monitoring Instrument (OMI) aboard NASAs Aura satellite along with detection efficiency-adjusted lightning data from the World Wide Lightning Location Network (WWLLN). A special algorithm was developed to retrieve the lightning NOx [(LNO(sub x)] signal from OMI. The algorithm in its general form takes the total slant column NO2 from OMI and removes the stratospheric contribution and tropospheric background and includes an air mass factor appropriate for the profile of lightning NO(sub x) to convert the slant column LNO2 to a vertical column of LNO(sub x). WWLLN flashes are totaled over a period of 3 h prior to OMI overpass, which is the time an air parcel is expected to remain in a 1 deg. x 1 deg. grid box. The analysis is conducted for grid cells containing flash counts greater than a threshold value of 3000 flashes that yields an expected LNO(sub x) signal greater than the background. Pixels with cloud radiance fraction greater than a criterion value (0.9) indicative of highly reflective clouds are used. Results for the summer seasons during 2007-2011 yield mean LNO(sub x) production of approximately 80 +/- 45 mol per flash over the region for the two analysis methods after accounting for biases and uncertainties in the estimation method. These results are consistent with literature estimates and more robust than many prior estimates due to the large number of storms considered but are sensitive to several substantial sources of uncertainty.

TRMM .25 deg x .25 deg Gridded Precipitation Text Product

NASA Technical Reports Server (NTRS)

Stocker, Erich; Kelley, Owen

2009-01-01

Since the launch of the Tropical Rainfall Measuring Mission (TRMM), the Precipitation Measurement Missions science team has endeavored to provide TRMM precipitation retrievals in a variety of formats that are more easily usable by the broad science community than the standard Hierarchical Data Format (HDF) in which TRMM data is produced and archived. At the request of users, the Precipitation Processing System (PPS) has developed a .25 x .25 gridded product in an easily used ASCII text format. The entire TRMM mission data has been made available in this format. The paper provides the details of this new precipitation product that is designated with the TRMM designator 3G68.25. The format is packaged into daily files. It provides hourly precipitation information from the TRMM microwave imager (TMI), precipitation radar (PR), and TMI/PR combined rain retrievals. A major advantage of this approach is the inclusion only of rain data, compression when a particular grid has no rain from the PR or combined, and its direct ASCII text format. For those interested only in rain retrievals and whether rain is convection or stratiform, these products provide a huge reduction in the data volume inherent in the standard TRMM products. This paper provides examples of the 3G68 data products and their uses. It also provides information about C tools that can be used to aggregate daily files into larger time samples. In addition, it describes the possibilities inherent in the spatial sampling which allows resampling into coarser spatial sampling. The paper concludes with information about downloading the gridded text data products.

Effect of stiffness characteristics on the response of composite grid-stiffened structures

NASA Technical Reports Server (NTRS)

Ambur, Damodar R.; Rehfield, Lawrence W.

1991-01-01

A study of the effect of stiffness discontinuities and structural parameters on the response of continuous-filament grid-stiffened flat panels is presented. The buckling load degradation due to manufacturing-introduced stiffener discontinuities associated with a filament cut-and-add approach at the stiffener intersections is investigated. The degradation of buckling resistance in isogrid flat panels subjected to uni-axial compression and combined axial compression and shear loading conditions and induced damage is quantified using FEM. The combined loading case is the most critical one. Nonsolid stiffener cross sections, such as a foam-filled blade or hat with a 0-deg dominant cap, result in grid-stiffened structures that are structurally very efficient for wing and fuselage applications. The results of a study of the ability of grid-stiffened structural concepts to enhance the effective Poisson's ratio of a panel are presented. Grid-stiffened concepts create a highly effective Poisson's ratio, which can produce large camber deformations for certain elastic tailoring applications.

North Polar Radiative Flux Variability from 2002 Through 2014

NASA Technical Reports Server (NTRS)

Rutan, David; Rose, Fred; Doelling, David; Kato, Seiji; Smith, Bill, Jr.

2017-01-01

NASA's Clouds and the Earth's Radiant Energy System (CERES) project produces the SYN1Deg data product. SYN1deg provides global, 1deg gridded, hourly estimates of Top of Atmosphere (TOA) (CERES observations and calculations) and atmospheric and surface radiative flux (calculations). Examples of 12 year North Polar averages of some variables are shown to the right. Given recent interest in polar science we focus here on TOA and Surface validation of calculated irradiant fluxes. TOA upward longwave irradiance calculations match the CERES observations well both spatially and temporally with correlations remaining strong through PC 6. Compare SYN1Deg Calculations & Meteorological Teleconnections. TOA reflected shortwave irradiance calculations match the CERES observations well both spatially and temporally with correlations remaining string through PC 7. Comparing SYN1Deg calculations to teleconnection patterns requires expanding the area to 30N for EOF analyses. Correlating the Principal Components of various variables to teleconnection time series indicates which variable is most highly correlated with which teleconnection signal. The tables indicate the Pacific North American Oscillation is most correlated to the OLR EOF 1, and the North American Oscillation is correlated most closely to surface LW flux down EOF 1.

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.

The prediction and mapping of geoidal undulations from GEOS-3 altimetry. [gravity anomalies

NASA Technical Reports Server (NTRS)

Kearsley, W.

1978-01-01

From the adjusted altimeter data an approximation to the geoid height in ocean areas is obtained. Methods are developed to produce geoid maps in these areas. Geoid heights are obtained for grid points in the region to be mapped, and two of the parameters critical to the production of an accurate map are investigated. These are the spacing of the grid, which must be related to the half-wavelength of the altimeter signal whose amplitude is the desired accuracy of the contour; and the method adopted to predict the grid values. Least squares collocation was used to find geoid undulations on a 1 deg grid in the mapping area. Twenty maps, with their associated precisions, were produced and are included. These maps cover the Indian Ocean, Southwestern and Northeastern portions of the Pacific Ocean, and Southwest Atlantic and the U.S. Calibration Area.

Comparative analysis of single-cell RNA sequencing data from mouse spermatogonial and mesenchymal stem cells to identify differentially expressed genes and transcriptional regulators of germline cells.

PubMed

Sisakhtnezhad, Sajjad; Heshmati, Parvin

2018-07-01

Identifying effective internal factors for regulating germline commitment during development and for maintaining spermatogonial stem cells (SSCs) self-renewal is important to understand the molecular basis of spermatogenesis process, and to develop new protocols for the production of the germline cells from other cell sources. Therefore, this study was designed to investigate single-cell RNA-sequencing data for identification of differentially expressed genes (DEGs) in 12 mouse-derived single SSCs (mSSCs) in compare with 16 mouse-derived single mesenchymal stem cells. We also aimed to find transcriptional regulators of DEGs. Collectively, 1,584 up-regulated DEGs were identified that are associated with 32 biological processes. Moreover, investigation of the expression profiles of genes including in spermatogenesis process revealed that Dazl, Ddx4, Sall4, Fkbp6, Tex15, Tex19.1, Rnf17, Piwil2, Taf7l, Zbtb16, and Cadm1 are presented in the first 30 up-regulated DEGs. We also found 12 basal transcription factors (TFs) and three sequence-specific TFs that control the expression of DEGs. Our findings also indicated that MEIS1, SMC3, TAF1, KAT2A, STAT3, GTF3C2, SIN3A, BDP1, PHC1, and EGR1 are the main central regulators of DEGs in mSSCs. In addition, we collectively detected two significant protein complexes in the protein-protein interactions network for DEGs regulators. Finally, this study introduces the major upstream kinases for the main central regulators of DEGs and the components of core protein complexes. In conclusion, this study provides a molecular blueprint to uncover the molecular mechanisms behind the biology of SSCs and offers a list of candidate factors for cell type conversion approaches and production of germ cells. © 2017 Wiley Periodicals, Inc.

A new approach for the construction of gridded emission inventories from satellite data

NASA Astrophysics Data System (ADS)

Kourtidis, Konstantinos; Georgoulias, Aristeidis; Mijling, Bas; van der A, Ronald; Zhang, Qiang; Ding, Jieying

2017-04-01

We present a new method for the derivation of anthropogenic emission estimates for SO2. The method, which we term Enhancement Ratio Method (ERM), uses observed relationships between measured OMI satellite tropospheric columnar levels of SO2 and NOx in each 0.25 deg X 0.25 deg grid box at low wind speeds, and the Daily Emission estimates Constrained by Satellite Observations (DECSO) versions v1 and v3a NOx emission estimates to scale the SO2 emissions. The method is applied over China, and emission estimates for SO2 are derived for different seasons and years (2007-2011), thus allowing an insight into the interannual evolution of the emissions. The inventory shows a large decrease of emissions during 2007-2009 and a modest increase between 2010-2011. The evolution in emission strength over time calculated here is in general agreement with bottom-up inventories, although differences exist, not only between the current inventory and other inventories but also among the bottom up inventories themselves. The gridded emission estimates derived appear to be consistent, both in their spatial distribution and their magnitude, with the Multi-resolution Emission Inventory for China (MEIC). The total emissions correlate very well with most existing inventories. This research has been financed under the FP7 Programme MarcoPolo (Grand Number 606953, Theme SPA.2013.3.2-01).

Microwave limb sounder. [measuring trace gases in the upper atmosphere

NASA Technical Reports Server (NTRS)

Gustincic, J. J. (Inventor)

1981-01-01

Trace gases in the upper atmosphere can be measured by comparing spectral noise content of limb soundings with the spectral noise content of cold space. An offset Cassegrain antenna system and tiltable input mirror alternately look out at the limb and up at cold space at an elevation angle of about 22. The mirror can also be tilted to look at a black body calibration target. Reflection from the mirror is directed into a radiometer whose head functions as a diplexer to combine the input radiation and a local ocillator (klystron) beam. The radiometer head is comprised of a Fabry-Perot resonator consisting of two Fabry-Perot cavities spaced a number of half wavelengths apart. Incoming radiation received on one side is reflected and rotated 90 deg in polarization by the resonator so that it will be reflected by an input grid into a mixer, while the klystron beam received on the other side is also reflected and rotated 90 deg, but not without passing some energy to be reflected by the input grid into the mixer.

High-resolution Local Gravity Model of the South Pole of the Moon from GRAIL Extended Mission Data

NASA Technical Reports Server (NTRS)

Goossens, Sander Johannes; Sabaka, Terence J.; Nicholas, Joseph B.; Lemoine, Frank G.; Rowlands, David D.; Mazarico, Erwan; Neumann, Gregory A.; Smith, David E.; Zuber, Maria T.

2014-01-01

We estimated a high-resolution local gravity field model over the south pole of the Moon using data from the Gravity Recovery and Interior Laboratory's extended mission. Our solution consists of adjustments with respect to a global model expressed in spherical harmonics. The adjustments are expressed as gridded gravity anomalies with a resolution of 1/6deg by 1/6deg (equivalent to that of a degree and order 1080 model in spherical harmonics), covering a cap over the south pole with a radius of 40deg. The gravity anomalies have been estimated from a short-arc analysis using only Ka-band range-rate (KBRR) data over the area of interest. We apply a neighbor-smoothing constraint to our solution. Our local model removes striping present in the global model; it reduces the misfit to the KBRR data and improves correlations with topography to higher degrees than current global models.

Some new worldwide cloud-cover models

NASA Technical Reports Server (NTRS)

Bean, S. J.; Somerville, P. N.

1981-01-01

Using daily measurements of day and night infrared, and incoming and absorbed solar radiation obtained from a Tiros satellite over a period of approximately 45 months, and integrated over 2.5 deg latitude-longitude grids, the proportion of cloud cover over each grid each day was derived for the entire period. For each of four 3-month periods, for each grid location, estimates a and b of the two parameters of the best-fit beta distribution were obtained. The (a, b) plane was divided into a number of regions. All the geographical locations whose (a, b) estimates were in the same region in the (a, b) plane were said to have the same cloud cover type for that season. For each season, the world is thus divided into separate cloud-cover types.

Phosphorylated DegU Manipulates Cell Fate Differentiation in the Bacillus subtilis Biofilm

PubMed Central

Marlow, Victoria L.; Porter, Michael; Hobley, Laura; Kiley, Taryn B.; Swedlow, Jason R.; Davidson, Fordyce A.

2014-01-01

Cell differentiation is ubiquitous and facilitates division of labor and development. Bacteria are capable of multicellular behaviors that benefit the bacterial community as a whole. A striking example of bacterial differentiation occurs throughout the formation of a biofilm. During Bacillus subtilis biofilm formation, a subpopulation of cells differentiates into a specialized population that synthesizes the exopolysaccharide and the TasA amyloid components of the extracellular matrix. The differentiation process is indirectly controlled by the transcription factor Spo0A that facilitates transcription of the eps and tapA (tasA) operons. DegU is a transcription factor involved in regulating biofilm formation. Here, using a combination of genetics and live single-cell cytological techniques, we define the mechanism of biofilm inhibition at high levels of phosphorylated DegU (DegU∼P) by showing that transcription from the eps and tapA promoter regions is inhibited. Data demonstrating that this is not a direct regulatory event are presented. We demonstrate that DegU∼P controls the frequency with which cells activate transcription from the operons needed for matrix biosynthesis in favor of an off state. Subsequent experimental analysis led us to conclude that DegU∼P functions to increase the level of Spo0A∼P, driving cell fate differentiation toward the terminal developmental process of sporulation. PMID:24123822

Cross-disease transcriptomics: Unique IL-17A signaling in psoriasis lesions and an autoimmune PBMC signature

PubMed Central

Sarkar, Mrinal K.; Liang, Yun; Xing, Xianying; Gudjonsson, Johann E.

2016-01-01

Transcriptome studies of psoriasis have identified robust changes in mRNA expression through large-scale analysis of patient cohorts. These studies, however, have analyzed all mRNA changes in aggregate, without distinguishing between disease-specific and non-specific differentially expressed genes (DEGs). In this study, RNA-seq meta-analysis was used to identify (1) psoriasis-specific DEGs altered in few diseases besides psoriasis and (2) non-specific DEGs similarly altered in many other skin conditions. We show that few cutaneous DEGs are psoriasis-specific and that the two DEG classes differ in their cell type and cytokine associations. Psoriasis-specific DEGs are expressed by keratinocytes and induced by IL-17A, whereas non-specific DEGs are expressed by inflammatory cells and induced by IFN-gamma and TNF. PBMC-derived DEGs were more psoriasis-specific than cutaneous DEGs. Nonetheless, PBMC DEGs associated with MHC class I and NK cells were commonly downregulated in psoriasis and other autoimmune diseases (e.g., multiple sclerosis, sarcoidosis and juvenile rheumatoid arthritis). These findings demonstrate “cross-disease” transcriptomics as an approach to gain insights into the cutaneous and non-cutaneous psoriasis transcriptomes. This highlighted unique contributions of IL-17A to the cytokine network and uncovered a blood-based gene signature that links psoriasis to other diseases of autoimmunity. PMID:27206706

Impact of Spatial Sampling on Continuity of MODIS-VIIRS Land Surface Reflectance Products: A Simulation Approach

NASA Technical Reports Server (NTRS)

Pahlevan, Nima; Sarkar, Sudipta; Devadiga, Sadashiva; Wolfe, Robert E.; Roman, Miguel; Vermote, Eric; Lin, Guoqing; Xiong, Xiaoxiong

2016-01-01

With the increasing need to construct long-term climate-quality data records to understand, monitor, and predict climate variability and change, it is vital to continue systematic satellite measurements along with the development of new technology for more quantitative and accurate observations. The Suomi National Polar-orbiting Partnership mission provides continuity in monitoring the Earths surface and its atmosphere in a similar fashion as the heritage MODIS instruments onboard the National Aeronautics and Space Administrations Terra and Aqua satellites. In this paper, we aim at quantifying the consistency of Aqua MODIS and Suomi-NPP Visible Infrared Imaging Radiometer Suite (VIIRS) Land Surface Reflectance (LSR) and NDVI products as related to their inherent spatial sampling characteristics. To avoid interferences from sources of measurement and/or processing errors other than spatial sampling, including calibration, atmospheric correction, and the effects of the bidirectional reflectance distribution function, the MODIS and VIIRSLSR products were simulated using the Landsat-8s Operational Land Imager (OLI) LSR products. The simulations were performed using the instruments point spread functions on a daily basis for various OLI scenes over a 16-day orbit cycle. It was found that the daily mean differences due to discrepancies in spatial sampling remain below 0.0015 (1) in absolute surface reflectance at subgranule scale (i.e., OLI scene size).We also found that the MODISVIIRS product intercomparisons appear to be minimally impacted when differences in the corresponding view zenith angles (VZAs) are within the range of -15deg to -35deg (VZA(sub v) - VZA(sub m)), where VIIRS and MODIS footprints resemble in size. In general, depending on the spatial heterogeneity of the OLI scene contents, per-grid-cell differences can reach up to 20.Further spatial analysis of the simulated NDVI and LSR products revealed that, depending on the user accuracy requirements for product intercomparisons, spatial aggregations may be used. It was found that if per-grid-cell differences on the order of 10(in LSR or NDVI) are tolerated, the product intercomparisons are expected to be immune from differences in spatial sampling.

Probabilistic Learning by Rodent Grid Cells

PubMed Central

Cheung, Allen

2016-01-01

Mounting evidence shows mammalian brains are probabilistic computers, but the specific cells involved remain elusive. Parallel research suggests that grid cells of the mammalian hippocampal formation are fundamental to spatial cognition but their diverse response properties still defy explanation. No plausible model exists which explains stable grids in darkness for twenty minutes or longer, despite being one of the first results ever published on grid cells. Similarly, no current explanation can tie together grid fragmentation and grid rescaling, which show very different forms of flexibility in grid responses when the environment is varied. Other properties such as attractor dynamics and grid anisotropy seem to be at odds with one another unless additional properties are assumed such as a varying velocity gain. Modelling efforts have largely ignored the breadth of response patterns, while also failing to account for the disastrous effects of sensory noise during spatial learning and recall, especially in darkness. Here, published electrophysiological evidence from a range of experiments are reinterpreted using a novel probabilistic learning model, which shows that grid cell responses are accurately predicted by a probabilistic learning process. Diverse response properties of probabilistic grid cells are statistically indistinguishable from rat grid cells across key manipulations. A simple coherent set of probabilistic computations explains stable grid fields in darkness, partial grid rescaling in resized arenas, low-dimensional attractor grid cell dynamics, and grid fragmentation in hairpin mazes. The same computations also reconcile oscillatory dynamics at the single cell level with attractor dynamics at the cell ensemble level. Additionally, a clear functional role for boundary cells is proposed for spatial learning. These findings provide a parsimonious and unified explanation of grid cell function, and implicate grid cells as an accessible neuronal population readout of a set of probabilistic spatial computations. PMID:27792723

Identification of Key Transcription Factors Associated with Lung Squamous Cell Carcinoma

PubMed Central

Zhang, Feng; Chen, Xia; Wei, Ke; Liu, Daoming; Xu, Xiaodong; Zhang, Xing; Shi, Hong

2017-01-01

Background Lung squamous cell carcinoma (lung SCC) is a common type of lung cancer, but its mechanism of pathogenesis is unclear. The aim of this study was to identify key transcription factors in lung SCC and elucidate its mechanism. Material/Methods Six published microarray datasets of lung SCC were downloaded from Gene Expression Omnibus (GEO) for integrated bioinformatics analysis. Significance analysis of microarrays was used to identify differentially expressed genes (DEGs) between lung SCC and normal controls. The biological functions and signaling pathways of DEGs were mapped in the Gene Otology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, respectively. A transcription factor gene regulatory network was used to obtain insights into the functions of DEGs. Results A total of 1,011 genes, including 539 upregulated genes and 462 downregulated genes, were filtered as DEGs between lung SCC and normal controls. DEGs were significantly enriched in cell cycle, DNA replication, p53 signaling pathway, pathways in cancer, adherens junction, and cell adhesion molecules signaling pathways. There were 57 transcription factors identified, which were used to construct a regulatory network. The network consisted of 736 interactions between 49 transcription factors and 486 DEGs. NFIC, BRCA1, and NFATC2 were the top 3 transcription factors that had the highest connectivity with DEGs and that regulated 83, 82, and 75 DEGs in the network, respectively. Conclusions NFIC, BRCA1, and NFATC2 might be the key transcription factors in the development of lung SCC by regulating the genes involved in cell cycle and DNA replication pathways. PMID:28081052

During running in place, grid cells integrate elapsed time and distance run

PubMed Central

Kraus, Benjamin J.; Brandon, Mark P.; Robinson, Robert J.; Connerney, Michael A.; Hasselmo, Michael E.; Eichenbaum, Howard

2015-01-01

Summary The spatial scale of grid cells may be provided by self-generated motion information or by external sensory information from environmental cues. To determine whether grid cell activity reflects distance traveled or elapsed time independent of external information, we recorded grid cells as animals ran in place on a treadmill. Grid cell activity was only weakly influenced by location but most grid cells and other neurons recorded from the same electrodes strongly signaled a combination of distance and time, with some signaling only distance or time. Grid cells were more sharply tuned to time and distance than non-grid cells. Many grid cells exhibited multiple firing fields during treadmill running, parallel to the periodic firing fields observed in open fields, suggesting a common mode of information processing. These observations indicate that, in the absence of external dynamic cues, grid cells integrate self-generated distance and time information to encode a representation of experience. PMID:26539893

76 FR 82035 - Public Notice for Waiver of Aeronautical Land-Use Assurance; Ohio State University Airport...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-29

... subject to all easements, restrictions and rights- of-way of record. The bearings shown herein are based on the Grid Bearing of North 79[deg] 49' 22'' West for the centerline of Dublin-Granville Road, as.... Mayfield, Jr., Manager, Detroit Airports District Office, FAA, Great Lakes Region. [FR Doc. 2011-33469...

Vortical Flow Prediction Using an Adaptive Unstructured Grid Method

NASA Technical Reports Server (NTRS)

Pirzadeh, Shahyar Z.

2001-01-01

A computational fluid dynamics (CFD) method has been employed to compute vortical flows around slender wing/body configurations. The emphasis of the paper is on the effectiveness of an adaptive grid procedure in "capturing" concentrated vortices generated at sharp edges or flow separation lines of lifting surfaces flying at high angles of attack. The method is based on a tetrahedral unstructured grid technology developed at the NASA Langley Research Center. Two steady-state, subsonic, inviscid and Navier-Stokes flow test cases are presented to demonstrate the applicability of the method for solving practical vortical flow problems. The first test case concerns vortex flow over a simple 65deg delta wing with different values of leading-edge bluntness, and the second case is that of a more complex fighter configuration. The superiority of the adapted solutions in capturing the vortex flow structure over the conventional unadapted results is demonstrated by comparisons with the windtunnel experimental data. The study shows that numerical prediction of vortical flows is highly sensitive to the local grid resolution and that the implementation of grid adaptation is essential when applying CFD methods to such complicated flow problems.

Hypersonic Shock Interactions About a 25 deg/65 deg Sharp Double Cone

NASA Technical Reports Server (NTRS)

Moss, James N.; LeBeau, Gerald J.; Glass, Christopher E.

2002-01-01

This paper presents the results of a numerical study of shock interactions resulting from Mach 10 air flow about a sharp double cone. Computations are made with the direct simulation Monte Carlo (DSMC) method by using two different codes: the G2 code of Bird and the DAC (DSMC Analysis Code) code of LeBeau. The flow conditions are the pretest nominal free-stream conditions specified for the ONERA R5Ch low-density wind tunnel. The focus is on the sensitivity of the interactions to grid resolution while providing information concerning the flow structure and surface results for the extent of separation, heating, pressure, and skin friction.

A diagnosis of the development of a winter anticyclone over North America

NASA Technical Reports Server (NTRS)

King, Melinda L.; Smith, Phillip J.; Lupo, Anthony R.

1995-01-01

This paper examines the 48-h life cycle of a winter anticyclone occurring over North America from 18 to 20 January 1979 using Goddard Laboratory for Atmospheres FGGE level 3b (SOP 1) global analyses on a 4 deg latitude by 5 deg longitude grid. Applying the relatively new methodology of the Zwack-Okossi equation, results show that anticyclonic vorticity advection and cold-air advection acted to develop the anticyclone, while adiabatic warming in the descending air opposed development. Other forcing processes made only small contributions to anticyclone changes. Vertical profiles of the development quantities reveal that vorticity and temperature advections, as well as the adiabatic warming, maximized in the 200-300-mb layer.

Transcriptome profiling identified differentially expressed genes and pathways associated with tamoxifen resistance in human breast cancer

PubMed Central

Men, Xin; Ma, Jun; Wu, Tong; Pu, Junyi; Wen, Shaojia; Shen, Jianfeng; Wang, Xun; Wang, Yamin; Chen, Chao; Dai, Penggao

2018-01-01

Tamoxifen (TAM) resistance is an important clinical problem in the treatment of breast cancer. In order to identify the mechanism of TAM resistance for estrogen receptor (ER)-positive breast cancer, we screened the transcriptome using RNA-seq and compared the gene expression profiles between the MCF-7 mamma carcinoma cell line and the TAM-resistant cell line TAMR/MCF-7, 52 significant differential expression genes (DEGs) were identified including SLIT2, ROBO, LHX, KLF, VEGFC, BAMBI, LAMA1, FLT4, PNMT, DHRS2, MAOA and ALDH. The DEGs were annotated in the GO, COG and KEGG databases. Annotation of the function of the DEGs in the KEGG database revealed the top three pathways enriched with the most DEGs, including pathways in cancer, the PI3K-AKT pathway, and focal adhesion. Then we compared the gene expression profiles between the Clinical progressive disease (PD) and the complete response (CR) from the cancer genome altas (TCGA). 10 common DEGs were identified through combining the clinical and cellular analysis results. Protein-protein interaction network was applied to analyze the association of ER signal pathway with the 10 DEGs. 3 significant genes (GFRA3, NPY1R and PTPRN2) were closely related to ER related pathway. These significant DEGs regulated many biological activities such as cell proliferation and survival, motility and migration, and tumor cell invasion. The interactions between these DEGs and drug resistance phenomenon need to be further elucidated at a functional level in further studies. Based on our findings, we believed that these DEGs could be therapeutic targets, which can be explored to develop new treatment options. PMID:29423105

Fuel Cell Backup Power System for Grid Service and Micro-Grid in Telecommunication Applications: Preprint

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

Ma, Zhiwen; Eichman, Joshua D; Kurtz, Jennifer M

This paper presents the feasibility and economics of using fuel cell backup power systems in telecommunication cell towers to provide grid services (e.g., ancillary services, demand response). The fuel cells are able to provide power for the cell tower during emergency conditions. This study evaluates the strategic integration of clean, efficient, and reliable fuel cell systems with the grid for improved economic benefits. The backup systems have potential as enhanced capability through information exchanges with the power grid to add value as grid services that depend on location and time. The economic analysis has been focused on the potential revenuemore » for distributed telecommunications fuel cell backup units to provide value-added power supply. This paper shows case studies on current fuel cell backup power locations and regional grid service programs. The grid service benefits and system configurations for different operation modes provide opportunities for expanding backup fuel cell applications responsive to grid needs.« less

The Global Precipitation Patterns Associated with Short-Term Extratropical Climate Fluctuations

NASA Technical Reports Server (NTRS)

Huffman, George J.; Adler, Robert F.; Bolvin, David T.

1999-01-01

Two globally-complete, observation-only precipitation datasets have recently been developed for the Global Precipitation Climatology Project (GPCP). Both depend heavily on a variety of satellite input, as well as gauge data over land. The first, Version 2x79, provides monthly estimates on a 2.5 deg. x 2.5 deg. lat/long grid for the period 1979 through late 1999 (by the time of the conference). The second, the One-Degree Daily (1DD), provides daily estimates on a 1 deg. x l deg. grid for the period 1997 through late 1999 (by the time of the conference). Both are in beta test preparatory to release as official GPCP products. These datasets provide a unique perspective on the hydrological effects of the various atmospheric flow anomalies that have been identified by meteorologists. In this paper we discuss the regional precipitation effects that result from persistent extratropical flow anomalies. We will focus on the Pacific-North America (PNA) and North Atlantic Oscillation (NAO) patterns. Each characteristically becomes established on synoptic time scales, but then persists for periods that can exceed a month. The onset phase of each appears to have systematic mobile features, while the mature phase tend to be more stationary. Accordingly, composites of monthly data for outstanding positive and negative events (separately) contained in the 20-year record reveal the climatological structure of the precipitation during the mature phase. The climatological anomalies of the positive, negative, and (positive-negative) composites show the expected storm-track-related shifts in precipitation, and provide the advantage of putting the known precipitation effects over land in the context of the total pattern over land and ocean. As well, this global perspective points out some unexpected areas of correlation. Day-by-day composites of daily data anchored to the onset date demonstrate the systematic features during the onset. Although the 1DD has a fairly short record, some preliminary results are shown and compared to previous work with numerical weather prediction models.

A Global Precipitation Perspective on Persistent Extratropical Flow Anomalies

NASA Technical Reports Server (NTRS)

Huffman, George J.; Adler, Robert F.; Bolvin, David T.

1999-01-01

Two globally-complete, observation-only precipitation datasets have recently been developed for the Global Precipitation Climatology Project (GPCP). Both depend heavily on a variety of satellite input, as well as gauge data over land. The first, Version 2 x 79, provides monthly estimates on a 2.5 deg x 2.5 deg lat/long grid for the period 1979 through late 1999 (by the time of the conference). The second, the One-Degree Daily (1DD), provides daily estimates on a 1 deg x 1 deg grid for the period 1997 through late 1999 (by the time of the conference). Both are in beta test preparatory to release as official GPCP products. These datasets provide a unique perspective on the hydrological effects of the various atmospheric flow anomalies that have been identified by meteorologists. In this paper we discuss the regional precipitation effects that result from persistent extratropical flow anomalies. We will focus on the Pacific-North America (PNA) and North Atlantic Oscillation (NAO) patterns. Each characteristically becomes established on synoptic time scales, but then persists for periods that can exceed a month. The onset phase of each appears to have systematic mobile features, while the mature phase tend to be more stationary. Accordingly, composites of monthly data for outstanding positive and negative events (separately) contained in the 20-year record reveal the climatological structure of the precipitation during the mature phase. The climatological anomalies of the positive, negative, and (positive-negative) composites show the expected storm-track-related shifts in precipitation, and provide the advantage of putting the known precipitation effects over land in the context of the total pattern over land and ocean. As well, this global perspective points out some unexpected areas of correlation. Day-by-day composites of daily data anchored to the onset date demonstrate the systematic features during the onset. Although the 1DD has a fairly short record, some preliminary results are shown and compared to previous work with numerical weather prediction models.

The effect of Reynolds number and turbulence on airfoil aerodynamics at -90 degrees incidence

NASA Technical Reports Server (NTRS)

Stremel, Paul M.

1993-01-01

A method has been developed for calculating the viscous flow about airfoils in with and without deflected flaps at -90 deg incidence. This method provides for the solution of the unsteady incompressible Navier-Stokes equations by means of an implicit technique. The solution is calculated on a body-fitted computational mesh using a staggered grid method. The vorticity is defined at the node points, and the velocity components are defined at the mesh-cell sides. The staggered-grid orientation provides for accurate representation of vorticity at the node points and the continuity equation at the mesh-cell centers. The method provides for the direct solution of the flow field and satisfies the continuity equation to machine zero at each time-step. The method is evaluated in terms of its ability to predict two-dimensional flow about an airfoil at -90 degrees incidence for varying Reynolds number and different boundary layer models. A laminar and a turbulent boundary layer models. A laminar and a turbulent boundary layer model are considered in the evaluation of the method. The variation of the average loading and surface pressure distribution due to flap deflection, Reynolds number, and laminar or turbulent flow are presented and compared with experimental results. The comparisons indicate that the calculated drag and drag reduction caused by flap deflection and the calculated average surface pressure are in excellent agreement with the measured results at a similar Reynolds number.

The chemokine receptor CCR1 is identified in mast cell-derived exosomes.

PubMed

Liang, Yuting; Qiao, Longwei; Peng, Xia; Cui, Zelin; Yin, Yue; Liao, Huanjin; Jiang, Min; Li, Li

2018-01-01

Mast cells are important effector cells of the immune system, and mast cell-derived exosomes carrying RNAs play a role in immune regulation. However, the molecular function of mast cell-derived exosomes is currently unknown, and here, we identify differentially expressed genes (DEGs) in mast cells and exosomes. We isolated mast cells derived exosomes through differential centrifugation and screened the DEGs from mast cell-derived exosomes, using the GSE25330 array dataset downloaded from the Gene Expression Omnibus database. Biochemical pathways were analyzed by Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway on the online tool DAVID. DEGs-associated protein-protein interaction networks (PPIs) were constructed using the STRING database and Cytoscape software. The genes identified from these bioinformatics analyses were verified by qRT-PCR and Western blot in mast cells and exosomes. We identified 2121 DEGs (843 up and 1278 down-regulated genes) in HMC-1 cell-derived exosomes and HMC-1 cells. The up-regulated DEGs were classified into two significant modules. The chemokine receptor CCR1 was screened as a hub gene and enriched in cytokine-mediated signaling pathway in module one. Seven genes, including CCR1, CD9, KIT, TGFBR1, TLR9, TPSAB1 and TPSB2 were screened and validated through qRT-PCR analysis. We have achieved a comprehensive view of the pivotal genes and pathways in mast cells and exosomes and identified CCR1 as a hub gene in mast cell-derived exosomes. Our results provide novel clues with respect to the biological processes through which mast cell-derived exosomes modulate immune responses.

Numerical Solutions for the CAWAPI Configuration on Structured Grids at NASA LaRC, United States. Chapter 7

NASA Technical Reports Server (NTRS)

Elmiligui, Alaa A.; Abdol-Hamid, Khaled S.; Massey, Steven J.

2009-01-01

In this chapter numerical simulations of the flow around F-16XL are performed as a contribution to the Cranked Arrow Wing Aerodynamic Project International (CAWAPI) using the PAB3D CFD code. Two turbulence models are used in the calculations: a standard k-epsilon model, and the Shih-Zhu-Lumley (SZL) algebraic stress model. Seven flight conditions are simulated for the flow around the F-16XL where the free stream Mach number varies from 0.242 to 0.97. The range of angles of attack varies from 0 deg to 20 deg. Computational results, surface static pressure, boundary layer velocity profiles, and skin friction are presented and compared with flight data. Numerical results are generally in good agreement with flight data, considering that only one grid resolution is utilized for the different flight conditions simulated in this study. The Algebraic Stress Model (ASM) results are closer to the flight data than the k-epsilon model results. The ASM predicted a stronger primary vortex, however, the origin of the vortex and footprint is approximately the same as in the k-epsilon predictions.

Climate Controls on Tree Growth in the Western Mediterranean

NASA Technical Reports Server (NTRS)

Touchan, Ramzi; Anchukaitis, Kevin J.; Meko, David M.; Kerchouche, Dalila; Slimani, Said; Ilmen, Rachid; Hasnaoui, Fouad; Guibal, Frederic; Canarerim Hesys Hykui; Sanchez-Salguero, Raul;

CFD Validation Studies for Hypersonic Flow Prediction

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.

2001-01-01

A series of experiments to measure pressure and heating for code validation involving hypersonic, laminar, separated flows was conducted at the Calspan-University at Buffalo Research Center (CUBRC) in the Large Energy National Shock (LENS) tunnel. The experimental data serves as a focus for a code validation session but are not available to the authors until the conclusion of this session. The first set of experiments considered here involve Mach 9.5 and Mach 11.3 N, flow over a hollow cylinder-flare with 30 deg flare angle at several Reynolds numbers sustaining laminar, separated flow. Truncated and extended flare configurations are considered. The second set of experiments, at similar conditions, involves flow over a sharp, double cone with fore-cone angle of 25 deg and aft-cone angle of 55 deg. Both sets of experiments involve 30 deg compressions. Location of the separation point in the numerical simulation is extremely sensitive to the level of grid refinement in the numerical predictions. The numerical simulations also show a significant influence of Reynolds number on extent of separation. Flow unsteadiness was easily introduced into the double cone simulations using aggressive relaxation parameters that normally promote convergence.

Spectral study of wintertime kinetic energy of the Northern Hemisphere in the troposphere

NASA Technical Reports Server (NTRS)

Lee, H. N.; Zhao, Z.; Kao, S. K.

1983-01-01

Characteristics of the kinetic energy of wind fields at various pressure levels were analyzed, and significant wavenumbers in the wavenumber-frequency domain were identified. The nonlinear interaction terms of the kinetic energy equation were examined, and the distribution of the kinetic energy at the 850 mb, 500 mb, and 200 mb levels was calculated. A 5 deg latitude-longitude square grid was used, with NMC data for the 1975-1976 winter in the 20-60 deg N at 500 mb and 20-85 deg N for the 200 mb and 850 mb levels. The kinetic energy distribution was determined to be geography-dependent, with wavenumbers 6-9 westerly waves in the midfrequency range contributing significantly to kinetic energy maxima over the North Pacific and the east coast of North America. The contribution of the nonlinear interactions of these waves, which correspond to the longitudinal convergence of the kinetic energy flux, was found to be larger than the meridional convergence of the kinetic energy flux, and to occur mainly between 30-50 deg N. The nonlinear interactions were a negative contribution over the North Pacific at the 200 mb level.

Spiking Neurons in a Hierarchical Self-Organizing Map Model Can Learn to Develop Spatial and Temporal Properties of Entorhinal Grid Cells and Hippocampal Place Cells

PubMed Central

Pilly, Praveen K.; Grossberg, Stephen

2013-01-01

Medial entorhinal grid cells and hippocampal place cells provide neural correlates of spatial representation in the brain. A place cell typically fires whenever an animal is present in one or more spatial regions, or places, of an environment. A grid cell typically fires in multiple spatial regions that form a regular hexagonal grid structure extending throughout the environment. Different grid and place cells prefer spatially offset regions, with their firing fields increasing in size along the dorsoventral axes of the medial entorhinal cortex and hippocampus. The spacing between neighboring fields for a grid cell also increases along the dorsoventral axis. This article presents a neural model whose spiking neurons operate in a hierarchy of self-organizing maps, each obeying the same laws. This spiking GridPlaceMap model simulates how grid cells and place cells may develop. It responds to realistic rat navigational trajectories by learning grid cells with hexagonal grid firing fields of multiple spatial scales and place cells with one or more firing fields that match neurophysiological data about these cells and their development in juvenile rats. The place cells represent much larger spaces than the grid cells, which enable them to support navigational behaviors. Both self-organizing maps amplify and learn to categorize the most frequent and energetic co-occurrences of their inputs. The current results build upon a previous rate-based model of grid and place cell learning, and thus illustrate a general method for converting rate-based adaptive neural models, without the loss of any of their analog properties, into models whose cells obey spiking dynamics. New properties of the spiking GridPlaceMap model include the appearance of theta band modulation. The spiking model also opens a path for implementation in brain-emulating nanochips comprised of networks of noisy spiking neurons with multiple-level adaptive weights for controlling autonomous adaptive robots capable of spatial navigation. PMID:23577130

Global Population Distribution (1990),Terrestrial Area and Country Name Information on a One by One Degree Grid Cell Basis

DOE Data Explorer

Li, Yi-Fan [Canadian Global Emissions Inventory Centre, Downsview, Ontario (Canada); Brenkert, A. L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

1996-01-01

This data base contains gridded (one degree by one degree) information on the world-wide distribution of the population for 1990 and country-specific information on the percentage of the country's population present in each grid cell (Li, 1996a). Secondly, the data base contains the percentage of a country's total area in a grid cell and the country's percentage of the grid cell that is terrestrial (Li, 1996b). Li (1996b) also developed an indicator signifying how many countries are represented in a grid cell and if a grid cell is part of the sea; this indicator is only relevant for the land, countries, and sea-partitioning information of the grid cell. Thirdly, the data base includes the latitude and longitude coordinates of each grid cell; a grid code number, which is a translation of the latitude/longitude value and is used in the Global Emission Inventory Activity (GEIA) data bases; the country or region's name; and the United Nations three-digit country code that represents that name.

Chemistry Simulations using the MERRA-2 Reanalysis with the GMI CTM and Replay in Support of the Atmospheric Composition Community

NASA Technical Reports Server (NTRS)

Oman, Luke D.; Strahan, Susan E.

2017-01-01

Simulations using reanalysis meteorological fields have long been used to understand the causes of atmospheric composition change in the recent past. Using the new MERRA-2 reanalysis, we are conducting chemistry simulations to create products covering 1980-2016 for the atmospheric composition community. These simulations use the Global Modeling Initiative (GMI) chemical mechanism in two different models: the GMI Chemical Transport Model (CTM) and the GEOS-5 model in Replay mode. Replay mode means an integration of the GEOS-5 general circulation model that is incrementally adjusted each time step toward the MERRA-2 reanalysis. The GMI CTM is a 1 deg x 1.25 deg simulation and the MERRA-2 GMI Replay simulation uses the native MERRA-2 grid of approximately 1/2 deg horizontal resolution on the cubed sphere. A specialized set of transport diagnostics is included in both runs to better understand trace gas transport and its variability in the recent past.

Turbulence Model Comparisons for a High-Speed Aircraft

NASA Technical Reports Server (NTRS)

Rivers, Melissa B.; Wahls, Richard A.

1999-01-01

Four turbulence models are described and evaluated for transonic flows over the High-Speed Research/industry baseline configuration known as Reference H by using the thin-layer, upwind, Navier-Stokes solver known as CFL3D. The turbulence models studied are the equilibrium model of Baldwin-Lomax (B-L) with the Degani-Schiff (D-S) modifications, the one-equation Baldwin-Barth (B-B) model, the one-equation Spalart-Allmaras (S-A) model, and Menter's two-equation Shear Stress Transport (SST) model. The flow conditions, which correspond to tests performed in the National Transonic Facility (NTF) at Langley Research Center, are a Mach number of 0.90 and a Reynolds number of 30 x 10 (exp. 6) based on mean aerodynamic chord for angles of attack of 1 deg., 5 deg., and 10 deg. The effects of grid topology and the representation of the actual wind tunnel model geometry are also investigated. Computed forces and surface pressures compare reasonably well with the experimental data for all four turbulence models.

Effect of particle size of Martian dust on the degradation of photovoltaic cell performance

NASA Technical Reports Server (NTRS)

Gaier, James R.; Perez-Davis, Marla E.

1991-01-01

Glass coverglass and SiO2 covered and uncovered silicon photovoltaic (PV) cells were subjected to conditions simulating a Mars dust storm, using the Martian Surface Wind Tunnel, to assess the effect of particle size on the performance of PV cells in the Martian environment. The dust used was an artificial mineral of the approximate elemental composition of Martian soil, which was sorted into four different size ranges. Samples were tested both initially clean and initially dusted. The samples were exposed to clear and dust laden winds, wind velocities varying from 23 to 116 m/s, and attack angles from 0 to 90 deg. It was found that transmittance through the coverglass approximates the power produced by a dusty PV cell. Occultation by the dust was found to dominate the performance degradation for wind velocities below 50 m/s, whereas abrasion dominates the degradation at wind velocities above 85 m/s. Occultation is most severe at 0 deg (parallel to the wind), is less pronounced from 22.5 to 67.5 deg, and is somewhat larger at 90 deg (perpendicular to the wind). Abrasion is negligible at 0 deg, and increases to a maximum at 90 deg. Occultation is more of a problem with small particles, whereas large particles (unless they are agglomerates) cause more abrasion.

Design of a global soil moisture initialization procedure for the simple biosphere model

NASA Technical Reports Server (NTRS)

Liston, G. E.; Sud, Y. C.; Walker, G. K.

1993-01-01

Global soil moisture and land-surface evapotranspiration fields are computed using an analysis scheme based on the Simple Biosphere (SiB) soil-vegetation-atmosphere interaction model. The scheme is driven with observed precipitation, and potential evapotranspiration, where the potential evapotranspiration is computed following the surface air temperature-potential evapotranspiration regression of Thomthwaite (1948). The observed surface air temperature is corrected to reflect potential (zero soil moisture stress) conditions by letting the ratio of actual transpiration to potential transpiration be a function of normalized difference vegetation index (NDVI). Soil moisture, evapotranspiration, and runoff data are generated on a daily basis for a 10-year period, January 1979 through December 1988, using observed precipitation gridded at a 4 deg by 5 deg resolution.

When the swimming gets tough, the tough form a biofilm.

PubMed

Belas, Robert

2013-10-01

Bacteria live either as independent planktonic cells or as members of surface-attached communities called biofilms. Motility and biofilm development are mutually exclusive events, and control of the phase of this 'swim-or-stick' switch involves the ability of the bacterium to sense and respond appropriately to a surface. Cairns et al. (2013) report that the Bacillus subtilis flagellum functions in surface-sensing. Using mutants of B. subtilis that prevent flagellum rotation, they measured the expression and activity of DegU, the response regulator of the two-component DegS-DegU circuit. DegU activity and degU transcription increased when flagellum rotation was prevented, and were dependent on the DegS kinase. Inhibiting flagellar rotation by overexpressing the EpsE flagellar 'clutch' or addition of anti-flagellin antiserum also increased degU transcription and activity. These results suggest B. subtilis senses restriction of flagellum rotation as the cell nears a surface. Inhibition of the flagellum activates the DegS-DegU circuit to turn on biofilm formation, i.e. the flagellum is acting as a mechanosensor of surfaces. B. subtilis joins an ever-expanding group of bacteria, including species of Vibrio, Proteus and Caulobacter that use the flagellum as a surface sensor. © 2013 John Wiley & Sons Ltd.

The chemokine receptor CCR1 is identified in mast cell-derived exosomes

PubMed Central

Liang, Yuting; Qiao, Longwei; Peng, Xia; Cui, Zelin; Yin, Yue; Liao, Huanjin; Jiang, Min; Li, Li

2018-01-01

Mast cells are important effector cells of the immune system, and mast cell-derived exosomes carrying RNAs play a role in immune regulation. However, the molecular function of mast cell-derived exosomes is currently unknown, and here, we identify differentially expressed genes (DEGs) in mast cells and exosomes. We isolated mast cells derived exosomes through differential centrifugation and screened the DEGs from mast cell-derived exosomes, using the GSE25330 array dataset downloaded from the Gene Expression Omnibus database. Biochemical pathways were analyzed by Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway on the online tool DAVID. DEGs-associated protein-protein interaction networks (PPIs) were constructed using the STRING database and Cytoscape software. The genes identified from these bioinformatics analyses were verified by qRT-PCR and Western blot in mast cells and exosomes. We identified 2121 DEGs (843 up and 1278 down-regulated genes) in HMC-1 cell-derived exosomes and HMC-1 cells. The up-regulated DEGs were classified into two significant modules. The chemokine receptor CCR1 was screened as a hub gene and enriched in cytokine-mediated signaling pathway in module one. Seven genes, including CCR1, CD9, KIT, TGFBR1, TLR9, TPSAB1 and TPSB2 were screened and validated through qRT-PCR analysis. We have achieved a comprehensive view of the pivotal genes and pathways in mast cells and exosomes and identified CCR1 as a hub gene in mast cell-derived exosomes. Our results provide novel clues with respect to the biological processes through which mast cell-derived exosomes modulate immune responses. PMID:29511430

Bioinformatics analysis of gene expression profiles in B cells of postmenopausal osteoporosis patients.

PubMed

Ma, Min; Luo, Shulin; Zhou, Wei; Lu, Liangyu; Cai, Junfeng; Yuan, Feng; Yin, Feng

2017-04-01

The aim of this study was to gain a better understanding of the molecular mechanisms and identify more critical genes associated with the pathogenesis of postmenopausal osteoporosis (PMOP). Microarray data of GSE13850 were download from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified either in B cells from postmenopausal female nonsmokers with high bone mineral density (BMD) compared with those with low BMD (defined as DEG1 group) or in B cells from postmenopausal female smokers with high BMD compared with postmenopausal female nonsmokers with high BMD (defined as DEG2 group). Gene ontology and immune-related functional enrichment analysis of DEGs were performed. Additionally, the protein-protein interaction network of all DEGs was constructed and subnetworks of the hub genes were extracted. A total of 51 DEGs were identified in the DEG1 group, including 30 up- and 21 downregulated genes. Besides, 86 DEGs were identified in the DEG2 group, of which 46 were upregulated and 40 were downregulated. Immune enrichment analysis showed DEGs were mainly enriched in functions of CD molecules and chemokines and receptor, and the upregulated gene interleukin 4 receptor (IL-4R) was significantly enriched. Moreover, guanine nucleotide-binding protein G (GNAI2), filamin A alpha (FLNA), and transforming growth factor-β1 (TGFB1) were hub proteins in the protein-protein interaction network. IL-4R, GNAI2, FLNA, and TGFB1 may be potential target genes associated with the pathogenesis of PMOP. In particular, FLNA, and TGFB1 may be affected by smoking, a risk factor of PMOP. Copyright © 2017. Published by Elsevier B.V.

Optimizing solar-cell grid geometry

NASA Technical Reports Server (NTRS)

Crossley, A. P.

1969-01-01

Trade-off analysis and mathematical expressions calculate optimum grid geometry in terms of various cell parameters. Determination of the grid geometry provides proper balance between grid resistance and cell output to optimize the energy conversion process.

The functional micro-organization of grid cells revealed by cellular-resolution imaging

PubMed Central

Heys, James G.; Rangarajan, Krsna V.; Dombeck, Daniel A.

2015-01-01

Summary Establishing how grid cells are anatomically arranged, on a microscopic scale, in relation to their firing patterns in the environment would facilitate a greater micro-circuit level understanding of the brain’s representation of space. However, all previous grid cell recordings used electrode techniques that provide limited descriptions of fine-scale organization. We therefore developed a technique for cellular-resolution functional imaging of medial entorhinal cortex (MEC) neurons in mice navigating a virtual linear track, enabling a new experimental approach to study MEC. Using these methods, we show that grid cells are physically clustered in MEC compared to non-grid cells. Additionally, we demonstrate that grid cells are functionally micro-organized: The similarity between the environment firing locations of grid cell pairs varies as a function of the distance between them according to a “Mexican Hat” shaped profile. This suggests that, on average, nearby grid cells have more similar spatial firing phases than those further apart. PMID:25467986

The NASA POWER SSE: Deriving the Direct Normal Counterpart from the CERES SYN1deg Hourly Global Horizontal Irradiance during Early 2000 to Near Present

NASA Astrophysics Data System (ADS)

Zhang, T.; Stackhouse, P. W., Jr.; Westberg, D. J.

2017-12-01

The NASA Prediction of Worldwide Energy Resource (POWER) Surface meteorology and Solar Energy (SSE) provides solar direct normal irradiance (DNI) data as well as a variety of other solar parameters. The currently available DNIs are monthly means on a quasi-equal-area grid system with grid boxes roughly equivalent to 1 degree longitude by 1 degree latitude around the equator from July 1983 to June 2005, and the data were derived from the GEWEX Surface Radiation Budget (SRB) monthly mean global horizontal irradiance (GHI, Release 3) and regression analysis of the Baseline Surface Radiation Network (BSRN) data. To improve the quality of the DNI data and push the temporal coverage of the data to near present, we have applied a modified version of the DIRINDEX global-to-beam model to the GEWEX SRB (Release 3) all-sky and clear-sky 3-hourly GHI data and derived their DNI counterparts for the period from July 1983 to December 2007. The results have been validated against the BSRN data. To further expand the data in time to near present, we are now applying the DIRINDEX model to the Clouds and the Earth's Radiant Energy System (CERES) data. The CERES SYN1deg (Edition 4A) offers hourly all-sky and clear-sky GHIs on a 1 degree longitude by 1 degree latitude grid system from March 2000 to October 2016 as of this writing. Comparisons of the GHIs with their BSRN counterparts show remarkable agreements. Besides the GHIs, the inputs will also include the atmospheric water vapor and surface pressure from the Modern Era Retrospective-Analysis for Research and Applications (MERRA) and the aerosol optical depth from the Max-Planck Institute Climatology (MAC-v1). Based on the performance of the DIRINDEX model with the GEWEX SRB GHI data, we expect at least equally good or even better results. In this paper, we will show the derived hourly, daily, and monthly mean DNIs from the CERES SYN1deg hourly GHIs from March 2000 to October 2016 and how they compare with the BSRN data.

Analyses and forecasts with LAWS winds

NASA Technical Reports Server (NTRS)

Wang, Muyin; Paegle, Jan

1994-01-01

Horizontal fluxes of atmospheric water vapor are studied for summer months during 1989 and 1992 over North and South America based on analyses from European Center for Medium Range Weather Forecasts, US National Meteorological Center, and United Kingdom Meteorological Office. The calculations are performed over 20 deg by 20 deg box-shaped midlatitude domains located to the east of the Rocky Mountains in North America, and to the east of the Andes Mountains in South America. The fluxes are determined from operational center gridded analyses of wind and moisture. Differences in the monthly mean moisture flux divergence determined from these analyses are as large as 7 cm/month precipitable water equivalent over South America, and 3 cm/month over North America. Gridded analyses at higher spatial and temporal resolution exhibit better agreement in the moisture budget study. However, significant discrepancies of the moisture flux divergence computed from different gridded analyses still exist. The conclusion is more pessimistic than Rasmusson's estimate based on station data. Further analysis reveals that the most significant sources of error result from model surface elevation fields, gaps in the data archive, and uncertainties in the wind and specific humidity analyses. Uncertainties in the wind analyses are the most important problem. The low-level jets, in particular, are substantially different in the different data archives. Part of the reason for this may be due to the way the different analysis models parameterized physical processes affecting low-level jets. The results support the inference that the noise/signal ratio of the moisture budget may be improved more rapidly by providing better wind observations and analyses than by providing better moisture data.

Deletion of degQ gene enhances outer membrane vesicle production of Shewanella oneidensis cells.

PubMed

Ojima, Yoshihiro; Mohanadas, Thivagaran; Kitamura, Kosei; Nunogami, Shota; Yajima, Reiki; Taya, Masahito

2017-04-01

Shewanella oneidensis is a Gram-negative facultative anaerobe that can use a wide variety of terminal electron acceptors for anaerobic respiration. In this study, S. oneidensis degQ gene, encoding a putative periplasmic serine protease, was cloned and expressed. The activity of purified DegQ was inhibited by diisopropyl fluorophosphate, a typical serine protease-specific inhibitor, indicating that DegQ is a serine protease. In-frame deletion and subsequent complementation of the degQ were carried out to examine the effect of envelope stress on the production of outer membrane vesicles (OMVs). Analysis of periplasmic proteins from the resulting S. oneidensis strain showed that deletion of degQ induced protein accumulation and resulted in a significant decrease in protease activity within the periplasmic space. OMVs from the wild-type and mutant strains were purified and observed by transmission electron microscopy. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the OMVs showed a prominent band at ~37 kDa. Nanoliquid chromatography-tandem mass spectrometry analysis identified three outer membrane porins (SO3896, SO1821, and SO3545) as dominant components of the band, suggesting that these proteins could be used as indices for comparing OMV production by S. oneidensis strains. Quantitative evaluation showed that degQ-deficient cells had a fivefold increase in OMV production compared with wild-type cells. Thus, the increased OMV production following the deletion of DegQ in S. oneidensis may be responsible for the increase in envelope stress.

A single-cell spiking model for the origin of grid-cell patterns

PubMed Central

Kempter, Richard

2017-01-01

Spatial cognition in mammals is thought to rely on the activity of grid cells in the entorhinal cortex, yet the fundamental principles underlying the origin of grid-cell firing are still debated. Grid-like patterns could emerge via Hebbian learning and neuronal adaptation, but current computational models remained too abstract to allow direct confrontation with experimental data. Here, we propose a single-cell spiking model that generates grid firing fields via spike-rate adaptation and spike-timing dependent plasticity. Through rigorous mathematical analysis applicable in the linear limit, we quantitatively predict the requirements for grid-pattern formation, and we establish a direct link to classical pattern-forming systems of the Turing type. Our study lays the groundwork for biophysically-realistic models of grid-cell activity. PMID:28968386

Grid scale drives the scale and long-term stability of place maps

PubMed Central

Mallory, Caitlin S; Hardcastle, Kiah; Bant, Jason S; Giocomo, Lisa M

2018-01-01

Medial entorhinal cortex (MEC) grid cells fire at regular spatial intervals and project to the hippocampus, where place cells are active in spatially restricted locations. One feature of the grid population is the increase in grid spatial scale along the dorsal-ventral MEC axis. However, the difficulty in perturbing grid scale without impacting the properties of other functionally-defined MEC cell types has obscured how grid scale influences hippocampal coding and spatial memory. Here, we use a targeted viral approach to knock out HCN1 channels selectively in MEC, causing grid scale to expand while leaving other MEC spatial and velocity signals intact. Grid scale expansion resulted in place scale expansion in fields located far from environmental boundaries, reduced long-term place field stability and impaired spatial learning. These observations, combined with simulations of a grid-to-place cell model and position decoding of place cells, illuminate how grid scale impacts place coding and spatial memory. PMID:29335607

File Specification for the 7-km GEOS-5 Nature Run, Ganymed Release Non-Hydrostatic 7-km Global Mesoscale Simulation

NASA Technical Reports Server (NTRS)

da Silva, Arlindo M.; Putman, William; Nattala, J.

2014-01-01

This document describes the gridded output files produced by a two-year global, non-hydrostatic mesoscale simulation for the period 2005-2006 produced with the non-hydrostatic version of GEOS-5 Atmospheric Global Climate Model (AGCM). In addition to standard meteorological parameters (wind, temperature, moisture, surface pressure), this simulation includes 15 aerosol tracers (dust, sea-salt, sulfate, black and organic carbon), O3, CO and CO2. This model simulation is driven by prescribed sea-surface temperature and sea-ice, daily volcanic and biomass burning emissions, as well as high-resolution inventories of anthropogenic sources. A description of the GEOS-5 model configuration used for this simulation can be found in Putman et al. (2014). The simulation is performed at a horizontal resolution of 7 km using a cubed-sphere horizontal grid with 72 vertical levels, extending up to to 0.01 hPa (approximately 80 km). For user convenience, all data products are generated on two logically rectangular longitude-latitude grids: a full-resolution 0.0625 deg grid that approximately matches the native cubed-sphere resolution, and another 0.5 deg reduced-resolution grid. The majority of the full-resolution data products are instantaneous with some fields being time-averaged. The reduced-resolution datasets are mostly time-averaged, with some fields being instantaneous. Hourly data intervals are used for the reduced-resolution datasets, while 30-minute intervals are used for the full-resolution products. All full-resolution output is on the model's native 72-layer hybrid sigma-pressure vertical grid, while the reduced-resolution output is given on native vertical levels and on 48 pressure surfaces extending up to 0.02 hPa. Section 4 presents additional details on horizontal and vertical grids. Information of the model surface representation can be found in Appendix B. The GEOS-5 product is organized into file collections that are described in detail in Appendix C. Additional details about variables listed in this file specification can be found in a separate document, the GEOS-5 File Specification Variable Definition Glossary. Documentation about the current access methods for products described in this document can be found on the GEOS-5 Nature Run portal: http://gmao.gsfc.nasa.gov/projects/G5NR. Information on the scientific quality of this simulation will appear in a forthcoming NASA Technical Report Series on Global Modeling and Data Assimilation to be available from http://gmao.gsfc.nasa.gov/pubs/tm/.

Framing the grid: effect of boundaries on grid cells and navigation.

PubMed

Krupic, Julija; Bauza, Marius; Burton, Stephen; O'Keefe, John

2016-11-15

Cells in the mammalian hippocampal formation subserve neuronal representations of environmental location and support navigation in familiar environments. Grid cells constitute one of the main cell types in the hippocampal formation and are widely believed to represent a universal metric of space independent of external stimuli. Recent evidence showing that grid symmetry is distorted in non-symmetrical environments suggests that a re-examination of this hypothesis is warranted. In this review we will discuss behavioural and physiological evidence for how environmental shape and in particular enclosure boundaries influence grid cell firing properties. We propose that grid cells encode the geometric layout of enclosures. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

ENaC/DEG in Tumor Development and Progression

PubMed Central

Liu, Cui; Zhu, Li-Li; Xu, Si-Guang; Ji, Hong-Long; Li, Xiu-Min

2016-01-01

The epithelial Na+ channel/degenerin (ENaC/DEG) superfamily, including the acid-sensing ion channels (ASICs), is characterized by a high degree of similarity in structure but highly diverse in physiological functions. These ion channels have been shown to be important in several physiological functions of normal epithelial cells, including salt homeostasis, fluid transportation and cell mobility. There is increasing evidence suggesting that ENaC/DEG channels are critically engaged in cancer cell biology, such as proliferation, migration, invasion and apoptosis, playing a role in tumor development and progression. In this review, we will discuss recent studies showing the role of ENaC and ASIC channels in epithelial cells and its relationship to the oncogenesis. PMID:27698929

Methodological Caveats in the Detection of Coordinated Replay between Place Cells and Grid Cells.

PubMed

Trimper, John B; Trettel, Sean G; Hwaun, Ernie; Colgin, Laura Lee

2017-01-01

At rest, hippocampal "place cells," neurons with receptive fields corresponding to specific spatial locations, reactivate in a manner that reflects recently traveled trajectories. These "replay" events have been proposed as a mechanism underlying memory consolidation, or the transfer of a memory representation from the hippocampus to neocortical regions associated with the original sensory experience. Accordingly, it has been hypothesized that hippocampal replay of a particular experience should be accompanied by simultaneous reactivation of corresponding representations in the neocortex and in the entorhinal cortex, the primary interface between the hippocampus and the neocortex. Recent studies have reported that coordinated replay may occur between hippocampal place cells and medial entorhinal cortex grid cells, cells with multiple spatial receptive fields. Assessing replay in grid cells is problematic, however, as the cells exhibit regularly spaced spatial receptive fields in all environments and, therefore, coordinated replay between place cells and grid cells may be detected by chance. In the present report, we adapted analytical approaches utilized in recent studies of grid cell and place cell replay to determine the extent to which coordinated replay is spuriously detected between grid cells and place cells recorded from separate rats. For a subset of the employed analytical methods, coordinated replay was detected spuriously in a significant proportion of cases in which place cell replay events were randomly matched with grid cell firing epochs of equal duration. More rigorous replay evaluation procedures and minimum spike count requirements greatly reduced the amount of spurious findings. These results provide insights into aspects of place cell and grid cell activity during rest that contribute to false detection of coordinated replay. The results further emphasize the need for careful controls and rigorous methods when testing the hypothesis that place cells and grid cells exhibit coordinated replay.

Membrane potential dynamics of grid cells

PubMed Central

Domnisoru, Cristina; Kinkhabwala, Amina A.; Tank, David W.

2014-01-01

During navigation, grid cells increase their spike rates in firing fields arranged on a strikingly regular triangular lattice, while their spike timing is often modulated by theta oscillations. Oscillatory interference models of grid cells predict theta amplitude modulations of membrane potential during firing field traversals, while competing attractor network models predict slow depolarizing ramps. Here, using in-vivo whole-cell recordings, we tested these models by directly measuring grid cell intracellular potentials in mice running along linear tracks in virtual reality. Grid cells had large and reproducible ramps of membrane potential depolarization that were the characteristic signature tightly correlated with firing fields. Grid cells also exhibited intracellular theta oscillations that influenced their spike timing. However, the properties of theta amplitude modulations were not consistent with the view that they determine firing field locations. Our results support cellular and network mechanisms in which grid fields are produced by slow ramps, as in attractor models, while theta oscillations control spike timing. PMID:23395984

Grid-Optimization Program for Photovoltaic Cells

NASA Technical Reports Server (NTRS)

Daniel, R. E.; Lee, T. S.

1986-01-01

CELLOPT program developed to assist in designing grid pattern of current-conducting material on photovoltaic cell. Analyzes parasitic resistance losses and shadow loss associated with metallized grid pattern on both round and rectangular solar cells. Though performs sensitivity studies, used primarily to optimize grid design in terms of bus bar and grid lines by minimizing power loss. CELLOPT written in APL.

Modelling effects on grid cells of sensory input during self‐motion

PubMed Central

Raudies, Florian; Hinman, James R.

2016-01-01

Abstract The neural coding of spatial location for memory function may involve grid cells in the medial entorhinal cortex, but the mechanism of generating the spatial responses of grid cells remains unclear. This review describes some current theories and experimental data concerning the role of sensory input in generating the regular spatial firing patterns of grid cells, and changes in grid cell firing fields with movement of environmental barriers. As described here, the influence of visual features on spatial firing could involve either computations of self‐motion based on optic flow, or computations of absolute position based on the angle and distance of static visual cues. Due to anatomical selectivity of retinotopic processing, the sensory features on the walls of an environment may have a stronger effect on ventral grid cells that have wider spaced firing fields, whereas the sensory features on the ground plane may influence the firing of dorsal grid cells with narrower spacing between firing fields. These sensory influences could contribute to the potential functional role of grid cells in guiding goal‐directed navigation. PMID:27094096

Specific gene expression signatures induced by the multiple oncogenic alterations that occur within the PTEN/PI3K/AKT pathway in lung cancer.

PubMed

De Marco, Carmela; Laudanna, Carmelo; Rinaldo, Nicola; Oliveira, Duarte Mendes; Ravo, Maria; Weisz, Alessandro; Ceccarelli, Michele; Caira, Elvira; Rizzuto, Antonia; Zoppoli, Pietro; Malanga, Donatella; Viglietto, Giuseppe

2017-01-01

Hyperactivation of the phosphatydil-inositol-3' phosphate kinase (PI3K)/AKT pathway is observed in most NSCLCs, promoting proliferation, migration, invasion and resistance to therapy. AKT can be activated through several mechanisms that include loss of the negative regulator PTEN, activating mutations of the catalytic subunit of PI3K (PIK3CA) and/or mutations of AKT1 itself. However, number and identity of downstream targets of activated PI3K/AKT pathway are poorly defined. To identify the genes that are targets of constitutive PI3K/AKT signalling in lung cancer cells, we performed a comparative transcriptomic analysis of human lung epithelial cells (BEAS-2B) expressing active mutant AKT1 (AKT1-E17K), active mutant PIK3CA (PIK3CA-E545K) or that are silenced for PTEN. We found that, altogether, aberrant PI3K/AKT signalling in lung epithelial cells regulated the expression of 1,960/20,436 genes (9%), though only 30 differentially expressed genes (DEGs) (15 up-regulated, 12 down-regulated and 3 discordant) out of 20,436 that were common among BEAS-AKT1-E17K, BEAS-PIK3CA-E545K and BEAS-shPTEN cells (0.1%). Conversely, DEGs specific for mutant AKT1 were 133 (85 up-regulated; 48 down-regulated), DEGs specific for mutant PIK3CA were 502 (280 up-regulated; 222 down-regulated) and DEGs specific for PTEN loss were 1549 (799 up-regulated, 750 down-regulated). The results obtained from array analysis were confirmed by quantitative RT-PCR on selected up- and down-regulated genes (n = 10). Treatment of BEAS-C cells and the corresponding derivatives with pharmacological inhibitors of AKT (MK2206) or PI3K (LY294002) further validated the significance of our findings. Moreover, mRNA expression of selected DEGs (SGK1, IGFBP3, PEG10, GDF15, PTGES, S100P, respectively) correlated with the activation status of the PI3K/AKT pathway assessed by S473 phosphorylation in NSCLC cell lines (n = 6). Finally, we made use of Ingenuity Pathway Analysis (IPA) to investigate the relevant BioFunctions enriched by the costitutive activation of AKT1-, PI3K- or PTEN-dependent signalling in lung epithelial cells. Expectedly, the analysis of the DEGs common to all three alterations highlighted a group of BioFunctions that included Cell Proliferation of tumor cell lines (14 DEGs), Invasion of cells (10 DEGs) and Migration of tumour cell lines (10 DEGs), with a common core of 5 genes (ATF3, CDKN1A, GDF15, HBEGF and LCN2) that likely represent downstream effectors of the pro-oncogenic activities of PI3K/AKT signalling. Conversely, IPA analysis of exclusive DEGs led to the identification of different downstream effectors that are modulated by mutant AKT1 (TGFBR2, CTSZ, EMP1), mutant PIK3CA (CCND2, CDK2, IGFBP2, TRIB1) and PTEN loss (ASNS, FHL2). These findings not only shed light on the molecular mechanisms that are activated by aberrant signalling through the PI3K/AKT pathway in lung epithelial cells, but also contribute to the identification of previously unrecognised molecules whose regulation takes part in the development of lung cancer.

Effects of Model Resolution and Ocean Mixing on Forced Ice-Ocean Physical and Biogeochemical Simulations Using Global and Regional System Models

NASA Astrophysics Data System (ADS)

Jin, Meibing; Deal, Clara; Maslowski, Wieslaw; Matrai, Patricia; Roberts, Andrew; Osinski, Robert; Lee, Younjoo J.; Frants, Marina; Elliott, Scott; Jeffery, Nicole; Hunke, Elizabeth; Wang, Shanlin

2018-01-01

The current coarse-resolution global Community Earth System Model (CESM) can reproduce major and large-scale patterns but is still missing some key biogeochemical features in the Arctic Ocean, e.g., low surface nutrients in the Canada Basin. We incorporated the CESM Version 1 ocean biogeochemical code into the Regional Arctic System Model (RASM) and coupled it with a sea-ice algal module to investigate model limitations. Four ice-ocean hindcast cases are compared with various observations: two in a global 1° (40˜60 km in the Arctic) grid: G1deg and G1deg-OLD with/without new sea-ice processes incorporated; two on RASM's 1/12° (˜9 km) grid R9km and R9km-NB with/without a subgrid scale brine rejection parameterization which improves ocean vertical mixing under sea ice. Higher-resolution and new sea-ice processes contributed to lower model errors in sea-ice extent, ice thickness, and ice algae. In the Bering Sea shelf, only higher resolution contributed to lower model errors in salinity, nitrate (NO3), and chlorophyll-a (Chl-a). In the Arctic Basin, model errors in mixed layer depth (MLD) were reduced 36% by brine rejection parameterization, 20% by new sea-ice processes, and 6% by higher resolution. The NO3 concentration biases were caused by both MLD bias and coarse resolution, because of excessive horizontal mixing of high NO3 from the Chukchi Sea into the Canada Basin in coarse resolution models. R9km showed improvements over G1deg on NO3, but not on Chl-a, likely due to light limitation under snow and ice cover in the Arctic Basin.

Absence of Visual Input Results in the Disruption of Grid Cell Firing in the Mouse.

PubMed

Chen, Guifen; Manson, Daniel; Cacucci, Francesca; Wills, Thomas Joseph

2016-09-12

Grid cells are spatially modulated neurons within the medial entorhinal cortex whose firing fields are arranged at the vertices of tessellating equilateral triangles [1]. The exquisite periodicity of their firing has led to the suggestion that they represent a path integration signal, tracking the organism's position by integrating speed and direction of movement [2-10]. External sensory inputs are required to reset any errors that the path integrator would inevitably accumulate. Here we probe the nature of the external sensory inputs required to sustain grid firing, by recording grid cells as mice explore familiar environments in complete darkness. The absence of visual cues results in a significant disruption of grid cell firing patterns, even when the quality of the directional information provided by head direction cells is largely preserved. Darkness alters the expression of velocity signaling within the entorhinal cortex, with changes evident in grid cell firing rate and the local field potential theta frequency. Short-term (<1.5 s) spike timing relationships between grid cell pairs are preserved in the dark, indicating that network patterns of excitatory and inhibitory coupling between grid cells exist independently of visual input and of spatially periodic firing. However, we find no evidence of preserved hexagonal symmetry in the spatial firing of single grid cells at comparable short timescales. Taken together, these results demonstrate that visual input is required to sustain grid cell periodicity and stability in mice and suggest that grid cells in mice cannot perform accurate path integration in the absence of reliable visual cues. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

The Global Precipitation Climatology Project (GPCP) Combined Precipitation Dataset

NASA Technical Reports Server (NTRS)

Huffman, George J.; Adler, Robert F.; Arkin, Philip; Chang, Alfred; Ferraro, Ralph; Gruber, Arnold; Janowiak, John; McNab, Alan; Rudolf, Bruno; Schneider, Udo

1997-01-01

The Global Precipitation Climatology Project (GPCP) has released the GPCP Version 1 Combined Precipitation Data Set, a global, monthly precipitation dataset covering the period July 1987 through December 1995. The primary product in the dataset is a merged analysis incorporating precipitation estimates from low-orbit-satellite microwave data, geosynchronous-orbit -satellite infrared data, and rain gauge observations. The dataset also contains the individual input fields, a combination of the microwave and infrared satellite estimates, and error estimates for each field. The data are provided on 2.5 deg x 2.5 deg latitude-longitude global grids. Preliminary analyses show general agreement with prior studies of global precipitation and extends prior studies of El Nino-Southern Oscillation precipitation patterns. At the regional scale there are systematic differences with standard climatologies.

A Preliminary, Full Spectrum, Magnetic Anomaly Grid of the United States with Improved Long Wavelengths for Studying Continental Dynamics: A Website for Distribution of Data

USGS Publications Warehouse

Ravat, D.; Finn, C.; Hill, P.; Kucks, R.; Phillips, J.; Blakely, R.; Bouligand, C.; Sabaka, T.; Elshayat, A.; Aref, A.; Elawadi, E.

2009-01-01

Under an initiative started by Thomas G. Hildenbrand of the U.S. Geological Survey, we have improved the long-wavelength (50-2,500 km) content of the regional magnetic anomaly compilation for the conterminous United States by utilizing a nearly homogeneous set of National Uranium Resource Evaluation (NURE) magnetic surveys flown from 1975 to 1981. The surveys were flown in quadrangles of 2 deg of longitude by 1 deg of latitude with east-west flight lines spaced 4.8 to 9.6 km apart, north-south tie lines variably spaced, and a nominal terrain clearance of 122 m. Many of the surveys used base-station magnetometers to remove external field variations.

Coordinated learning of grid cell and place cell spatial and temporal properties: multiple scales, attention and oscillations.

PubMed

Grossberg, Stephen; Pilly, Praveen K

2014-02-05

A neural model proposes how entorhinal grid cells and hippocampal place cells may develop as spatial categories in a hierarchy of self-organizing maps (SOMs). The model responds to realistic rat navigational trajectories by learning both grid cells with hexagonal grid firing fields of multiple spatial scales, and place cells with one or more firing fields, that match neurophysiological data about their development in juvenile rats. Both grid and place cells can develop by detecting, learning and remembering the most frequent and energetic co-occurrences of their inputs. The model's parsimonious properties include: similar ring attractor mechanisms process linear and angular path integration inputs that drive map learning; the same SOM mechanisms can learn grid cell and place cell receptive fields; and the learning of the dorsoventral organization of multiple spatial scale modules through medial entorhinal cortex to hippocampus (HC) may use mechanisms homologous to those for temporal learning through lateral entorhinal cortex to HC ('neural relativity'). The model clarifies how top-down HC-to-entorhinal attentional mechanisms may stabilize map learning, simulates how hippocampal inactivation may disrupt grid cells, and explains data about theta, beta and gamma oscillations. The article also compares the three main types of grid cell models in the light of recent data.

The functional micro-organization of grid cells revealed by cellular-resolution imaging.

PubMed

Heys, James G; Rangarajan, Krsna V; Dombeck, Daniel A

2014-12-03

Establishing how grid cells are anatomically arranged, on a microscopic scale, in relation to their firing patterns in the environment would facilitate a greater microcircuit-level understanding of the brain's representation of space. However, all previous grid cell recordings used electrode techniques that provide limited descriptions of fine-scale organization. We therefore developed a technique for cellular-resolution functional imaging of medial entorhinal cortex (MEC) neurons in mice navigating a virtual linear track, enabling a new experimental approach to study MEC. Using these methods, we show that grid cells are physically clustered in MEC compared to nongrid cells. Additionally, we demonstrate that grid cells are functionally micro-organized: the similarity between the environment firing locations of grid cell pairs varies as a function of the distance between them according to a "Mexican hat"-shaped profile. This suggests that, on average, nearby grid cells have more similar spatial firing phases than those further apart. Copyright © 2014 Elsevier Inc. All rights reserved.

Grid and non-grid cells in medial entorhinal cortex represent spatial location and environmental features with complementary coding schemes

PubMed Central

Diehl, Geoffrey W.; Hon, Olivia J.; Leutgeb, Stefan; Leutgeb, Jill K.

2017-01-01

Summary The medial entorhinal cortex (mEC) has been identified as a hub for spatial information processing by the discovery of grid, border, and head-direction cells. Here we find that in addition to these well characterized classes, nearly all of the remaining two thirds of mEC cells can be categorized as spatially selective. We refer to these cells as non-grid spatial cells and confirmed that their spatial firing patterns were unrelated to running speed and highly reproducible within the same environment. However, in response to manipulations of environmental features, such as box shape or box color, non-grid spatial cells completely reorganized their spatial firing patterns. At the same time, grid cells retained their spatial alignment and predominantly responded with redistributed firing rates across their grid fields. Thus, mEC contains a joint representation of both spatial and environmental feature content, with specialized cell types showing different types of integrated coding of multimodal information. PMID:28343867

Extracting grid cell characteristics from place cell inputs using non-negative principal component analysis

PubMed Central

Dordek, Yedidyah; Soudry, Daniel; Meir, Ron; Derdikman, Dori

2016-01-01

Many recent models study the downstream projection from grid cells to place cells, while recent data have pointed out the importance of the feedback projection. We thus asked how grid cells are affected by the nature of the input from the place cells. We propose a single-layer neural network with feedforward weights connecting place-like input cells to grid cell outputs. Place-to-grid weights are learned via a generalized Hebbian rule. The architecture of this network highly resembles neural networks used to perform Principal Component Analysis (PCA). Both numerical results and analytic considerations indicate that if the components of the feedforward neural network are non-negative, the output converges to a hexagonal lattice. Without the non-negativity constraint, the output converges to a square lattice. Consistent with experiments, grid spacing ratio between the first two consecutive modules is −1.4. Our results express a possible linkage between place cell to grid cell interactions and PCA. DOI: http://dx.doi.org/10.7554/eLife.10094.001 PMID:26952211

Wind Code Application to External Forebody Flowfields with Comparisons to Experimental Results

NASA Technical Reports Server (NTRS)

Frate, F. C.; Kim, H. D.

2001-01-01

The WIND Code, a general purpose Navier-Stokes solver, has been utilized to obtain supersonic external flowfield Computational Fluid Dynamics (CFD) solutions over an axisymmetric, parabolic forebody with comparisons made to wind tunnel experimental results. Various cases have been investigated at supersonic freestream conditions ranging from Mach 2.0 to 3.5, at 0 deg and 3 deg angles-of-attack, and with either a sharp-nose or blunt-nose forebody configuration. Both a turbulent (Baldwin-Lomax algebraic turbulence model) and a laminar model have been implemented in the CFD. Obtaining the solutions involved utilizing either the parabolized- or full-Navier-Stokes analyses supplied in WIND. Comparisons have been made with static pressure measurements, with boundary-layer rake and flowfield rake pitot pressure measurements, and with temperature sensitive paint experimental results. Using WIND's parabolized Navier-Stokes capability, grid sequencing, and the Baldwin-Lomax algebraic turbulence model allowed for significant reductions in computational time while still providing good agreement with experiment. Given that CFD and experiment compare well, WIND is found to be a good computational platform for solving this type of forebody problem, and the grids developed in conjunction with it will be used in the future to investigate varying freestream conditions not tested experimentally.

Anisotropic encoding of three-dimensional space by place cells and grid cells

PubMed Central

Hayman, R.; Verriotis, M.; Jovalekic, A.; Fenton, A.A.; Jeffery, K.J.

2011-01-01

The subjective sense of space may result in part from the combined activity of place cells, in the hippocampus, and grid cells in posterior cortical regions such as entorhinal cortex and pre/parasubiculum. In horizontal planar environments, place cells provide focal positional information while grid cells supply odometric (distance-measuring) information. How these cells operate in three dimensions is unknown, even though the real world is three–dimensional. The present study explored this issue in rats exploring two different kinds of apparatus, a climbing wall (the “pegboard”) and a helix. Place and grid cell firing fields had normal horizontal characteristics but were elongated vertically, with grid fields forming stripes. It appears that grid cell odometry (and by implication path integration) is impaired/absent in the vertical domain, at least when the animal itself remains horizontal. These findings suggest that the mammalian encoding of three-dimensional space is anisotropic. PMID:21822271

The abrupt development of adult-like grid cell firing in the medial entorhinal cortex

PubMed Central

Wills, Thomas J.; Barry, Caswell; Cacucci, Francesca

2012-01-01

Understanding the development of the neural circuits subserving specific cognitive functions such as navigation remains a central problem in neuroscience. Here, we characterize the development of grid cells in the medial entorhinal cortex, which, by nature of their regularly spaced firing fields, are thought to provide a distance metric to the hippocampal neural representation of space. Grid cells emerge at the time of weaning in the rat, at around 3 weeks of age. We investigated whether grid cells in young rats are functionally equivalent to those observed in the adult as soon as they appear, or if instead they follow a gradual developmental trajectory. We find that, from the very youngest ages at which reproducible grid firing is observed (postnatal day 19): grid cells display adult-like firing fields that tessellate to form a coherent map of the local environment; that this map is universal, maintaining its internal structure across different environments; and that grid cells in young rats, as in adults, also encode a representation of direction and speed. To further investigate the developmental processes leading up to the appearance of grid cells, we present data from individual medial entorhinal cortex cells recorded across more than 1 day, spanning the period before and after the grid firing pattern emerged. We find that increasing spatial stability of firing was correlated with increasing gridness. PMID:22557949

Differences in Visual-Spatial Input May Underlie Different Compression Properties of Firing Fields for Grid Cell Modules in Medial Entorhinal Cortex

PubMed Central

Raudies, Florian; Hasselmo, Michael E.

2015-01-01

Firing fields of grid cells in medial entorhinal cortex show compression or expansion after manipulations of the location of environmental barriers. This compression or expansion could be selective for individual grid cell modules with particular properties of spatial scaling. We present a model for differences in the response of modules to barrier location that arise from different mechanisms for the influence of visual features on the computation of location that drives grid cell firing patterns. These differences could arise from differences in the position of visual features within the visual field. When location was computed from the movement of visual features on the ground plane (optic flow) in the ventral visual field, this resulted in grid cell spatial firing that was not sensitive to barrier location in modules modeled with small spacing between grid cell firing fields. In contrast, when location was computed from static visual features on walls of barriers, i.e. in the more dorsal visual field, this resulted in grid cell spatial firing that compressed or expanded based on the barrier locations in modules modeled with large spacing between grid cell firing fields. This indicates that different grid cell modules might have differential properties for computing location based on visual cues, or the spatial radius of sensitivity to visual cues might differ between modules. PMID:26584432

Chromosomal aberrations in Sigmodon hispidus from a Superfund site

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

Bowers, B.; McBee, K.; Lochmiller, R.

1995-12-31

Cotton rats (Sigmodon hispidus) were collected from an EPA Superfund site located on an abandoned oil refinery. Three trapping grids were located on the refinery and three similar grids were located at uncontaminated localities which served as reference sites. Bone marrow metaphase chromosome preparations were examined for chromosomal damage. For each individual, 50 cells were scored for six classes of chromosomal lesions. For the fall 1991 trapping period, mean number of aberrant cells per individual was 2.33, 0.85, and 1.50 for the three Superfund grids., Mean number of aberrant cells per individual was 2.55, 2.55, and 2.12 from the referencemore » grids. Mean number of lesions per cell was 2.77, 0.86, and 1.9 from the Superfund grids, and 3.55, 2.77, and 2.50 from the reference grids. For the spring 1992 trapping period, more damage was observed in animals from both Superfund and reference sites; however, animals from Superfund grids had more damage than animals from reference grids. Mean number of aberrant cells per individual was 3.50, 3.25, and 3.70 from the Superfund grids, and 2.40, 2.11, and 1.40 from the reference grids. Mean number of lesions per cell was 4.80, 4.25, and 5.50 from the Superfund grids, and 2.60, 2.33, and 1.50 from the reference grids. These data suggest animals may be more susceptible to chromosomal damage during winter months, and animals from the Superfund grids appear to be more severely affected than animals from reference grids.« less

Optimizing Grid Patterns on Photovoltaic Cells

NASA Technical Reports Server (NTRS)

Burger, D. R.

1984-01-01

CELCAL computer program helps in optimizing grid patterns for different photovoltaic cell geometries and metalization processes. Five different powerloss phenomena associated with front-surface metal grid pattern on photovoltaic cells.

Methodological Caveats in the Detection of Coordinated Replay between Place Cells and Grid Cells

PubMed Central

Trimper, John B.; Trettel, Sean G.; Hwaun, Ernie; Colgin, Laura Lee

2017-01-01

At rest, hippocampal “place cells,” neurons with receptive fields corresponding to specific spatial locations, reactivate in a manner that reflects recently traveled trajectories. These “replay” events have been proposed as a mechanism underlying memory consolidation, or the transfer of a memory representation from the hippocampus to neocortical regions associated with the original sensory experience. Accordingly, it has been hypothesized that hippocampal replay of a particular experience should be accompanied by simultaneous reactivation of corresponding representations in the neocortex and in the entorhinal cortex, the primary interface between the hippocampus and the neocortex. Recent studies have reported that coordinated replay may occur between hippocampal place cells and medial entorhinal cortex grid cells, cells with multiple spatial receptive fields. Assessing replay in grid cells is problematic, however, as the cells exhibit regularly spaced spatial receptive fields in all environments and, therefore, coordinated replay between place cells and grid cells may be detected by chance. In the present report, we adapted analytical approaches utilized in recent studies of grid cell and place cell replay to determine the extent to which coordinated replay is spuriously detected between grid cells and place cells recorded from separate rats. For a subset of the employed analytical methods, coordinated replay was detected spuriously in a significant proportion of cases in which place cell replay events were randomly matched with grid cell firing epochs of equal duration. More rigorous replay evaluation procedures and minimum spike count requirements greatly reduced the amount of spurious findings. These results provide insights into aspects of place cell and grid cell activity during rest that contribute to false detection of coordinated replay. The results further emphasize the need for careful controls and rigorous methods when testing the hypothesis that place cells and grid cells exhibit coordinated replay. PMID:28824388

Selforganization of modular activity of grid cells

PubMed Central

Urdapilleta, Eugenio; Si, Bailu

2017-01-01

Abstract A unique topographical representation of space is found in the concerted activity of grid cells in the rodent medial entorhinal cortex. Many among the principal cells in this region exhibit a hexagonal firing pattern, in which each cell expresses its own set of place fields (spatial phases) at the vertices of a triangular grid, the spacing and orientation of which are typically shared with neighboring cells. Grid spacing, in particular, has been found to increase along the dorso‐ventral axis of the entorhinal cortex but in discrete steps, that is, with a modular structure. In this study, we show that such a modular activity may result from the self‐organization of interacting units, which individually would not show discrete but rather continuously varying grid spacing. Within our “adaptation” network model, the effect of a continuously varying time constant, which determines grid spacing in the isolated cell model, is modulated by recurrent collateral connections, which tend to produce a few subnetworks, akin to magnetic domains, each with its own grid spacing. In agreement with experimental evidence, the modular structure is tightly defined by grid spacing, but also involves grid orientation and distortion, due to interactions across modules. Thus, our study sheds light onto a possible mechanism, other than simply assuming separate networks a priori, underlying the formation of modular grid representations. PMID:28768062

Purely Translational Realignment in Grid Cell Firing Patterns Following Nonmetric Context Change

PubMed Central

Marozzi, Elizabeth; Ginzberg, Lin Lin; Alenda, Andrea; Jeffery, Kate J.

2015-01-01

Grid cells in entorhinal and parahippocampal cortices contribute to a network, centered on the hippocampal place cell system, that constructs a representation of spatial context for use in navigation and memory. In doing so, they use metric cues such as the distance and direction of nearby boundaries to position and orient their firing field arrays (grids). The present study investigated whether they also use purely nonmetric “context” information such as color and odor of the environment. We found that, indeed, purely nonmetric cues—sufficiently salient to cause changes in place cell firing patterns—can regulate grid positioning; they do so independently of orientation, and thus interact with linear but not directional spatial inputs. Grid cells responded homogeneously to context changes. We suggest that the grid and place cell networks receive context information directly and also from each other; the information is used by place cells to compute the final decision of the spatial system about which context the animal is in, and by grid cells to help inform the system about where the animal is within it. PMID:26048956

Grid cells form a global representation of connected environments.

PubMed

Carpenter, Francis; Manson, Daniel; Jeffery, Kate; Burgess, Neil; Barry, Caswell

2015-05-04

The firing patterns of grid cells in medial entorhinal cortex (mEC) and associated brain areas form triangular arrays that tessellate the environment [1, 2] and maintain constant spatial offsets to each other between environments [3, 4]. These cells are thought to provide an efficient metric for navigation in large-scale space [5-8]. However, an accurate and universal metric requires grid cell firing patterns to uniformly cover the space to be navigated, in contrast to recent demonstrations that environmental features such as boundaries can distort [9-11] and fragment [12] grid patterns. To establish whether grid firing is determined by local environmental cues, or provides a coherent global representation, we recorded mEC grid cells in rats foraging in an environment containing two perceptually identical compartments connected via a corridor. During initial exposures to the multicompartment environment, grid firing patterns were dominated by local environmental cues, replicating between the two compartments. However, with prolonged experience, grid cell firing patterns formed a single, continuous representation that spanned both compartments. Thus, we provide the first evidence that in a complex environment, grid cell firing can form the coherent global pattern necessary for them to act as a metric capable of supporting large-scale spatial navigation. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Grid Cells Form a Global Representation of Connected Environments

PubMed Central

Carpenter, Francis; Manson, Daniel; Jeffery, Kate; Burgess, Neil; Barry, Caswell

2015-01-01

Summary The firing patterns of grid cells in medial entorhinal cortex (mEC) and associated brain areas form triangular arrays that tessellate the environment [1, 2] and maintain constant spatial offsets to each other between environments [3, 4]. These cells are thought to provide an efficient metric for navigation in large-scale space [5–8]. However, an accurate and universal metric requires grid cell firing patterns to uniformly cover the space to be navigated, in contrast to recent demonstrations that environmental features such as boundaries can distort [9–11] and fragment [12] grid patterns. To establish whether grid firing is determined by local environmental cues, or provides a coherent global representation, we recorded mEC grid cells in rats foraging in an environment containing two perceptually identical compartments connected via a corridor. During initial exposures to the multicompartment environment, grid firing patterns were dominated by local environmental cues, replicating between the two compartments. However, with prolonged experience, grid cell firing patterns formed a single, continuous representation that spanned both compartments. Thus, we provide the first evidence that in a complex environment, grid cell firing can form the coherent global pattern necessary for them to act as a metric capable of supporting large-scale spatial navigation. PMID:25913404

Implementation of the Baldwin-Barth turbulence model into the ZETA code and its diagnosis. M.S. Thesis

NASA Technical Reports Server (NTRS)

Low, Scott L.

1993-01-01

The Baldwin-Barth turbulence model was implemented into Zeta, a time-accurate, zonal, integro-differential code for incompressible laminar and turbulent flows. The implementation procedure is patterned after the model subroutine in ARC2D. The results of ZETA with the Baldwin-Barth turbulence model were compared with experimental data, with ZETA using Baldwin-Lomax model, and with ARC2D using the Baldwin-Barth model. The Baldwin-Barth model subroutine was tested by inputting an ARC2D velocity solution of an NACA-0012 airfoil at R(sub e) = 3.9 x 10(exp 6) and alpha = 5 deg. The resultant turbulent viscosity and Reynolds stresses compared favorably with the original data. For the same grid having grid points inside the laminar sublayer, which is necessary due to the one-equation nature of the model, ZETA however predicts early separation. It was found that the current ZETA has problem with such a fine grid. Further work is in progress to solve this problem.

Integrated polarization-dependent sensor for autonomous navigation

NASA Astrophysics Data System (ADS)

Liu, Ze; Zhang, Ran; Wang, Zhiwen; Guan, Le; Li, Bin; Chu, Jinkui

2015-01-01

Based on the navigation strategy of insects utilizing the polarized skylight, an integrated polarization-dependent sensor for autonomous navigation is presented. The navigation sensor has the features of compact structure, high precision, strong robustness, and a simple manufacture technique. The sensor is composed by integrating a complementary-metal-oxide-semiconductor sensor with a multiorientation nanowire grid polarizer. By nanoimprint lithography, the multiorientation nanowire polarizer is fabricated in one step and the alignment error is eliminated. The statistical theory is added to the interval-division algorithm to calculate the polarization angle of the incident light. The laboratory and outdoor tests for the navigation sensor are implemented and the errors of the measured angle are ±0.02 deg and ±1.3 deg, respectively. The results show that the proposed sensor has potential for application in autonomous navigation.

Tabulations of ambient ozone data obtained by GASP (Global Air Sampling Program) airliners, March 1975 to July 1979

NASA Technical Reports Server (NTRS)

Jasperson, W. H.; Holdeman, J. D.

1984-01-01

Tabulations are given of GASP ambient ozone mean, standard deviation, median, 84th percentile, and 98th percentile values, by month, flight level, and geographical region. These data are tabulated to conform to the temporal and spatial resolution required by FAA Advisory Circular 120-38 (monthly by 2000 ft in altitude by 5 deg in latitude) for climatological data used to show compliance with cabin ozone regulations. In addition seasonal x 10 deg latitude tabulations are included which are directly comparable to and supersede the interim GASP ambient ozone tabulations given in appendix B of FAA-EE-80-43 (NASA TM-81528). Selected probability variations are highlighted to illustrate the spatial and temporal variability of ambient ozone and to compare results from the coarse and fine grid analyses.

Hair cell tufts and afferent innervation of the bullfrog crista ampullaris

NASA Technical Reports Server (NTRS)

Myers, Steven F.; Lewis, Edwin R.

1990-01-01

Within the bullfrog semicircular canal crista, hair cell tuft types were defined and mapped with the aid of scanning electron microscopy. Dye-filled planar afferent axons had mean distal axonal diameters of 1.6-4.9 microns, highly branched arbors, and contacted 11-24 hair cells. Dye-filled isthmus afferent axons had mean distal axonal diameters of 1.8-7.9 microns, with either small or large field arbors contacting 4-9 or 25-31 hair cells. The estimated mean number of contacts per innervated hair cell was 2.2 for planar and 1.3 for isthmus afferent neurons. Data on evoked afferent responses were available only for isthmus units that were observed to respond to our microrotational stimuli. Of 21 such afferent neurons, eight were successfully dye-filled. Within this sample, high-gain units had large field arbors and lower-gain units had small field arbors. The sensitivity of each afferent neuron was analyzed in terms of noise equivalent input (NEI), the stimulus amplitude for which the afferent response amplitude is just equivalent to the rms deviation of the instantaneous spike rate. NEI for isthmus units varied from 0.63 to 8.2 deg/s; the mean was 3.2 deg/s.

Nuclear reactor spacer grid and ductless core component

DOEpatents

Christiansen, David W.; Karnesky, Richard A.

1989-01-01

The invention relates to a nuclear reactor spacer grid member for use in a liquid cooled nuclear reactor and to a ductless core component employing a plurality of these spacer grid members. The spacer grid member is of the egg-shell type and is constructed so that the walls of the cell members of the grid member are formed of a single thickness of metal to avoid tolerance problems. Within each cell member is a hydraulic spring which laterally constrains the nuclear material bearing rod which passes through each cell member against a hardstop in response to coolant flow through the cell member. This hydraulic spring is also suitable for use in a water cooled nuclear reactor. A core component constructed of, among other components, a plurality of these spacer grid members, avoids the use of a full length duct by providing spacer sleeves about the sodium tubes passing through the spacer grid members at locations between the grid members, thereby maintaining a predetermined space between adjacent grid members.

Method of making a back contacted solar cell

DOEpatents

Gee, James M.

1995-01-01

A back-contacted solar cell having laser-drilled vias connecting the front-surface carrier-collector junction to an electrode grid on the back surface. The structure may also include a rear surface carrier-collector junction connected to the same grid. The substrate is connected to a second grid which is interdigitated with the first. Both grids are configured for easy series connection with neighboring cells. Several processes are disclosed to produce the cell.

Retrovirus-mediated conditional immortalization and analysis of established cell lines of osteoclast precursor cells

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

Kawata, Shigehisa; Suzuki, Jun; Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871

2006-11-10

Osteoclast precursor cells (OPCs) have previously been established from bone marrow cells of SV40 temperature-sensitive T antigen-expressing transgenic mice. Here, we use retrovirus-mediated gene transfer to conditionally immortalize OPCs by expressing temperature-sensitive large T antigen (tsLT) from wild type bone marrow cells. The immortalized OPCs proliferated at the permissive temperature of 33.5 deg. C, but stopped growing at the non-permissive temperature of 39 deg. C. In the presence of receptor activator of NF{kappa}B ligand (RANKL), the OPCs differentiated into tartrate-resistant acid phosphatase (TRAP)-positive cells and formed multinucleate osteoclasts at 33.5 deg. C. From these OPCs, we cloned two types ofmore » cell lines. Both differentiated into TRAP-positive cells, but one formed multinucleate osteoclasts while the other remained unfused in the presence of RANKL. These results indicate that the established cell lines are useful for analyzing mechanisms of differentiation, particularly multinucleate osteoclast formation. Retrovirus-mediated conditional immortalization should be a useful method to immortalize OPCs from primary bone marrow cells.« less

In silico analysis of single-cell RNA sequencing data from 3 and 7 days old mouse spermatogonial stem cells to identify their differentially expressed genes and transcriptional regulators.

PubMed

Sisakhtnezhad, Sajjad

2018-05-11

Spermatogonial stem cells (SSCs), which are at the basis of spermatogenesis process, are valuable cells with different applications in biotechnology and regenerative medicine. Understanding the molecular basis of SSC self-renewal and differentiation at various developmental stages of the male organism is crucial to find key factors in the SSCs fate and function. Therefore, this study was aimed to use single-cell RNA-sequencing dataset analysis for identification of differentially expressed genes (DEGs) and their regulators in 3 and 7 days old mouse-derived single SSCs (mSSCs). Results showed 68 upregulated and 203 downregulated genes in 7 days old mouse-derived SSCs compared to 3 days old mSSCs, which were associated with 1493 and 3077 biological processes, respectively. It also found that DAZL, FKBP6, PAIP2, DDX4, H3F3B, TEX15, XRN2, MAEL, and SOD1 are important factors with the higher gene expression pattern, which may be pivotal for mSSCs fate and function during development of germ cells. Moreover, NR3C1, RXRA, NCOA, ESR1, PML, ATF2, BMI1, POU5F1, and CHD1 were the main central regulators for the upregulated DEGs, while HNF1A, C/EBPα, and NFATC1 were the master regulators for the downregulated DEGs. In this regard, two significant protein complexes were found in the protein-protein interactions network for the upregulated DEGs regulators. Furthermore, 24 protein kinases detected upstream of the main central regulators of DEGs. In conclusion, this study presents DEGs and their transcriptional regulators that are crucial for inducing and regulating SSCs commitment during development, and for developing efficient protocols to identify and isolate SSCs for different applications. © 2018 Wiley Periodicals, Inc.

The analysis of polar clouds from AVHRR satellite data using pattern recognition techniques

NASA Technical Reports Server (NTRS)

Smith, William L.; Ebert, Elizabeth

1990-01-01

The cloud cover in a set of summertime and wintertime AVHRR data from the Arctic and Antarctic regions was analyzed using a pattern recognition algorithm. The data were collected by the NOAA-7 satellite on 6 to 13 Jan. and 1 to 7 Jul. 1984 between 60 deg and 90 deg north and south latitude in 5 spectral channels, at the Global Area Coverage (GAC) resolution of approximately 4 km. This data embodied a Polar Cloud Pilot Data Set which was analyzed by a number of research groups as part of a polar cloud algorithm intercomparison study. This study was intended to determine whether the additional information contained in the AVHRR channels (beyond the standard visible and infrared bands on geostationary satellites) could be effectively utilized in cloud algorithms to resolve some of the cloud detection problems caused by low visible and thermal contrasts in the polar regions. The analysis described makes use of a pattern recognition algorithm which estimates the surface and cloud classification, cloud fraction, and surface and cloudy visible (channel 1) albedo and infrared (channel 4) brightness temperatures on a 2.5 x 2.5 deg latitude-longitude grid. In each grid box several spectral and textural features were computed from the calibrated pixel values in the multispectral imagery, then used to classify the region into one of eighteen surface and/or cloud types using the maximum likelihood decision rule. A slightly different version of the algorithm was used for each season and hemisphere because of differences in categories and because of the lack of visible imagery during winter. The classification of the scene is used to specify the optimal AVHRR channel for separating clear and cloudy pixels using a hybrid histogram-spatial coherence method. This method estimates values for cloud fraction, clear and cloudy albedos and brightness temperatures in each grid box. The choice of a class-dependent AVHRR channel allows for better separation of clear and cloudy pixels than does a global choice of a visible and/or infrared threshold. The classification also prevents erroneous estimates of large fractional cloudiness in areas of cloudfree snow and sea ice. The hybrid histogram-spatial coherence technique and the advantages of first classifying a scene in the polar regions are detailed. The complete Polar Cloud Pilot Data Set was analyzed and the results are presented and discussed.

An application of the MPP to the interactive manipulation of stereo images of digital terrain models

NASA Technical Reports Server (NTRS)

Pol, Sanjay; Mcallister, David; Davis, Edward

1987-01-01

Massively Parallel Processor algorithms were developed for the interactive manipulation of flat shaded digital terrain models defined over grids. The emphasis is on real time manipulation of stereo images. Standard graphics transformations are applied to a 128 x 128 grid of elevations followed by shading and a perspective projection to produce the right eye image. The surface is then rendered using a simple painter's algorithm for hidden surface removal. The left eye image is produced by rotating the surface 6 degs about the viewer's y axis followed by a perspective projection and rendering of the image as described above. The left and right eye images are then presented on a graphics device using standard stereo technology. Performance evaluations and comparisons are presented.

GRIDGEN Version 1.0: a computer program for generating unstructured finite-volume grids

USGS Publications Warehouse

Lien, Jyh-Ming; Liu, Gaisheng; Langevin, Christian D.

2015-01-01

GRIDGEN is a computer program for creating layered quadtree grids for use with numerical models, such as the MODFLOW–USG program for simulation of groundwater flow. The program begins by reading a three-dimensional base grid, which can have variable row and column widths and spatially variable cell top and bottom elevations. From this base grid, GRIDGEN will continuously divide into four any cell intersecting user-provided refinement features (points, lines, and polygons) until the desired level of refinement is reached. GRIDGEN will then smooth, or balance, the grid so that no two adjacent cells, including overlying and underlying cells, differ by more than a user-specified level tolerance. Once these gridding processes are completed, GRIDGEN saves a tree structure file so that the layered quadtree grid can be quickly reconstructed as needed. Once a tree structure file has been created, GRIDGEN can then be used to (1) export the layered quadtree grid as a shapefile, (2) export grid connectivity and cell information as ASCII text files for use with MODFLOW–USG or other numerical models, and (3) intersect the grid with shapefiles of points, lines, or polygons, and save intersection output as ASCII text files and shapefiles. The GRIDGEN program is demonstrated by creating a layered quadtree grid for the Biscayne aquifer in Miami-Dade County, Florida, using hydrologic features to control where refinement is added.

HELP - A Multimaterial Eulerian Program in Two Space Dimensions and Time

DTIC Science & Technology

1976-04-01

ASSUMPTIONS 3-1 3.2 STRENGTH PHASE (SPHASE) 3-1 3.2.1 Definition of Strain Rate Derivatives for Cells at a Grid Boundary 3-3 3.2.2 Definition...of Interpolated Strain Rates and Stresses for Cells at a Grid Boundary 3-4 3.2.3 Definition of Velocities and Deviator Stresses at Grid Boundaries...Grid Boundaries 3-9 3.4.2 Change of Momentum for Cells at Reflective Grid Boundaries in TPHASE.. 3-10 3.4.3 Correction to Theoretical Energy for

Optimal configurations of spatial scale for grid cell firing under noise and uncertainty

PubMed Central

Towse, Benjamin W.; Barry, Caswell; Bush, Daniel; Burgess, Neil

2014-01-01

We examined the accuracy with which the location of an agent moving within an environment could be decoded from the simulated firing of systems of grid cells. Grid cells were modelled with Poisson spiking dynamics and organized into multiple ‘modules’ of cells, with firing patterns of similar spatial scale within modules and a wide range of spatial scales across modules. The number of grid cells per module, the spatial scaling factor between modules and the size of the environment were varied. Errors in decoded location can take two forms: small errors of precision and larger errors resulting from ambiguity in decoding periodic firing patterns. With enough cells per module (e.g. eight modules of 100 cells each) grid systems are highly robust to ambiguity errors, even over ranges much larger than the largest grid scale (e.g. over a 500 m range when the maximum grid scale is 264 cm). Results did not depend strongly on the precise organization of scales across modules (geometric, co-prime or random). However, independent spatial noise across modules, which would occur if modules receive independent spatial inputs and might increase with spatial uncertainty, dramatically degrades the performance of the grid system. This effect of spatial uncertainty can be mitigated by uniform expansion of grid scales. Thus, in the realistic regimes simulated here, the optimal overall scale for a grid system represents a trade-off between minimizing spatial uncertainty (requiring large scales) and maximizing precision (requiring small scales). Within this view, the temporary expansion of grid scales observed in novel environments may be an optimal response to increased spatial uncertainty induced by the unfamiliarity of the available spatial cues. PMID:24366144

Method of making a back contacted solar cell

DOEpatents

Gee, J.M.

1995-11-21

A back-contacted solar cell is described having laser-drilled vias connecting the front-surface carrier-collector junction to an electrode grid on the back surface. The structure may also include a rear surface carrier-collector junction connected to the same grid. The substrate is connected to a second grid which is interdigitated with the first. Both grids are configured for easy series connection with neighboring cells. Several processes are disclosed to produce the cell. 2 figs.

Grid cell spatial tuning reduced following systemic muscarinic receptor blockade

PubMed Central

Newman, Ehren L.; Climer, Jason R.; Hasselmo, Michael E.

2014-01-01

Grid cells of the medial entorhinal cortex exhibit a periodic and stable pattern of spatial tuning that may reflect the output of a path integration system. This grid pattern has been hypothesized to serve as a spatial coordinate system for navigation and memory function. The mechanisms underlying the generation of this characteristic tuning pattern remain poorly understood. Systemic administration of the muscarinic antagonist scopolamine flattens the typically positive correlation between running speed and entorhinal theta frequency in rats. The loss of this neural correlate of velocity, an important signal for the calculation of path integration, raises the question of what influence scopolamine has on the grid cell tuning as a read out of the path integration system. To test this, the spatial tuning properties of grid cells were compared before and after systemic administration of scopolamine as rats completed laps on a circle track for food rewards. The results show that the spatial tuning of the grid cells was reduced following scopolamine administration. The tuning of head direction cells, in contrast, was not reduced by scopolamine. This is the first report to demonstrate a link between cholinergic function and grid cell tuning. This work suggests that the loss of tuning in the grid cell network may underlie the navigational disorientation observed in Alzheimer's patients and elderly individuals with reduced cholinergic tone. PMID:24493379

Coarse Grid Modeling of Turbine Film Cooling Flows Using Volumetric Source Terms

NASA Technical Reports Server (NTRS)

Heidmann, James D.; Hunter, Scott D.

2001-01-01

The recent trend in numerical modeling of turbine film cooling flows has been toward higher fidelity grids and more complex geometries. This trend has been enabled by the rapid increase in computing power available to researchers. However, the turbine design community requires fast turnaround time in its design computations, rendering these comprehensive simulations ineffective in the design cycle. The present study describes a methodology for implementing a volumetric source term distribution in a coarse grid calculation that can model the small-scale and three-dimensional effects present in turbine film cooling flows. This model could be implemented in turbine design codes or in multistage turbomachinery codes such as APNASA, where the computational grid size may be larger than the film hole size. Detailed computations of a single row of 35 deg round holes on a flat plate have been obtained for blowing ratios of 0.5, 0.8, and 1.0, and density ratios of 1.0 and 2.0 using a multiblock grid system to resolve the flows on both sides of the plate as well as inside the hole itself. These detailed flow fields were spatially averaged to generate a field of volumetric source terms for each conservative flow variable. Solutions were also obtained using three coarse grids having streamwise and spanwise grid spacings of 3d, 1d, and d/3. These coarse grid solutions used the integrated hole exit mass, momentum, energy, and turbulence quantities from the detailed solutions as volumetric source terms. It is shown that a uniform source term addition over a distance from the wall on the order of the hole diameter is able to predict adiabatic film effectiveness better than a near-wall source term model, while strictly enforcing correct values of integrated boundary layer quantities.

Spatially Fractionated Radiation Induces Cytotoxicity and Changes in Gene Expression in Bystander and Radiation Adjacent Murine Carcinoma Cells

PubMed Central

Asur, Rajalakshmi S.; Sharma, Sunil; Chang, Ching-Wei; Penagaricano, Jose; Kommuru, Indira M.; Moros, Eduardo G.; Corry, Peter M.; Griffin, Robert J.

2012-01-01

Radiation-induced bystander effects have been extensively studied at low doses, since evidence of bystander induced cell killing and other effects on unirradiated cells were found to be predominant at doses up to 0.5 Gy. Therefore, few studies have examined bystander effects induced by exposure to higher doses of radiation, such as spatially fractionated radiation (GRID) treatment. In the present study, we evaluate the ability of GRID treatment to induce changes in GRID adjacent (bystander) regions, in two different murine carcinoma cell lines following exposure to a single irradiation dose of 10 Gy. Murine SCK mammary carcinoma cells and SCCVII squamous carcinoma cells were irradiated using a brass collimator to create a GRID pattern of nine circular fields 12 mm in diameter with a center-to-center distance of 18 mm. Similar to the typical clinical implementation of GRID, this is approximately a 50:50 ratio of direct and bystander exposure. We also performed experiments by irradiating separate cultures and transferring the medium to unirradiated bystander cultures. Clonogenic survival was evaluated in both cell lines to determine the occurrence of radiation-induced bystander effects. For the purpose of our study, we have defined bystander cells as GRID adjacent cells that received approximately 1 Gy scatter dose or unirradiated cells receiving conditioned medium from irradiated cells. We observed significant bystander killing of cells adjacent to the GRID irradiated regions compared to sham treated controls. We also observed bystander killing of SCK and SCCVII cells cultured in conditioned medium obtained from cells irradiated with 10 Gy. Therefore, our results confirm the occurrence of bystander effects following exposure to a high-dose of radiation and suggest that cell-to-cell contact is not required for these effects. In addition, the gene expression profile for DNA damage and cellular stress response signaling in SCCVII cells after GRID exposure was studied. The occurrence of GRID-induced bystander gene expression changes in significant numbers of DNA damage and cellular stress response signaling genes, providing molecular evidence for possible mechanisms of bystander cell killing. PMID:22559204

Passive Transport Disrupts Grid Signals in the Parahippocampal Cortex.

PubMed

Winter, Shawn S; Mehlman, Max L; Clark, Benjamin J; Taube, Jeffrey S

2015-10-05

Navigation is usually thought of relative to landmarks, but neural signals representing space also use information generated by an animal's movements. These signals include grid cells, which fire at multiple locations, forming a repeating grid pattern. Grid cell generation depends upon theta rhythm, a 6-10 Hz electroencephalogram (EEG) oscillation that is modulated by the animals' movement velocity. We passively moved rats in a clear cart to eliminate motor related self-movement cues that drive moment-to-moment changes in theta rhythmicity. We found that passive movement maintained theta power and frequency at levels equivalent to low active movement velocity, spared overall head-direction (HD) cell characteristics, but abolished both velocity modulation of theta rhythmicity and grid cell firing patterns. These results indicate that self-movement motor cues are necessary for generating grid-specific firing patterns, possibly by driving velocity modulation of theta rhythmicity, which may be used as a speed signal to generate the repeating pattern of grid cells. Copyright © 2015 Elsevier Ltd. All rights reserved.

Passive Transport Disrupts Grid Signals in the Parahippocampal Cortex

PubMed Central

Winter, Shawn S.; Mehlman, Max L.; Clark, Benjamin J.; Taube, Jeffrey S.

2015-01-01

Summary Navigation is usually thought of relative to landmarks, but neural signals representing space also use information generated by an animal’s movements. These signals include grid cells, which fire at multiple locations forming a repeating grid pattern. Grid cell generation depends upon theta rhythm, a 6-10 Hz EEG oscillation that is modulated by the animals’ movement velocity. We passively moved rats in a clear cart to eliminate motor related self-movement cues that drive moment-to-moment changes in theta rhythmicity. We found that passive movement maintained theta power and frequency at levels equivalent to low active movement velocity, spared overall HD cell characteristics, and abolished velocity modulation of theta rhythmicity and grid cell firing patterns. These results indicate that self-movement motor cues are necessary for generating grid-specific firing patterns, possibly by driving velocity modulation of theta rhythmicity. Velocity modulation of theta may be used as a speed signal to generate the repeating pattern of grid cells. PMID:26387719

Beam efflux measurements

NASA Technical Reports Server (NTRS)

Komatsu, G. K.; Stellen, J. M., Jr.

1976-01-01

Measurements have been made of the high energy thrust ions, (Group I), high angle/high energy ions (Group II), and high angle/low energy ions (Group IV) of a mercury electron bombardment thruster in the angular divergence range from 0 deg to greater than 90 deg. The measurements have been made as a function of thrust ion current, propellant utilization efficiency, bombardment discharge voltage, screen and accelerator grid potential (accel-decel ratio) and neutralizer keeper potential. The shape of the Group IV (charge exchange) ion plume has remained essentially fixed within the range of variation of the engine operation parameters. The magnitude of the charge exchange ion flux scales with thrust ion current, for good propellant utilization conditions. For fixed thrust ion current, charge exchange ion flux increases for diminishing propellant utilization efficiency. Facility effects influence experimental accuracies within the range of propellant utilization efficiency used in the experiments. The flux of high angle/high energy Group II ions is significantly diminished by the use of minimum decel voltages on the accelerator grid. A computer model of charge exchange ion production and motion has been developed. The program allows computation of charge exchange ion volume production rate, total production rate, and charge exchange ion trajectories for "genuine" and "facilities effects" particles. In the computed flux deposition patterns, the Group I and Group IV ion plumes exhibit a counter motion.

Deg proteases and their role in protein quality control and processing in different subcellular compartments of the plant cell.

PubMed

Schuhmann, Holger; Adamska, Iwona

2012-05-01

Degradation of periplasmic proteins (Deg)/high temperature requirement A (HtrA) proteases are ATP-independent serine endopeptidases found in almost every organism. Database searches revealed that 16 Deg paralogues are encoded by the genome of Arabidopsis thaliana, six of which were experimentally shown to be located in chloroplasts, one in peroxisomes, one in mitochondria and one in the nucleus. Two more Deg proteases are predicted to reside in chloroplasts, five in mitochondria (one of them with a dual chloroplastidial/mitochondrial localization) and the subcellular location of one protein is uncertain. This review summarizes the current knowledge on the role of Deg proteases in maintaining protein homeostasis and protein processing in various subcompartments of the plant cell. The chloroplast Deg proteases are the best examined so far, especially with respect to their role in the degradation of photodamaged photosynthetic proteins and in biogenesis of photosystem II (PSII). A combined action of thylakoid lumen and stroma Deg proteases in the primary cleavage of photodamaged D1 protein from PSII reaction centre is discussed on the basis of a recently resolved crystal structure of plant Deg1. The peroxisomal Deg protease is a processing enzyme responsible for the cleavage of N-terminal peroxisomal targeting signals (PTSs). A. thaliana mutants lacking this enzyme show reduced peroxisomal β-oxidation, indicating for the first time the impact of protein processing on peroxisomal functions in plants. Much less data is available for mitochondrial and nuclear Deg proteases. Based on the available expression data we hypothesize a role in general protein quality control and during acquired heat resistance. Copyright © Physiologia Plantarum 2011.

Grid cells on steeply sloping terrain: evidence for planar rather than volumetric encoding

PubMed Central

Hayman, Robin M. A.; Casali, Giulio; Wilson, Jonathan J.; Jeffery, Kate J.

2015-01-01

Neural encoding of navigable space involves a network of structures centered on the hippocampus, whose neurons –place cells – encode current location. Input to the place cells includes afferents from the entorhinal cortex, which contains grid cells. These are neurons expressing spatially localized activity patches, or firing fields, that are evenly spaced across the floor in a hexagonal close-packed array called a grid. It is thought that grids function to enable the calculation of distances. The question arises as to whether this odometry process operates in three dimensions, and so we queried whether grids permeate three-dimensional (3D) space – that is, form a lattice – or whether they simply follow the environment surface. If grids form a 3D lattice then this lattice would ordinarily be aligned horizontally (to explain the usual hexagonal pattern observed). A tilted floor would transect several layers of this putative lattice, resulting in interruption of the hexagonal pattern. We model this prediction with simulated grid lattices, and show that the firing of a grid cell on a 40°-tilted surface should cover proportionally less of the surface, with smaller field size, fewer fields, and reduced hexagonal symmetry. However, recording of real grid cells as animals foraged on a 40°-tilted surface found that firing of grid cells was almost indistinguishable, in pattern or rate, from that on the horizontal surface, with if anything increased coverage and field number, and preserved field size. It thus appears unlikely that the sloping surface transected a lattice. However, grid cells on the slope displayed slightly degraded firing patterns, with reduced coherence and slightly reduced symmetry. These findings collectively suggest that the grid cell component of the metric representation of space is not fixed in absolute 3D space but is influenced both by the surface the animal is on and by the relationship of this surface to the horizontal, supporting the hypothesis that the neural map of space is “multi-planar” rather than fully volumetric. PMID:26236245

Molecular transformers in the cell: lessons learned from the DegP protease-chaperone.

PubMed

Sawa, Justyna; Heuck, Alexander; Ehrmann, Michael; Clausen, Tim

2010-04-01

Structure-function analysis of DegP revealed a novel mechanism for protease and chaperone regulation. Binding of unfolded proteins induces the oligomer reassembly from the resting hexamer (DegP6) into the functional protease-chaperone DegP12/24. The newly formed cage exhibits the characteristics of a proteolytic folding chamber, shredding those proteins that are severely misfolded while stabilizing and protecting proteins present in their native state. Isolation of native DegP complexes with folded outer membrane proteins (OMPs) highlights the importance of DegP in OMP biogenesis. The encapsulated OMP beta-barrel is significantly stabilized in the hydrophobic chamber of DegP12/24 and thus DegP seems to employ a reciprocal mechanism to those chaperones assisting the folding of water soluble proteins via polar interactions. In addition, we discuss in this review similarities to other complex proteolytic machines that, like DegP, are under control of a substrate-induced or stress-induced oligomer conversion.

Three-dimensional hybrid grid generation using advancing front techniques

NASA Technical Reports Server (NTRS)

Steinbrenner, John P.; Noack, Ralph W.

1995-01-01

A new 3-dimensional hybrid grid generation technique has been developed, based on ideas of advancing fronts for both structured and unstructured grids. In this approach, structured grids are first generate independently around individual components of the geometry. Fronts are initialized on these structure grids, and advanced outward so that new cells are extracted directly from the structured grids. Employing typical advancing front techniques, cells are rejected if they intersect the existing front or fail other criteria When no more viable structured cells exist further cells are advanced in an unstructured manner to close off the overall domain, resulting in a grid of 'hybrid' form. There are two primary advantages to the hybrid formulation. First, generating blocks with limited regard to topology eliminates the bottleneck encountered when a multiple block system is used to fully encapsulate a domain. Individual blocks may be generated free of external constraints, which will significantly reduce the generation time. Secondly, grid points near the body (presumably with high aspect ratio) will still maintain a structured (non-triangular or tetrahedral) character, thereby maximizing grid quality and solution accuracy near the surface.

Unstructured viscous grid generation by advancing-front method

NASA Technical Reports Server (NTRS)

Pirzadeh, Shahyar

1993-01-01

A new method of generating unstructured triangular/tetrahedral grids with high-aspect-ratio cells is proposed. The method is based on new grid-marching strategy referred to as 'advancing-layers' for construction of highly stretched cells in the boundary layer and the conventional advancing-front technique for generation of regular, equilateral cells in the inviscid-flow region. Unlike the existing semi-structured viscous grid generation techniques, the new procedure relies on a totally unstructured advancing-front grid strategy resulting in a substantially enhanced grid flexibility and efficiency. The method is conceptually simple but powerful, capable of producing high quality viscous grids for complex configurations with ease. A number of two-dimensional, triangular grids are presented to demonstrate the methodology. The basic elements of the method, however, have been primarily designed with three-dimensional problems in mind, making it extendible for tetrahedral, viscous grid generation.

OxfordGrid: a web interface for pairwise comparative map views.

PubMed

Yang, Hongyu; Gingle, Alan R

2005-12-01

OxfordGrid is a web application and database schema for storing and interactively displaying genetic map data in a comparative, dot-plot, fashion. Its display is composed of a matrix of cells, each representing a pairwise comparison of mapped probe data for two linkage groups or chromosomes. These are arranged along the axes with one forming grid columns and the other grid rows with the degree and pattern of synteny/colinearity between the two linkage groups manifested in the cell's dot density and structure. A mouse click over the selected grid cell launches an image map-based display for the selected cell. Both individual and linear groups of mapped probes can be selected and displayed. Also, configurable links can be used to access other web resources for mapped probe information. OxfordGrid is implemented in C#/ASP.NET and the package, including MySQL schema creation scripts, is available at ftp://cggc.agtec.uga.edu/OxfordGrid/.

Generation of a composite grid for turbine flows and consideration of a numerical scheme

NASA Technical Reports Server (NTRS)

Choo, Y.; Yoon, S.; Reno, C.

1986-01-01

A composite grid was generated for flows in turbines. It consisted of the C-grid (or O-grid) in the immediate vicinity of the blade and the H-grid in the middle of the blade passage between the C-grids and in the upstream region. This new composite grid provides better smoothness, resolution, and orthogonality than any single grid for a typical turbine blade with a large camber and rounded leading and trailing edges. The C-H (or O-H) composite grid has an unusual grid point that is connected to more than four neighboring nodes in two dimensions (more than six neighboring nodes in three dimensions). A finite-volume lower-upper (LU) implicit scheme to be used on this grid poses no problem and requires no special treatment because each interior cell of this composite grid has only four neighboring cells in two dimensions (six cells in three dimensions). The LU implicit scheme was demonstrated to be efficient and robust for external flows in a broad flow regime and can be easily applied to internal flows and extended from two to three dimensions.

Environmental tests of metallization systems for terrestrial photovoltaic cells

NASA Technical Reports Server (NTRS)

Alexander, P., Jr.

1985-01-01

Seven different solar cell metallization systems were subjected to temperature cycling tests and humidity tests. Temperature cycling excursions were -50 deg C to 150 deg C per cycle. Humidity conditions were 70 deg C at 98% relative humidity. The seven metallization systems were: Ti/Ag, Ti/Pd/Ag, Ti/Pd/Cu, Ni/Cu, Pd/Ni/Solder, Cr/Pd/Ag, and thick film Ag. All metallization systems showed a slight to moderate decrease in cell efficiencies after subjection to 1000 temperature cycles. Six of the seven metallization systems also evidenced slight increases in cell efficiencies after moderate numbers of cycles, generally less than 100 cycles. The copper based systems showed the largest decrease in cell efficiencies after temperature cycling. All metallization systems showed moderate to large decreases in cell efficiencies after 123 days of humidity exposure. The copper based systems again showed the largest decrease in cell efficiencies after humidity exposure. Graphs of the environmental exposures versus cell efficiencies are presented for each metallization system, as well as environmental exposures versus fill factors or series resistance.

Framing of grid cells within and beyond navigation boundaries

PubMed Central

Savelli, Francesco; Luck, JD; Knierim, James J

2017-01-01

Grid cells represent an ideal candidate to investigate the allocentric determinants of the brain’s cognitive map. Most studies of grid cells emphasized the roles of geometric boundaries within the navigational range of the animal. Behaviors such as novel route-taking between local environments indicate the presence of additional inputs from remote cues beyond the navigational borders. To investigate these influences, we recorded grid cells as rats explored an open-field platform in a room with salient, remote cues. The platform was rotated or translated relative to the room frame of reference. Although the local, geometric frame of reference often exerted the strongest control over the grids, the remote cues demonstrated a consistent, sometimes dominant, countervailing influence. Thus, grid cells are controlled by both local geometric boundaries and remote spatial cues, consistent with prior studies of hippocampal place cells and providing a rich representational repertoire to support complex navigational (and perhaps mnemonic) processes. DOI: http://dx.doi.org/10.7554/eLife.21354.001 PMID:28084992

Welding interconnects to 50-micron silicon solar cells

NASA Technical Reports Server (NTRS)

Patterson, R. E.; Mesch, H. G.

1983-01-01

A program was conducted to develop technologies for welding interconnects to 50-micron thick, 2 by 2 cm solar cells obtained from three suppliers. The cells were characterized with respect to electrical performance, cell thickness, silver contact thickness, contact waviness, bowing, and fracture strength. Weld schedules were independently developed for each of the three cell types and were coincidentally identical. Thermal shock tests (100 cycles from 100 deg to -180 deg C) were performed on 16-cell coupons for each cell type without any weld joint failures or electrical degradation. Three 48-cell modules (one for each cell type) were assembled with 50-micron thick cells, frosted fused silica covers, silver clad Invar interconnectors, and Kapton substrates.

Refinement Of Hexahedral Cells In Euler Flow Computations

NASA Technical Reports Server (NTRS)

Melton, John E.; Cappuccio, Gelsomina; Thomas, Scott D.

1996-01-01

Topologically Independent Grid, Euler Refinement (TIGER) computer program solves Euler equations of three-dimensional, unsteady flow of inviscid, compressible fluid by numerical integration on unstructured hexahedral coordinate grid refined where necessary to resolve shocks and other details. Hexahedral cells subdivided, each into eight smaller cells, as needed to refine computational grid in regions of high flow gradients. Grid Interactive Refinement and Flow-Field Examination (GIRAFFE) computer program written in conjunction with TIGER program to display computed flow-field data and to assist researcher in verifying specified boundary conditions and refining grid.

The Beauty and Complexity of the Brunt Ice Shelf from MOA and ICESat

NASA Technical Reports Server (NTRS)

Humbert, Angelika; Shuman, Christopher A.

2005-01-01

Beginning in February 2003, NASA's Ice, Cloud, and land Elevation Satellite (ICESat) has determined surface elevations from approx. 86degN to 86degS latitude. To date, altimetry data have been acquired in a series of observation periods in repeated track patterns using all three Geoscience Laser Altimeter System (GLAS) lasers. This paper will focus on ice shelf elevation data that were obtained in 2003 across the Brunt Ice Shelf and the Stancomb-Wills Ice Tongue. Integrating the altimetry with the recently available MODIS Mosaic of Antarctica (MOA), quantifies the relative accuracy and precision of the resulting ice shelf elevations. Furthermore, the elevation data was processed onto an elevation grid, by regional interpolation across the area s complex glacial features only. Ice thickness estimation from the altimetry of the floating ice is discussed. ICESat operates at 40Hz and its elevation data is obtained every 172m along track. These elevations have a relative accuracy of about 14cm based on the standard deviation of low-slope crossover differences and a precision of close to 2cm for the Laser 2a, Release 21, GLA12 data used here.

Heat Transfer Measurements and Predictions on a Power Generation Gas Turbine Blade

NASA Technical Reports Server (NTRS)

Giel, Paul W.; Bunker, Ronald S.; VanFossen, G. James; Boyle, Robert J.

2000-01-01

Detailed heat transfer measurements and predictions are given for a power generation turbine rotor with 129 deg of nominal turning and an axial chord of 137 mm. Data were obtained for a set of four exit Reynolds numbers comprised of the design point of 628,000, -20%, +20%, and +40%. Three ideal exit pressure ratios were examined including the design point of 1.378, -10%, and +10%. Inlet incidence angles of 0 deg and +/-2 deg were also examined. Measurements were made in a linear cascade with highly three-dimensional blade passage flows that resulted from the high flow turning and thick inlet boundary layers. Inlet turbulence was generated with a blown square bar grid. The purpose of the work is the extension of three-dimensional predictive modeling capability for airfoil external heat transfer to engine specific conditions including blade shape, Reynolds numbers, and Mach numbers. Data were obtained by a steady-state technique using a thin-foil heater wrapped around a low thermal conductivity blade. Surface temperatures were measured using calibrated liquid crystals. The results show the effects of strong secondary vortical flows, laminar-to-turbulent transition, and also show good detail in the stagnation region.

Short-circuit current improvement in thin cells with a gridded back contact

NASA Technical Reports Server (NTRS)

Giuliano, M.; Wohlgemuth, J.

1980-01-01

The use of gridded back contact on thin silicon solar cells 50 micrometers was investigated. An unexpected increase in short circuit current of almost 10 percent was experienced for 2 cm x 2 cm cells. Control cells with the standard continuous contact metallization were fabricated at the same time as the gridded back cells with all processes identical up to the formation of the back contact. The gridded back contact pattern was delineated by evaporation of Ti-Pd over a photo-resist mask applied to the back of the wafer; the Ti-Pd film on the controls was applied in the standard fashion in a continuous layer over the back of the cell. The Ti-Pd contacts were similarly applied to the front of the wafer, and the grid pattern on both sides of the cell was electroplated with 8-10 micrometers of silver.

Analysis of selective chopper radiometer data

NASA Technical Reports Server (NTRS)

Roe, J.; Hovland, D.; Wilcox, R.

1983-01-01

Data from SCR-B on Nimbus 5 have been processed to yield global, orbital temperatures at 10, 5, 2, 1, and 0.4 mb for the period January 1977 through April 1978 under the current task. In addition gridded values at 10 deg latitude by 20 deg longitude were prepared by space-time interpolation for the period January 1975 through April 1978. Temperature retrieval was based on regression of radiances against Meteorological Rocket Network data, with regressions recomputed at approximately six-month intervals. This data now completes a consistent time series from April 1970 to April 1978 for all available radiance data from SCR A and SCR B on Nimbus 4 and 5. The processing details for the current period are discussed, but is also applicable to the previous data periods. The accuracy of the temperature retrievals for each 6-month period for the entire eight years is given in the Appendices.

Production of long-term global water vapor and liquid water data set using ultra-fast methods to assimilate multi-satellite and radiosonde observations

NASA Technical Reports Server (NTRS)

Vonderhaar, Thomas H.; Randel, David L.; Reinke, Donald L.; Stephens, Graeme L.; Ringerud, Mark A.; Combs, Cynthia L.; Greenwald, Thomas J.; Wittmeyer, Ian L.

1994-01-01

In recent years climate research scientists have recognized the need for increased time and space resolution precipitable and liquid water data sets. This project is designed to meet those needs. Specifically, NASA is funding STC-METSAT to develop a total integrated column and layered precipitable water data set. This is complemented by a total column liquid water data set. These data are global in extent, 1 deg x 1 deg in resolution, with daily grids produced. Precipitable water is measured by a combination of in situ radiosonde observations and satellite derived infrared and microwave retrievals from four satellites. This project combines these data into a coherent merged product for use in global climate research. This report is the Year 2 Annual Report from this NASA-sponsored project and includes progress-to-date on the assigned tasks.

Planar ion trap (retarding potential analyzer) experiment for atmosphere explorer

NASA Technical Reports Server (NTRS)

Hanson, W. B.; Sanatani, S.; Lippincott, C. R.; Zuccaro, D. R.

1982-01-01

The retarding potential analyzer and drift meter were carried aboard all three Atmosphere Explorer spacecraft. These instruments measure the total thermal ion concentration and temperature, the bulk thermal ion velocity vector and some limited properties of the relative abundance of H(+), He(+), O(+) and molecular ions. These instruments functioned with no internal failures on all the spacecraft. On AE-E there existed some evidence for external surface contamination that damaged the integrity of the RPA sweep grids. This led to some difficulties in data reduction and interpretation that did not prove to be a disastrous problem. The AE-D spacecraft functioned for only a few months before it re-entered. During this time the satellite suffered from a nutation about the spin axis of about + or - 2 deg. This 2 deg modulation was superimposed upon the ion drift meter horizontal ion arrival angle output requiring the employment of filtering techniques to retrieve the real data.

Flight summaries and temperature climatology at airliner cruise altitudes from GASP (Global Atmospheric Sampling Program) data

NASA Technical Reports Server (NTRS)

Nastrom, G. D.; Jasperson, W. H.

1983-01-01

Temperature data obtained by the Global Atmospheric Sampling Program (GASP) during the period March 1975 to July 1979 are compiled to form flight summaries of static air temperature and a geographic temperature climatology. The flight summaries include the height and location of the coldest observed temperature and the mean flight level, temperature and the standard deviation of temperature for each flight as well as for flight segments. These summaries are ordered by route and month. The temperature climatology was computed for all statistically independent temperture data for each flight. The grid used consists of 5 deg latitude, 30 deg longitude and 2000 feet vertical resolution from FL270 to FL430 for each month of the year. The number of statistically independent observations, their mean, standard deviation and the empirical 98, 50, 16, 2 and .3 probability percentiles are presented.

Sexy DEG/ENaC channels involved in gustatory detection of fruit fly pheromones.

PubMed

Pikielny, Claudio W

2012-11-06

Hydrocarbon pheromones on the cuticle of Drosophila melanogaster modulate the complex courtship behavior of males. Recently, three members of the degenerin/epithelial Na+ channel (DEG/ENaC) family of sodium channel subunits, Ppk25, Ppk23, and Ppk29 (also known as Nope), have been shown to function in gustatory perception of courtship-modulating contact pheromones. All three proteins are required for the activation of male courtship by female pheromones. Specific interactions between two of them have been demonstrated in cultured cells, suggesting that, in a subset of cells where they are coexpressed, these three subunits function within a common heterotrimeric DEG/ENaC channel. Such a DEG/ENaC channel may be gated by pheromones, either directly or indirectly, or alternatively may control the excitability of pheromone-sensing cells. In addition, these studies identify taste neurons that respond specifically to courtship-modulating pheromones and mediate their effects on male behavior. Two types of pheromone-sensing taste neurons, F and M cells, have been defined on the basis of their specific response to either female or male pheromones. These reports set the stage for the dissection of the molecular and cellular mechanisms that mediate gustatory detection of contact pheromones.

Linear Look-Ahead in Conjunctive Cells: An Entorhinal Mechanism for Vector-Based Navigation

PubMed Central

Kubie, John L.; Fenton, André A.

2012-01-01

The crisp organization of the “firing bumps” of entorhinal grid cells and conjunctive cells leads to the notion that the entorhinal cortex may compute linear navigation routes. Specifically, we propose a process, termed “linear look-ahead,” by which a stationary animal could compute a series of locations in the direction it is facing. We speculate that this computation could be achieved through learned patterns of connection strengths among entorhinal neurons. This paper has three sections. First, we describe the minimal grid cell properties that will be built into our network. Specifically, the network relies on “rigid modules” of neurons, where all members have identical grid scale and orientation, but differ in spatial phase. Additionally, these neurons must be densely interconnected with synapses that are modifiable early in the animal’s life. Second, we investigate whether plasticity during short bouts of locomotion could induce patterns of connections amongst grid cells or conjunctive cells. Finally, we run a simulation to test whether the learned connection patterns can exhibit linear look-ahead. Our results are straightforward. A simulated 30-min walk produces weak strengthening of synapses between grid cells that do not support linear look-ahead. Similar training in a conjunctive cell module produces a small subset of very strong connections between cells. These strong pairs have three properties: the pre- and post-synaptic cells have similar heading direction. The cell pairs have neighboring grid bumps. Finally, the spatial offset of firing bumps of the cell pair is in the direction of the common heading preference. Such a module can produce strong and accurate linear look-ahead starting in any location and extending in any direction. We speculate that this process may: (1) compute linear paths to goals; (2) update grid cell firing during navigation; and (3) stabilize the rigid modules of grid cells and conjunctive cells. PMID:22557948

Transcriptomic meta-analysis identifies gene expression characteristics in various samples of HIV-infected patients with nonprogressive disease.

PubMed

Zhang, Le-Le; Zhang, Zi-Ning; Wu, Xian; Jiang, Yong-Jun; Fu, Ya-Jing; Shang, Hong

2017-09-12

A small proportion of HIV-infected patients remain clinically and/or immunologically stable for years, including elite controllers (ECs) who have undetectable viremia (<50 copies/ml) and long-term nonprogressors (LTNPs) who maintain normal CD4 + T cell counts for prolonged periods (>10 years). However, the mechanism of nonprogression needs to be further resolved. In this study, a transcriptome meta-analysis was performed on nonprogressor and progressor microarray data to identify differential transcriptome pathways and potential biomarkers. Using the INMEX (integrative meta-analysis of expression data) program, we performed the meta-analysis to identify consistently differentially expressed genes (DEGs) in nonprogressors and further performed functional interpretation (gene ontology analysis and pathway analysis) of the DEGs identified in the meta-analysis. Five microarray datasets (81 cases and 98 controls in total), including whole blood, CD4 + and CD8 + T cells, were collected for meta-analysis. We determined that nonprogressors have reduced expression of important interferon-stimulated genes (ISGs), CD38, lymphocyte activation gene 3 (LAG-3) in whole blood, CD4 + and CD8 + T cells. Gene ontology (GO) analysis showed a significant enrichment in DEGs that function in the type I interferon signaling pathway. Upregulated pathways, including the PI3K-Akt signaling pathway in whole blood, cytokine-cytokine receptor interaction in CD4 + T cells and the MAPK signaling pathway in CD8 + T cells, were identified in nonprogressors compared with progressors. In each metabolic functional category, the number of downregulated DEGs was more than the upregulated DEGs, and almost all genes were downregulated DEGs in the oxidative phosphorylation (OXPHOS) and tricarboxylic acid (TCA) cycle in the three types of samples. Our transcriptomic meta-analysis provides a comprehensive evaluation of the gene expression profiles in major blood types of nonprogressors, providing new insights in the understanding of HIV pathogenesis and developing strategies to delay HIV disease progression.

Downscaling GISS ModelE Boreal Summer Climate over Africa

NASA Technical Reports Server (NTRS)

Druyan, Leonard M.; Fulakeza, Matthew

2015-01-01

The study examines the perceived added value of downscaling atmosphere-ocean global climate model simulations over Africa and adjacent oceans by a nested regional climate model. NASA/Goddard Institute for Space Studies (GISS) coupled ModelE simulations for June- September 1998-2002 are used to form lateral boundary conditions for synchronous simulations by the GISS RM3 regional climate model. The ModelE computational grid spacing is 2deg latitude by 2.5deg longitude and the RM3 grid spacing is 0.44deg. ModelE precipitation climatology for June-September 1998-2002 is shown to be a good proxy for 30-year means so results based on the 5-year sample are presumed to be generally representative. Comparison with observational evidence shows several discrepancies in ModelE configuration of the boreal summer inter-tropical convergence zone (ITCZ). One glaring shortcoming is that ModelE simulations do not advance the West African rain band northward during the summer to represent monsoon precipitation onset over the Sahel. Results for 1998-2002 show that onset simulation is an important added value produced by downscaling with RM3. ModelE Eastern South Atlantic Ocean computed sea-surface temperatures (SST) are some 4 K warmer than reanalysis, contributing to large positive biases in overlying surface air temperatures (Tsfc). ModelE Tsfc are also too warm over most of Africa. RM3 downscaling somewhat mitigates the magnitude of Tsfc biases over the African continent, it eliminates the ModelE double ITCZ over the Atlantic and it produces more realistic orographic precipitation maxima. Parallel ModelE and RM3 simulations with observed SST forcing (in place of the predicted ocean) lower Tsfc errors but have mixed impacts on circulation and precipitation biases. Downscaling improvements of the meridional movement of the rain band over West Africa and the configuration of orographic precipitation maxima are realized irrespective of the SST biases.

SEASAT-A SASS wind processing

NASA Technical Reports Server (NTRS)

Langland, R. A.; Stephens, P. L.; Pihos, G. G.

1980-01-01

The techniques used for ingesting SEASAT-A SASS wind retrievals into the existing operational software are described. The intent is to assess the impact of SEASAT data in he marine wind fields produced by the global marine wind/sea level pressure analysis. This analysis is performed on a 21/2 deg latitude/longitude global grid which executes at three hourly time increments. Wind fields with and without SASS winds are being compared. The problems of data volume reduction and aliased wind retrieval ambiquity are treated.

Enhanced gamma-ray emission from the microquasar Cygnus X-3 detected by AGILE

NASA Astrophysics Data System (ADS)

Piano, G.; Pittori, C.; Verrecchia, F.; Tavani, M.; Bulgarelli, A.; Fioretti, V.; Zoli, A.; Munar-Adrover, P.; Lucarelli, F.; Donnarumma, I.; Vercellone, S.; Striani, E.; Cardillo, M.; Gianotti, F.; Trifoglio, M.; Giuliani, A.; Mereghetti, S.; Caraveo, P.; Perotti, F.; Chen, A.; Argan, A.; Costa, E.; Del Monte, E.; Evangelista, Y.; Feroci, M.; Lazzarotto, F.; Lapshov, I.; Pacciani, L.; Soffitta, P.; Sabatini, S.; Vittorini, V.; Pucella, G.; Rapisarda, M.; Di Cocco, G.; Fuschino, F.; Galli, M.; Labanti, C.; Marisaldi, M.; Pellizzoni, A.; Pilia, M.; Trois, A.; Barbiellini, G.; Vallazza, E.; Longo, F.; Morselli, A.; Picozza, P.; Prest, M.; Lipari, P.; Zanello, D.; Cattaneo, P. W.; Rappoldi, A.; Colafrancesco, S.; Parmiggiani, N.; Ferrari, A.; Antonelli, A.; Giommi, P.; Salotti, L.; Valentini, G.; D'Amico, F.

2016-04-01

Integrating from 2016-04-16 00:00 UT to 2016-04-19 00:00 UT, the AGILE-GRID detector is revealing gamma-ray emission above 100 MeV from a source positionally consistent with Cygnus X-3 at Galactic coordinates (l, b) = (79.4, 0.2) +/- 0.6 (stat.) +/- 0.1 (syst.) deg, with flux F( > 100 MeV) = (2.0 +/- 0.8) x 10^-6 photons/cm^2/s, as determined by a multi-source likelihood analysis.

Direct CFD Predictions of Low Frequency Sounds Generated by a Helicopter Main Rotor

DTIC Science & Technology

2010-05-01

modeling and grid constraints. NOTATION α Shaft tilt (corrected) or tip-path-plane angle BPF Blade passing frequency CT/σ Thrust coefficient to rotor...cyclic pitch angle, deg. LFSPL Low frequency sound metric (1st-6th BPF ), dB MFSPL Mid frequency sound metric (> 6th BPF ), dB OASPL Overall sound metric...Tunnel of the National Full- Scale Aerodynamic Complex (NFAC) at NASA Ames Research Center in 2008 (Fig. 2a), as a guide for prediction validation. The

Grid Fin Stabilization of the Orion Launch Abort Vehicle

NASA Technical Reports Server (NTRS)

Pruzan, Daniel A.; Mendenhall, Michael R.; Rose, William C.; Schuster, David M.

2011-01-01

Wind tunnel tests were conducted by Nielsen Engineering & Research (NEAR) and Rose Engineering & Research (REAR) in conjunction with the NASA Engineering & Safety Center (NESC) on a 6%-scale model of the Orion launch abort vehicle (LAV) configured with four grid fins mounted near the base of the vehicle. The objectives of these tests were to 1) quantify LAV stability augmentation provided by the grid fins from subsonic through supersonic Mach numbers, 2) assess the benefits of swept grid fins versus unswept grid fins on the LAV, 3) determine the effects of the LAV abort motors on grid fin aerodynamics, and 4) generate an aerodynamic database for use in the future application of grid fins to small length-to-diameter ratio vehicles similar to the LAV. The tests were conducted in NASA Ames Research Center's 11x11-foot transonic wind tunnel from Mach 0.5 through Mach 1.3 and in their 9x7-foot supersonic wind tunnel from Mach 1.6 through Mach 2.5. Force- and moment-coefficient data were collected for the complete vehicle and for each individual grid fin as a function of angle of attack and sideslip angle. Tests were conducted with both swept and unswept grid fins with the simulated abort motors (cold jets) off and on. The swept grid fins were designed with a 22.5deg aft sweep angle for both the frame and the internal lattice so that the frontal projection of the swept fins was the same as for the unswept fins. Data from these tests indicate that both unswept and swept grid fins provide significant improvements in pitch stability as compared to the baseline vehicle over the Mach number range investigated. The swept fins typically provide improved stability as compared to the unswept fins, but the performance gap diminished as Mach number was increased. The aerodynamic performance of the fins was not observed to degrade when the abort motors were turned on. Results from these tests indicate that grid fins can be a robust solution for stabilizing the Orion LAV over a wide range of operating conditions.

High resolution Fourier interferometer-spectrophotopolarimeter

NASA Technical Reports Server (NTRS)

Fymat, A. L. (Inventor)

1976-01-01

A high-resolution Fourier interferometer-spectrophotopolarimeter is provided using a single linear polarizer-analyzer the transmission axis azimuth of which is positioned successively in the three orientations of 0 deg, 45 deg, and 90 deg, in front of a detector; four flat mirrors, three of which are switchable to either of two positions to direct an incoming beam from an interferometer to the polarizer-analyzer around a sample cell transmitted through a medium in a cell and reflected by medium in the cell; and four fixed focussing lenses, all located in a sample chamber attached at the exit side of the interferometer. This arrangement can provide the distribution of energy and complete polarization state across the spectrum of the reference light entering from the interferometer; the same light after a fixed-angle reflection from the sample cell containing a medium to be analyzed; and the same light after direct transmission through the same sample cell, with the spectral resolution provided by the interferometer.

Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post-chemotherapy tissues.

PubMed

Tong, Mengsha; Zheng, Weicheng; Lu, Xingrong; Ao, Lu; Li, Xiangyu; Guan, Qingzhou; Cai, Hao; Li, Mengyao; Yan, Haidan; Guo, You; Chi, Pan; Guo, Zheng

2015-12-01

Until recently, few molecular signatures of drug resistance identified in drug-induced resistant cancer cell models can be translated into clinical practice. Here, we defined differentially expressed genes (DEGs) between pre-chemotherapy colorectal cancer (CRC) tissue samples of non-responders and responders for 5-fluorouracil and oxaliplatin-based therapy as clinically relevant drug resistance genes (CRG5-FU/L-OHP). Taking CRG5-FU/L-OHP as reference, we evaluated the clinical relevance of several types of genes derived from HCT116 CRC cells with resistance to 5-fluorouracil and oxaliplatin, respectively. The results revealed that DEGs between parental and resistant cells, when both were treated with the corresponding drug for a certain time, were significantly consistent with the CRG5-FU/L-OHP as well as the DEGs between the post-chemotherapy CRC specimens of responders and non-responders. This study suggests a novel strategy to extract clinically relevant drug resistance genes from both drug-induced resistant cell models and post-chemotherapy cancer tissue specimens.

From grid cells to place cells with realistic field sizes

PubMed Central

2017-01-01

While grid cells in the medial entorhinal cortex (MEC) of rodents have multiple, regularly arranged firing fields, place cells in the cornu ammonis (CA) regions of the hippocampus mostly have single spatial firing fields. Since there are extensive projections from MEC to the CA regions, many models have suggested that a feedforward network can transform grid cell firing into robust place cell firing. However, these models generate place fields that are consistently too small compared to those recorded in experiments. Here, we argue that it is implausible that grid cell activity alone can be transformed into place cells with robust place fields of realistic size in a feedforward network. We propose two solutions to this problem. Firstly, weakly spatially modulated cells, which are abundant throughout EC, provide input to downstream place cells along with grid cells. This simple model reproduces many place cell characteristics as well as results from lesion studies. Secondly, the recurrent connections between place cells in the CA3 network generate robust and realistic place fields. Both mechanisms could work in parallel in the hippocampal formation and this redundancy might account for the robustness of place cell responses to a range of disruptions of the hippocampal circuitry. PMID:28750005

Development of the Orion Crew Module Static Aerodynamic Database. Part 1; Hypersonic

NASA Technical Reports Server (NTRS)

Bibb, Karen L.; Walker, Eric L.; Robinson, Philip E.

2011-01-01

The Orion aerodynamic database provides force and moment coefficients given the velocity, attitude, configuration, etc. of the Crew Exploration Vehicle (CEV). The database is developed and maintained by the NASA CEV Aerosciences Project team from computational and experimental aerodynamic simulations. The database is used primarily by the Guidance, Navigation, and Control (GNC) team to design vehicle trajectories and assess flight performance. The initial hypersonic re-entry portion of the Crew Module (CM) database was developed in 2006. Updates incorporating additional data and improvements to the database formulation and uncertainty methodologies have been made since then. This paper details the process used to develop the CM database, including nominal values and uncertainties, for Mach numbers greater than 8 and angles of attack between 140deg and 180deg. The primary available data are more than 1000 viscous, reacting gas chemistry computational simulations using both the Laura and Dplr codes, over a range of Mach numbers from 2 to 37 and a range of angles of attack from 147deg to 172deg. Uncertainties were based on grid convergence, laminar-turbulent solution variations, combined altitude and code-to-code variations, and expected heatshield asymmetry. A radial basis function response surface tool, NEAR-RS, was used to fit the coefficient data smoothly in a velocity-angle-of-attack space. The resulting database is presented and includes some data comparisons and a discussion of the predicted variation of trim angle of attack and lift-to-drag ratio. The database provides a variation in trim angle of attack on the order of +/-2deg, and a range in lift-to-drag ratio of +/-0.035 for typical vehicle flight conditions.

On-site fuel cell field test support program

NASA Astrophysics Data System (ADS)

Staniunas, J. W.; Merten, G. P.

1982-01-01

In order to assess the impact of grid connection on the potential market for fuel cell service, applications studies were conducted to identify the fuel cell operating modes and corresponding fuel cell sizing criteria which offer the most potential for initial commercial service. The market for grid-connected fuel cell service was quantified using United's market analysis program and computerized building data base. Electric and gas consumption data for 268 buildings was added to our surveyed building data file, bringing the total to 407 buildings. These buildings were analyzed for grid-isolated and grid-connected fuel cell service. The results of the analyses indicated that the nursing home, restaurant and health club building sectors offer significant potential for fuel cell service.

Getting the current out

NASA Astrophysics Data System (ADS)

Burger, D. R.

1983-11-01

Progress of a photovoltaic (PV) device from a research concept to a competitive power-generation source requires an increasing concern with current collection. The initial metallization focus is usually on contact resistance, since a good ohmic contact is desirable for accurate device characterization measurements. As the device grows in size, sheet resistance losses become important and a metal grid is usually added to reduce the effective sheet resistance. Later, as size and conversion efficiency continue to increase, grid-line resistance and cell shadowing must be considered simultaneously, because grid-line resistance is inversely related to total grid-line area and cell shadowing is directly related. A PV cell grid design must consider the five power-loss phenomena mentioned above: sheet resistance, contact resistance, grid resistance, bus-bar resistance and cell shadowing. Although cost, reliability and usage are important factors in deciding upon the best metallization system, this paper will focus only upon grid-line design and substrate material problems for flat-plate solar arrays.

Intrinsic electrophysiological properties of entorhinal cortex stellate cells and their contribution to grid cell firing fields

PubMed Central

Pastoll, Hugh; Ramsden, Helen L.; Nolan, Matthew F.

2012-01-01

The medial entorhinal cortex (MEC) is an increasingly important focus for investigation of mechanisms for spatial representation. Grid cells found in layer II of the MEC are likely to be stellate cells, which form a major projection to the dentate gyrus. Entorhinal stellate cells are distinguished by distinct intrinsic electrophysiological properties, but how these properties contribute to representation of space is not yet clear. Here, we review the ionic conductances, synaptic, and excitable properties of stellate cells, and examine their implications for models of grid firing fields. We discuss why existing data are inconsistent with models of grid fields that require stellate cells to generate periodic oscillations. An alternative possibility is that the intrinsic electrophysiological properties of stellate cells are tuned specifically to control integration of synaptic input. We highlight recent evidence that the dorsal-ventral organization of synaptic integration by stellate cells, through differences in currents mediated by HCN and leak potassium channels, influences the corresponding organization of grid fields. Because accurate cellular data will be important for distinguishing mechanisms for generation of grid fields, we introduce new data comparing properties measured with whole-cell and perforated patch-clamp recordings. We find that clustered patterns of action potential firing and the action potential after-hyperpolarization (AHP) are particularly sensitive to recording condition. Nevertheless, with both methods, these properties, resting membrane properties and resonance follow a dorsal-ventral organization. Further investigation of the molecular basis for synaptic integration by stellate cells will be important for understanding mechanisms for generation of grid fields. PMID:22536175

Transverse Injection into Subsonic Crossflow with Various Injector Orifice Geometries

NASA Technical Reports Server (NTRS)

Foster, Lancert E.; Zaman, Khairul B.

2010-01-01

Computational and experimental results are presented for a case study of single injectors employed in 90 deg transverse injection into a non-reacting subsonic flow. Different injector orifice shapes are used (including circular, square, diamond-shaped, and wide rectangular slot), all with constant cross-sectional area, to observe the effects of this variation on injector penetration and mixing. Whereas the circle, square, and diamond injector produce similar jet plumes, the wide rectangular slot produces a plume with less vertical penetration than the others. There is also some evidence that the diamond injector produces slightly faster penetration with less mixing of the injected fluid. In addition, a variety of rectangular injectors were analyzed, with varying length/width ratios. Both experimental and computational data show improved plume penetration with increased streamwise orifice length. 3-D Reynolds-Averaged Navier-Stokes (RANS) results are obtained for the various injector geometries using NCC (National Combustion Code) with the kappa-epsilon turbulence model in multi-species modes on an unstructured grid. Grid sensitivity results are also presented which indicate consistent qualitative trends in the injector performance comparisons with increasing grid refinement.

Efficient Unstructured Cartesian/Immersed-Boundary Method with Local Mesh Refinement to Simulate Flows in Complex 3D Geometries

NASA Astrophysics Data System (ADS)

de Zelicourt, Diane; Ge, Liang; Sotiropoulos, Fotis; Yoganathan, Ajit

2008-11-01

Image-guided computational fluid dynamics has recently gained attention as a tool for predicting the outcome of different surgical scenarios. Cartesian Immersed-Boundary methods constitute an attractive option to tackle the complexity of real-life anatomies. However, when such methods are applied to the branching, multi-vessel configurations typically encountered in cardiovascular anatomies the majority of the grid nodes of the background Cartesian mesh end up lying outside the computational domain, increasing the memory and computational overhead without enhancing the numerical resolution in the region of interest. To remedy this situation, the method presented here superimposes local mesh refinement onto an unstructured Cartesian grid formulation. A baseline unstructured Cartesian mesh is generated by eliminating all nodes that reside in the exterior of the flow domain from the grid structure, and is locally refined in the vicinity of the immersed-boundary. The potential of the method is demonstrated by carrying out systematic mesh refinement studies for internal flow problems ranging in complexity from a 90 deg pipe bend to an actual, patient-specific anatomy reconstructed from magnetic resonance.

Identification of downstream metastasis-associated target genes regulated by LSD1 in colon cancer cells.

PubMed

Chen, Jiang; Ding, Jie; Wang, Ziwei; Zhu, Jian; Wang, Xuejian; Du, Jiyi

2017-03-21

This study aims to identify downstream target genes regulated by lysine-specific demethylase 1 (LSD1) in colon cancer cells and investigate the molecular mechanisms of LSD1 influencing invasion and metastasis of colon cancer. We obtained the expression changes of downstream target genes regulated by small-interfering RNA-LSD1 and LSD1-overexpression via gene expression profiling in two human colon cancer cell lines. An Affymetrix Human Transcriptome Array 2.0 was used to identify differentially expressed genes (DEGs). We screened out LSD1-target gene associated with proliferation, metastasis, and invasion from DEGs via Gene Ontology and Pathway Studio. Subsequently, four key genes (CABYR, FOXF2, TLE4, and CDH1) were computationally predicted as metastasis-related LSD1-target genes. ChIp-PCR was applied after RT-PCR and Western blot validations to detect the occupancy of LSD1-target gene promoter-bound LSD1. A total of 3633 DEGs were significantly upregulated, and 4642 DEGs were downregulated in LSD1-silenced SW620 cells. A total of 4047 DEGs and 4240 DEGs were upregulated and downregulated in LSD1-overexpressed HT-29 cells, respectively. RT-PCR and Western blot validated the microarray analysis results. ChIP assay results demonstrated that LSD1 might be negative regulators for target genes CABYR and CDH1. The expression level of LSD1 is negatively correlated with mono- and dimethylation of histone H3 lysine4(H3K4) at LSD1- target gene promoter region. No significant mono-methylation and dimethylation of H3 lysine9 methylation was detected at the promoter region of CABYR and CDH1. LSD1- depletion contributed to the upregulation of CABYR and CDH1 through enhancing the dimethylation of H3K4 at the LSD1-target genes promoter. LSD1- overexpression mediated the downregulation of CABYR and CDH1expression through decreasing the mono- and dimethylation of H3K4 at LSD1-target gene promoter in colon cancer cells. CABYR and CDH1 might be potential LSD1-target genes in colon carcinogenesis.

An efficient coding theory for a dynamic trajectory predicts non-uniform allocation of entorhinal grid cells to modules.

PubMed

Mosheiff, Noga; Agmon, Haggai; Moriel, Avraham; Burak, Yoram

2017-06-01

Grid cells in the entorhinal cortex encode the position of an animal in its environment with spatially periodic tuning curves with different periodicities. Recent experiments established that these cells are functionally organized in discrete modules with uniform grid spacing. Here we develop a theory for efficient coding of position, which takes into account the temporal statistics of the animal's motion. The theory predicts a sharp decrease of module population sizes with grid spacing, in agreement with the trend seen in the experimental data. We identify a simple scheme for readout of the grid cell code by neural circuitry, that can match in accuracy the optimal Bayesian decoder. This readout scheme requires persistence over different timescales, depending on the grid cell module. Thus, we propose that the brain may employ an efficient representation of position which takes advantage of the spatiotemporal statistics of the encoded variable, in similarity to the principles that govern early sensory processing.

An efficient coding theory for a dynamic trajectory predicts non-uniform allocation of entorhinal grid cells to modules

PubMed Central

Mosheiff, Noga; Agmon, Haggai; Moriel, Avraham

2017-01-01

Grid cells in the entorhinal cortex encode the position of an animal in its environment with spatially periodic tuning curves with different periodicities. Recent experiments established that these cells are functionally organized in discrete modules with uniform grid spacing. Here we develop a theory for efficient coding of position, which takes into account the temporal statistics of the animal’s motion. The theory predicts a sharp decrease of module population sizes with grid spacing, in agreement with the trend seen in the experimental data. We identify a simple scheme for readout of the grid cell code by neural circuitry, that can match in accuracy the optimal Bayesian decoder. This readout scheme requires persistence over different timescales, depending on the grid cell module. Thus, we propose that the brain may employ an efficient representation of position which takes advantage of the spatiotemporal statistics of the encoded variable, in similarity to the principles that govern early sensory processing. PMID:28628647

The spatial distribution of two dimensional electron gas at the LaTiO3/KTaO3 interface

NASA Astrophysics Data System (ADS)

Song, Qi; Peng, Rui; Xu, Haichao; Feng, Donglai

2017-08-01

We report the photoemission spectroscopy studies on the newly discovered two dimensional electron gas (2DEG) system LaTiO3/KTaO3, whose interfacial carriers show much higher mobility than that in LaAlO3/SrTiO3 at room temperature, thus raising the application prospect of transition metal oxide-based 2DEG. By measuring the density of states at the Fermi energy (EF), we directly reveal the spatial distribution of the conducting electrons at the interface. The density of states near EF of the topmost LTO reaches the highest when LTO is 2-unit-cell thick, and diminishes at the 5th unit cell of LTO. We discussed the origin of such a spacial distribution of conducting electrons and its relation with 2DEG, and proposed two possible scenarios based on electrostatic relaxations and chemical reconstructions. These results offer experimental clues in understanding the characteristics and origin of the 2DEG, and also shed light on improving the performance of 2DEG.

The spatial distribution of two dimensional electron gas at the LaTiO3/KTaO3 interface.

PubMed

Song, Qi; Peng, Rui; Xu, Haichao; Feng, Donglai

2017-08-09

We report the photoemission spectroscopy studies on the newly discovered two dimensional electron gas (2DEG) system LaTiO 3 /KTaO 3 , whose interfacial carriers show much higher mobility than that in LaAlO 3 /SrTiO 3 at room temperature, thus raising the application prospect of transition metal oxide-based 2DEG. By measuring the density of states at the Fermi energy (E F ), we directly reveal the spatial distribution of the conducting electrons at the interface. The density of states near E F of the topmost LTO reaches the highest when LTO is 2-unit-cell thick, and diminishes at the 5th unit cell of LTO. We discussed the origin of such a spacial distribution of conducting electrons and its relation with 2DEG, and proposed two possible scenarios based on electrostatic relaxations and chemical reconstructions. These results offer experimental clues in understanding the characteristics and origin of the 2DEG, and also shed light on improving the performance of 2DEG.

Numerical generation of two-dimensional grids by the use of Poisson equations with grid control at boundaries

NASA Technical Reports Server (NTRS)

Sorenson, R. L.; Steger, J. L.

1980-01-01

A method for generating boundary-fitted, curvilinear, two dimensional grids by the use of the Poisson equations is presented. Grids of C-type and O-type were made about airfoils and other shapes, with circular, rectangular, cascade-type, and other outer boundary shapes. Both viscous and inviscid spacings were used. In all cases, two important types of grid control can be exercised at both inner and outer boundaries. First is arbitrary control of the distances between the boundaries and the adjacent lines of the same coordinate family, i.e., stand-off distances. Second is arbitrary control of the angles with which lines of the opposite coordinate family intersect the boundaries. Thus, both grid cell size (or aspect ratio) and grid cell skewness are controlled at boundaries. Reasonable cell size and shape are ensured even in cases wherein extreme boundary shapes would tend to cause skewness or poorly controlled grid spacing. An inherent feature of the Poisson equations is that lines in the interior of the grid smoothly connect the boundary points (the grid mapping functions are second order differentiable).

Large Scale Ice Water Path and 3-D Ice Water Content

DOE Data Explorer

Liu, Guosheng

2008-01-15

Cloud ice water concentration is one of the most important, yet poorly observed, cloud properties. Developing physical parameterizations used in general circulation models through single-column modeling is one of the key foci of the ARM program. In addition to the vertical profiles of temperature, water vapor and condensed water at the model grids, large-scale horizontal advective tendencies of these variables are also required as forcing terms in the single-column models. Observed horizontal advection of condensed water has not been available because the radar/lidar/radiometer observations at the ARM site are single-point measurement, therefore, do not provide horizontal distribution of condensed water. The intention of this product is to provide large-scale distribution of cloud ice water by merging available surface and satellite measurements. The satellite cloud ice water algorithm uses ARM ground-based measurements as baseline, produces datasets for 3-D cloud ice water distributions in a 10 deg x 10 deg area near ARM site. The approach of the study is to expand a (surface) point measurement to an (satellite) areal measurement. That is, this study takes the advantage of the high quality cloud measurements at the point of ARM site. We use the cloud characteristics derived from the point measurement to guide/constrain satellite retrieval, then use the satellite algorithm to derive the cloud ice water distributions within an area, i.e., 10 deg x 10 deg centered at ARM site.

An optimized top contact design for solar cell concentrators

NASA Technical Reports Server (NTRS)

Desalvo, Gregory C.; Barnett, Allen M.

1985-01-01

A new grid optimization scheme is developed for point focus solar cell concentrators which employs a separated grid and busbar concept. Ideally, grid lines act as the primary current collectors and receive all of the current from the semiconductor region. Busbars are the secondary collectors which pick up current from the grids and carry it out of the active region of the solar cell. This separation of functions leads to a multithickness metallization design, where the busbars are made larger in cross section than the grids. This enables the busbars to carry more current per unit area of shading, which is advantageous under high solar concentration where large current densities are generated. Optimized grid patterns using this multilayer concept can provide a 1.6 to 20 percent increase in output power efficiency over optimized single thickness grids.

Vector-based navigation using grid-like representations in artificial agents.

PubMed

Banino, Andrea; Barry, Caswell; Uria, Benigno; Blundell, Charles; Lillicrap, Timothy; Mirowski, Piotr; Pritzel, Alexander; Chadwick, Martin J; Degris, Thomas; Modayil, Joseph; Wayne, Greg; Soyer, Hubert; Viola, Fabio; Zhang, Brian; Goroshin, Ross; Rabinowitz, Neil; Pascanu, Razvan; Beattie, Charlie; Petersen, Stig; Sadik, Amir; Gaffney, Stephen; King, Helen; Kavukcuoglu, Koray; Hassabis, Demis; Hadsell, Raia; Kumaran, Dharshan

2018-05-01

Deep neural networks have achieved impressive successes in fields ranging from object recognition to complex games such as Go 1,2 . Navigation, however, remains a substantial challenge for artificial agents, with deep neural networks trained by reinforcement learning 3-5 failing to rival the proficiency of mammalian spatial behaviour, which is underpinned by grid cells in the entorhinal cortex 6 . Grid cells are thought to provide a multi-scale periodic representation that functions as a metric for coding space 7,8 and is critical for integrating self-motion (path integration) 6,7,9 and planning direct trajectories to goals (vector-based navigation) 7,10,11 . Here we set out to leverage the computational functions of grid cells to develop a deep reinforcement learning agent with mammal-like navigational abilities. We first trained a recurrent network to perform path integration, leading to the emergence of representations resembling grid cells, as well as other entorhinal cell types 12 . We then showed that this representation provided an effective basis for an agent to locate goals in challenging, unfamiliar, and changeable environments-optimizing the primary objective of navigation through deep reinforcement learning. The performance of agents endowed with grid-like representations surpassed that of an expert human and comparison agents, with the metric quantities necessary for vector-based navigation derived from grid-like units within the network. Furthermore, grid-like representations enabled agents to conduct shortcut behaviours reminiscent of those performed by mammals. Our findings show that emergent grid-like representations furnish agents with a Euclidean spatial metric and associated vector operations, providing a foundation for proficient navigation. As such, our results support neuroscientific theories that see grid cells as critical for vector-based navigation 7,10,11 , demonstrating that the latter can be combined with path-based strategies to support navigation in challenging environments.

Use of upscaled elevation and surface roughness data in two-dimensional surface water models

USGS Publications Warehouse

Hughes, J.D.; Decker, J.D.; Langevin, C.D.

2011-01-01

In this paper, we present an approach that uses a combination of cell-block- and cell-face-averaging of high-resolution cell elevation and roughness data to upscale hydraulic parameters and accurately simulate surface water flow in relatively low-resolution numerical models. The method developed allows channelized features that preferentially connect large-scale grid cells at cell interfaces to be represented in models where these features are significantly smaller than the selected grid size. The developed upscaling approach has been implemented in a two-dimensional finite difference model that solves a diffusive wave approximation of the depth-integrated shallow surface water equations using preconditioned Newton–Krylov methods. Computational results are presented to show the effectiveness of the mixed cell-block and cell-face averaging upscaling approach in maintaining model accuracy, reducing model run-times, and how decreased grid resolution affects errors. Application examples demonstrate that sub-grid roughness coefficient variations have a larger effect on simulated error than sub-grid elevation variations.

Grid cell hexagonal patterns formed by fast self-organized learning within entorhinal cortex.

PubMed

Mhatre, Himanshu; Gorchetchnikov, Anatoli; Grossberg, Stephen

2012-02-01

Grid cells in the dorsal segment of the medial entorhinal cortex (dMEC) show remarkable hexagonal activity patterns, at multiple spatial scales, during spatial navigation. It has previously been shown how a self-organizing map can convert firing patterns across entorhinal grid cells into hippocampal place cells that are capable of representing much larger spatial scales. Can grid cell firing fields also arise during navigation through learning within a self-organizing map? This article describes a simple and general mathematical property of the trigonometry of spatial navigation which favors hexagonal patterns. The article also develops a neural model that can learn to exploit this trigonometric relationship. This GRIDSmap self-organizing map model converts path integration signals into hexagonal grid cell patterns of multiple scales. GRIDSmap creates only grid cell firing patterns with the observed hexagonal structure, predicts how these hexagonal patterns can be learned from experience, and can process biologically plausible neural input and output signals during navigation. These results support an emerging unified computational framework based on a hierarchy of self-organizing maps for explaining how entorhinal-hippocampal interactions support spatial navigation. Copyright © 2010 Wiley Periodicals, Inc.

Psoriatic T cells reduce epidermal turnover time and affect cell proliferation contributed from differential gene expression.

PubMed

Li, Junqin; Li, Xinhua; Hou, Ruixia; Liu, Ruifeng; Zhao, Xincheng; Dong, Feng; Wang, Chunfang; Yin, Guohua; Zhang, Kaiming

2015-09-01

Psoriasis is mediated primarily by T cells, which reduce epidermal turnover time and affect keratinocyte proliferation. We aimed to identify differentially expressed genes (DEG) in T cells from normal, five pairs of monozygotic twins concordant or discordant for psoriasis, to determine whether these DEG may account for the influence to epidermal turnover time and keratinocyte proliferation. The impact of T cells on keratinocyte proliferation and epidermal turnover time were investigated separately by immunohistochemistry and cultured with (3) H-TdR. mRNA expression patterns were investigated by RNA sequencing and verified by real-time reverse transcription polymerase chain reaction. After co-culture with psoriatic T cells, the expression of Ki-67, c-Myc and p53 increased, while expression of Bcl-2 and epidermal turnover time decreased. There were 14 DEG which were found to participate in the regulation of cell proliferation or differentiation. Psoriatic T cells exhibited the ability to decrease epidermal turnover time and affect keratinocyte proliferation because of the differential expression of PPIL1, HSPH1, SENP3, NUP54, FABP5, PLEKHG3, SLC9A9 and CHCHD4. © 2015 Japanese Dermatological Association.

Identification of the Key Genes and Pathways in Esophageal Carcinoma.

PubMed

Su, Peng; Wen, Shiwang; Zhang, Yuefeng; Li, Yong; Xu, Yanzhao; Zhu, Yonggang; Lv, Huilai; Zhang, Fan; Wang, Mingbo; Tian, Ziqiang

2016-01-01

Objective . Esophageal carcinoma (EC) is a frequently common malignancy of gastrointestinal cancer in the world. This study aims to screen key genes and pathways in EC and elucidate the mechanism of it. Methods . 5 microarray datasets of EC were downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) were screened by bioinformatics analysis. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network construction were performed to obtain the biological roles of DEGs in EC. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the expression level of DEGs in EC. Results . A total of 1955 genes were filtered as DEGs in EC. The upregulated genes were significantly enriched in cell cycle and the downregulated genes significantly enriched in Endocytosis. PPI network displayed CDK4 and CCT3 were hub proteins in the network. The expression level of 8 dysregulated DEGs including CDK4, CCT3, THSD4, SIM2, MYBL2, CENPF, CDCA3, and CDKN3 was validated in EC compared to adjacent nontumor tissues and the results were matched with the microarray analysis. Conclusion . The significantly DEGs including CDK4, CCT3, THSD4, and SIM2 may play key roles in tumorigenesis and development of EC involved in cell cycle and Endocytosis.

Flow cytometry of human embryonic kidney cells: A light scattering approach

NASA Technical Reports Server (NTRS)

Kunze, M. E.; Goolsby, C. L.; Todd, P. W.; Morrison, D. R.; Lewis, M. L.

1985-01-01

The mammalian kidney contains cells that transport water, convert vitamin D to active forms, synthesize hormones such a renin and erythropoietin, and produce enzymes such as urokinase, a plasminogen activator. Several of these functions are maintained by human embryonic kidney cells (HEK) cultivated in vitro. Biochemical study of these functions in their individual cell types in vitro requires purified populations of cells. Light-scattering activated cell sorting (LACS) was explored as a means of achieving such purifications. It was found that HEK cells at the first 1 to 5 passages in culture were heterogeneous with respect to 2-parameter light scattering intensity distribution, in which combined measurements included forward angle scattering (2.5 to 19 deg), 90 deg scattering, and time-of-flight size measurements. Size was measured at a resolution of 0.15 microns/channel in 256 channels using pulse-height independent pulse-width measurements. Two-parameter distributions combining these measurements were obtained for HEK cell subpopulations that had been purified by microgravity electrophoresis and subsequently propagated in culture. These distributions contained at least 3 subpopulations in all purified fractions, and results of experiments with prepurified cultured HEK cells indicated that subpopulations of living cells that were high in plasminogen-activator activity also contained the highest per cent of cells with high 90 deg light scatter intensity.

The identification of key genes and pathways in hepatocellular carcinoma by bioinformatics analysis of high-throughput data.

PubMed

Zhang, Chaoyang; Peng, Li; Zhang, Yaqin; Liu, Zhaoyang; Li, Wenling; Chen, Shilian; Li, Guancheng

2017-06-01

Liver cancer is a serious threat to public health and has fairly complicated pathogenesis. Therefore, the identification of key genes and pathways is of much importance for clarifying molecular mechanism of hepatocellular carcinoma (HCC) initiation and progression. HCC-associated gene expression dataset was downloaded from Gene Expression Omnibus database. Statistical software R was used for significance analysis of differentially expressed genes (DEGs) between liver cancer samples and normal samples. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, based on R software, were applied for the identification of pathways in which DEGs significantly enriched. Cytoscape software was for the construction of protein-protein interaction (PPI) network and module analysis to find the hub genes and key pathways. Finally, weighted correlation network analysis (WGCNA) was conducted to further screen critical gene modules with similar expression pattern and explore their biological significance. Significance analysis identified 1230 DEGs with fold change >2, including 632 significantly down-regulated DEGs and 598 significantly up-regulated DEGs. GO term enrichment analysis suggested that up-regulated DEG significantly enriched in immune response, cell adhesion, cell migration, type I interferon signaling pathway, and cell proliferation, and the down-regulated DEG mainly enriched in response to endoplasmic reticulum stress and endoplasmic reticulum unfolded protein response. KEGG pathway analysis found DEGs significantly enriched in five pathways including complement and coagulation cascades, focal adhesion, ECM-receptor interaction, antigen processing and presentation, and protein processing in endoplasmic reticulum. The top 10 hub genes in HCC were separately GMPS, ACACA, ALB, TGFB1, KRAS, ERBB2, BCL2, EGFR, STAT3, and CD8A, which resulted from PPI network. The top 3 gene interaction modules in PPI network enriched in immune response, organ development, and response to other organism, respectively. WGCNA revealed that the confirmed eight gene modules significantly enriched in monooxygenase and oxidoreductase activity, response to endoplasmic reticulum stress, type I interferon signaling pathway, processing, presentation and binding of peptide antigen, cellular response to cadmium and zinc ion, cell locomotion and differentiation, ribonucleoprotein complex and RNA processing, and immune system process, respectively. In conclusion, we identified some key genes and pathways closely related with HCC initiation and progression by a series of bioinformatics analysis on DEGs. These screened genes and pathways provided for a more detailed molecular mechanism underlying HCC occurrence and progression, holding promise for acting as biomarkers and potential therapeutic targets.

Ossification of the posterior longitudinal ligament related genes identification using microarray gene expression profiling and bioinformatics analysis.

PubMed

He, Hailong; Mao, Lingzhou; Xu, Peng; Xi, Yanhai; Xu, Ning; Xue, Mingtao; Yu, Jiangming; Ye, Xiaojian

2014-01-10

Ossification of the posterior longitudinal ligament (OPLL) is a kind of disease with physical barriers and neurological disorders. The objective of this study was to explore the differentially expressed genes (DEGs) in OPLL patient ligament cells and identify the target sites for the prevention and treatment of OPLL in clinic. Gene expression data GSE5464 was downloaded from Gene Expression Omnibus; then DEGs were screened by limma package in R language, and changed functions and pathways of OPLL cells compared to normal cells were identified by DAVID (The Database for Annotation, Visualization and Integrated Discovery); finally, an interaction network of DEGs was constructed by string. A total of 1536 DEGs were screened, with 31 down-regulated and 1505 up-regulated genes. Response to wounding function and Toll-like receptor signaling pathway may involve in the development of OPLL. Genes, such as PDGFB, PRDX2 may involve in OPLL through response to wounding function. Toll-like receptor signaling pathway enriched genes such as TLR1, TLR5, and TLR7 may involve in spine cord injury in OPLL. PIK3R1 was the hub gene in the network of DEGs with the highest degree; INSR was one of the most closely related genes of it. OPLL related genes screened by microarray gene expression profiling and bioinformatics analysis may be helpful for elucidating the mechanism of OPLL. © 2013.

Effect of Dynamic Rolling Oscillations on Twin Tail Buffet Response

NASA Technical Reports Server (NTRS)

Sheta, Essam F.; Kandil, Osama A.

1999-01-01

The effect of dynamic rolling oscillations of delta-wing/twin-tail configuration on twin-tail buffet response is investigated. The computational model consists of a sharp-edged delta wing of aspect ratio one and swept-back flexible twin tail with taper ratio of 0.23. The configuration model is statically pitched at 30 deg. angle of attack and then forced to oscillate in roll around the symmetry axis at a constant amplitude of 4 deg. and reduced frequency of pi and 2(pi). The freestream Mach number and Reynolds number are 0.3 and 1.25 million, respectively. This multidisciplinary problem is solved using three sets of equations on a dynamic multi-block grid structure. The first set is the unsteady, full Navier-Stokes equations, the second set is the aeroelastic equations for coupled bending and torsion vibrations of the tails, and the third set is the grid-displacement equations. The configuration is investigated for inboard position of the twin tails which corresponds to a separation distance between the twin tails of 33% wing span. The computed results are compared with the results of stationary configuration, which previously have been validated using experimental data. The results conclusively showed that the rolling oscillations of the configuration have led to higher loads, higher deflections, and higher excitation peaks than those of the stationary configuration. Moreover, increasing the reduced frequency has led to higher loads and excitation peaks and lower bending and torsion deflections and acceleration.

Accurate path integration in continuous attractor network models of grid cells.

PubMed

Burak, Yoram; Fiete, Ila R

2009-02-01

Grid cells in the rat entorhinal cortex display strikingly regular firing responses to the animal's position in 2-D space and have been hypothesized to form the neural substrate for dead-reckoning. However, errors accumulate rapidly when velocity inputs are integrated in existing models of grid cell activity. To produce grid-cell-like responses, these models would require frequent resets triggered by external sensory cues. Such inadequacies, shared by various models, cast doubt on the dead-reckoning potential of the grid cell system. Here we focus on the question of accurate path integration, specifically in continuous attractor models of grid cell activity. We show, in contrast to previous models, that continuous attractor models can generate regular triangular grid responses, based on inputs that encode only the rat's velocity and heading direction. We consider the role of the network boundary in the integration performance of the network and show that both periodic and aperiodic networks are capable of accurate path integration, despite important differences in their attractor manifolds. We quantify the rate at which errors in the velocity integration accumulate as a function of network size and intrinsic noise within the network. With a plausible range of parameters and the inclusion of spike variability, our model networks can accurately integrate velocity inputs over a maximum of approximately 10-100 meters and approximately 1-10 minutes. These findings form a proof-of-concept that continuous attractor dynamics may underlie velocity integration in the dorsolateral medial entorhinal cortex. The simulations also generate pertinent upper bounds on the accuracy of integration that may be achieved by continuous attractor dynamics in the grid cell network. We suggest experiments to test the continuous attractor model and differentiate it from models in which single cells establish their responses independently of each other.

The National Grid Project: A system overview

NASA Technical Reports Server (NTRS)

Gaither, Adam; Gaither, Kelly; Jean, Brian; Remotigue, Michael; Whitmire, John; Soni, Bharat; Thompson, Joe; Dannenhoffer,, John; Weatherill, Nigel

1995-01-01

The National Grid Project (NGP) is a comprehensive numerical grid generation software system that is being developed at the National Science Foundation (NSF) Engineering Research Center (ERC) for Computational Field Simulation (CFS) at Mississippi State University (MSU). NGP is supported by a coalition of U.S. industries and federal laboratories. The objective of the NGP is to significantly decrease the amount of time it takes to generate a numerical grid for complex geometries and to increase the quality of these grids to enable computational field simulations for applications in industry. A geometric configuration can be discretized into grids (or meshes) that have two fundamental forms: structured and unstructured. Structured grids are formed by intersecting curvilinear coordinate lines and are composed of quadrilateral (2D) and hexahedral (3D) logically rectangular cells. The connectivity of a structured grid provides for trivial identification of neighboring points by incrementing coordinate indices. Unstructured grids are composed of cells of any shape (commonly triangles, quadrilaterals, tetrahedra and hexahedra), but do not have trivial identification of neighbors by incrementing an index. For unstructured grids, a set of points and an associated connectivity table is generated to define unstructured cell shapes and neighboring points. Hybrid grids are a combination of structured grids and unstructured grids. Chimera (overset) grids are intersecting or overlapping structured grids. The NGP system currently provides a user interface that integrates both 2D and 3D structured and unstructured grid generation, a solid modeling topology data management system, an internal Computer Aided Design (CAD) system based on Non-Uniform Rational B-Splines (NURBS), a journaling language, and a grid/solution visualization system.

Tau Pathology Induces Excitatory Neuron Loss, Grid Cell Dysfunction and Spatial Memory Deficits Reminiscent of Early Alzheimer's Disease

PubMed Central

Fu, Hongjun; Rodriguez, Gustavo A.; Herman, Mathieu; Emrani, Sheina; Nahmani, Eden; Barrett, Geoffrey; Figueroa, Helen Y.; Goldberg, Eliana

2017-01-01

Summary The earliest stages of Alzheimer's disease (AD) are characterized by the formation of mature tangles in the entorhinal cortex and disorientation and confusion navigating familiar places. The medial entorhinal cortex (MEC) contains specialized neurons called grid cells that form part of the spatial navigation system. Here we show in a transgenic mouse model expressing mutant human tau predominantly in the EC that the formation of mature tangles in old mice was associated with excitatory cell loss and deficits in grid cell function, including destabilized grid fields and reduced firing rates, as well as altered network activity. Overt tau pathology in the aged mice was accompanied by spatial memory deficits. Therefore, tau pathology initiated in the entorhinal cortex could lead to deficits in grid cell firing and underlie the deterioration of spatial cognition seen in human AD. PMID:28111080

Combining Livestock Production Information in a Process-Based Vegetation Model to Reconstruct the History of Grassland Management

NASA Technical Reports Server (NTRS)

Chang, Jinfeng; Ciais, Philippe; Herrero, Mario; Havlik, Petr; Campioli, Matteo; Zhang, Xianzhou; Bai, Yongfei; Viovy, Nicolas; Joiner, Joanna; Wang, Xuhui;

Light coupling into the Whispering Gallery Modes of a fiber array thin film solar cell for fixed partial Sun tracking

PubMed Central

Mariano, Marina; Rodríguez, Francisco J.; Romero-Gomez, Pablo; Kozyreff, Gregory; Martorell, Jordi

2014-01-01

We propose the use of whispering gallery mode coupling in a novel configuration based on implementing a thin film cell on the backside of an array of parallel fibers. We performed numerical calculations using the parameters of a thin film organic cell which demonstrate that light coupling becomes more effective as the angle for the incident light relative to the fiber array normal increases up to an optimal angle close to 55 deg. At this angle the power conversion efficiency of the fiber array solar cell we propose becomes 30% times larger than the one from an equivalent planar cell configuration. We demonstrate that the micro fiber array solar cell we propose may perform an effective partial tracking of the sun movement for over 100 degrees without any mechanical help. In addition, in the event that such fiber array cell would be installed with the adequate orientation on a vertical façade, an optimal photon-to-charge conversion would be reached for sunlight incident at 55 deg with respect to the horizon line, very close to the yearly average position for the sun at Latitude of 40 deg.

A regional analysis of cloudy mean spherical albedo over the marine stratocumulus region and the tropical Atlantic Ocean. M.S. Thesis

NASA Technical Reports Server (NTRS)

Ginger, Kathryn M.

1993-01-01

Since clouds are the largest variable in Earth's radiation budget, it is critical to determine both the spatial and temporal characteristics of their radiative properties. The relationships between cloud properties and cloud fraction are studied in order to supplement grid scale parameterizations. The satellite data used is from three hourly ISCCP (International Satellite Cloud Climatology Project) and monthly ERBE (Earth Radiation Budget Experiment) data on a 2.5 deg x 2.5 deg latitude-longitude grid. Mean cloud spherical albedo, the mean optical depth distribution, and cloud fraction are examined and compared off the coast of California and the mid-tropical Atlantic for July 1987 and 1988. Individual grid boxes and spatial averages over several grid boxes are correlated to Coakley's theory of reflection for uniform and broken layered cloud and to Kedem, et al.'s findings that rainfall volume and fractional area of rain in convective systems is linear. Kedem's hypothesis can be expressed in terms of cloud properties. That is, the total volume of liquid in a box is a linear function of cloud fraction. Results for the marine stratocumulus regime indicate that albedo is often invariant for cloud fractions of 20% to 80%. Coakley's satellite model of small and large clouds with cores (1 km) and edges (100 m) is consistent with this observation. The cores maintain high liquid water concentrations and large droplets while the edges contain low liquid water concentrations and small droplets. Large clouds are just a collection of cores. The mean optical depth (TAU) distributions support the above observation with TAU values of 3.55 to 9.38 favored across all cloud fractions. From these results, a method based upon Kedem, et al's theory is proposed to separate the cloud fraction and liquid water path (LWP) calculations in a general circulation model (GCM). In terms of spatial averaging, a linear relationship between albedo and cloud fraction is observed. For tropical locations outside the Intertropical Convergence Zone (ITCZ), results of cloud fraction and albedo spatial averaging followed that of the stratus boxes containing few overcast scenes. Both the ideas of Coakley and Kedem, et al. apply. Within the ITCZ, the grid boxes tended to have the same statistical properties as stratus boxes containing many overcast scenes. Because different dynamical forcing mechanisms are present, it is difficult to devise a method for determining subgrid scale variations. Neither of the theories proposed by Kedem, et al. or Coakley works well for the boxes with numerous overcast scenes.

Temporally structured replay of neural activity in a model of entorhinal cortex, hippocampus and postsubiculum

PubMed Central

Hasselmo, Michael E.

2008-01-01

The spiking activity of hippocampal neurons during REM sleep exhibits temporally structured replay of spiking occurring during previously experienced trajectories (Louie and Wilson, 2001). Here, temporally structured replay of place cell activity during REM sleep is modeled in a large-scale network simulation of grid cells, place cells and head direction cells. During simulated waking behavior, the movement of the simulated rat drives activity of a population of head direction cells that updates the activity of a population of entorhinal grid cells. The population of grid cells drives the activity of place cells coding individual locations. Associations between location and movement direction are encoded by modification of excitatory synaptic connections from place cells to speed modulated head direction cells. During simulated REM sleep, the population of place cells coding an experienced location activates the head direction cells coding the associated movement direction. Spiking of head direction cells then causes frequency shifts within the population of entorhinal grid cells to update a phase representation of location. Spiking grid cells then activate new place cells that drive new head direction activity. In contrast to models that perform temporally compressed sequence retrieval similar to sharp wave activity, this model can simulate data on temporally structured replay of hippocampal place cell activity during REM sleep at time scales similar to those observed during waking. These mechanisms could be important for episodic memory of trajectories. PMID:18973557

Comparison of Node-Centered and Cell-Centered Unstructured Finite-Volume Discretizations: Inviscid Fluxes

NASA Technical Reports Server (NTRS)

Diskin, Boris; Thomas, James L.

2010-01-01

Cell-centered and node-centered approaches have been compared for unstructured finite-volume discretization of inviscid fluxes. The grids range from regular grids to irregular grids, including mixed-element grids and grids with random perturbations of nodes. Accuracy, complexity, and convergence rates of defect-correction iterations are studied for eight nominally second-order accurate schemes: two node-centered schemes with weighted and unweighted least-squares (LSQ) methods for gradient reconstruction and six cell-centered schemes two node-averaging with and without clipping and four schemes that employ different stencils for LSQ gradient reconstruction. The cell-centered nearest-neighbor (CC-NN) scheme has the lowest complexity; a version of the scheme that involves smart augmentation of the LSQ stencil (CC-SA) has only marginal complexity increase. All other schemes have larger complexity; complexity of node-centered (NC) schemes are somewhat lower than complexity of cell-centered node-averaging (CC-NA) and full-augmentation (CC-FA) schemes. On highly anisotropic grids typical of those encountered in grid adaptation, discretization errors of five of the six cell-centered schemes converge with second order on all tested grids; the CC-NA scheme with clipping degrades solution accuracy to first order. The NC schemes converge with second order on regular and/or triangular grids and with first order on perturbed quadrilaterals and mixed-element grids. All schemes may produce large relative errors in gradient reconstruction on grids with perturbed nodes. Defect-correction iterations for schemes employing weighted least-square gradient reconstruction diverge on perturbed stretched grids. Overall, the CC-NN and CC-SA schemes offer the best options of the lowest complexity and secondorder discretization errors. On anisotropic grids over a curved body typical of turbulent flow simulations, the discretization errors converge with second order and are small for the CC-NN, CC-SA, and CC-FA schemes on all grids and for NC schemes on triangular grids; the discretization errors of the CC-NA scheme without clipping do not converge on irregular grids. Accurate gradient reconstruction can be achieved by introducing a local approximate mapping; without approximate mapping, only the NC scheme with weighted LSQ method provides accurate gradients. Defect correction iterations for the CC-NA scheme without clipping diverge; for the NC scheme with weighted LSQ method, the iterations either diverge or converge very slowly. The best option in curved geometries is the CC-SA scheme that offers low complexity, second-order discretization errors, and fast convergence.

Sparse grid techniques for particle-in-cell schemes

NASA Astrophysics Data System (ADS)

Ricketson, L. F.; Cerfon, A. J.

2017-02-01

We propose the use of sparse grids to accelerate particle-in-cell (PIC) schemes. By using the so-called ‘combination technique’ from the sparse grids literature, we are able to dramatically increase the size of the spatial cells in multi-dimensional PIC schemes while paying only a slight penalty in grid-based error. The resulting increase in cell size allows us to reduce the statistical noise in the simulation without increasing total particle number. We present initial proof-of-principle results from test cases in two and three dimensions that demonstrate the new scheme’s efficiency, both in terms of computation time and memory usage.

Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content.

PubMed

Cesar, Aline S M; Regitano, Luciana C A; Poleti, Mirele D; Andrade, Sónia C S; Tizioto, Polyana C; Oliveira, Priscila S N; Felício, Andrezza M; do Nascimento, Michele L; Chaves, Amália S; Lanna, Dante P D; Tullio, Rymer R; Nassu, Renata T; Koltes, James E; Fritz-Waters, Eric; Mourão, Gerson B; Zerlotini-Neto, Adhemar; Reecy, James M; Coutinho, Luiz L

2016-11-22

Lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. In the last few decades, it has been reported that long-chain fatty acids (FAs) are involved in several biological functions from transcriptional regulation to physiological processes. Several fatty acids have been both positively and negatively implicated in different biological processes in skeletal muscle and other tissues. To gain insight into biological processes associated with fatty acid content in skeletal muscle, the aim of the present study was to identify differentially expressed genes (DEGs) and functional pathways related to gene expression regulation associated with FA content in cattle. Skeletal muscle transcriptome analysis of 164 Nellore steers revealed no differentially expressed genes (DEGs, FDR 10%) for samples with extreme values for linoleic acid (LA) or stearic acid (SA), and only a few DEGs for eicosapentaenoic acid (EPA, 5 DEGs), docosahexaenoic acid (DHA, 4 DEGs) and palmitic acid (PA, 123 DEGs), while large numbers of DEGs were associated with oleic acid (OA, 1134 DEGs) and conjugated linoleic acid cis9 trans11 (CLA-c9t11, 872 DEGs). Functional annotation and functional enrichment from OA DEGs identified important genes, canonical pathways and upstream regulators such as SCD, PLIN5, UCP3, CPT1, CPT1B, oxidative phosphorylation mitochondrial dysfunction, PPARGC1A, and FOXO1. Two important genes associated with lipid metabolism, gene expression and cancer were identified as DEGs between animals with high and low CLA-c9t11, specifically, epidermal growth factor receptor (EGFR) and RNPS. Only two out of seven classes of molecules of FA studied were associated with large changes in the expression profile of skeletal muscle. OA and CLA-c9t11 content had significant effects on the expression level of genes related to important biological processes associated with oxidative phosphorylation, and cell growth, survival, and migration. These results contribute to our understanding of how some FAs modulate metabolism and may have protective health function.

Janus kinase 1 inhibition suppresses interferon-induced B cell activating factor production in human salivary gland: potential therapeutic strategy for primary Sjögren's syndrome.

PubMed

Lee, Jaeseon; Lee, Jennifer; Kwok, Seung-Ki; Baek, SeungYe; Jang, Se Gwang; Hong, Seung-Min; Min, Jae-Woong; Choi, Sun Shim; Lee, Juhyun; Cho, Mi-La; Park, Sung-Hwan

2018-06-21

To examine whether a JAK inhibitor regulates functional responses of human salivary gland epithelial cells (SGEC) and disease parameters in a Sjögren's syndrome animal model. Common differentially expressed genes (DEGs) were analyzed among peripheral blood mononuclear cells from patients with primary Sjögren's syndrome (pSS) and other datasets, using blood and salivary gland (SG) tissue. Validation of expression in SG was analyzed by focus score. Inhibition of mRNA expression of DEGs and BAFF by filgotinib was analyzed using real-time PCR in primary SGECs. SG organoid cultures were used to determine the association between DEGs and B cell activating factor (BAFF) via knockdown using siRNAs or regulation of BAFF by JAK inhibitor. Filgotinib (1.5 mg/kg) was intraperitoneally injected into 8-week-old NOD/ShiLtJ mice three times per week to analyze manifestations of disease. Finally, STAT signaling was assessed in human and mouse SGECs. Expression of DEGs IFNG and BAFF increased in pSS patient SGs, as assessed by focus score. There was significant correlation between IFIT2 and BAFF expression. JAK inhibitor suppressed IFN-induced transcription of DEGs and BAFF in human pSGECs. Knockdown of DEGs, or inhibition of JAK caused reduced secretion of BAFF in human SG organoid cultures. In addition, filgotinib-treated mice exhibited increased salivary flow rates and marked reductions in lymphocytic infiltration of the SG. JAK inhibitor regulated pSTAT1 Y701 , pSTAT3 Y705 , and PIAS3 in IFN-induced human SGECs, and pSTAT1 Y701 , pSTAT3 S727 , PIAS1 in IFNγ-induced mouse SGECs. JAK inhibition controls aberrant activation of SGECs and may be a novel therapeutic approach for pSS. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Gene expression analysis of TIL rich HPV-driven head and neck tumors reveals a distinct B-cell signature when compared to HPV independent tumors.

PubMed

Wood, Oliver; Woo, Jeongmin; Seumois, Gregory; Savelyeva, Natalia; McCann, Katy J; Singh, Divya; Jones, Terry; Peel, Lailah; Breen, Michael S; Ward, Matthew; Garrido Martin, Eva; Sanchez-Elsner, Tilman; Thomas, Gareth; Vijayanand, Pandurangan; Woelk, Christopher H; King, Emma; Ottensmeier, Christian

2016-08-30

Human papilloma virus (HPV)-associated head and neck squamous cell carcinoma (HNSCC) has a better prognosis than it's HPV negative (HPV(-)) counterpart. This may be due to the higher numbers of tumor-infiltrating lymphocytes (TILs) in HPV positive (HPV(+)) tumors. RNA-Sequencing (RNA-Seq) was used to evaluate whether the differences in clinical behaviour simply reflect a numerical difference in TILs or whether there is a fundamental behavioural difference between TILs in these two settings. Thirty-nine HNSCC tumors were scored for TIL density by immunohistochemistry. After the removal of 16 TILlow tumors, RNA-Seq analysis was performed on 23 TILhigh/med tumors (HPV(+) n=10 and HPV(-) n=13). Using EdgeR, differentially expressed genes (DEG) were identified. Immune subset analysis was performed using Functional Analysis of Individual RNA-Seq/ Microarray Expression (FAIME) and immune gene RNA transcript count analysis. In total, 1,634 DEGs were identified, with a dominant immune signature observed in HPV(+) tumors. After normalizing the expression profiles to account for differences in B- and T-cell number, 437 significantly DEGs remained. A B-cell associated signature distinguished HPV(+) from HPV(-) tumors, and included the DEGs CD200, GGA2, ADAM28, STAG3, SPIB, VCAM1, BCL2 and ICOSLG; the immune signal relative to T-cells was qualitatively similar between TILs of both tumor cohorts. Our findings were validated and confirmed in two independent cohorts using TCGA data and tumor-infiltrating B-cells from additional HPV(+) HNSCC patients. A B-cell associated signal segregated tumors relative to HPV status. Our data suggests that the role of B-cells in the adaptive immune response to HPV(+) HNSCC requires re-assessment.

Cellular dissection of psoriasis for transcriptome analyses and the post-GWAS era

PubMed Central

2014-01-01

Background Genome-scale studies of psoriasis have been used to identify genes of potential relevance to disease mechanisms. For many identified genes, however, the cell type mediating disease activity is uncertain, which has limited our ability to design gene functional studies based on genomic findings. Methods We identified differentially expressed genes (DEGs) with altered expression in psoriasis lesions (n = 216 patients), as well as candidate genes near susceptibility loci from psoriasis GWAS studies. These gene sets were characterized based upon their expression across 10 cell types present in psoriasis lesions. Susceptibility-associated variation at intergenic (non-coding) loci was evaluated to identify sites of allele-specific transcription factor binding. Results Half of DEGs showed highest expression in skin cells, although the dominant cell type differed between psoriasis-increased DEGs (keratinocytes, 35%) and psoriasis-decreased DEGs (fibroblasts, 33%). In contrast, psoriasis GWAS candidates tended to have highest expression in immune cells (71%), with a significant fraction showing maximal expression in neutrophils (24%, P < 0.001). By identifying candidate cell types for genes near susceptibility loci, we could identify and prioritize SNPs at which susceptibility variants are predicted to influence transcription factor binding. This led to the identification of potentially causal (non-coding) SNPs for which susceptibility variants influence binding of AP-1, NF-κB, IRF1, STAT3 and STAT4. Conclusions These findings underscore the role of innate immunity in psoriasis and highlight neutrophils as a cell type linked with pathogenetic mechanisms. Assignment of candidate cell types to genes emerging from GWAS studies provides a first step towards functional analysis, and we have proposed an approach for generating hypotheses to explain GWAS hits at intergenic loci. PMID:24885462

Synergistic effects of arsenic trioxide combined with ascorbic acid in human osteosarcoma MG-63 cells: a systems biology analysis.

PubMed

Huang, X C; Maimaiti, X Y M; Huang, C W; Zhang, L; Li, Z B; Chen, Z G; Gao, X; Chen, T Y

2014-01-01

To further understand the synergistic mechanism of As2O3 and asscorbic acid (AA) in human osteosarcoma MG-63 cells by systems biology analysis. Human osteosarcoma MG-63 cells were treated by As2O3 (1 µmol/L), AA (62.5 µmol/L) and combined drugs (1 µmol/L As2O3 plus 62.5 µmol/L AA). Dynamic morphological characteristics were recorded by Cell-IQ system, and growth rate was calculated. Illumina beadchip assay was used to analyze the differential expression genes in different groups. Synergic effects on differential expression genes (DEGs) were analyzed by mixture linear model and singular value decomposition model. KEGG pathway annotations and GO enrichment analysis were performed to figure out the pathways involved in the synergic effects. We captured 1987 differential expression genes in combined therapy MG-63 cells. FAT1 gene was significantly upregulated in all three groups, which is a promising drug target as an important tumor suppressor analogue; meanwhile, HIST1H2BD gene was markedly downregulated in the As2O3 monotherapy group and the combined therapy group, which was found to be upregulated in prostatic cancer. These two genes might play critical roles in synergetic effects of AA and As2O3, although the exact mechanism needs further investigation. KEGG pathway analysis showed many DEGs were related with tight junction, and GO analysis also indicated that DEGs in the combined therapy cells gathered in occluding junction, apical junction complex, cell junction, and tight junction. AA potentiates the efficacy of As2O3 in MG-63 cells. Systems biology analysis showed the synergic effect on the DEGs.

Gene expression analysis of TIL rich HPV-driven head and neck tumors reveals a distinct B-cell signature when compared to HPV independent tumors

PubMed Central

Savelyeva, Natalia; McCann, Katy J.; Singh, Divya; Jones, Terry; Peel, Lailah; Breen, Michael S.; Ward, Matthew; Martin, Eva Garrido

2016-01-01

Human papilloma virus (HPV)-associated head and neck squamous cell carcinoma (HNSCC) has a better prognosis than it's HPV negative (HPV(−)) counterpart. This may be due to the higher numbers of tumor-infiltrating lymphocytes (TILs) in HPV positive (HPV(+)) tumors. RNA-Sequencing (RNA-Seq) was used to evaluate whether the differences in clinical behaviour simply reflect a numerical difference in TILs or whether there is a fundamental behavioural difference between TILs in these two settings. Thirty-nine HNSCC tumors were scored for TIL density by immunohistochemistry. After the removal of 16 TILlow tumors, RNA-Seq analysis was performed on 23 TILhigh/med tumors (HPV(+) n=10 and HPV(−) n=13). Using EdgeR, differentially expressed genes (DEG) were identified. Immune subset analysis was performed using Functional Analysis of Individual RNA-Seq/ Microarray Expression (FAIME) and immune gene RNA transcript count analysis. In total, 1,634 DEGs were identified, with a dominant immune signature observed in HPV(+) tumors. After normalizing the expression profiles to account for differences in B- and T-cell number, 437 significantly DEGs remained. A B-cell associated signature distinguished HPV(+) from HPV(−) tumors, and included the DEGs CD200, GGA2, ADAM28, STAG3, SPIB, VCAM1, BCL2 and ICOSLG; the immune signal relative to T-cells was qualitatively similar between TILs of both tumor cohorts. Our findings were validated and confirmed in two independent cohorts using TCGA data and tumor-infiltrating B-cells from additional HPV(+) HNSCC patients. A B-cell associated signal segregated tumors relative to HPV status. Our data suggests that the role of B-cells in the adaptive immune response to HPV(+) HNSCC requires re-assessment. PMID:27462861

Streamline integration as a method for two-dimensional elliptic grid generation

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

Wiesenberger, M., E-mail: Matthias.Wiesenberger@uibk.ac.at; Held, M.; Einkemmer, L.

We propose a new numerical algorithm to construct a structured numerical elliptic grid of a doubly connected domain. Our method is applicable to domains with boundaries defined by two contour lines of a two-dimensional function. Furthermore, we can adapt any analytically given boundary aligned structured grid, which specifically includes polar and Cartesian grids. The resulting coordinate lines are orthogonal to the boundary. Grid points as well as the elements of the Jacobian matrix can be computed efficiently and up to machine precision. In the simplest case we construct conformal grids, yet with the help of weight functions and monitor metricsmore » we can control the distribution of cells across the domain. Our algorithm is parallelizable and easy to implement with elementary numerical methods. We assess the quality of grids by considering both the distribution of cell sizes and the accuracy of the solution to elliptic problems. Among the tested grids these key properties are best fulfilled by the grid constructed with the monitor metric approach. - Graphical abstract: - Highlights: • Construct structured, elliptic numerical grids with elementary numerical methods. • Align coordinate lines with or make them orthogonal to the domain boundary. • Compute grid points and metric elements up to machine precision. • Control cell distribution by adaption functions or monitor metrics.« less

A computational and experimental investigation of a delta wing with vertical tails

NASA Technical Reports Server (NTRS)

Krist, Sherrie L.; Washburn, Anthony E.; Visser, Kenneth D.

1993-01-01

The flow over an aspect ratio 1 delta wing with twin vertical tails is studied in a combined computational and experimental investigation. This research is conducted in an effort to understand the vortex and fin interaction process. The computational algorithm used solves both the thin-layer Navier-Stokes and the inviscid Euler equations and utilizes a chimera grid-overlapping technique. The results are compared with data obtained from a detailed experimental investigation. The laminar case presented is for an angle of attack of 20 deg and a Reynolds number of 500,000. Good agreement is observed for the physics of the flow field, as evidenced by comparisons of computational pressure contours with experimental flow-visualization images, as well as by comparisons of vortex-core trajectories. While comparisons of the vorticity magnitudes indicate that the computations underpredict the magnitude in the wing primary-vortex-core region, grid embedding improves the computational prediction.

Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post- chemotherapy tissues

PubMed Central

Tong, Mengsha; Zheng, Weicheng; Lu, Xingrong; Ao, Lu; Li, Xiangyu; Guan, Qingzhou; Cai, Hao; Li, Mengyao; Yan, Haidan; Guo, You; Chi, Pan; Guo, Zheng

2015-01-01

Until recently, few molecular signatures of drug resistance identified in drug-induced resistant cancer cell models can be translated into clinical practice. Here, we defined differentially expressed genes (DEGs) between pre-chemotherapy colorectal cancer (CRC) tissue samples of non-responders and responders for 5-fluorouracil and oxaliplatin-based therapy as clinically relevant drug resistance genes (CRG5-FU/L-OHP). Taking CRG5-FU/L-OHP as reference, we evaluated the clinical relevance of several types of genes derived from HCT116 CRC cells with resistance to 5-fluorouracil and oxaliplatin, respectively. The results revealed that DEGs between parental and resistant cells, when both were treated with the corresponding drug for a certain time, were significantly consistent with the CRG5-FU/L-OHP as well as the DEGs between the post-chemotherapy CRC specimens of responders and non-responders. This study suggests a novel strategy to extract clinically relevant drug resistance genes from both drug-induced resistant cell models and post-chemotherapy cancer tissue specimens. PMID:26515599

Possible role of acetylcholine in regulating spatial novelty effects on theta rhythm and grid cells

PubMed Central

Barry, Caswell; Heys, James G.; Hasselmo, Michael E.

2012-01-01

Existing pharmacological and lesion data indicate that acetylcholine plays an important role in memory formation. For example, increased levels of acetylcholine in the hippocampal formation are known to be associated with successful encoding while disruption of the cholinergic system leads to impairments on a range of mnemonic tasks. However, cholinergic signaling from the medial septum also plays a central role in generating and pacing theta-band oscillations throughout the hippocampal formation. Recent experimental results suggest a potential link between these distinct phenomena. Environmental novelty, a condition associated with strong cholinergic drive, has been shown to induce an expansion in the firing pattern of entorhinal grid cells and a reduction in the frequency of theta measured from the LFP. Computational modeling suggests the spatial activity of grid cells is produced by interference between neuronal oscillators; scale being determined by theta-band oscillations impinging on entorhinal stellate cells, the frequency of which is modulated by acetylcholine. Here we propose that increased cholinergic signaling in response to environmental novelty triggers grid expansion by reducing the frequency of the oscillations. Furthermore, we argue that cholinergic induced grid expansion may enhance, or even induce, encoding by producing a mismatch between expanded grid cells and other spatial inputs to the hippocampus, such as boundary vector cells. Indeed, a further source of mismatch is likely to occur between grid cells of different native scales which may expand by different relative amounts. PMID:22363266

A principle of economy predicts the functional architecture of grid cells.

PubMed

Wei, Xue-Xin; Prentice, Jason; Balasubramanian, Vijay

2015-09-03

Grid cells in the brain respond when an animal occupies a periodic lattice of 'grid fields' during navigation. Grids are organized in modules with different periodicity. We propose that the grid system implements a hierarchical code for space that economizes the number of neurons required to encode location with a given resolution across a range equal to the largest period. This theory predicts that (i) grid fields should lie on a triangular lattice, (ii) grid scales should follow a geometric progression, (iii) the ratio between adjacent grid scales should be √e for idealized neurons, and lie between 1.4 and 1.7 for realistic neurons, (iv) the scale ratio should vary modestly within and between animals. These results explain the measured grid structure in rodents. We also predict optimal organization in one and three dimensions, the number of modules, and, with added assumptions, the ratio between grid periods and field widths.

RNA-Seq Expression Analysis of Enteric Neuron Cells with Rotenone Treatment and Prediction of Regulated Pathways.

PubMed

Guan, Qiang; Wang, Xijin; Jiang, Yanyan; Zhao, Lijuan; Nie, Zhiyu; Jin, Lingjing

2017-02-01

The enteric nervous system (ENS) is involved in the initiation and development of the pathological process of Parkinson's disease (PD). The effect of rotenone on the ENS may trigger the progression of PD through the central nervous system (CNS). In this study, we used RNA-sequencing (RNA-seq) analysis to examine differential expression genes (DEGs) and pathways induced by in vitro treatment of rotenone in the enteric nervous cells isolated from rats. We identified 45 up-regulated and 30 down-regulated genes. The functional categorization revealed that the DEGs were involved in the regulation of cell differentiation and development, response to various stimuli, and regulation of neurogenesis. In addition, the pathway and network analysis showed that the Mitogen Activated Protein Kinase (MAPK), Toll-like receptor, Wnt, and Ras signaling pathways were intensively involved in the effect of rotenone on the ENS. Additionally, the quantitative real-time polymerase chain reaction result for the selected seven DEGs matched those of the RNA-seq analysis. Our results present a significant step in the identification of DEGs and provide new insight into the progression of PD in the rotenone-induced model.

Continuous Attractor Network Model for Conjunctive Position-by-Velocity Tuning of Grid Cells

PubMed Central

Si, Bailu; Romani, Sandro; Tsodyks, Misha

2014-01-01

The spatial responses of many of the cells recorded in layer II of rodent medial entorhinal cortex (MEC) show a triangular grid pattern, which appears to provide an accurate population code for animal spatial position. In layer III, V and VI of the rat MEC, grid cells are also selective to head-direction and are modulated by the speed of the animal. Several putative mechanisms of grid-like maps were proposed, including attractor network dynamics, interactions with theta oscillations or single-unit mechanisms such as firing rate adaptation. In this paper, we present a new attractor network model that accounts for the conjunctive position-by-velocity selectivity of grid cells. Our network model is able to perform robust path integration even when the recurrent connections are subject to random perturbations. PMID:24743341

Decadal changes in shortwave irradiance at the surface in the period from 1960 to 2000 estimated from Global Energy Balance Archive Data

NASA Astrophysics Data System (ADS)

Gilgen, H.; Roesch, A.; Wild, M.; Ohmura, A.

2009-05-01

Decadal changes in shortwave irradiance at the Earth's surface are estimated for the period from approximately 1960 through to 2000 from pyranometer records stored in the Global Energy Balance Archive. For this observational period, estimates could be calculated for a total of 140 cells of the International Satellite Cloud Climatology Project grid (an equal area 2.5° × 2.5° grid at the equator) using regression models allowing for station effects. In large regions worldwide, shortwave irradiance decreases in the first half of the observational period, recovers from the decrease in the 1980s, and thereafter increases, in line with previous reports. Years of trend reversals are determined for the grid cells which are best described with a second-order polynomial model. This reversal of the trend is observed in the majority of the grid cells in the interior of Europe and in Japan. In China, shortwave irradiance recovers during the 1990s in the majority of the grid cells in the southeast and northeast from the decrease observed in the period from 1960 through to 1990. A reversal of the trend in the 1980s or early 1990s is also observed for two grid cells in North America, and for the grid cells containing the Kuala Lumpur (Malaysia), Singapore, Casablanca (Morocco), Valparaiso (Chile) sites, and, noticeably, the remote South Pole and American Samoa sites. Negative trends persist, i.e., shortwave radiation decreases, for the observational period 1960 through to 2000 at the European coasts, in central and northwest China, and for three grid cells in India and two in Africa.

Context-dependent spatially periodic activity in the human entorhinal cortex

PubMed Central

Nguyen, T. Peter; Török, Ágoston; Shen, Jason Y.; Briggs, Deborah E.; Modur, Pradeep N.; Buchanan, Robert J.

2017-01-01

The spatially periodic activity of grid cells in the entorhinal cortex (EC) of the rodent, primate, and human provides a coordinate system that, together with the hippocampus, informs an individual of its location relative to the environment and encodes the memory of that location. Among the most defining features of grid-cell activity are the 60° rotational symmetry of grids and preservation of grid scale across environments. Grid cells, however, do display a limited degree of adaptation to environments. It remains unclear if this level of environment invariance generalizes to human grid-cell analogs, where the relative contribution of visual input to the multimodal sensory input of the EC is significantly larger than in rodents. Patients diagnosed with nontractable epilepsy who were implanted with entorhinal cortical electrodes performing virtual navigation tasks to memorized locations enabled us to investigate associations between grid-like patterns and environment. Here, we report that the activity of human entorhinal cortical neurons exhibits adaptive scaling in grid period, grid orientation, and rotational symmetry in close association with changes in environment size, shape, and visual cues, suggesting scale invariance of the frequency, rather than the wavelength, of spatially periodic activity. Our results demonstrate that neurons in the human EC represent space with an enhanced flexibility relative to neurons in rodents because they are endowed with adaptive scalability and context dependency. PMID:28396399

A computer program for converting rectangular coordinates to latitude-longitude coordinates

USGS Publications Warehouse

Rutledge, A.T.

1989-01-01

A computer program was developed for converting the coordinates of any rectangular grid on a map to coordinates on a grid that is parallel to lines of equal latitude and longitude. Using this program in conjunction with groundwater flow models, the user can extract data and results from models with varying grid orientations and place these data into grid structure that is oriented parallel to lines of equal latitude and longitude. All cells in the rectangular grid must have equal dimensions, and all cells in the latitude-longitude grid measure one minute by one minute. This program is applicable if the map used shows lines of equal latitude as arcs and lines of equal longitude as straight lines and assumes that the Earth 's surface can be approximated as a sphere. The program user enters the row number , column number, and latitude and longitude of the midpoint of the cell for three test cells on the rectangular grid. The latitude and longitude of boundaries of the rectangular grid also are entered. By solving sets of simultaneous linear equations, the program calculates coefficients that are used for making the conversion. As an option in the program, the user may build a groundwater model file based on a grid that is parallel to lines of equal latitude and longitude. The program reads a data file based on the rectangular coordinates and automatically forms the new data file. (USGS)

Bayesian Non-Stationary Index Gauge Modeling of Gridded Precipitation Extremes

NASA Astrophysics Data System (ADS)

Verdin, A.; Bracken, C.; Caldwell, J.; Balaji, R.; Funk, C. C.

2017-12-01

We propose a Bayesian non-stationary model to generate watershed scale gridded estimates of extreme precipitation return levels. The Climate Hazards Group Infrared Precipitation with Stations (CHIRPS) dataset is used to obtain gridded seasonal precipitation extremes over the Taylor Park watershed in Colorado for the period 1981-2016. For each year, grid cells within the Taylor Park watershed are aggregated to a representative "index gauge," which is input to the model. Precipitation-frequency curves for the index gauge are estimated for each year, using climate variables with significant teleconnections as proxies. Such proxies enable short-term forecasting of extremes for the upcoming season. Disaggregation ratios of the index gauge to the grid cells within the watershed are computed for each year and preserved to translate the index gauge precipitation-frequency curve to gridded precipitation-frequency maps for select return periods. Gridded precipitation-frequency maps are of the same spatial resolution as CHIRPS (0.05° x 0.05°). We verify that the disaggregation method preserves spatial coherency of extremes in the Taylor Park watershed. Validation of the index gauge extreme precipitation-frequency method consists of ensuring extreme value statistics are preserved on a grid cell basis. To this end, a non-stationary extreme precipitation-frequency analysis is performed on each grid cell individually, and the resulting frequency curves are compared to those produced by the index gauge disaggregation method.

Uncertainty in gridded CO 2 emissions estimates

DOE PAGES

Hogue, Susannah; Marland, Eric; Andres, Robert J.; ...

2016-05-19

We are interested in the spatial distribution of fossil-fuel-related emissions of CO 2 for both geochemical and geopolitical reasons, but it is important to understand the uncertainty that exists in spatially explicit emissions estimates. Working from one of the widely used gridded data sets of CO 2 emissions, we examine the elements of uncertainty, focusing on gridded data for the United States at the scale of 1° latitude by 1° longitude. Uncertainty is introduced in the magnitude of total United States emissions, the magnitude and location of large point sources, the magnitude and distribution of non-point sources, and from themore » use of proxy data to characterize emissions. For the United States, we develop estimates of the contribution of each component of uncertainty. At 1° resolution, in most grid cells, the largest contribution to uncertainty comes from how well the distribution of the proxy (in this case population density) represents the distribution of emissions. In other grid cells, the magnitude and location of large point sources make the major contribution to uncertainty. Uncertainty in population density can be important where a large gradient in population density occurs near a grid cell boundary. Uncertainty is strongly scale-dependent with uncertainty increasing as grid size decreases. In conclusion, uncertainty for our data set with 1° grid cells for the United States is typically on the order of ±150%, but this is perhaps not excessive in a data set where emissions per grid cell vary over 8 orders of magnitude.« less

Comparison of local grid refinement methods for MODFLOW

USGS Publications Warehouse

Mehl, S.; Hill, M.C.; Leake, S.A.

2006-01-01

Many ground water modeling efforts use a finite-difference method to solve the ground water flow equation, and many of these models require a relatively fine-grid discretization to accurately represent the selected process in limited areas of interest. Use of a fine grid over the entire domain can be computationally prohibitive; using a variably spaced grid can lead to cells with a large aspect ratio and refinement in areas where detail is not needed. One solution is to use local-grid refinement (LGR) whereby the grid is only refined in the area of interest. This work reviews some LGR methods and identifies advantages and drawbacks in test cases using MODFLOW-2000. The first test case is two dimensional and heterogeneous; the second is three dimensional and includes interaction with a meandering river. Results include simulations using a uniform fine grid, a variably spaced grid, a traditional method of LGR without feedback, and a new shared node method with feedback. Discrepancies from the solution obtained with the uniform fine grid are investigated. For the models tested, the traditional one-way coupled approaches produced discrepancies in head up to 6.8% and discrepancies in cell-to-cell fluxes up to 7.1%, while the new method has head and cell-to-cell flux discrepancies of 0.089% and 0.14%, respectively. Additional results highlight the accuracy, flexibility, and CPU time trade-off of these methods and demonstrate how the new method can be successfully implemented to model surface water-ground water interactions. Copyright ?? 2006 The Author(s).

Comparison of Node-Centered and Cell-Centered Unstructured Finite-Volume Discretizations. Part 1; Viscous Fluxes

NASA Technical Reports Server (NTRS)

Diskin, Boris; Thomas, James L.; Nielsen, Eric J.; Nishikawa, Hiroaki; White, Jeffery A.

2009-01-01

Discretization of the viscous terms in current finite-volume unstructured-grid schemes are compared using node-centered and cell-centered approaches in two dimensions. Accuracy and efficiency are studied for six nominally second-order accurate schemes: a node-centered scheme, cell-centered node-averaging schemes with and without clipping, and cell-centered schemes with unweighted, weighted, and approximately mapped least-square face gradient reconstruction. The grids considered range from structured (regular) grids to irregular grids composed of arbitrary mixtures of triangles and quadrilaterals, including random perturbations of the grid points to bring out the worst possible behavior of the solution. Two classes of tests are considered. The first class of tests involves smooth manufactured solutions on both isotropic and highly anisotropic grids with discontinuous metrics, typical of those encountered in grid adaptation. The second class concerns solutions and grids varying strongly anisotropically over a curved body, typical of those encountered in high-Reynolds number turbulent flow simulations. Results from the first class indicate the face least-square methods, the node-averaging method without clipping, and the node-centered method demonstrate second-order convergence of discretization errors with very similar accuracies per degree of freedom. The second class of tests are more discriminating. The node-centered scheme is always second order with an accuracy and complexity in linearization comparable to the best of the cell-centered schemes. In comparison, the cell-centered node-averaging schemes are less accurate, have a higher complexity in linearization, and can fail to converge to the exact solution when clipping of the node-averaged values is used. The cell-centered schemes using least-square face gradient reconstruction have more compact stencils with a complexity similar to the complexity of the node-centered scheme. For simulations on highly anisotropic curved grids, the least-square methods have to be amended either by introducing a local mapping of the surface anisotropy or modifying the scheme stencil to reflect the direction of strong coupling.

Homogeneity and EPR metrics for assessment of regular grids used in CW EPR powder simulations.

PubMed

Crăciun, Cora

2014-08-01

CW EPR powder spectra may be approximated numerically using a spherical grid and a Voronoi tessellation-based cubature. For a given spin system, the quality of simulated EPR spectra depends on the grid type, size, and orientation in the molecular frame. In previous work, the grids used in CW EPR powder simulations have been compared mainly from geometric perspective. However, some grids with similar homogeneity degree generate different quality simulated spectra. This paper evaluates the grids from EPR perspective, by defining two metrics depending on the spin system characteristics and the grid Voronoi tessellation. The first metric determines if the grid points are EPR-centred in their Voronoi cells, based on the resonance magnetic field variations inside these cells. The second metric verifies if the adjacent Voronoi cells of the tessellation are EPR-overlapping, by computing the common range of their resonance magnetic field intervals. Beside a series of well known regular grids, the paper investigates a modified ZCW grid and a Fibonacci spherical code, which are new in the context of EPR simulations. For the investigated grids, the EPR metrics bring more information than the homogeneity quantities and are better related to the grids' EPR behaviour, for different spin system symmetries. The metrics' efficiency and limits are finally verified for grids generated from the initial ones, by using the original or magnetic field-constraint variants of the Spherical Centroidal Voronoi Tessellation method. Copyright © 2014 Elsevier Inc. All rights reserved.

Calculation of wind-driven surface currents in the North Atlantic Ocean

NASA Technical Reports Server (NTRS)

Rees, T. H.; Turner, R. E.

1976-01-01

Calculations to simulate the wind driven near surface currents of the North Atlantic Ocean are described. The primitive equations were integrated on a finite difference grid with a horizontal resolution of 2.5 deg in longitude and latitude. The model ocean was homogeneous with a uniform depth of 100 m and with five levels in the vertical direction. A form of the rigid-lid approximation was applied. Generally, the computed surface current patterns agreed with observed currents. The development of a subsurface equatorial countercurrent was observed.

Parallel alignment of bacteria using near-field optical force array for cell sorting

NASA Astrophysics Data System (ADS)

Zhao, H. T.; Zhang, Y.; Chin, L. K.; Yap, P. H.; Wang, K.; Ser, W.; Liu, A. Q.

2017-08-01

This paper presents a near-field approach to align multiple rod-shaped bacteria based on the interference pattern in silicon nano-waveguide arrays. The bacteria in the optical field will be first trapped by the gradient force and then rotated by the scattering force to the equilibrium position. In the experiment, the Shigella bacteria is rotated 90 deg and aligned to horizontal direction in 9.4 s. Meanwhile, 150 Shigella is trapped on the surface in 5 min and 86% is aligned with angle < 5 deg. This method is a promising toolbox for the research of parallel single-cell biophysical characterization, cell-cell interaction, etc.

Analysis of CrIS/ATMS using AIRS Version-7 Retrieval and QC Methodology

NASA Astrophysics Data System (ADS)

Susskind, J.; Kouvaris, L. C.; Blaisdell, J. M.; Iredell, L. F.

2017-12-01

The objective of the proposed research is to develop, implement, test, and refine a CrIS/ATMS retrieval algorithm which will produce monthly mean data products that are compatible with those of the soon to be operational AIRS V7 retrieval algorithm. This is a necessary condition for CrIS/ATMS on NPP and future missions to serve as adequate follow-ons to AIRS for the monitoring of climate variability and trends. Of particular importance toward this end is achieving agreement of monthly mean fields of CrIS and AIRS geophysical parameters on a 1 deg by 1 deg spatial scale, and, more significantly, agreement of their interannual differences. Indications are that the best way to achieve this is to use scientific retrieval and Quality Control (QC) methodology for CrIS/ATMS which is analogous to that which will be used in AIRS V7. We refer to the current scientific candidate for AIRS V7 as AIRS Sounder Research Team (SRT) V6.42, which currently runs at JPL on the AIRS Team Leader Scientific Facility (TLSCF). We ported CrIS SRT V6.42 Level 2 (L2) retrieval code and QC methodology to run at the Sounder SIPS at JPL. The months of January and July 2015 were both processed at JPL using AIRS and CrIS at the TLSCF and SIPS respectively. This paper shows excellent agreement of AIRS and CrIS single day and monthly mean products on a 1 deg lat by 1 deg long spatial grid with each other and with the other satellites measures of the same products.

Comparison of Node-Centered and Cell-Centered Unstructured Finite-Volume Discretizations: Viscous Fluxes

NASA Technical Reports Server (NTRS)

Diskin, Boris; Thomas, James L.; Nielsen, Eric J.; Nishikawa, Hiroaki; White, Jeffery A.

2010-01-01

Discretization of the viscous terms in current finite-volume unstructured-grid schemes are compared using node-centered and cell-centered approaches in two dimensions. Accuracy and complexity are studied for four nominally second-order accurate schemes: a node-centered scheme and three cell-centered schemes - a node-averaging scheme and two schemes with nearest-neighbor and adaptive compact stencils for least-square face gradient reconstruction. The grids considered range from structured (regular) grids to irregular grids composed of arbitrary mixtures of triangles and quadrilaterals, including random perturbations of the grid points to bring out the worst possible behavior of the solution. Two classes of tests are considered. The first class of tests involves smooth manufactured solutions on both isotropic and highly anisotropic grids with discontinuous metrics, typical of those encountered in grid adaptation. The second class concerns solutions and grids varying strongly anisotropically over a curved body, typical of those encountered in high-Reynolds number turbulent flow simulations. Tests from the first class indicate the face least-square methods, the node-averaging method without clipping, and the node-centered method demonstrate second-order convergence of discretization errors with very similar accuracies per degree of freedom. The tests of the second class are more discriminating. The node-centered scheme is always second order with an accuracy and complexity in linearization comparable to the best of the cell-centered schemes. In comparison, the cell-centered node-averaging schemes may degenerate on mixed grids, have a higher complexity in linearization, and can fail to converge to the exact solution when clipping of the node-averaged values is used. The cell-centered schemes using least-square face gradient reconstruction have more compact stencils with a complexity similar to that of the node-centered scheme. For simulations on highly anisotropic curved grids, the least-square methods have to be amended either by introducing a local mapping based on a distance function commonly available in practical schemes or modifying the scheme stencil to reflect the direction of strong coupling. The major conclusion is that accuracies of the node centered and the best cell-centered schemes are comparable at equivalent number of degrees of freedom.

Dual Identification and Analysis of Differentially Expressed Transcripts of Porcine PK-15 Cells and Toxoplasma gondii during in vitro Infection

PubMed Central

Zhou, Chun-Xue; Elsheikha, Hany M.; Zhou, Dong-Hui; Liu, Qing; Zhu, Xing-Quan; Suo, Xun

2016-01-01

Toxoplasma gondii is responsible for causing toxoplasmosis, one of the most prevalent zoonotic parasitoses worldwide. The mechanisms that mediate T. gondii infection of pigs (the most common source of human infection) and renal tissues are still unknown. To identify the critical alterations that take place in the transcriptome of both porcine kidney (PK-15) cells and T. gondii following infection, infected cell samples were collected at 1, 3, 6, 9, 12, 18, and 24 h post infection and RNA-Seq data were acquired using Illumina Deep Sequencing. Differential Expression of Genes (DEGs) analysis was performed to study the concomitant gene-specific temporal patterns of induction of mRNA expression of PK-15 cells and T. gondii. High sequence coverage enabled us to thoroughly characterize T. gondii transcriptome and identify the activated molecular pathways in host cells. More than 6G clean bases/sample, including >40 million clean reads were obtained. These were aligned to the reference genome of T. gondii and wild boar (Sus scrofa). DEGs involved in metabolic activities of T. gondii showed time-dependent down-regulation. However, DEGs involved in immune or disease related pathways of PK-15 cells peaked at 6 h PI, and were highly enriched as evidenced by KEGG analysis. Protein-protein interaction analysis revealed that TGME49_120110 (PCNA), TGME49_049180 (DHFR-TS), TGME49_055320, and TGME49_002300 (ITPase) are the four hub genes with most interactions with T. gondii at the onset of infection. These results reveal altered profiles of gene expressed by PK-15 cells and T. gondii during infection and provide the groundwork for future virulence studies to uncover the mechanisms of T. gondii interaction with porcine renal tissue by functional analysis of these DEGs. PMID:27242740

Application of spatially gridded temperature and land cover data sets for urban heat island analysis

USGS Publications Warehouse

Gallo, Kevin; Xian, George Z.

2014-01-01

Two gridded data sets that included (1) daily mean temperatures from 2006 through 2011 and (2) satellite-derived impervious surface area, were combined for a spatial analysis of the urban heat-island effect within the Dallas-Ft. Worth Texas region. The primary advantage of using these combined datasets included the capability to designate each 1 × 1 km grid cell of available temperature data as urban or rural based on the level of impervious surface area within the grid cell. Generally, the observed differences in urban and rural temperature increased as the impervious surface area thresholds used to define an urban grid cell were increased. This result, however, was also dependent on the size of the sample area included in the analysis. As the spatial extent of the sample area increased and included a greater number of rural defined grid cells, the observed urban and rural differences in temperature also increased. A cursory comparison of the spatially gridded temperature observations with observations from climate stations suggest that the number and location of stations included in an urban heat island analysis requires consideration to assure representative samples of each (urban and rural) environment are included in the analysis.

New fixed-point mini-cell to investigate thermocouple drift in a high-temperature environment under neutron irradiation

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

Laurie, M.; Vlahovic, L.; Rondinella, V.V.

Temperature measurements in the nuclear field require a high degree of reliability and accuracy. Despite their sheathed form, thermocouples subjected to nuclear radiations undergo changes due to radiation damage and transmutation that lead to significant EMF drift during long-term fuel irradiation experiment. For the purpose of a High Temperature Reactor fuel irradiation to take place in the High Flux Reactor Petten, a dedicated fixed-point cell was jointly developed by LNE-Cnam and JRC-IET. The developed cell to be housed in the irradiation rig was tailor made to quantify the thermocouple drift during the irradiation (about two year duration) and withstand highmore » temperature (in the range 950 deg. C - 1100 deg. C) in the presence of contaminated helium in a graphite environment. Considering the different levels of temperature achieved in the irradiation facility and the large palette of thermocouple types aimed at surveying the HTR fuel pebble during the qualification test both copper (1084.62 deg. C) and gold (1064.18 deg. C) fixed-point materials were considered. The aim of this paper is to first describe the fixed-point mini-cell designed to be embedded in the reactor rig and to discuss the preliminary results achieved during some out of pile tests as much as some robustness tests representative of the reactor scram scenarios. (authors)« less

The importance of non-quasigeostrophic forcing during the development of a blocking anticyclone

NASA Technical Reports Server (NTRS)

Tsou, Chih-Hua; Smith, Phillip J.

1990-01-01

This study examines the impact of non-quasigeostrophic (NQG) processes during the development of a blocking anticyclone (January 21, 1979 over the southern tip of Greenland) and a precursor, upstream intense cyclone (January 18, 1979). Energy quantities and height tendencies determined from quasigeostrophic estimates are compared with the same quantities obtained from more general formulations. GLA FGGE Level III-b analysis on a 4 deg lat by 5 deg long grid was used to obtain energetics results. It is concluded that NQG processes strengthened the intensity of the block and a precursor explosive cyclone and that a portion of this increase resulted from enhanced baroclinic conversion of eddy potential to eddy kinetic energy and reduced barotropic energy conversion from eddy to zonal flow. It is suggested that NQG vorticity advection, instead of moderating wave developments, enhanced the block development, and it is also suggested that QG forcing might not have been adequate to produce the observed block development.

Analysis of a high speed civil transport configuration at subsonic flow conditions using a Navier-Stokes solver

NASA Technical Reports Server (NTRS)

Lessard, Victor R.

1993-01-01

Computations of three dimensional vortical flows over a generic High Speed Civil Transport (HSCT) configuration with an aspect ratio of 3.04 are performed using a thin-layer Navier-Stokes solver. The HSCT cruise configuration is modeled without leading or trailing edge flap deflections and without engine nacelles. The flow conditions, which correspond to tests done in the NASA Langley 8-Foot Transonic Pressure Tunnel (TPT), are a subsonic Mach number of 0.3 and Reynolds number of 4.4 million for a range-of-attack (-.23 deg to 17.78 deg). The effects of the farfield boundary location with respect to the body are investigated. The boundary layer is assumed turbulent and simulated using an algebraic turbulence model. The key features of the vortices and their interactions are captured. Grid distribution in the vortex regions is critical for predicting the correct induced lift. Computed forces and surface pressures compare reasonably well with the experimental TPT data.

The impact of global warming on river runoff

NASA Technical Reports Server (NTRS)

Miller, James R.; Russell, Gary L.

1992-01-01

A global atmospheric model is used to calculate the annual river runoff for 33 of the world's major rivers for the present climate and for a doubled CO2 climate. The model has a horizontal resolution of 4 x 5 deg, but the runoff from each model grid box is quartered and added to the appropriate river drainage basin on a 2 x 2.5 deg resolution. The computed runoff depends on the model's precipitation, evapotranspiration, and soil moisture storage. For the doubled CO2 climate, the runoff increased for 25 of the 33 rivers, and in most cases the increases coincide with increased rainfall within the drainage basins. There were runoff increases in all rivers in high northern latitudes, with a maximum increase of 47 percent. At low latitudes there were both increases and decreases ranging from a 96 increase to a 43 percent decrease. The effect of the simplified model assumptions of land-atmosphere interactions on the results is discussed.

Spectral and diurnal variations in clear sky planetary albedo

NASA Technical Reports Server (NTRS)

Briegleb, B.; Ramanathan, V.

1982-01-01

Spectral and diurnal variations in the clear sky planetary albedo of the earth are calculated using a radiative transfer model to obtain January and July values for a 5 deg x 5 deg global grid. The model employs observed climatological values of temperatures, humidities, snow and sea-ice cover. The diurnal cycle of clear sky albedo is calculated in the following intervals: 0.2-0.5, 0.5-0.7, and 0.7-4 microns. Observed ozone distribution is specified as a function of latitude and season. The 0.2-0.5 micron spectral albedo is 10-20% higher than the total albedo for all latitudes because of Rayleigh scattering; the 0.5-0.7 micron albedo differs from the total albedo by 1-2% for most latitudes, while the 0.7-4 micron albedo is 5-10% lower than the total because of strong atmospheric absorption. Planetary albedo decreases from morning to local noon, with diurnal variations being particularly strong over water.

Use of MAGSAT anomaly data for crustal structure and mineral resources in the US Midcontinent

NASA Technical Reports Server (NTRS)

Carmichael, R. S. (Principal Investigator)

1981-01-01

The analysis and preliminary interpretation of investigator-B MAGSAT data are addressed. The data processing included: (1) removal of spurious data points; (2) statistical smoothing along individual data tracks, to reduce the effect of geomagnetic transient disturbances; (3) comparison of data profiles spatially coincident in track location but acquired at different times; (4) reduction of data by weighted averaging to a grid with 1 deg xl deg latitude/longitude spacing, and with elevations interpolated and weighted to a common datum of 400 km; (5) wavelength filtering; and (6) reduction of the anomaly map to the magnetic pole. Agreement was found between a magnitude data anomaly map and a reduce-to-the-pole map supporting the general assumption that, on a large scale (long wavelength), it is induced crustal magnetization which is responsible for major anamalies. Anomalous features are identified and explanations are suggested with regard to crustal structure, petrologic characteristics, and Curie temperature isotherms.

Reliable Detection and Smart Deletion of Malassez Counting Chamber Grid in Microscopic White Light Images for Microbiological Applications.

PubMed

Denimal, Emmanuel; Marin, Ambroise; Guyot, Stéphane; Journaux, Ludovic; Molin, Paul

2015-08-01

In biology, hemocytometers such as Malassez slides are widely used and are effective tools for counting cells manually. In a previous work, a robust algorithm was developed for grid extraction in Malassez slide images. This algorithm was evaluated on a set of 135 images and grids were accurately detected in most cases, but there remained failures for the most difficult images. In this work, we present an optimization of this algorithm that allows for 100% grid detection and a 25% improvement in grid positioning accuracy. These improvements make the algorithm fully reliable for grid detection. This optimization also allows complete erasing of the grid without altering the cells, which eases their segmentation.

Transcript Profiling Identifies Gene Cohorts Controlled by Each Signal Regulating Trans-Differentiation of Epidermal Cells of Vicia faba Cotyledons to a Transfer Cell Phenotype

PubMed Central

Zhang, Hui-Ming; Wheeler, Simon L.; Xia, Xue; Colyvas, Kim; Offler, Christina E.; Patrick, John W.

2017-01-01

Transfer cells (TCs) support high rates of membrane transport of nutrients conferred by a plasma membrane area amplified by lining a wall labyrinth comprised of an uniform wall layer (UWL) upon which intricate wall ingrowth (WI) papillae are deposited. A signal cascade of auxin, ethylene, extracellular hydrogen peroxide (H2O2) and cytosolic Ca2+ regulates wall labyrinth assembly. To identify gene cohorts regulated by each signal, a RNA- sequencing study was undertaken using Vicia faba cotyledons. When cotyledons are placed in culture, their adaxial epidermal cells spontaneously undergo trans-differentiation to epidermal TCs (ETCs). Expressed genes encoding proteins central to wall labyrinth formation (signaling, intracellular organization, cell wall) and TC function of nutrient transport were assembled. Transcriptional profiles identified 9,742 annotated ETC-specific differentially expressed genes (DEGs; Log2fold change > 1; FDR p ≤ 0.05) of which 1,371 belonged to signaling (50%), intracellular organization (27%), cell wall (15%) and nutrient transporters (9%) functional categories. Expression levels of 941 ETC-specific DEGs were found to be sensitive to the known signals regulating ETC trans-differentiation. Significantly, signals acting alone, or in various combinations, impacted similar numbers of ETC-specific DEGs across the four functional gene categories. Amongst the signals acting alone, H2O2 exerted most influence affecting expression levels of 56% of the ETC-specific DEGs followed by Ca2+ (21%), auxin (18%) and ethylene (5%). The dominance by H2O2 was evident across all functional categories, but became more attenuated once trans-differentiation transitioned into WI papillae formation. Amongst the eleven signal combinations, H2O2/Ca2+ elicited the greatest impact across all functional categories accounting for 20% of the ETC-specific DEG cohort. The relative influence of the other signals acting alone, or in various combinations, varied across the four functional categories and two phases of wall labyrinth construction. These transcriptome data provide a powerful information platform from which to examine signal transduction pathways and how these regulate expression of genes encoding proteins engaged in intracellular organization, cell wall construction and nutrient transport. PMID:29234338

Transcript Profiling Identifies Gene Cohorts Controlled by Each Signal Regulating Trans-Differentiation of Epidermal Cells of Vicia faba Cotyledons to a Transfer Cell Phenotype.

PubMed

Zhang, Hui-Ming; Wheeler, Simon L; Xia, Xue; Colyvas, Kim; Offler, Christina E; Patrick, John W

2017-01-01

Transfer cells (TCs) support high rates of membrane transport of nutrients conferred by a plasma membrane area amplified by lining a wall labyrinth comprised of an uniform wall layer (UWL) upon which intricate wall ingrowth (WI) papillae are deposited. A signal cascade of auxin, ethylene, extracellular hydrogen peroxide (H 2 O 2 ) and cytosolic Ca 2+ regulates wall labyrinth assembly. To identify gene cohorts regulated by each signal, a RNA- sequencing study was undertaken using Vicia faba cotyledons. When cotyledons are placed in culture, their adaxial epidermal cells spontaneously undergo trans -differentiation to epidermal TCs (ETCs). Expressed genes encoding proteins central to wall labyrinth formation (signaling, intracellular organization, cell wall) and TC function of nutrient transport were assembled. Transcriptional profiles identified 9,742 annotated ETC-specific differentially expressed genes (DEGs; Log 2 fold change > 1; FDR p ≤ 0.05) of which 1,371 belonged to signaling (50%), intracellular organization (27%), cell wall (15%) and nutrient transporters (9%) functional categories. Expression levels of 941 ETC-specific DEGs were found to be sensitive to the known signals regulating ETC trans -differentiation. Significantly, signals acting alone, or in various combinations, impacted similar numbers of ETC-specific DEGs across the four functional gene categories. Amongst the signals acting alone, H 2 O 2 exerted most influence affecting expression levels of 56% of the ETC-specific DEGs followed by Ca 2+ (21%), auxin (18%) and ethylene (5%). The dominance by H 2 O 2 was evident across all functional categories, but became more attenuated once trans -differentiation transitioned into WI papillae formation. Amongst the eleven signal combinations, H 2 O 2 /Ca 2+ elicited the greatest impact across all functional categories accounting for 20% of the ETC-specific DEG cohort. The relative influence of the other signals acting alone, or in various combinations, varied across the four functional categories and two phases of wall labyrinth construction. These transcriptome data provide a powerful information platform from which to examine signal transduction pathways and how these regulate expression of genes encoding proteins engaged in intracellular organization, cell wall construction and nutrient transport.

Computational Aeroelastic Analysis of Ares Crew Launch Vehicle Bi-Modal Loading

NASA Technical Reports Server (NTRS)

Massey, Steven J.; Chwalowski, Pawel

2010-01-01

A Reynolds averaged Navier-Stokes analysis, with and without dynamic aeroelastic effects, is presented for the Ares I-X launch vehicle at transonic Mach numbers and flight Reynolds numbers for two grid resolutions and two angles of attack. The purpose of the study is to quantify the force and moment increment imparted by the sudden transition from fully separated flow around the crew module - service module junction to that of the bi-modal flow state in which only part of the flow reattaches. The bi-modal flow phenomenon is of interest to the guidance, navigation and control community because it causes a discontinuous jump in forces and moments. Computations with a rigid structure at zero zero angle of attack indicate significant increases in normal force and pitching moment. Dynamic aeroelastic computations indicate the bi-modal flow state is insensitive to vehicle flexibility due to the resulting deflections imparting only very small changes in local angle of attack. At an angle of attack of 2.5deg, the magnitude of the pitching moment increment resulting from the bi-modal state nearly triples, while occurring at a slightly lower Mach number. Significant grid induced variations between the solutions indicate that further grid refinement is warranted.

An Adaptively-Refined, Cartesian, Cell-Based Scheme for the Euler and Navier-Stokes Equations. Ph.D. Thesis - Michigan Univ.

NASA Technical Reports Server (NTRS)

Coirier, William John

1994-01-01

A Cartesian, cell-based scheme for solving the Euler and Navier-Stokes equations in two dimensions is developed and tested. Grids about geometrically complicated bodies are generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, polygonal 'cut' cells are created. The geometry of the cut cells is computed using polygon-clipping algorithms. The grid is stored in a binary-tree data structure which provides a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive refinement. The Euler and Navier-Stokes equations are solved on the resulting grids using a finite-volume formulation. The convective terms are upwinded, with a limited linear reconstruction of the primitive variables used to provide input states to an approximate Riemann solver for computing the fluxes between neighboring cells. A multi-stage time-stepping scheme is used to reach a steady-state solution. Validation of the Euler solver with benchmark numerical and exact solutions is presented. An assessment of the accuracy of the approach is made by uniform and adaptive grid refinements for a steady, transonic, exact solution to the Euler equations. The error of the approach is directly compared to a structured solver formulation. A non smooth flow is also assessed for grid convergence, comparing uniform and adaptively refined results. Several formulations of the viscous terms are assessed analytically, both for accuracy and positivity. The two best formulations are used to compute adaptively refined solutions of the Navier-Stokes equations. These solutions are compared to each other, to experimental results and/or theory for a series of low and moderate Reynolds numbers flow fields. The most suitable viscous discretization is demonstrated for geometrically-complicated internal flows. For flows at high Reynolds numbers, both an altered grid-generation procedure and a different formulation of the viscous terms are shown to be necessary. A hybrid Cartesian/body-fitted grid generation approach is demonstrated. In addition, a grid-generation procedure based on body-aligned cell cutting coupled with a viscous stensil-construction procedure based on quadratic programming is presented.

A principle of economy predicts the functional architecture of grid cells

PubMed Central

Wei, Xue-Xin; Prentice, Jason; Balasubramanian, Vijay

2015-01-01

Grid cells in the brain respond when an animal occupies a periodic lattice of ‘grid fields’ during navigation. Grids are organized in modules with different periodicity. We propose that the grid system implements a hierarchical code for space that economizes the number of neurons required to encode location with a given resolution across a range equal to the largest period. This theory predicts that (i) grid fields should lie on a triangular lattice, (ii) grid scales should follow a geometric progression, (iii) the ratio between adjacent grid scales should be √e for idealized neurons, and lie between 1.4 and 1.7 for realistic neurons, (iv) the scale ratio should vary modestly within and between animals. These results explain the measured grid structure in rodents. We also predict optimal organization in one and three dimensions, the number of modules, and, with added assumptions, the ratio between grid periods and field widths. DOI: http://dx.doi.org/10.7554/eLife.08362.001 PMID:26335200

Assessment of in situ butanol recovery by vacuum during acetone butanol ethanol (ABE) fermentation

USDA-ARS?s Scientific Manuscript database

Butanol fermentation is product limiting due to butanol toxicity to microbial cells. Butanol (boiling point: 118 deg C) boils at a greater temperature than water (boiling point: 100 deg C) and application of vacuum technology to integrated acetone-butanol-ethanol (ABE) fermentation and recovery may ...

Therapeutic benefits in grid irradiation on Tomotherapy for bulky, radiation-resistant tumors.

PubMed

Narayanasamy, Ganesh; Zhang, Xin; Meigooni, Ali; Paudel, Nava; Morrill, Steven; Maraboyina, Sanjay; Peacock, Loverd; Penagaricano, Jose

2017-08-01

Spatially fractionated radiation therapy (SFRT or grid therapy) has proven to be effective in management of bulky tumors. The aim of this project is to study the therapeutic ratio (TR) of helical Tomotherapy (HT)-based grid therapy using linear-quadratic cell survival model. HT-based grid (or HT-GRID) plan was generated using a patient-specific virtual grid pattern of high-dose cylindrical regions using MLCs. TR was defined as the ratio of normal tissue surviving fraction (SF) under HT-GRID irradiation to an open debulking field of an equivalent dose that result in the same tumor cell SF. TR was estimated from DVH data on ten HT-GRID patient plans with deep seated, bulky tumor. Dependence of the TR values on radiosensitivity of the tumor cells and prescription dose was analyzed. The mean ± standard deviation (SD) of TR was 4.0 ± 0.7 (range: 3.1-5.5) for the 10 patients with single fraction maximum dose of 20 Gy to GTV assuming a tumor cell SF at 2 Gy (SF2 t ) value of 0·5. In addition, the mean ± SD of TR values for SF2 t values of 0.3 and 0.7 were found to be 1 ± 0.1 and 18.0 ± 5.1, respectively. Reducing the prescription dose to 15 and 10 Gy lowered the respective TR values to 2.0 ± 0.2 and 1.2 ± 0.04 for a SF2 t value of 0.5. HT-GRID therapy demonstrates a significant therapeutic advantage over uniform dose from an open field irradiation for the same tumor cell kill. TR increases with the radioresistance of the tumor cells and with prescription dose.

MODFLOW–USG version 1: An unstructured grid version of MODFLOW for simulating groundwater flow and tightly coupled processes using a control volume finite-difference formulation

USGS Publications Warehouse

Panday, Sorab; Langevin, Christian D.; Niswonger, Richard G.; Ibaraki, Motomu; Hughes, Joseph D.

2013-01-01

A new version of MODFLOW, called MODFLOW–USG (for UnStructured Grid), was developed to support a wide variety of structured and unstructured grid types, including nested grids and grids based on prismatic triangles, rectangles, hexagons, and other cell shapes. Flexibility in grid design can be used to focus resolution along rivers and around wells, for example, or to subdiscretize individual layers to better represent hydrostratigraphic units. MODFLOW–USG is based on an underlying control volume finite difference (CVFD) formulation in which a cell can be connected to an arbitrary number of adjacent cells. To improve accuracy of the CVFD formulation for irregular grid-cell geometries or nested grids, a generalized Ghost Node Correction (GNC) Package was developed, which uses interpolated heads in the flow calculation between adjacent connected cells. MODFLOW–USG includes a Groundwater Flow (GWF) Process, based on the GWF Process in MODFLOW–2005, as well as a new Connected Linear Network (CLN) Process to simulate the effects of multi-node wells, karst conduits, and tile drains, for example. The CLN Process is tightly coupled with the GWF Process in that the equations from both processes are formulated into one matrix equation and solved simultaneously. This robustness results from using an unstructured grid with unstructured matrix storage and solution schemes. MODFLOW–USG also contains an optional Newton-Raphson formulation, based on the formulation in MODFLOW–NWT, for improving solution convergence and avoiding problems with the drying and rewetting of cells. Because the existing MODFLOW solvers were developed for structured and symmetric matrices, they were replaced with a new Sparse Matrix Solver (SMS) Package developed specifically for MODFLOW–USG. The SMS Package provides several methods for resolving nonlinearities and multiple symmetric and asymmetric linear solution schemes to solve the matrix arising from the flow equations and the Newton-Raphson formulation, respectively.

Identification of targets of miRNA-221 and miRNA-222 in fulvestrant-resistant breast cancer

PubMed Central

Liu, Pengfei; Sun, Manna; Jiang, Wenhua; Zhao, Jinkun; Liang, Chunyong; Zhang, Huilai

2016-01-01

The present study aimed to identify the differentially expressed genes (DEGs) regulated by microRNA (miRNA)-221 and miRNA-222 that are associated with the resistance of breast cancer to fulvestrant. The GSE19777 transcription profile was downloaded from the Gene Expression Omnibus database, and includes data from three samples of antisense miRNA-221-transfected fulvestrant-resistant MCF7-FR breast cancer cells, three samples of antisense miRNA-222-transfected fulvestrant-resistant MCF7-FR cells and three samples of control inhibitor (green fluorescent protein)-treated fulvestrant-resistant MCF7-FR cells. The linear models for microarray data package in R/Bioconductor was employed to screen for DEGs in the miRNA-transfected cells, and the pheatmap package in R was used to perform two-way clustering. Pathway enrichment was conducted using the Gene Set Enrichment Analysis tool. Furthermore, a miRNA-messenger (m) RNA regulatory network depicting interactions between miRNA-targeted upregulated DEGs was constructed and visualized using Cytoscape. In total, 492 and 404 DEGs were identified for the antisense miRNA-221-transfected MCF7-FR cells and the antisense miRNA-222-transfected MCF7-FR cells, respectively. Genes of the pentose phosphate pathway (PPP) were significantly enriched in the antisense miRNA-221-transfected MCF7-FR cells. In addition, components of the Wnt signaling pathway and cell adhesion molecules (CAMs) were significantly enriched in the antisense miRNA-222-transfected MCF7-FR cells. In the miRNA-mRNA regulatory network, miRNA-222 was demonstrated to target protocadherin 10 (PCDH10). The results of the present study suggested that the PPP and Wnt signaling pathways, as well as CAMs and PCDH10, may be associated with the resistance of breast cancer to fulvestrant. PMID:27895744

Comparison of TRMM Ground Validation and Satellite Rain Intensity Estimates

NASA Technical Reports Server (NTRS)

Wolff, David B.; Lawrence, Richard

2005-01-01

The Tropical Rainfall Measuring Mission (TRMM) Ground Validation (GV) Program began in the late 1980's and has provided a wealth of data and resources for validating TRMM satellite estimates. The TRMM GV program's main operational task is to provide rainfall products for four sites: Darwin, Australia (DARW); Houston, Texas (HSTN); Kwajalein, Republic of the Marshall Islands (KWAJ); and, Melbourne, Florida (MELB). A comparison between TRMM Ground Validation (Version 5) and Satellite (Version 6) rain intensity estimates is presented. The full suite of Version 6 satellite data is currently being generated by the TRMM Science Data and Information System (TSDIS) and should be completed some time near the end of 2005. The gridded satellite product (3G68) will be compared to GV Level II rain-intensity and -type maps (2A53 and 2A54, respectively). The 3G68 product represents a 0.5 deg x 0.5 deg data grid providing estimates of rain intensities from the TRMM Precipitation Radar (PR), Microwave Imager (TMI) and Combined (COM) algorithms. The comparisons will be sub-setted according to geographical type (land, coast and ocean). A bias statistic will be presented that provides quantification of the relative differences between the various estimators. Previous comparisons of an interim satellite product (Version 6a) showed that all of the estimates (GV and satellite) are converging, with some expected discrepancies. The convergence of the GV and satellite estimates bodes well for expectations for the proposed Global Precipitation Measurement (GPM) program and this study and others are being leveraged towards planning GV goals for GPM.

Computational Simulations of Convergent Nozzles for the AIAA 1st Propulsion Aerodynamics Workshop

NASA Technical Reports Server (NTRS)

Dippold, Vance F., III

2014-01-01

Computational Fluid Dynamics (CFD) simulations were completed for a series of convergent nozzles in participation of the American Institute of Aeronautics and Astronautics (AIAA) 1st Propulsion Aerodynamics Workshop. The simulations were performed using the Wind-US flow solver. Discharge and thrust coefficients were computed for four axisymmetric nozzles with nozzle pressure ratios (NPR) ranging from 1.4 to 7.0. The computed discharge coefficients showed excellent agreement with available experimental data; the computed thrust coefficients captured trends observed in the experimental data, but over-predicted the thrust coefficient by 0.25 to 1.0 percent. Sonic lines were computed for cases with NPR >= 2.0 and agreed well with experimental data for NPR >= 2.5. Simulations were also performed for a 25 deg. conic nozzle bifurcated by a flat plate at NPR = 4.0. The jet plume shock structure was compared with and without the splitter plate to the experimental data. The Wind-US simulations predicted the shock structure well, though lack of grid resolution in the plume reduced the sharpness of the shock waves. Unsteady Reynolds-Averaged Navier-Stokes (URANS) simulations and Detached Eddy Simulations (DES) were performed at NPR = 1.6 for the 25 deg conic nozzle with splitter plate. The simulations predicted vortex shedding from the trailing edge of the splitter plate. However, the vortices of URANS and DES solutions appeared to dissipate earlier than observed experimentally. It is believed that a lack of grid resolution in the region of the vortex shedding may have caused the vortices to break down too soon

Characterization of three types of silicon solar cells for SEPS Deep Space Mission. Volume 3: Current-voltage characteristics of spectrolab sculptured BSR/P+ (K7), BSR/P+ (K6.5) and BSR (K4.5) cells as a function of temperature and intensity

NASA Technical Reports Server (NTRS)

Whitaker, A. F.; Little, S. A.; Wooden, V. A.; Carter, D. E.; Cothren, B. E.; Torstenson, C. A.

1980-01-01

Three types of high performance silicon solar cells, sculptured BSR/P+(K7), BSR/P+(K6.5) and BSR(K4.5) manufactured by Spectrolab were evaluated for their low temperature and low intensity performance. Sixteen cells of each type were subjected to 11 temperatures and 9 intensities. The sculptured BSR/P+(K7) cells provided the greatest maximum power output both at 1 AU and at LTLI conditions. The average efficiencies of this cell were 14.4 percent at 1 SC/+25 deg C and 18.5 percent at 0.086 SC/-100 deg C.

A robust, efficient equidistribution 2D grid generation method

NASA Astrophysics Data System (ADS)

Chacon, Luis; Delzanno, Gian Luca; Finn, John; Chung, Jeojin; Lapenta, Giovanni

2007-11-01

We present a new cell-area equidistribution method for two- dimensional grid adaptation [1]. The method is able to satisfy the equidistribution constraint to arbitrary precision while optimizing desired grid properties (such as isotropy and smoothness). The method is based on the minimization of the grid smoothness integral, constrained to producing a given positive-definite cell volume distribution. The procedure gives rise to a single, non-linear scalar equation with no free-parameters. We solve this equation numerically with the Newton-Krylov technique. The ellipticity property of the linearized scalar equation allows multigrid preconditioning techniques to be effectively used. We demonstrate a solution exists and is unique. Therefore, once the solution is found, the adapted grid cannot be folded due to the positivity of the constraint on the cell volumes. We present several challenging tests to show that our new method produces optimal grids in which the constraint is satisfied numerically to arbitrary precision. We also compare the new method to the deformation method [2] and show that our new method produces better quality grids. [1] G.L. Delzanno, L. Chac'on, J.M. Finn, Y. Chung, G. Lapenta, A new, robust equidistribution method for two-dimensional grid generation, in preparation. [2] G. Liao and D. Anderson, A new approach to grid generation, Appl. Anal. 44, 285--297 (1992).

GSRP/David Marshall: Fully Automated Cartesian Grid CFD Application for MDO in High Speed Flows

NASA Technical Reports Server (NTRS)

2003-01-01

With the renewed interest in Cartesian gridding methodologies for the ease and speed of gridding complex geometries in addition to the simplicity of the control volumes used in the computations, it has become important to investigate ways of extending the existing Cartesian grid solver functionalities. This includes developing methods of modeling the viscous effects in order to utilize Cartesian grids solvers for accurate drag predictions and addressing the issues related to the distributed memory parallelization of Cartesian solvers. This research presents advances in two areas of interest in Cartesian grid solvers, viscous effects modeling and MPI parallelization. The development of viscous effects modeling using solely Cartesian grids has been hampered by the widely varying control volume sizes associated with the mesh refinement and the cut cells associated with the solid surface. This problem is being addressed by using physically based modeling techniques to update the state vectors of the cut cells and removing them from the finite volume integration scheme. This work is performed on a new Cartesian grid solver, NASCART-GT, with modifications to its cut cell functionality. The development of MPI parallelization addresses issues associated with utilizing Cartesian solvers on distributed memory parallel environments. This work is performed on an existing Cartesian grid solver, CART3D, with modifications to its parallelization methodology.

Comparative Transcriptional Analysis of Loquat Fruit Identifies Major Signal Networks Involved in Fruit Development and Ripening Process.

PubMed

Song, Huwei; Zhao, Xiangxiang; Hu, Weicheng; Wang, Xinfeng; Shen, Ting; Yang, Liming

2016-11-04

Loquat ( Eriobotrya japonica Lindl.) is an important non-climacteric fruit and rich in essential nutrients such as minerals and carotenoids. During fruit development and ripening, thousands of the differentially expressed genes (DEGs) from various metabolic pathways cause a series of physiological and biochemical changes. To better understand the underlying mechanism of fruit development, the Solexa/Illumina RNA-seq high-throughput sequencing was used to evaluate the global changes of gene transcription levels. More than 51,610,234 high quality reads from ten runs of fruit development were sequenced and assembled into 48,838 unigenes. Among 3256 DEGs, 2304 unigenes could be annotated to the Gene Ontology database. These DEGs were distributed into 119 pathways described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A large number of DEGs were involved in carbohydrate metabolism, hormone signaling, and cell-wall degradation. The real-time reverse transcription (qRT)-PCR analyses revealed that several genes related to cell expansion, auxin signaling and ethylene response were differentially expressed during fruit development. Other members of transcription factor families were also identified. There were 952 DEGs considered as novel genes with no annotation in any databases. These unigenes will serve as an invaluable genetic resource for loquat molecular breeding and postharvest storage.

Velocity field calculation for non-orthogonal numerical grids

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

Flach, G. P.

2015-03-01

Computational grids containing cell faces that do not align with an orthogonal (e.g. Cartesian, cylindrical) coordinate system are routinely encountered in porous-medium numerical simulations. Such grids are referred to in this study as non-orthogonal grids because some cell faces are not orthogonal to a coordinate system plane (e.g. xy, yz or xz plane in Cartesian coordinates). Non-orthogonal grids are routinely encountered at the Savannah River Site in porous-medium flow simulations for Performance Assessments and groundwater flow modeling. Examples include grid lines that conform to the sloping roof of a waste tank or disposal unit in a 2D Performance Assessment simulation,more » and grid surfaces that conform to undulating stratigraphic surfaces in a 3D groundwater flow model. Particle tracking is routinely performed after a porous-medium numerical flow simulation to better understand the dynamics of the flow field and/or as an approximate indication of the trajectory and timing of advective solute transport. Particle tracks are computed by integrating the velocity field from cell to cell starting from designated seed (starting) positions. An accurate velocity field is required to attain accurate particle tracks. However, many numerical simulation codes report only the volumetric flowrate (e.g. PORFLOW) and/or flux (flowrate divided by area) crossing cell faces. For an orthogonal grid, the normal flux at a cell face is a component of the Darcy velocity vector in the coordinate system, and the pore velocity for particle tracking is attained by dividing by water content. For a non-orthogonal grid, the flux normal to a cell face that lies outside a coordinate plane is not a true component of velocity with respect to the coordinate system. Nonetheless, normal fluxes are often taken as Darcy velocity components, either naively or with accepted approximation. To enable accurate particle tracking or otherwise present an accurate depiction of the velocity field for a non-orthogonal grid, Darcy velocity components are rigorously derived in this study from normal fluxes to cell faces, which are assumed to be provided by or readily computed from porous-medium simulation code output. The normal fluxes are presumed to satisfy mass balances for every computational cell, and if so, the derived velocity fields are consistent with these mass balances. Derivations are provided for general two-dimensional quadrilateral and three-dimensional hexagonal systems, and for the commonly encountered special cases of perfectly vertical side faces in 2D and 3D and a rectangular footprint in 3D.« less

Rebound spiking in layer II medial entorhinal cortex stellate cells: Possible mechanism of grid cell function

PubMed Central

Shay, Christopher F.; Ferrante, Michele; Chapman, G. William; Hasselmo, Michael E.

2015-01-01

Rebound spiking properties of medial entorhinal cortex (mEC) stellate cells induced by inhibition may underlie their functional properties in awake behaving rats, including the temporal phase separation of distinct grid cells and differences in grid cell firing properties. We investigated rebound spiking properties using whole cell patch recording in entorhinal slices, holding cells near spiking threshold and delivering sinusoidal inputs, superimposed with realistic inhibitory synaptic inputs to test the capacity of cells to selectively respond to specific phases of inhibitory input. Stellate cells showed a specific phase range of hyperpolarizing inputs that elicited spiking, but non-stellate cells did not show phase specificity. In both cell types, the phase range of spiking output occurred between the peak and subsequent descending zero crossing of the sinusoid. The phases of inhibitory inputs that induced spikes shifted earlier as the baseline sinusoid frequency increased, while spiking output shifted to later phases. Increases in magnitude of the inhibitory inputs shifted the spiking output to earlier phases. Pharmacological blockade of h-current abolished the phase selectivity of hyperpolarizing inputs eliciting spikes. A network computational model using cells possessing similar rebound properties as found in vitro produces spatially periodic firing properties resembling grid cell firing when a simulated animal moves along a linear track. These results suggest that the ability of mEC stellate cells to fire rebound spikes in response to a specific range of phases of inhibition could support complex attractor dynamics that provide completion and separation to maintain spiking activity of specific grid cell populations. PMID:26385258

Obstacle-avoiding navigation system

DOEpatents

Borenstein, Johann; Koren, Yoram; Levine, Simon P.

1991-01-01

A system for guiding an autonomous or semi-autonomous vehicle through a field of operation having obstacles thereon to be avoided employs a memory for containing data which defines an array of grid cells which correspond to respective subfields in the field of operation of the vehicle. Each grid cell in the memory contains a value which is indicative of the likelihood, or probability, that an obstacle is present in the respectively associated subfield. The values in the grid cells are incremented individually in response to each scan of the subfields, and precomputation and use of a look-up table avoids complex trigonometric functions. A further array of grid cells is fixed with respect to the vehicle form a conceptual active window which overlies the incremented grid cells. Thus, when the cells in the active window overly grid cell having values which are indicative of the presence of obstacles, the value therein is used as a multiplier of the precomputed vectorial values. The resulting plurality of vectorial values are summed vectorially in one embodiment of the invention to produce a virtual composite repulsive vector which is then summed vectorially with a target-directed vector for producing a resultant vector for guiding the vehicle. In an alternative embodiment, a plurality of vectors surrounding the vehicle are computed, each having a value corresponding to obstacle density. In such an embodiment, target location information is used to select between alternative directions of travel having low associated obstacle densities.

Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome

PubMed Central

Shen, Haoran; Liang, Zhou; Zheng, Saihua; Li, Xuelian

2017-01-01

The purpose of this study was to identify promising candidate genes and pathways in polycystic ovary syndrome (PCOS). Microarray dataset GSE345269 obtained from the Gene Expression Omnibus database includes 7 granulosa cell samples from PCOS patients, and 3 normal granulosa cell samples. Differentially expressed genes (DEGs) were screened between PCOS and normal samples. Pathway enrichment analysis was conducted for DEGs using ClueGO and CluePedia plugin of Cytoscape. A Reactome functional interaction (FI) network of the DEGs was built using ReactomeFIViz, and then network modules were extracted, followed by pathway enrichment analysis for the modules. Expression of DEGs in granulosa cell samples was measured using quantitative RT-PCR. A total of 674 DEGs were retained, which were significantly enriched with inflammation and immune-related pathways. Eight modules were extracted from the Reactome FI network. Pathway enrichment analysis revealed significant pathways of each module: module 0, Regulation of RhoA activity and Signaling by Rho GTPases pathways shared ARHGAP4 and ARHGAP9; module 2, GlycoProtein VI-mediated activation cascade pathway was enriched with RHOG; module 3, Thromboxane A2 receptor signaling, Chemokine signaling pathway, CXCR4-mediated signaling events pathways were enriched with LYN, the hub gene of module 3. Results of RT-PCR confirmed the finding of the bioinformatic analysis that ARHGAP4, ARHGAP9, RHOG and LYN were significantly upregulated in PCOS. RhoA-related pathways, GlycoProtein VI-mediated activation cascade pathway, ARHGAP4, ARHGAP9, RHOG and LYN may be involved in the pathogenesis of PCOS. PMID:28949383

Orbiter Capability for Providing Water to the International Space Station according to the Most Probable Flight Attitudes

NASA Technical Reports Server (NTRS)

Dunaway, Brian; Edeen, Marybeth

2000-01-01

Water to be generated by, delivered to, and processed by the International Space Station (ISS) is a critical Environmental Control and Life Support (ECLS) element, especially for the early ISS missions. A significant portion of the water required by the ISS shall be provided by the Shuttle Transportation System (STS) Orbiter. The balance of water generated by the Orbiter Fuel Cells (FC), minus that water consumed by the Orbiter Flash Evaporator System (FES) and crew, is available for transfer to the ISS. During later missions, crew respired and perspired water, as well as effluent water from the Orbiter LiOH canisters, will be collected as condensate and available for transfer to the ISS. Orbiter radiator performance provides the most variance in determining the amount of net Orbiter water available for transfer to the ISS. As radiator performance decreases, the dependence upon the FES (and FC water) increases for rejecting Orbiter waste heat. Generally, radiator performance decreases as the ISS assembly size increases (especially as solar arrays are added), and also as beta angle increases. ISS solar array deployment necessitates the use of models with articulating solar arrays (for Earth local-vertical attitudes), as array position dramatically affects Orbiter radiator performance. Recent developments in the relaxation of beta angle limitations have also increased the complexity and difficulty of providing water to the ISS. Other factors that may hinder the ability to transfer water are the number of empty Contingency Water Containers (CWCs) available, duration of open-hatch time, crew activity timeline, and full CWC storage capability. A parametric study has been accomplished that provides a quick-reference table for determining expected water generation rates for ISS missions 2A.2 through 7A.1. An hourly Orbiter water generation rate is reported according to a matrix that consists of: (1) (six) significant changes in ISS assembly configuration; (2) (four) beta angles (0 deg. , +37 deg., +53 deg. , and +75 deg.); (3) the (three) most representative ISS attitudes (XPOP-O, XPOP-180 and +XVV); (4) (four) Orbiter radiator configurations (both stowed, starboard deployed, port deployed, and both deployed) and (5) the (two) conditions (radiator inlet temperatures and fuel cell power) most consistent with sleep and wake periods. Those permutations of higher probability of occurrence than others have been identified. Another parametric study has been accomplished that provides a quick-reference table for determining expected water generation rates for ISS assembly complete missions. An hourly Orbiter water generation rate is reported according to a matrix that consists of: (1) (seven) beta angles (-75 deg., -60 deg., -30 deg., 0 deg., +30 deg., +60 deg., and +75 deg.); (2) the (nine) PYR angles that define the corners of the envelope; (3) (four) Orbiter radiator configurations (both stowed, starboard deployed, port deployed, and both deployed) and (4) the (two) conditions (radiator inlet temperatures and fuel cell power) most consistent with sleep and wake periods.

The Semicircular Canal Microphonic

NASA Technical Reports Server (NTRS)

Rabbitt, R. D.; Boyle, R.; Highstein, S. M.; Dalton, Bonnie P. (Technical Monitor)

2002-01-01

Present experiments were designed to quantify the alternating current (AC) component of the semicircular canal microphonic for angular motion stimulation as a function of stimulus frequency and amplitude. The oyster toadfish, Opsanus tau, was used as the experimental model. Calibrated mechanical indentation of the horizontal canal duct was used as a stimulus to generate hair-cell and afferent responses reproducing those present during head rotation. Sensitivity to polarization of the endolymph DC voltage re: perilymph was also investigated. Modulation of endolymph voltage was recorded using conventional glass electrodes and lock-in amplification over the frequency range 0.2-80 Hz. Access to the endolymph for inserting voltage recording and current passing electrodes was obtained by sectioning the anterior canal at its apex and isolating the cut ends in air. For sinusoidal stimulation below approx.10 Hz, the horizontal semicircular canal AC microphonic was nearly independent of stimulus frequency and equal to approximately 4 microV per micron indent (equivalent to approx. 1 microV per deg/s). A saturating nonlinearity decreasing the microphonic gain was present for stimuli exceeding approx.3 micron indent (approx. 12 deg/s angular velocity). The phase was not sensitive to the saturating nonlinearity. The microphonic exhibited a resonance near 30Hz consistent with basolateral current hair cell resonance observed previously in voltage-clamp records from semicircular canal hair cells. The magnitude and phase of the microphonic exhibited sensitivity to endolymphatic polarization consistent with electro-chemical reversal of hair cell transduction currents.

A secretory multifunctional serine protease, DegP of Plasmodium falciparum, plays an important role in thermo-oxidative stress, parasite growth and development.

PubMed

Sharma, Shweta; Jadli, Mohit; Singh, Anu; Arora, Kavita; Malhotra, Pawan

2014-03-01

Plasmodium falciparum heat shock proteins and proteases are known for their indispensable roles in parasite virulence and survival in the host cell. They neutralize various host-derived stress responses that are deleterious for parasite growth and invasion. We report identification and functional characterization of the first DegP from an apicomplexan (P. falciparum). To determine the molecular identity and functions of the parasite-encoded DegP, we complemented the Escherichia coli degP null mutant with a putative PfdegP gene, and the results showed that PfDegP complements the growth defect of the temperature sensitive DegP-deficient mutant and imparts resistance to non-permissive temperatures and oxidative stress. Molecular interaction studies showed that PfDegP exists as a complex with parasite-encoded heat shock protein 70, iron superoxide dismutase and enolase. DegP expression is significantly induced in parasite culture upon heat shock/oxidative stress. Our data suggest that the PfDegP protein may play a role in the growth and development of P. falciparum through its ability to confer protection against thermal/oxidative stress. Antibody against DegP showed anti-plasmodial activity against blood-stage parasites in vitro, suggesting that PfDegP and its associated complex may be a potential focus for new anti-malarial therapies. ●PfDegP physically interacts with PfHsp70 and PfEno by anti-bait co-immunoprecipitation (View interaction) ●PfDegP physically interacts with PfEno, PfSod, PfOat, PfHsp70, PfLDH and PfGpi by anti-bait co-immunoprecipitation (View interaction) ●PfHsp-70 and PfDegP co-localize by fluorescence microscopy (View interaction) ●PfDegP physically interacts with PfOat, PfHsp70, PfEno, PfSod, PfGpi and PfLDH by surface plasmon resonance (View interaction) ●PfEno and PfDegP co-localize by fluorescence microscopy (View interaction) ●PfDegP and PfHsp70 co-localize by co-sedimentation through density gradient (View interaction). © 2014 FEBS.

Ray tracing a three dimensional scene using a grid

DOEpatents

Wald, Ingo; Ize, Santiago; Parker, Steven G; Knoll, Aaron

2013-02-26

Ray tracing a three-dimensional scene using a grid. One example embodiment is a method for ray tracing a three-dimensional scene using a grid. In this example method, the three-dimensional scene is made up of objects that are spatially partitioned into a plurality of cells that make up the grid. The method includes a first act of computing a bounding frustum of a packet of rays, and a second act of traversing the grid slice by slice along a major traversal axis. Each slice traversal includes a first act of determining one or more cells in the slice that are overlapped by the frustum and a second act of testing the rays in the packet for intersection with any objects at least partially bounded by the one or more cells overlapped by the frustum.

Semantic 3d City Model to Raster Generalisation for Water Run-Off Modelling

NASA Astrophysics Data System (ADS)

Verbree, E.; de Vries, M.; Gorte, B.; Oude Elberink, S.; Karimlou, G.

2013-09-01

Water run-off modelling applied within urban areas requires an appropriate detailed surface model represented by a raster height grid. Accurate simulations at this scale level have to take into account small but important water barriers and flow channels given by the large-scale map definitions of buildings, street infrastructure, and other terrain objects. Thus, these 3D features have to be rasterised such that each cell represents the height of the object class as good as possible given the cell size limitations. Small grid cells will result in realistic run-off modelling but with unacceptable computation times; larger grid cells with averaged height values will result in less realistic run-off modelling but fast computation times. This paper introduces a height grid generalisation approach in which the surface characteristics that most influence the water run-off flow are preserved. The first step is to create a detailed surface model (1:1.000), combining high-density laser data with a detailed topographic base map. The topographic map objects are triangulated to a set of TIN-objects by taking into account the semantics of the different map object classes. These TIN objects are then rasterised to two grids with a 0.5m cell-spacing: one grid for the object class labels and the other for the TIN-interpolated height values. The next step is to generalise both raster grids to a lower resolution using a procedure that considers the class label of each cell and that of its neighbours. The results of this approach are tested and validated by water run-off model runs for different cellspaced height grids at a pilot area in Amersfoort (the Netherlands). Two national datasets were used in this study: the large scale Topographic Base map (BGT, map scale 1:1.000), and the National height model of the Netherlands AHN2 (10 points per square meter on average). Comparison between the original AHN2 height grid and the semantically enriched and then generalised height grids shows that water barriers are better preserved with the new method. This research confirms the idea that topographical information, mainly the boundary locations and object classes, can enrich the height grid for this hydrological application.

Elliptic generation of composite three-dimensional grids about realistic aircraft

NASA Technical Reports Server (NTRS)

Sorenson, R. L.

1986-01-01

An elliptic method for generating composite grids about realistic aircraft is presented. A body-conforming grid is first generated about the entire aircraft by the solution of Poisson's differential equation. This grid has relatively coarse spacing, and it covers the entire physical domain. At boundary surfaces, cell size is controlled and cell skewness is nearly eliminated by inhomogeneous terms, which are found automatically by the program. Certain regions of the grid in which high gradients are expected, and which map into rectangular solids in the computational domain, are then designated for zonal refinement. Spacing in the zonal grids is reduced by adding points with a simple, algebraic scheme. Details of the grid generation method are presented along with results of the present application, a wing-body configuration based on the F-16 fighter aircraft.

A 'digital' technique for manual extraction of data from aerial photography

NASA Technical Reports Server (NTRS)

Istvan, L. B.; Bondy, M. T.

1977-01-01

The interpretation procedure described uses a grid cell approach. In addition, a random point is located in each cell. The procedure required that the cell/point grid be established on a base map, and identical grids be made to precisely match the scale of the photographic frames. The grid is then positioned on the photography by visual alignment to obvious features. Several alignments on one frame are sometimes required to make a precise match of all points to be interpreted. This system inherently corrects for distortions in the photography. Interpretation is then done cell by cell. In order to meet the time constraints, first order interpretation should be maintained. The data is put onto coding forms, along with other appropriate data, if desired. This 'digital' manual interpretation technique has proven to be efficient, and time and cost effective, while meeting strict requirements for data format and accuracy.

Correlations and Functional Connections in a Population of Grid Cells

PubMed Central

Roudi, Yasser

2015-01-01

We study the statistics of spike trains of simultaneously recorded grid cells in freely behaving rats. We evaluate pairwise correlations between these cells and, using a maximum entropy kinetic pairwise model (kinetic Ising model), study their functional connectivity. Even when we account for the covariations in firing rates due to overlapping fields, both the pairwise correlations and functional connections decay as a function of the shortest distance between the vertices of the spatial firing pattern of pairs of grid cells, i.e. their phase difference. They take positive values between cells with nearby phases and approach zero or negative values for larger phase differences. We find similar results also when, in addition to correlations due to overlapping fields, we account for correlations due to theta oscillations and head directional inputs. The inferred connections between neurons in the same module and those from different modules can be both negative and positive, with a mean close to zero, but with the strongest inferred connections found between cells of the same module. Taken together, our results suggest that grid cells in the same module do indeed form a local network of interconnected neurons with a functional connectivity that supports a role for attractor dynamics in the generation of grid pattern. PMID:25714908

Medial Entorhinal Grid Cells and Head Direction Cells Rotate with a T-Maze More Often During Less Recently Experienced Rotations

PubMed Central

Gupta, Kishan; Beer, Nathan J.; Keller, Lauren A.; Hasselmo, Michael E.

2014-01-01

Prior studies of head direction (HD) cells indicate strong landmark control over the preferred firing direction of these cells, with few studies exhibiting shifts away from local reference frames over time. We recorded spiking activity of grid and HD cells in the medial entorhinal cortex of rats, testing correlations of local environmental cues with the spatial tuning curves of these cells' firing fields as animals performed continuous spatial alternation on a T-maze that shared the boundaries of an open-field arena. The environment was rotated into configurations the animal had either seen or not seen in the past recording week. Tuning curves of both cell types demonstrated commensurate shifts of tuning with T-maze rotations during less recent rotations, more so than recent rotations. This strongly suggests that animals are shifting their reference frame away from the local environmental cues over time, learning to use a different reference frame more likely reliant on distal or idiothetic cues. In addition, grid fields demonstrated varying levels of “fragmentation” on the T-maze. The propensity for fragmentation does not depend on grid spacing and grid score, nor animal trajectory, indicating the cognitive treatment of environmental subcompartments is likely driven by task demands. PMID:23382518

Electrophysiological and biochemical evidence that DEG/ENaC cation channels are composed of nine subunits.

PubMed

Snyder, P M; Cheng, C; Prince, L S; Rogers, J C; Welsh, M J

1998-01-09

Members of the DEG/ENaC protein family form ion channels with diverse functions. DEG/ENaC subunits associate as hetero- and homomultimers to generate channels; however the stoichiometry of these complexes is unknown. To determine the subunit stoichiometry of the human epithelial Na+ channel (hENaC), we expressed the three wild-type hENaC subunits (alpha, beta, and gamma) with subunits containing mutations that alter channel inhibition by methanethiosulfonates. The data indicate that hENaC contains three alpha, three beta, and three gamma subunits. Sucrose gradient sedimentation of alphahENaC translated in vitro, as well as alpha-, beta-, and gammahENaC coexpressed in cells, was consistent with complexes containing nine subunits. FaNaCh and BNC1, two related DEG/ENaC channels, produced complexes of similar mass. Our results suggest a novel nine-subunit stoichiometry for the DEG/ENaC family of ion channels.

Improved ground hydrology calculations for global climate models (GCMs) - Soil water movement and evapotranspiration

NASA Technical Reports Server (NTRS)

Abramopoulos, F.; Rosenzweig, C.; Choudhury, B.

1988-01-01

A physically based ground hydrology model is presented that includes the processes of transpiration, evaporation from intercepted precipitation and dew, evaporation from bare soil, infiltration, soil water flow, and runoff. Data from the Goddard Institute for Space Studies GCM were used as inputs for off-line tests of the model in four 8 x 10 deg regions, including Brazil, Sahel, Sahara, and India. Soil and vegetation input parameters were caculated as area-weighted means over the 8 x 10 deg gridbox; the resulting hydrological quantities were compared to ground hydrology model calculations performed on the 1 x 1 deg cells which comprise the 8 x 10 deg gridbox. Results show that the compositing procedure worked well except in the Sahel, where low soil water levels and a heterogeneous land surface produce high variability in hydrological quantities; for that region, a resolution better than 8 x 10 deg is needed.

An Investigation of Aerosol and Ozone Measurements from the Cryogenic Limb Array Etalon Spectrometer: Validation and Relation to Other Chemical Species

NASA Technical Reports Server (NTRS)

Deshler, Terry

1997-01-01

Throughout this study we focused on comparisons of CLAES and in situ measurements of ozone and aerosol extinction. Thus the comparison is between satellite data representative of large spatial regions and in situ data representative of nearly point samples. Both instruments provide vertical profiles, but the region of overlap is limited to between approximately 10 and 100 mb. CLAES Version 7 ozone measurements have been compared to electrochemical cell ozonesonde measurements over McMurdo Station, Antarctica (78 deg S, 167 deg E), Dumont d'Urville, Antarctica (66.7 deg S, 140 deg E), Laramie, Wyoming (41 deg N, 106 deg W), and Bear Island, Norway (74.3 deg N, 19 deg E). Comparisons were made between vertical ozone profiles, and between integrated column ozone over the region of overlap of the measurements. Comparisons using CLAES Version 8 data are underway. CLAES Version 8 aerosol extinction measurements at all wavelengths have also been compared to University of Wyoming aerosol extinctions over McMurdo Station, Antarctica, and over Laramie, Wyoming. Coincidences in all cases were determined by minimizing the distance between the CLAES observations and the surface station, and the time separation between the satellite and in situ measurements.

The Art of Grid Fields: Geometry of Neuronal Time

PubMed Central

Shilnikov, Andrey L.; Maurer, Andrew Porter

2016-01-01

The discovery of grid cells in the entorhinal cortex has both elucidated our understanding of spatial representations in the brain, and germinated a large number of theoretical models regarding the mechanisms of these cells’ striking spatial firing characteristics. These models cross multiple neurobiological levels that include intrinsic membrane resonance, dendritic integration, after hyperpolarization characteristics and attractor dynamics. Despite the breadth of the models, to our knowledge, parallels can be drawn between grid fields and other temporal dynamics observed in nature, much of which was described by Art Winfree and colleagues long before the initial description of grid fields. Using theoretical and mathematical investigations of oscillators, in a wide array of mediums far from the neurobiology of grid cells, Art Winfree has provided a substantial amount of research with significant and profound similarities. These theories provide specific inferences into the biological mechanisms and extraordinary resemblances across phenomenon. Therefore, this manuscript provides a novel interpretation on the phenomenon of grid fields, from the perspective of coupled oscillators, postulating that grid fields are the spatial representation of phase resetting curves in the brain. In contrast to prior models of gird cells, the current manuscript provides a sketch by which a small network of neurons, each with oscillatory components can operate to form grid cells, perhaps providing a unique hybrid between the competing attractor neural network and oscillatory interference models. The intention of this new interpretation of the data is to encourage novel testable hypotheses. PMID:27013981

Investigation of candidate genes for osteoarthritis based on gene expression profiles.

PubMed

Dong, Shuanghai; Xia, Tian; Wang, Lei; Zhao, Qinghua; Tian, Jiwei

2016-12-01

To explore the mechanism of osteoarthritis (OA) and provide valid biological information for further investigation. Gene expression profile of GSE46750 was downloaded from Gene Expression Omnibus database. The Linear Models for Microarray Data (limma) package (Bioconductor project, http://www.bioconductor.org/packages/release/bioc/html/limma.html) was used to identify differentially expressed genes (DEGs) in inflamed OA samples. Gene Ontology function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis of DEGs were performed based on Database for Annotation, Visualization and Integrated Discovery data, and protein-protein interaction (PPI) network was constructed based on the Search Tool for the Retrieval of Interacting Genes/Proteins database. Regulatory network was screened based on Encyclopedia of DNA Elements. Molecular Complex Detection was used for sub-network screening. Two sub-networks with highest node degree were integrated with transcriptional regulatory network and KEGG functional enrichment analysis was processed for 2 modules. In total, 401 up- and 196 down-regulated DEGs were obtained. Up-regulated DEGs were involved in inflammatory response, while down-regulated DEGs were involved in cell cycle. PPI network with 2392 protein interactions was constructed. Moreover, 10 genes including Interleukin 6 (IL6) and Aurora B kinase (AURKB) were found to be outstanding in PPI network. There are 214 up- and 8 down-regulated transcription factor (TF)-target pairs in the TF regulatory network. Module 1 had TFs including SPI1, PRDM1, and FOS, while module 2 contained FOSL1. The nodes in module 1 were enriched in chemokine signaling pathway, while the nodes in module 2 were mainly enriched in cell cycle. The screened DEGs including IL6, AGT, and AURKB might be potential biomarkers for gene therapy for OA by being regulated by TFs such as FOS and SPI1, and participating in the cell cycle and cytokine-cytokine receptor interaction pathway. Copyright © 2016 Turkish Association of Orthopaedics and Traumatology. Production and hosting by Elsevier B.V. All rights reserved.

Geosat Data Assimilation with Application to the Eastern North Atlantic

NASA Technical Reports Server (NTRS)

Stammer, Detlef

1997-01-01

An attempt is made to determine the three-dimensional ocean circulation from satellite altimeter measurements by assimilating Geosat sea surface height data into an eddy-resolving QuasiGeostrophic (QG) model of the eastern North Atlantic Ocean. Results are tested against independent information from hydrographic field observations and moored current meter data collected during the Geosat ERM. The comparison supports the concept of inferring aspects of the three-dimensional flow field from sea surface height observations by combining altimetric measurements with the dynamics of ocean circulation models. A Holland-type QG model with open boundaries is set up on a 2000 km X 2000 km domain of the eastern North Atlantic between 25 deg. and 45 deg. N, 32 deg. and 8 deg. W. By using a simple nudging technique, about two years of Geosat altimeter data are assimilated into the model every five days as space-time objective analyses on the model grid. The error information resulting from the analysis is used during the assimilation procedure to account for data uncertainties. Results show an intense eddy field, which in the surface layer interacts with a meandering Azores Front. Compared to Geosat, the model leads to smoothed fields that follow the observations. Model simulations are significantly correlated with hydrographic data from March 1988 and June 1989, both close to the surface and in the subsurface. Good agreement is also found between the model velocity fields and moored current meter data in the top two model layers. The agreement is visually weak in the bottom layer, although a coherence analysis reveals an agreement between the model simulation and current meter data over the full water column at periods exceeding 80 days.

Conical Euler simulation and active suppression of delta wing rocking motion

NASA Technical Reports Server (NTRS)

Lee, Elizabeth M.; Batina, John T.

1990-01-01

A conical Euler code was developed to study unsteady vortex-dominated flows about rolling highly-swept delta wings, undergoing either forced or free-to-roll motions including active roll suppression. The flow solver of the code involves a multistage Runge-Kutta time-stepping scheme which uses a finite volume spatial discretization of the Euler equations on an unstructured grid of triangles. The code allows for the additional analysis of the free-to-roll case, by including the rigid-body equation of motion for its simultaneous time integration with the governing flow equations. Results are presented for a 75 deg swept sharp leading edge delta wing at a freestream Mach number of 1.2 and at alpha equal to 10 and 30 deg angle of attack. A forced harmonic analysis indicates that the rolling moment coefficient provides: (1) a positive damping at the lower angle of attack equal to 10 deg, which is verified in a free-to-roll calculation; (2) a negative damping at the higher angle of attack equal to 30 deg at the small roll amplitudes. A free-to-roll calculation for the latter case produces an initially divergent response, but as the amplitude of motion grows with time, the response transitions to a wing-rock type of limit cycle oscillation. The wing rocking motion may be actively suppressed, however, through the use of a rate-feedback control law and antisymmetrically deflected leading edge flaps. The descriptions of the conical Euler flow solver and the free-to-roll analysis are presented. Results are also presented which give insight into the flow physics associated with unsteady vortical flows about forced and free-to-roll delta wings, including the active roll suppression of this wing-rock phenomenon.

Distinct speed dependence of entorhinal island and ocean cells, including respective grid cells

PubMed Central

Sun, Chen; Kitamura, Takashi; Yamamoto, Jun; Martin, Jared; Pignatelli, Michele; Kitch, Lacey J.; Schnitzer, Mark J.; Tonegawa, Susumu

2015-01-01

Entorhinal–hippocampal circuits in the mammalian brain are crucial for an animal’s spatial and episodic experience, but the neural basis for different spatial computations remain unknown. Medial entorhinal cortex layer II contains pyramidal island and stellate ocean cells. Here, we performed cell type-specific Ca2+ imaging in freely exploring mice using cellular markers and a miniature head-mounted fluorescence microscope. We found that both oceans and islands contain grid cells in similar proportions, but island cell activity, including activity in a proportion of grid cells, is significantly more speed modulated than ocean cell activity. We speculate that this differential property reflects island cells’ and ocean cells’ contribution to different downstream functions: island cells may contribute more to spatial path integration, whereas ocean cells may facilitate contextual representation in downstream circuits. PMID:26170279

Reflectance model of a plant leaf

NASA Technical Reports Server (NTRS)

Kumar, R.; Silva, L.

1973-01-01

A light ray, incident at 5 deg to the normal, is geometrically plotted through the drawing of the cross section of a soybean leaf using Fresnel's Equations and Snell's Law. The optical mediums of the leaf considered for ray tracing are: air, cell sap, chloroplast, and cell wall. The above ray is also drawn through the same leaf cross section considering cell wall and air as the only optical mediums. The values of the reflection and transmission found from ray tracing agree closely with the experimental results obtained using a Beckman DK-2A Spectroreflectometer. Similarly a light ray, incident at about 60 deg to the normal, is drawn through the palisade cells of a soybean leaf to illustrate the pathway of light, incident at an oblique angle, through the palisade cells.

Spatial cell firing during virtual navigation of open arenas by head-restrained mice.

PubMed

Chen, Guifen; King, John Andrew; Lu, Yi; Cacucci, Francesca; Burgess, Neil

2018-06-18

We present a mouse virtual reality (VR) system which restrains head-movements to horizontal rotations, compatible with multi-photon imaging. This system allows expression of the spatial navigation and neuronal firing patterns characteristic of real open arenas (R). Comparing VR to R: place and grid, but not head-direction, cell firing had broader spatial tuning; place, but not grid, cell firing was more directional; theta frequency increased less with running speed; whereas increases in firing rates with running speed and place and grid cells' theta phase precession were similar. These results suggest that the omni-directional place cell firing in R may require local-cues unavailable in VR, and that the scale of grid and place cell firing patterns, and theta frequency, reflect translational motion inferred from both virtual (visual and proprioceptive) and real (vestibular translation and extra-maze) cues. By contrast, firing rates and theta phase precession appear to reflect visual and proprioceptive cues alone. © 2018, Chen et al.

Validation of Land-Surface Mosaic Heterogeneity in the GEOS DAS

NASA Technical Reports Server (NTRS)

Bosilovich, Michael G.; Molod, Andrea; Houser, Paul R.; Schubert, Siegfried

1999-01-01

The Mosaic Land-surface Model (LSM) has been included into the current GEOS Data Assimilation System (DAS). The LSM uses a more advanced representation of physical processes than previous versions of the GEOS DAS, including the representation of sub-grid heterogeneity of the land-surface through the Mosaic approach. As a first approximation, Mosaic assumes that all similar surface types within a grid-cell can be lumped together as a single'tile'. Within one GCM grid-cell, there might be 1 - 5 different tiles or surface types. All tiles are subjected to the grid-scale forcing (radiation, air temperature and specific humidity, and precipitation), and the sub-grid variability is a function of the tile characteristics. In this paper, we validate the LSM sub-grid scale variability (tiles) using a variety of surface observing stations from the Southern Great Plains (SGP) site of the Atmospheric Radiation Measurement (ARM) Program. One of the primary goals of SGP ARM is to study the variability of atmospheric radiation within a G,CM grid-cell. Enough surface data has been collected by ARM to extend this goal to sub-grid variability of the land-surface energy and water budgets. The time period of this study is the Summer of 1998 (June I - September 1). The ARM site data consists of surface meteorology, energy flux (eddy correlation and bowen ratio), soil water observations spread over an area similar to the size of a G-CM grid-cell. Various ARM stations are described as wheat and alfalfa crops, pasture and range land. The LSM tiles considered at the grid-space (2 x 2.5) nearest the ARM site include, grassland, deciduous forests, bare soil and dwarf trees. Surface energy and water balances for each tile type are compared with observations. Furthermore, we will discuss the land-surface sub-grid variability of both the ARM observations and the DAS.

Solving Navigational Uncertainty Using Grid Cells on Robots

PubMed Central

Milford, Michael J.; Wiles, Janet; Wyeth, Gordon F.

2010-01-01

To successfully navigate their habitats, many mammals use a combination of two mechanisms, path integration and calibration using landmarks, which together enable them to estimate their location and orientation, or pose. In large natural environments, both these mechanisms are characterized by uncertainty: the path integration process is subject to the accumulation of error, while landmark calibration is limited by perceptual ambiguity. It remains unclear how animals form coherent spatial representations in the presence of such uncertainty. Navigation research using robots has determined that uncertainty can be effectively addressed by maintaining multiple probabilistic estimates of a robot's pose. Here we show how conjunctive grid cells in dorsocaudal medial entorhinal cortex (dMEC) may maintain multiple estimates of pose using a brain-based robot navigation system known as RatSLAM. Based both on rodent spatially-responsive cells and functional engineering principles, the cells at the core of the RatSLAM computational model have similar characteristics to rodent grid cells, which we demonstrate by replicating the seminal Moser experiments. We apply the RatSLAM model to a new experimental paradigm designed to examine the responses of a robot or animal in the presence of perceptual ambiguity. Our computational approach enables us to observe short-term population coding of multiple location hypotheses, a phenomenon which would not be easily observable in rodent recordings. We present behavioral and neural evidence demonstrating that the conjunctive grid cells maintain and propagate multiple estimates of pose, enabling the correct pose estimate to be resolved over time even without uniquely identifying cues. While recent research has focused on the grid-like firing characteristics, accuracy and representational capacity of grid cells, our results identify a possible critical and unique role for conjunctive grid cells in filtering sensory uncertainty. We anticipate our study to be a starting point for animal experiments that test navigation in perceptually ambiguous environments. PMID:21085643

TU-H-BRC-07: Therapeutic Benefit in Spatially Fractionated Radiotherapy (GRID) Using Helical Tomotherapy

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

Narayanasamy, G; Zhang, X; Paudel, N

Purpose: The aim of this project is to study the therapeutic ratio (TR) for helical Tomotherapy (HT) based spatially fractionated radiotherapy (GRID). Estimation of TR was based on the linear-quadratic cell survival model by comparing the normal cell survival in a HT GRID to that of a uniform dose delivery in an open-field for the same tumor survival. Methods: HT GRID plan was generated using a patient specific virtual GRID block pattern of non-divergent, cylinder shaped holes using MLCs. TR was defined as the ratio of normal tissue surviving fraction (SF) under HT GRID irradiation to an open field irradiationmore » with an equivalent dose that result in the same tumor cell SF. The ratio was estimated from DVH data on ten patient plans with deep seated, bulky tumor approved by the treating radiation oncologist. Dependence of the TR values on radio-sensitivity of the tumor cells and prescription dose were also analyzed. Results: The mean ± standard deviation (SD) of TR was 4.0±0.7 (range: 3.1 to 5.5) for the 10 patients with single fraction dose of 20 Gy and tumor cell SF of 0.5 at 2 Gy. In addition, mean±SD of TR = 1±0.1 and 18.0±5.1 were found for tumor with SF of 0.3 and 0.7, respectively. Reducing the prescription dose to 15 and 10 Gy lowered the TR to 2.0±0.2 and 1.2±0.04 for a tumor cell SF of 0.5 at 2 Gy. In this study, the SF of normal cells was assumed to be 0.5 at 2 Gy. Conclusion: HT GRID displayed a significant therapeutic advantage over uniform dose from an open field irradiation. TR increases with the radioresistance of the tumor cells and with prescription dose.« less

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

PubMed

Liao, Wei; Jordaan, Gwen; Nham, Phillipp; Phan, Ryan T; Pelegrini, Matteo; Sharma, Sanjai

2015-10-16

To determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed. Ten CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system. An average of 48.5 million reads for B cells, and 50.6 million reads for CLL specimens were obtained with 10396 and 10448 assembled transcripts for normal B cells and primary CLL specimens respectively. With the Cuffdiff analysis, 2091 differentially expressed genes (DEG) between B cells and CLL specimens based on FPKM (fragments per kilobase of transcript per million reads and false discovery rate, FDR q < 0.05, fold change >2) were identified. Expression of selected DEGs (n = 32) with up regulated and down regulated expression in CLL from RNA-seq data were also analyzed by qRT-PCR in a test cohort of CLL specimens. Even though there was a variation in fold expression of DEG genes between RNA-seq and qRT-PCR; more than 90 % of analyzed genes were validated by qRT-PCR analysis. Analysis of RNA-seq data for splicing alterations in CLL and B cells was performed by Multivariate Analysis of Transcript Splicing (MATS analysis). Skipped exon was the most frequent splicing alteration in CLL specimens with 128 significant events (P-value <0.05, minimum inclusion level difference >0.1). The RNA-seq analysis of CLL specimens identifies novel DEG and alternatively spliced genes that are potential prognostic markers and therapeutic targets. High level of validation by qRT-PCR for a number of DEG genes supports the accuracy of this analysis. Global comparison of transcriptomes of B cells, IGVH non-mutated CLL (U-CLL) and mutated CLL specimens (M-CLL) with multidimensional scaling analysis was able to segregate CLL and B cell transcriptomes but the M-CLL and U-CLL transcriptomes were indistinguishable. The analysis of HTS RNA-seq data to identify alternative splicing events and other genetic abnormalities specific to CLL is an added advantage of RNA-seq that is not feasible with other genome wide analysis.

Persistence of Rift Valley fever virus in East Africa

NASA Astrophysics Data System (ADS)

Gachohi, J.; Hansen, F.; Bett, B.; Kitala, P.

2012-04-01

Rift Valley fever virus (RVFv) is a mosquito-borne pathogen of livestock, wildlife and humans that causes severe outbreaks in intervals of several years. One of the open questions is how the virus persists between outbreaks. We developed a spatially-explicit, individual-based simulation model of the RVFv transmission dynamics to investigate this question. The model, is based on livestock and mosquito population dynamics. Spatial aspects are explicitly represented by a set of grid cells that represent mosquito breeding sites. A grid cell measures 500 by 500m and the model considers a grid of 100 by 100 grid cells; the model thus operates on the regional scale of 2500km2. Livestock herds move between grid cells, and provide connectivity between the cells. The model is used to explore the spatio-temporal dynamics of RVFv persistence in absence of a wildlife reservoir in an east African semi-arid context. Specifically, the model assesses the importance of local virus persistence in mosquito breeding sites relative to global virus persistence mitigated by movement of hosts. Local persistence is determined by the length of time the virus remains in a mosquito breeding site once introduced. In the model, this is a function of the number of mosquitoes that emerge infected and their lifespan. Global persistence is determined by the level of connectivity between isolated grid cells. Our work gives insights into the ecological and epidemiological conditions under which RVFv persists. The implication for disease surveillance and management are discussed.

Domain decomposition by the advancing-partition method for parallel unstructured grid generation

NASA Technical Reports Server (NTRS)

Banihashemi, legal representative, Soheila (Inventor); Pirzadeh, Shahyar Z. (Inventor)

2012-01-01

In a method for domain decomposition for generating unstructured grids, a surface mesh is generated for a spatial domain. A location of a partition plane dividing the domain into two sections is determined. Triangular faces on the surface mesh that intersect the partition plane are identified. A partition grid of tetrahedral cells, dividing the domain into two sub-domains, is generated using a marching process in which a front comprises only faces of new cells which intersect the partition plane. The partition grid is generated until no active faces remain on the front. Triangular faces on each side of the partition plane are collected into two separate subsets. Each subset of triangular faces is renumbered locally and a local/global mapping is created for each sub-domain. A volume grid is generated for each sub-domain. The partition grid and volume grids are then merged using the local-global mapping.

Self-similar grid patterns in free-space shuffle-exchange networks

NASA Astrophysics Data System (ADS)

Haney, Michael W.

1993-12-01

Self-similar grid patterns are proposed as an alternative to rectangular grid, array optoelectronic sources, and detectors of smart pixels. For shuffle based multistage interconnection networks, it is suggested that smart pixel should not be arrayed on a rectangular grid and that smart pixel unit cell should be the kernel of a self-similar grid pattern.

Modulated two-dimensional charge-carrier density in LaTiO3-layer-doped LaAlO3/SrTiO3 heterostructure.

PubMed

Nazir, Safdar; Bernal, Camille; Yang, Kesong

2015-03-11

The highly mobile two-dimensional electron gas (2DEG) formed at the polar/nonpolar LaAlO3/SrTiO3 (LAO/STO) heterostructure (HS) is a matter of great interest because of its potential applications in nanoscale solid-state devices. To realize practical implementation of the 2DEG in device design, desired physical properties such as tuned charge carrier density and mobility are necessary. In this regard, polar perovskite-based transition metal oxides can act as doping layers at the interface and are expected to tune the electronic properties of 2DEG of STO-based HS systems dramatically. Herein, we investigated the doping effects of LaTiO3(LTO) layers on the electronic properties of 2DEG at n-type (LaO)(+1)/(TiO2)(0) interface in the LAO/STO HS using spin-polarized density functional theory calculations. Our results indicate an enhancement of orbital occupation near the Fermi energy, which increases with respect to the number of LTO unit cells, resulting in a higher charge carrier density of 2DEG than that of undoped system. The enhanced charge carrier density is attributed to an extra electron introduced by the Ti 3d(1) orbitals from the LTO dopant unit cells. This conclusion is consistent with the recent experimental findings (Appl. Phys. Lett. 2013, 102, 091601). Detailed charge density and partial density of states analysis suggests that the 2DEG in the LTO-doped HS systems primarily comes from partially occupied dyz and dxz orbitals.

Expression of chicken ovalbumin upstream promoter-transcription factor I (COUP-TFI) in bladder transitional cell carcinoma.

PubMed

Ham, Won Sik; Lee, Joo Hyoung; Yu, Ho Song; Choi, Young Deuk

2008-10-01

An analysis of differentially expressed genes (DEGs) between bladder transitional cell carcinoma (TCC) and the surrounding urothelium to help identify what lies behind the mechanism of multifocal tumor development has not yet been performed. We sought to find a new DEG related to the development of bladder TCC. Thirty-nine bladder TCC tissues paired with normal-appearing urothelium tissues obtained from the same patient were used as subjects. Initially, we compared the messenger RNA (mRNA) profiles between normal-appearing urothelium and TCC tissue of 1 patient by using annealing control primer (ACP)-based GeneFishing polymerase chain reaction (PCR) and selective amplification of family members (SAFM) PCR to identify potential DEGs. To validate the results of the ACP data, reverse transcriptase-polymerase chain reaction (RT-PCR) was performed on those of all 39 patients. Among the several DEGs discovered in the ACP data, 1 DEG was chosen as the candidate for the RT-PCR, that is present or markedly upregulated in normal-appearing urothelial tissue compared with TCC tissue. Gene sequence searching revealed that this DEG is chicken ovalbumin upstream promoter-transcription factor I (COUP-TFI). Downregulation of COUP-TFI mRNA expression in TCC tissue compared to normal-appearing urothelium tissue of the same patient, irrespective of tumor stage and grade, was confirmed by RT-PCR in 39 patients. Our results suggest that the loss of COUP-TFI may play a role in the transition from normal epithelium to TCC. Further characterization of the COUP-TFI gene is expected to give us informations about bladder TCC tumorigenesis.

Ca2+ permeability and Na+ conductance in cellular toxicity caused by hyperactive DEG/ENaC channels.

PubMed

Matthewman, Cristina; Miller-Fleming, Tyne W; Miller, David M; Bianchi, Laura

2016-12-01

Hyperactivated DEG/ENaC channels cause neuronal death mediated by intracellular Ca 2+ overload. Mammalian ASIC1a channels and MEC-4(d) neurotoxic channels in Caenorhabditis elegans both conduct Na + and Ca 2+ , raising the possibility that direct Ca 2+ influx through these channels contributes to intracellular Ca 2+ overload. However, we showed that the homologous C. elegans DEG/ENaC channel UNC-8(d) is not Ca 2+ permeable, yet it is neurotoxic, suggesting that Na + influx is sufficient to induce cell death. Interestingly, UNC-8(d) shows small currents due to extracellular Ca 2+ block in the Xenopus oocyte expression system. Thus, MEC-4(d) and UNC-8(d) differ both in current amplitude and Ca 2+ permeability. Given that these two channels show a striking difference in toxicity, we wondered how Na + conductance vs. Ca 2+ permeability contributes to cell death. To address this question, we built an UNC-8/MEC-4 chimeric channel that retains the calcium permeability of MEC-4 and characterized its properties in Xenopus oocytes. Our data support the hypothesis that for Ca 2+ -permeable DEG/ENaC channels, both Ca 2+ permeability and Na + conductance contribute to toxicity. However, for Ca 2+ -impermeable DEG/ENaCs (e.g., UNC-8), our evidence shows that constitutive Na + conductance is sufficient to induce toxicity, and that this effect is enhanced as current amplitude increases. Our work further refines the contribution of different channel properties to cellular toxicity induced by hyperactive DEG/ENaC channels. Copyright © 2016 the American Physiological Society.

Ca2+ permeability and Na+ conductance in cellular toxicity caused by hyperactive DEG/ENaC channels

PubMed Central

Matthewman, Cristina; Miller-Fleming, Tyne W.; Miller, David M.

2016-01-01

Hyperactivated DEG/ENaC channels cause neuronal death mediated by intracellular Ca2+ overload. Mammalian ASIC1a channels and MEC-4(d) neurotoxic channels in Caenorhabditis elegans both conduct Na+ and Ca2+, raising the possibility that direct Ca2+ influx through these channels contributes to intracellular Ca2+ overload. However, we showed that the homologous C. elegans DEG/ENaC channel UNC-8(d) is not Ca2+ permeable, yet it is neurotoxic, suggesting that Na+ influx is sufficient to induce cell death. Interestingly, UNC-8(d) shows small currents due to extracellular Ca2+ block in the Xenopus oocyte expression system. Thus, MEC-4(d) and UNC-8(d) differ both in current amplitude and Ca2+ permeability. Given that these two channels show a striking difference in toxicity, we wondered how Na+ conductance vs. Ca2+ permeability contributes to cell death. To address this question, we built an UNC-8/MEC-4 chimeric channel that retains the calcium permeability of MEC-4 and characterized its properties in Xenopus oocytes. Our data support the hypothesis that for Ca2+-permeable DEG/ENaC channels, both Ca2+ permeability and Na+ conductance contribute to toxicity. However, for Ca2+-impermeable DEG/ENaCs (e.g., UNC-8), our evidence shows that constitutive Na+ conductance is sufficient to induce toxicity, and that this effect is enhanced as current amplitude increases. Our work further refines the contribution of different channel properties to cellular toxicity induced by hyperactive DEG/ENaC channels. PMID:27760755

Differential gene expression in the intestine of sea cucumber (Apostichopus japonicus) under low and high salinity conditions.

PubMed

Zhang, Libin; Feng, Qiming; Sun, Lina; Ding, Kui; Huo, Da; Fang, Yan; Zhang, Tao; Yang, Hongsheng

2018-03-01

Sea cucumber, Apostichopus japonicus is an important species for aquaculture, and its behavior and physiology can change in response to changing salinity conditions. For this reason, it is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity. In this study, RNA-Seq provided a general overview of the gene expression profiles in the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environments. Screening for differentially expressed genes (DEGs) using the NOISeq method identified 109, 100, and 89 DEGs based on a fold change of ≥2 and divergence probability ≥0.8 according to the comparisons of SD20 vs. SD30, SD20 vs.SD40, and SD30 vs. SD40, respectively. Gene ontology analysis showed that the terms "metabolic process" and "catalytic activity" comprised the most enriched DEGs. These fell into the categories of "biological process" and "molecular function". While "cell" and "cell part" had the most enriched DEGs in the category of "cellular component". With these DEGs mapping to 2119, 159, and 160 pathways in the Kyoto Encyclopedia of Genes and Genomes database. Of these 51, 2, and 57 pathways were significantly enriched, respectively. The osmosis-specific DEGs identified in this study of A. japonicus will be important targets for further studies to understand the biochemical mechanisms involved with the adaption of sea cucumbers to changes in salinity. Copyright © 2017. Published by Elsevier Inc.

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data.

PubMed

Yip, Shun H; Sham, Pak Chung; Wang, Junwen

2018-02-21

Traditional RNA sequencing (RNA-seq) allows the detection of gene expression variations between two or more cell populations through differentially expressed gene (DEG) analysis. However, genes that contribute to cell-to-cell differences are not discoverable with RNA-seq because RNA-seq samples are obtained from a mixture of cells. Single-cell RNA-seq (scRNA-seq) allows the detection of gene expression in each cell. With scRNA-seq, highly variable gene (HVG) discovery allows the detection of genes that contribute strongly to cell-to-cell variation within a homogeneous cell population, such as a population of embryonic stem cells. This analysis is implemented in many software packages. In this study, we compare seven HVG methods from six software packages, including BASiCS, Brennecke, scLVM, scran, scVEGs and Seurat. Our results demonstrate that reproducibility in HVG analysis requires a larger sample size than DEG analysis. Discrepancies between methods and potential issues in these tools are discussed and recommendations are made.

Shearing-induced asymmetry in entorhinal grid cells.

PubMed

Stensola, Tor; Stensola, Hanne; Moser, May-Britt; Moser, Edvard I

2015-02-12

Grid cells are neurons with periodic spatial receptive fields (grids) that tile two-dimensional space in a hexagonal pattern. To provide useful information about location, grids must be stably anchored to an external reference frame. The mechanisms underlying this anchoring process have remained elusive. Here we show in differently sized familiar square enclosures that the axes of the grids are offset from the walls by an angle that minimizes symmetry with the borders of the environment. This rotational offset is invariably accompanied by an elliptic distortion of the grid pattern. Reversing the ellipticity analytically by a shearing transformation removes the angular offset. This, together with the near-absence of rotation in novel environments, suggests that the rotation emerges through non-coaxial strain as a function of experience. The systematic relationship between rotation and distortion of the grid pattern points to shear forces arising from anchoring to specific geometric reference points as key elements of the mechanism for alignment of grid patterns to the external world.

Cause and Cure-Deterioration in Accuracy of CFD Simulations with Use of High-Aspect-Ratio Triangular/Tetrahedral Grids

NASA Technical Reports Server (NTRS)

Chang, Sin-Chung; Chang, Chau-Lyan; Venkatachari, Balaji

2017-01-01

In the multi-dimensional space-time conservation element and solution element16 (CESE) method, triangles and tetrahedral mesh elements turn out to be the most natural building blocks for 2D and 3D spatial grids, respectively. As such, the CESE method is naturally compatible with the simplest 2D and 3D unstructured grids and thus can be easily applied to solve problems with complex geometries. However, because (a) accurate solution of a high-Reynolds number flow field near a solid wall requires that the grid intervals along the direction normal to the wall be much finer than those in a direction parallel to the wall and, as such, the use of grid cells with extremely high aspect ratio (103 to 106) may become mandatory, and (b) unlike quadrilateral hexahedral grids, it is well-known that accuracy of gradient computations involving triangular tetrahedral grids tends to deteriorate rapidly as cell aspect ratio increases. As a result, the use of triangular tetrahedral grid cells near a solid wall has long been deemed impractical by CFD researchers. In view of (a) the critical role played by triangular tetrahedral grids in the CESE development, and (b) the importance of accurate resolution of high-Reynolds number flow field near a solid wall, as will be presented in the main paper, a comprehensive and rigorous mathematical framework that clearly identifies the reasons behind the accuracy deterioration as described above has been developed for the 2D case involving triangular cells. By avoiding the pitfalls identified by the 2D framework, and its 3D extension, it has been shown numerically.

A terrestrial biosphere model optimized to atmospheric CO2 concentration and above ground woody biomass

NASA Astrophysics Data System (ADS)

Saito, M.; Ito, A.; Maksyutov, S. S.

2013-12-01

This study documents an optimization of a prognostic biosphere model (VISIT; Vegetation Integrative Similator for Trace gases) to observations of atmospheric CO2 concentration and above ground woody biomass by using a Bayesian inversion method combined with an atmospheric tracer transport model (NIES-TM; National Institute for Environmental Studies / Frontier Research Center for Global Change (NIES/FRCGC) off-line global atmospheric tracer transport model). The assimilated observations include 74 station records of surface atmospheric CO2 concentration and aggregated grid data sets of above ground woody biomass (AGB) and net primary productivity (NPP) over the globe. Both the biosphere model and the atmospheric transport model are used at a horizontal resolution of 2.5 deg x 2.5 deg grid with temporal resolutions of a day and an hour, respectively. The atmospheric transport model simulates atmospheric CO2 concentration with nine vertical levels using daily net ecosystem CO2 exchange rate (NEE) from the biosphere model, oceanic CO2 flux, and fossil fuel emission inventory. The models are driven by meteorological data from JRA-25 (Japanese 25-year ReAnalysis) and JCDAS (JMA Climate Data Assimilation System). Statistically optimum physiological parameters in the biosphere model are found by iterative minimization of the corresponding Bayesian cost function. We select thirteen physiological parameter with high sensitivity to NEE, NPP, and AGB for the minimization. Given the optimized physiological parameters, the model shows error reductions in seasonal variation of the CO2 concentrations especially in the northern hemisphere due to abundant observation stations, while errors remain at a few stations that are located in coastal coastal area and stations in the southern hemisphere. The model also produces moderate estimates of the mean magnitudes and probability distributions in AGB and NPP for each biome. However, the model fails in the simulation of the terrestrial vegetation compositions in some grids. These misfits are assumed to derive from simplified representation in the biosphere model without the impact of land use change and dire disturbance and the seasonal variability in the physiological parameters.

A multigrid nonoscillatory method for computing high speed flows

NASA Technical Reports Server (NTRS)

Li, C. P.; Shieh, T. H.

1993-01-01

A multigrid method using different smoothers has been developed to solve the Euler equations discretized by a nonoscillatory scheme up to fourth order accuracy. The best smoothing property is provided by a five-stage Runge-Kutta technique with optimized coefficients, yet the most efficient smoother is a backward Euler technique in factored and diagonalized form. The singlegrid solution for a hypersonic, viscous conic flow is in excellent agreement with the solution obtained by the third order MUSCL and Roe's method. Mach 8 inviscid flow computations for a complete entry probe have shown that the accuracy is at least as good as the symmetric TVD scheme of Yee and Harten. The implicit multigrid method is four times more efficient than the explicit multigrid technique and 3.5 times faster than the single-grid implicit technique. For a Mach 8.7 inviscid flow over a blunt delta wing at 30 deg incidence, the CPU reduction factor from the three-level multigrid computation is 2.2 on a grid of 37 x 41 x 73 nodes.

Experimental and analytical study of close-coupled ventral nozzles for ASTOVL aircraft

NASA Technical Reports Server (NTRS)

Mcardle, Jack G.; Smith, C. Frederic

1990-01-01

Flow in a generic ventral nozzle system was studied experimentally and analytically with a block version of the PARC3D computational fluid dynamics program (a full Navier-Stokes equation solver) in order to evaluate the program's ability to predict system performance and internal flow patterns. For the experimental work a one-third-size model tailpipe with a single large rectangular ventral nozzle mounted normal to the tailpipe axis was tested with unheated air at steady-state pressure ratios up to 4.0. The end of the tailpipe was closed to simulate a blocked exhaust nozzle. Measurements showed about 5 1/2 percent flow-turning loss, reasonable nozzle performance coefficients, and a significant aftward axial component of thrust due to flow turning loss, reasonable nozzle performance coefficients, and a significant aftward axial component of thrust due to flow turning more than 90 deg. Flow behavior into and through the ventral duct is discussed and illustrated with paint streak flow visualization photographs. For the analytical work the same ventral system configuration was modeled with two computational grids to evaluate the effect of grid density. Both grids gave good results. The finer-grid solution produced more detailed flow patterns and predicted performance parameters, such as thrust and discharge coefficient, within 1 percent of the measured values. PARC3D flow visualization images are shown for comparison with the paint streak photographs. Modeling and computational issues encountered in the analytical work are discussed.

Impact of dose size in single fraction spatially fractionated (grid) radiotherapy for melanoma

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

Zhang, Hualin, E-mail: hualin.zhang@northwestern.edu, E-mail: hualinzhang@yahoo.com; Zhong, Hualiang; Barth, Rolf F.

2014-02-15

Purpose: To evaluate the impact of dose size in single fraction, spatially fractionated (grid) radiotherapy for selectively killing infiltrated melanoma cancer cells of different tumor sizes, using different radiobiological models. Methods: A Monte Carlo technique was employed to calculate the 3D dose distribution of a commercially available megavoltage grid collimator in a 6 MV beam. The linear-quadratic (LQ) and modified linear quadratic (MLQ) models were used separately to evaluate the therapeutic outcome of a series of single fraction regimens that employed grid therapy to treat both acute and late responding melanomas of varying sizes. The dose prescription point was atmore » the center of the tumor volume. Dose sizes ranging from 1 to 30 Gy at 100% dose line were modeled. Tumors were either touching the skin surface or having their centers at a depth of 3 cm. The equivalent uniform dose (EUD) to the melanoma cells and the therapeutic ratio (TR) were defined by comparing grid therapy with the traditional open debulking field. The clinical outcomes from recent reports were used to verify the authors’ model. Results: Dose profiles at different depths and 3D dose distributions in a series of 3D melanomas treated with grid therapy were obtained. The EUDs and TRs for all sizes of 3D tumors involved at different doses were derived through the LQ and MLQ models, and a practical equation was derived. The EUD was only one fifth of the prescribed dose. The TR was dependent on the prescribed dose and on the LQ parameters of both the interspersed cancer and normal tissue cells. The results from the LQ model were consistent with those of the MLQ model. At 20 Gy, the EUD and TR by the LQ model were 2.8% higher and 1% lower than by the MLQ, while at 10 Gy, the EUD and TR as defined by the LQ model were only 1.4% higher and 0.8% lower, respectively. The dose volume histograms of grid therapy for a 10 cm tumor showed different dosimetric characteristics from those of conventional radiotherapy. A significant portion of the tumor volume received a very large dose in grid therapy, which ensures significant tumor cell killing in these regions. Conversely, some areas received a relatively small dose, thereby sparing interspersed normal cells and increasing radiation tolerance. The radiobiology modeling results indicated that grid therapy could be useful for treating acutely responding melanomas infiltrating radiosensitive normal tissues. The theoretical model predictions were supported by the clinical outcomes. Conclusions: Grid therapy functions by selectively killing infiltrating tumor cells and concomitantly sparing interspersed normal cells. The TR depends on the radiosensitivity of the cell population, dose, tumor size, and location. Because the volumes of very high dose regions are small, the LQ model can be used safely to predict the clinical outcomes of grid therapy. When treating melanomas with a dose of 15 Gy or higher, single fraction grid therapy is clearly advantageous for sparing interspersed normal cells. The existence of a threshold fraction dose, which was found in the authors’ theoretical simulations, was confirmed by clinical observations.« less

Land Cover Change Detection using Neural Network and Grid Cells Techniques

NASA Astrophysics Data System (ADS)

Bagan, H.; Li, Z.; Tangud, T.; Yamagata, Y.

2017-12-01

In recent years, many advanced neural network methods have been applied in land cover classification, each of which has both strengths and limitations. In which, the self-organizing map (SOM) neural network method have been used to solve remote sensing data classification problems and have shown potential for efficient classification of remote sensing data. In SOM, both the distribution and the topology of features of the input layer are identified by using an unsupervised, competitive, neighborhood learning method. The high-dimensional data are then projected onto a low-dimensional map (competitive layer), usually as a two-dimensional map. The neurons (nodes) in the competitive layer are arranged by topological order in the input space. Spatio-temporal analyses of land cover change based on grid cells have demonstrated that gridded data are useful for obtaining spatial and temporal information about areas that are smaller than municipal scale and are uniform in size. Analysis based on grid cells has many advantages: grid cells all have the same size allowing for easy comparison; grids integrate easily with other scientific data; grids are stable over time and thus facilitate the modelling and analysis of very large multivariate spatial data sets. This study chose time-series MODIS and Landsat images as data sources, applied SOM neural network method to identify the land utilization in Inner Mongolia Autonomous Region of China. Then the results were integrated into grid cell to get the dynamic change maps. Land cover change using MODIS data in Inner Mongolia showed that urban area increased more than fivefold in recent 15 years, along with the growth of mining area. In terms of geographical distribution, the most obvious place of urban expansion is Ordos in southwest Inner Mongolia. The results using Landsat images from 1986 to 2014 in northeastern part of the Inner Mongolia show degradation in grassland from 1986 to 2014. Grid-cell-based spatial correlation analysis also confirmed a strong negative correlation between grassland and barren land, indicating that grassland degradation in this region is due to the urbanization and coal mining activities over the past three decades.

Effects of salinity on the cellular physiological responses of Natrinema sp. J7-2

PubMed Central

Mei, Yunjun; Liu, Huan; Zhang, Shunxi; Yang, Ming; Hu, Chun; Zhang, Jian; Shen, Ping; Chen, Xiangdong

2017-01-01

The halophilic archaea (haloarchaea) live in hyersaline environments such as salt lakes, salt ponds and marine salterns. To cope with the salt stress conditions, haloarchaea have developed two fundamentally different strategies: the "salt-in" strategy and the "compatible-solute" strategy. Although investigation of the molecular mechanisms underlying the tolerance to high salt concentrations has made outstanding achievements, experimental study from the aspect of transcription is rare. In the present study, we monitored cellular physiology of Natrinema sp. J7-2 cells incubated in different salinity media (15%, 25% and 30% NaCl) from several aspects, such as cellular morphology, growth, global transcriptome and the content of intracellular free amino acids. The results showed that the cells were polymorphic and fragile at a low salt concentration (15% NaCl) but had a long, slender rod shape at high salt concentrations (25% and 30% NaCl). The cells grew best in 25% NaCl, mediocre in 30% NaCl and struggled in 15% NaCl. An RNA-seq analysis revealed differentially expressed genes (DEGs) in various salinity media. A total of 1,148 genes were differentially expressed, consisting of 719 DEGs (348 up-regulated and 371 down-regulated genes) between cells in 15% vs 25% NaCl, and 733 DEGs (521 up-regulated and 212 down-regulated genes) between cells in 25% vs 30% NaCl. Moreover, 304 genes were commonly differentially expressed in both 15% vs 25% and 25% vs30% NaCl. The DEGs were enriched in different KEGG metabolic pathways, such as amino acids, glycerolipid, ribosome, nitrogen, protoporphyrin, porphyrin and porhiniods. The intracellular predominant free amino acids consisted of the glutamate family (Glu, Arg and Pro), aspartate family (Asp) and aromatic amino acids (Phe and Trp), especially Glu and Asp. PMID:28926633

Development of a Dynamic Operational Scheduling Algorithm for an Independent Micro-Grid with Renewable Energy

NASA Astrophysics Data System (ADS)

Obara, Shin'ya

A micro-grid with the capacity for sustainable energy is expected to be a distributed energy system that exhibits quite a small environmental impact. In an independent micro-grid, “green energy,” which is typically thought of as unstable, can be utilized effectively by introducing a battery. In the past study, the production-of-electricity prediction algorithm (PAS) of the solar cell was developed. In PAS, a layered neural network is made to learn based on past weather data and the operation plan of the compound system of a solar cell and other energy systems was examined using this prediction algorithm. In this paper, a dynamic operational scheduling algorithm is developed using a neural network (PAS) and a genetic algorithm (GA) to provide predictions for solar cell power output. We also do a case study analysis in which we use this algorithm to plan the operation of a system that connects nine houses in Sapporo to a micro-grid composed of power equipment and a polycrystalline silicon solar cell. In this work, the relationship between the accuracy of output prediction of the solar cell and the operation plan of the micro-grid was clarified. Moreover, we found that operating the micro-grid according to the plan derived with PAS was far superior, in terms of equipment hours of operation, to that using past average weather data.

Transcriptomic profiling of chemical exposure reveals roles of Yap1 in protecting yeast cells from oxidative and other types of stresses.

PubMed

Zhang, Chao; Li, Zhouquan; Zhang, Xiaohua; Yuan, Li; Dai, Heping; Xiao, Wei

2016-01-01

Transcriptomic profiles are generated by comparing wild-type and the yeast yap1 mutant to various chemicals in an attempt to establish a correlation between this gene mutation and chemical exposure. Test chemicals include ClonNAT as a non-genotoxic agent, methyl methanesulphonate (MMS) as an alkylating agent, tert-butyl hydroperoxide (t-BHP) as an oxidative agent and the mixture of t-BHP and MMS to reflect complex natural exposure. Differentially expressed genes (DEGs) were identified and specific DEGs were obtained by excluding overlapping DEGs with the control group. In the MMS exposure group, deoxyribonucleotide biosynthetic processes were upregulated, while oxidation-reduction processes were downregulated. In the t-BHP exposure group, metabolic processes were upregulated while peroxisome and ion transport pathways were downregulated. In the mixture exposure group, the proteasome pathway was upregulated, while the aerobic respiration was downregulated. Homologue analysis of DEGs related to human diseases showed that many of DEGs were linked to cancer, ageing and neuronal degeneration. These observations confirm that the yap1 mutant is more sensitive to chemicals than wild-type cells and that the susceptible individuals carrying the YAP1-like gene defect may enhance risk to chemical exposure. Hence, this study offers a novel approach to environmental risk assessment, based on the genetic backgrounds of susceptible individuals. Copyright © 2015 John Wiley & Sons, Ltd.

Placing a Disrupted Degradation Motif at the C Terminus of Proteasome Substrates Attenuates Degradation without Impairing Ubiquitylation*

PubMed Central

Alfassy, Omri S.; Cohen, Itamar; Reiss, Yuval; Tirosh, Boaz; Ravid, Tommer

2013-01-01

Protein elimination by the ubiquitin-proteasome system requires the presence of a cis-acting degradation signal. Efforts to discern degradation signals of misfolded proteasome substrates thus far revealed a general mechanism whereby the exposure of cryptic hydrophobic motifs provides a degradation determinant. We have previously characterized such a determinant, employing the yeast kinetochore protein Ndc10 as a model substrate. Ndc10 is essentially a stable protein that is rapidly degraded upon exposure of a hydrophobic motif located at the C-terminal region. The degradation motif comprises two distinct and essential elements: DegA, encompassing two amphipathic helices, and DegB, a hydrophobic sequence within the loosely structured C-terminal tail of Ndc10. Here we show that the hydrophobic nature of DegB is irrelevant for the ubiquitylation of substrates containing the Ndc10 degradation motif, but is essential for proteasomal degradation. Mutant DegB, in which the hydrophobic sequence was disrupted, acted as a dominant degradation inhibitory element when expressed at the C-terminal regions of ubiquitin-dependent and -independent substrates of the 26S proteasome. This mutant stabilized substrates in both yeast and mammalian cells, indicative of a modular recognition moiety. The dominant function of the mutant DegB provides a powerful experimental tool for evaluating the physiological implications of stabilization of specific proteasome substrates in intact cells and for studying the associated pathological effects. PMID:23519465

Grid generation in three dimensions by Poisson equations with control of cell size and skewness at boundary surfaces

NASA Technical Reports Server (NTRS)

Sorenson, R. L.; Steger, J. L.

1983-01-01

An algorithm for generating computational grids about arbitrary three-dimensional bodies is developed. The elliptic partial differential equation (PDE) approach developed by Steger and Sorenson and used in the NASA computer program GRAPE is extended from two to three dimensions. Forcing functions which are found automatically by the algorithm give the user the ability to control mesh cell size and skewness at boundary surfaces. This algorithm, as is typical of PDE grid generators, gives smooth grid lines and spacing in the interior of the grid. The method is applied to a rectilinear wind-tunnel case and to two body shapes in spherical coordinates.

Al/Pb lightweight grids prepared by molten salt electroless plating for application in lead-acid batteries

NASA Astrophysics Data System (ADS)

Hong, Bo; Jiang, Liangxing; Hao, Ketao; Liu, Fangyang; Yu, Xiaoying; Xue, Haitao; Li, Jie; Liu, Yexiang

2014-06-01

In this paper, a lightweight Pb plated Al (Al/Pb) grid was prepared by molten salt electroless plating. The SEM and bonding strength test show that the lead coating is deposited with a smooth surface and firm combination. CV test shows that the electrochemical properties of Al/Pb electrodes are stable. 2.0 V single-cell flooded lead-acid batteries with Al/Pb grids as negative collectors are assembled and the performances including 20 h capacity, rate capacity, cycle life, internal resistance are investigated. The results show that the cycle life of Al/Pb-grid cells is about 475 cycles and can meet the requirement of lead-acid batteries. Al/Pb grids are conducive to the refinement of PbSO4 grain, and thereby reduce the internal resistance of battery and advance the utilization of active mass. Moreover, weight of Al/Pb grid is only 55.4% of the conventional-grid. In this way, mass specific capacity of Al/Pb-grid negatives is 17.8% higher and the utilization of active mass is 6.5% higher than conventional-grid negatives.

Gene expression microarray profiles of cumulus cells in lean and overweight-obese polycystic ovary syndrome patients.

PubMed

Kenigsberg, Shlomit; Bentov, Yaakov; Chalifa-Caspi, Vered; Potashnik, Gad; Ofir, Rivka; Birk, Ohad S

2009-02-01

The aim of this work was to study gene expression patterns of cultured cumulus cells from lean and overweight-obese polycystic ovary syndrome (PCOS) patients using genome-wide oligonucleotide microarray. The study included 25 patients undergoing in vitro fertilization and intra-cytoplasmic sperm injection: 12 diagnosed with PCOS and 13 matching controls. Each of the groups was subdivided into lean (body mass index (BMI) < 24) and overweight (BMI > 27) subgroups. The following comparisons of gene expression data were made: lean PCOS versus lean controls, lean PCOS versus overweight PCOS, all PCOS versus all controls, overweight PCOS versus overweight controls, overweight controls versus lean controls and all overweight versus all lean. The largest number of differentially expressed genes (DEGs), with fold change (FC) |FC| >or= 1.5 and P-value < 0.01, was found in the lean PCOS versus lean controls comparison (487) with most of these genes being down-regulated in PCOS. The second largest group of DEGs originated from the comparison of lean PCOS versus overweight PCOS (305). The other comparisons resulted in a much smaller number of DEGs (174, 109, 125 and 12, respectively). In the comparison of lean PCOS with lean controls, most DEGs were transcription factors and components of the extracellular matrix and two pathways, Wnt/beta-catenin and mitogen-activated protein kinase. When comparing overweight PCOS with overweight controls, most DEGs were of pathways related to insulin signaling, metabolism and energy production. The finding of unique gene expression patterns in cumulus cells from the two PCOS subtypes is in agreement with other studies that have found the two to be separate entities with potentially different pathophysiologies.

Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome.

PubMed

Shen, Haoran; Liang, Zhou; Zheng, Saihua; Li, Xuelian

2017-11-01

The purpose of this study was to identify promising candidate genes and pathways in polycystic ovary syndrome (PCOS). Microarray dataset GSE345269 obtained from the Gene Expression Omnibus database includes 7 granulosa cell samples from PCOS patients, and 3 normal granulosa cell samples. Differentially expressed genes (DEGs) were screened between PCOS and normal samples. Pathway enrichment analysis was conducted for DEGs using ClueGO and CluePedia plugin of Cytoscape. A Reactome functional interaction (FI) network of the DEGs was built using ReactomeFIViz, and then network modules were extracted, followed by pathway enrichment analysis for the modules. Expression of DEGs in granulosa cell samples was measured using quantitative RT-PCR. A total of 674 DEGs were retained, which were significantly enriched with inflammation and immune-related pathways. Eight modules were extracted from the Reactome FI network. Pathway enrichment analysis revealed significant pathways of each module: module 0, Regulation of RhoA activity and Signaling by Rho GTPases pathways shared ARHGAP4 and ARHGAP9; module 2, GlycoProtein VI-mediated activation cascade pathway was enriched with RHOG; module 3, Thromboxane A2 receptor signaling, Chemokine signaling pathway, CXCR4-mediated signaling events pathways were enriched with LYN, the hub gene of module 3. Results of RT-PCR confirmed the finding of the bioinformatic analysis that ARHGAP4, ARHGAP9, RHOG and LYN were significantly upregulated in PCOS. RhoA-related pathways, GlycoProtein VI-mediated activation cascade pathway, ARHGAP4, ARHGAP9, RHOG and LYN may be involved in the pathogenesis of PCOS.

Efficacy of the MEK Inhibitor Cobimetinib and its Potential Application to Colorectal Cancer Cells.

PubMed

Gong, Shu; Xu, Dongsheng; Zhu, Jialin; Zou, Fangdong; Peng, Rui

2018-05-22

Mutations in the Ras/Raf/MEK/ERK pathway are detected in 50% of colorectal cancer cases and play a crucial role in cancer development and progression. Cobimetinib is a MEK inhibitor approved for the treatment of advanced melanoma and inhibits the cell viability of other types of cancer cells. HCT116 colorectal cancer cells were treated with cobimetinib, and MTT assay, colony formation assay, and flow cytometry were used to evaluate cell viability, cell cycle, and apoptosis, respectively. The expression of genes associated with the cell cycle and apoptosis were evaluated by quantitative real-time PCR and western blotting. To explore use of cobimetinib in colorectal cancer treatment and further understand its mechanisms, RNA-seq technology was used to identify differentially expressed genes (DEGs) between cobimetinib-treated and untreated HCT116 cells. Furthermore, we compared these DEGs with Gene Expression Omnibus data from colorectal cancer tissues and normal colonic epithelial tissues. We found that cobimetinib not only inhibited cell proliferation but also induced G1 phase arrest and apoptosis in HCT116 colorectal cancer cells, suggesting that cobimetinib may useful in colorectal cancer therapy. After cobimetinib treatment, 3,495 DEGs were obtained, including 2,089 upregulated genes and 1,406 downregulated genes, and most of these DEGs were enriched in the cell cycle, DNA replication, and DNA damage repair pathways. Our results revealed that some genes with high expression in colorectal cancer tissues were downregulated by cobimetinib in HCT116 cells, including CCND1, E2F1, CDC25C, CCNE2, MYC, and PCNA. These genes have vital roles in DNA replication and the cell cycle. Furthermore, genes with low expression in colorectal cancer tissues were upregulated by cobimetinib, including PRKCA, PI3K, RTK, and PKC. Based on our results, the PKC and PI3K pathways were activated after cobimetinib treatment, and inhibition of these two pathways can increase the cytotoxicity of cobimetinib in HCT116 cells. Notably, cobimetinib appeared to enhance the efficacy of 5-fluorouracil (5-FU) by decreasing TYMS expression, high expression of which is responsible for 5-FU resistance in colorectal cancer. Our results suggest the potential use of cobimetinib in colorectal cancer therapy. © 2018 The Author(s). Published by S. Karger AG, Basel.

Position Papers for the First Workshop on Principles and Practice of Constraint Programming Held in Newport, Rhode Island on April 28-30, 1993

DTIC Science & Technology

1993-04-30

There are alternative methods to MBB’s, based on decomposition of space into disjoint cells. These include uniform grid method [Fr84], quadtree-based...space. The IIn grid and quadtree methods there is a trade off between the resolution of the cells (and thus quantity of the cells) and the effectiveness...Mathematics, 13, pp. 221-229, 1983. 9 IFr84] W.R. Franklin, Adaptive grids for geometric operations, Cartographica 21, 2 g 3, pp. 160-167, 1984. (Gun87

Coarse-grained hydrodynamics from correlation functions

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

Palmer, Bruce

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configuration from a molecular dynamics simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilbrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is applied to some simple hydrodynamic cases to determine the feasibility of applying this to realistic nanoscale systems.

Grid-cell representations in mental simulation

PubMed Central

Bellmund, Jacob LS; Deuker, Lorena; Navarro Schröder, Tobias; Doeller, Christian F

2016-01-01

Anticipating the future is a key motif of the brain, possibly supported by mental simulation of upcoming events. Rodent single-cell recordings suggest the ability of spatially tuned cells to represent subsequent locations. Grid-like representations have been observed in the human entorhinal cortex during virtual and imagined navigation. However, hitherto it remains unknown if grid-like representations contribute to mental simulation in the absence of imagined movement. Participants imagined directions between building locations in a large-scale virtual-reality city while undergoing fMRI without re-exposure to the environment. Using multi-voxel pattern analysis, we provide evidence for representations of absolute imagined direction at a resolution of 30° in the parahippocampal gyrus, consistent with the head-direction system. Furthermore, we capitalize on the six-fold rotational symmetry of grid-cell firing to demonstrate a 60° periodic pattern-similarity structure in the entorhinal cortex. Our findings imply a role of the entorhinal grid-system in mental simulation and future thinking beyond spatial navigation. DOI: http://dx.doi.org/10.7554/eLife.17089.001 PMID:27572056

Genes involved in prostate cancer progression determine MRI visibility

PubMed Central

Li, Ping; You, Sungyong; Nguyen, Christopher; Wang, Yanping; Kim, Jayoung; Sirohi, Deepika; Ziembiec, Asha; Luthringer, Daniel; Lin, Shih-Chieh; Daskivich, Timothy; Wu, Jonathan; Freeman, Michael R; Saouaf, Rola; Li, Debiao; Kim, Hyung L.

2018-01-01

MRI is used to image prostate cancer and target tumors for biopsy or therapeutic ablation. The objective was to understand the biology of tumors not visible on MRI that may go undiagnosed and untreated. Methods: Prostate cancers visible or invisible on multiparametric MRI were macrodissected and examined by RNAseq. Differentially expressed genes (DEGs) based on MRI visibility status were cross-referenced with publicly available gene expression databases to identify genes associated with disease progression. Genes with potential roles in determining MRI visibility and disease progression were knocked down in murine prostate cancer xenografts, and imaged by MRI. Results: RNAseq identified 1,654 DEGs based on MRI visibility status. Comparison of DEGs based on MRI visibility and tumor characteristics revealed that Gleason score (dissimilarity test, p<0.0001) and tumor size (dissimilarity test, p<0.039) did not completely determine MRI visibility. Genes in previously reported prognostic signatures significantly correlated with MRI visibility suggesting that MRI visibility was prognostic. Cross-referencing DEGs with external datasets identified four genes (PHYHD1, CENPF, ALDH2, GDF15) that predict MRI visibility, progression free survival and metastatic deposits. Genetic modification of a human prostate cancer cell line to induce miR-101 and suppress CENPF decreased cell migration and invasion. As prostate cancer xenografts in mice, these cells had decreased visibility on diffusion weighted MRI and decreased perfusion, which correlated with immunostaining showing decreased cell density and proliferation. Conclusions: Genes involved in prostate cancer prognosis and metastasis determine MRI visibility, indicating that MRI visibility has prognostic significance. MRI visibility was associated with genetic features linked to poor prognosis. PMID:29556354

Characterization of transcriptional complexity during pre-implantation development of the yak (Bos grunniens) using RNA-Seq.

PubMed

Zi, X-D; Luo, B; Xia, W; Zheng, Y-C; Xiong, X-R; Li, J; Zhong, J-C; Zhu, J-J; Zhang, Z-F

2018-06-01

The objective of this study was to investigate the mechanism that regulates pre-implantation development of the yak (Bos grunniens). We determined the transcriptomes of in vitro-produced yak embryos at two-cell, four-cell, eight-cell stages, and morula and blastocyst using the Illumina RNA-seq for the first time. We obtained 47.36-50.86 million clean reads for each stage, of which, 85.65%-90.02% reads were covered in the reference genome. A total of 17,368 genes were expressed during the two-cell stage to blastocyst of the yak, of which 7,236 genes were co-expressed at all stages, whereas 10,132 genes were stage-specific expression. Transcripts from 9,827 to 14,893 different genes were detected in various developmental stages. When |log 2 ratio| ≥ 1 and q-value <0.05 were set as thresholds for identifying differentially expressed genes (DEGs), we detected a total of 6,922-10,555 DEGs between any two consecutive stages. The GO distributions of these DEGs were classified into three categories: biological processes (23 terms), cellular components (22 terms) and molecular functions (22 terms). Pathway analysis revealed 310 pathways of the DEGs that were operative in early pre-implantation yak development, of which 32 were the significantly enriched pathways. In conclusion, this is the first report to investigate the mechanism that regulates yak embryonic development using high-throughput sequencing, which provides a comprehensive framework of transcriptome landscapes of yak pre-implantation embryos. © 2018 Blackwell Verlag GmbH.

RNA sequencing enables systematic identification of platelet transcriptomic alterations in NSCLC patients.

PubMed

Zhang, Qun; Hu, Huan; Liu, Hongda; Jin, Jiajia; Zhu, Peiyuan; Wang, Shujun; Shen, Kaikai; Hu, Yangbo; Li, Zhou; Zhan, Ping; Zhu, Suhua; Fan, Hang; Zhang, Jianya; Lv, Tangfeng; Song, Yong

2018-05-29

Platelets are implicated as key players in the metastatic dissemination of tumor cells. Previous evidence demonstrated platelets retained cytoplasmic RNAs with physiologically activity, splicing pre-mRNA to mRNA and translating into functional proteins in response to external stimulation. Recently, platelets gene profile of healthy or diseased individuals were characterized with the help of RNA sequencing (RNA-Seq) in some studies, leading to new insights into the mechanisms underlying disease pathogenesis. In this study, we performed RNA-seq in platelets from 7 healthy individuals and 15 non-small cell lung cancer (NSCLC) patients. Our data revealed a subset of near universal differently expressed gene (DEG) profiles in platelets of metastatic NSCLC compared to healthy individuals, including 626 up-regulated RNAs (mRNAs and ncRNAs) and 1497 down-regulated genes. The significant over-expressed genes showed enrichment in focal adhesion, platelets activation, gap junction and adherens junction pathways. The DEGs also included previously reported tumor-related genes such as PDGFR, VEGF, EGF, etc., verifying the consistence and significance of platelet RNA-Seq in oncology study. We also validated several up-regulated DEGs involved in tumor cell-induced platelet aggregation (TCIPA) and tumorigenesis. Additionally, transcriptomic comparison analyses of NSCLC subgroups were conducted. Between non-metastatic and metastatic NSCLC patients, 526 platelet DEGs were identified with the most altered expression. The outcomes from subgroup analysis between lung adenocarcinoma and lung squamous cell carcinoma demonstrated the diagnostic potential of platelet RNA-Seq on distinguishing tumor histological types. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Linking field-based ecological data with remotely sensed data using a geographic information system in two malaria endemic urban areas of Kenya.

PubMed

Eisele, Thomas P; Keating, Joseph; Swalm, Chris; Mbogo, Charles M; Githeko, Andrew K; Regens, James L; Githure, John I; Andrews, Linda; Beier, John C

2003-12-10

BACKGROUND: Remote sensing technology provides detailed spectral and thermal images of the earth's surface from which surrogate ecological indicators of complex processes can be measured. METHODS: Remote sensing data were overlaid onto georeferenced entomological and human ecological data randomly sampled during April and May 2001 in the cities of Kisumu (population asymptotically equal to 320,000) and Malindi (population asymptotically equal to 81,000), Kenya. Grid cells of 270 meters x 270 meters were used to generate spatial sampling units for each city for the collection of entomological and human ecological field-based data. Multispectral Thermal Imager (MTI) satellite data in the visible spectrum at five meter resolution were acquired for Kisumu and Malindi during February and March 2001, respectively. The MTI data were fit and aggregated to the 270 meter x 270 meter grid cells used in field-based sampling using a geographic information system. The normalized difference vegetation index (NDVI) was calculated and scaled from MTI data for selected grid cells. Regression analysis was used to assess associations between NDVI values and entomological and human ecological variables at the grid cell level. RESULTS: Multivariate linear regression showed that as household density increased, mean grid cell NDVI decreased (global F-test = 9.81, df 3,72, P-value = <0.01; adjusted R2 = 0.26). Given household density, the number of potential anopheline larval habitats per grid cell also increased with increasing values of mean grid cell NDVI (global F-test = 14.29, df 3,36, P-value = <0.01; adjusted R2 = 0.51). CONCLUSIONS: NDVI values obtained from MTI data were successfully overlaid onto georeferenced entomological and human ecological data spatially sampled at a scale of 270 meters x 270 meters. Results demonstrate that NDVI at such a scale was sufficient to describe variations in entomological and human ecological parameters across both cities.

Analyzing Gene Expression Profiles with Preliminary Validations in Cardiac Hypertrophy Induced by Pressure-overload.

PubMed

Gao, Jing; Li, Yuhong; Wang, Tongmei; Shi, Zhuo; Zhang, Yiqi; Liu, Shuang; Wen, Pushuai; Ma, Chunyan

2018-03-06

The aim of this study was to identify the key genes involved in the cardiac hypertrophy (CH) induced by pressure overload. mRNA microarray dataset GSE5500 and GSE18801 were downloaded from GEO database, and differentially expressed genes (DEGs) were screened using Limma package; then, functional and pathway enrichment analysis were performed for common DEGs using DAVID database. Furthermore, the top DEGs were further validated using qPCR in the hypertrophic heart tissue induced by Isoprenaline (ISO). A total of 113 common DEGs with absolute fold change >0.5, including 60 significantly up-regulated DEGs and 53 down-regulated DEGs were obtained. GO term enrichment analysis suggested that common up-regulated DEG mainly enriched in neutrophil chemotaxis, extracellular fibril organization and cell proliferation, and the common down-regulated genes were significantly enriched in ion transport, endoplasmic reticulum and dendritic spine. KEGG pathway analysis found that the common DEGs were mainly enriched in ECM-receptor interaction, phagosome, and focal adhesion. Additionally, the expression of Mfap4, Ltbp2, Aspn, Serpina3n, and Cnksr1 were up-regulated in the model of cardiac hypertrophy, while the expression of Anp32a was down-regulated. The current study identified the key deregulated genes and pathways involved in the CH, which could shed new light to understand the mechanism of CH.

Conceptual Design of the Everglades Depth Estimation Network (EDEN) Grid

USGS Publications Warehouse

Jones, John W.; Price, Susan D.

2007-01-01

INTRODUCTION The Everglades Depth Estimation Network (EDEN) offers a consistent and documented dataset that can be used to guide large-scale field operations, to integrate hydrologic and ecological responses, and to support biological and ecological assessments that measure ecosystem responses to the Comprehensive Everglades Restoration Plan (Telis, 2006). Ground elevation data for the greater Everglades and the digital ground elevation models derived from them form the foundation for all EDEN water depth and associated ecologic/hydrologic modeling (Jones, 2004, Jones and Price, 2007). To use EDEN water depth and duration information most effectively, it is important to be able to view and manipulate information on elevation data quality and other land cover and habitat characteristics across the Everglades region. These requirements led to the development of the geographic data layer described in this techniques and methods report. Relying on extensive experience in GIS data development, distribution, and analysis, a great deal of forethought went into the design of the geographic data layer used to index elevation and other surface characteristics for the Greater Everglades region. To allow for simplicity of design and use, the EDEN area was broken into a large number of equal-sized rectangles ('Cells') that in total are referred to here as the 'grid'. Some characteristics of this grid, such as the size of its cells, its origin, the area of Florida it is designed to represent, and individual grid cell identifiers, could not be changed once the grid database was developed. Therefore, these characteristics were selected to design as robust a grid as possible and to ensure the grid's long-term utility. It is desirable to include all pertinent information known about elevation and elevation data collection as grid attributes. Also, it is very important to allow for efficient grid post-processing, sub-setting, analysis, and distribution. This document details the conceptual design of the EDEN grid spatial parameters and cell attribute-table content.

Metal nano-grids for transparent conduction in solar cells

DOE PAGES

Muzzillo, Christopher P.

2017-05-11

A general procedure for predicting metal grid performance in solar cells was developed. Unlike transparent conducting oxides (TCOs) or other homogeneous films, metal grids induce more resistance in the neighbor layer. The resulting balance of transmittance, neighbor and grid resistance was explored in light of cheap lithography advances that have enabled metal nano-grid (MNG) fabrication. The patterned MNGs have junction resistances and degradation rates that are more favorable than solution-synthesized metal nanowires. Neighbor series resistance was simulated by the finite element method, although a simpler analytical model was sufficient in most cases. Finite-difference frequency-domain transmittance simulations were performed for MNGsmore » with minimum wire width (w) of 50 nm, but deviations from aperture transmittance were small in magnitude. Depending on the process, MNGs can exhibit increased series resistance as w is decreased. However, numerous experimental reports have already achieved transmittance-MNG sheet resistance trade-offs comparable to TCOs. The transmittance, neighbor and MNG series resistances were used to parameterize a grid fill factor for a solar cell. In conclusion, this new figure of merit was used to demonstrate that although MNGs have only been employed in low efficiency solar cells, substantial gains in performance are predicted for decreased w in all high efficiency absorber technologies.« less

Metal nano-grids for transparent conduction in solar cells

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

Muzzillo, Christopher P.

A general procedure for predicting metal grid performance in solar cells was developed. Unlike transparent conducting oxides (TCOs) or other homogeneous films, metal grids induce more resistance in the neighbor layer. The resulting balance of transmittance, neighbor and grid resistance was explored in light of cheap lithography advances that have enabled metal nano-grid (MNG) fabrication. The patterned MNGs have junction resistances and degradation rates that are more favorable than solution-synthesized metal nanowires. Neighbor series resistance was simulated by the finite element method, although a simpler analytical model was sufficient in most cases. Finite-difference frequency-domain transmittance simulations were performed for MNGsmore » with minimum wire width (w) of 50 nm, but deviations from aperture transmittance were small in magnitude. Depending on the process, MNGs can exhibit increased series resistance as w is decreased. However, numerous experimental reports have already achieved transmittance-MNG sheet resistance trade-offs comparable to TCOs. The transmittance, neighbor and MNG series resistances were used to parameterize a grid fill factor for a solar cell. In conclusion, this new figure of merit was used to demonstrate that although MNGs have only been employed in low efficiency solar cells, substantial gains in performance are predicted for decreased w in all high efficiency absorber technologies.« less

Entorhinal cortex receptive fields are modulated by spatial attention, even without movement

PubMed Central

König, Peter; König, Seth; Buffalo, Elizabeth A

2018-01-01

Grid cells in the entorhinal cortex allow for the precise decoding of position in space. Along with potentially playing an important role in navigation, grid cells have recently been hypothesized to make a general contribution to mental operations. A prerequisite for this hypothesis is that grid cell activity does not critically depend on physical movement. Here, we show that movement of covert attention, without any physical movement, also elicits spatial receptive fields with a triangular tiling of space. In monkeys trained to maintain central fixation while covertly attending to a stimulus moving in the periphery we identified a significant population (20/141, 14% neurons at a FDR <5%) of entorhinal cells with spatially structured receptive fields. This contrasts with recordings obtained in the hippocampus, where grid-like representations were not observed. Our results provide evidence that neurons in macaque entorhinal cortex do not rely on physical movement. PMID:29537964

Toward Verification of USM3D Extensions for Mixed Element Grids

NASA Technical Reports Server (NTRS)

Pandya, Mohagna J.; Frink, Neal T.; Ding, Ejiang; Parlette, Edward B.

2013-01-01

The unstructured tetrahedral grid cell-centered finite volume flow solver USM3D has been recently extended to handle mixed element grids composed of hexahedral, prismatic, pyramidal, and tetrahedral cells. Presently, two turbulence models, namely, baseline Spalart-Allmaras (SA) and Menter Shear Stress Transport (SST), support mixed element grids. This paper provides an overview of the various numerical discretization options available in the newly enhanced USM3D. Using the SA model, the flow solver extensions are verified on three two-dimensional test cases available on the Turbulence Modeling Resource website at the NASA Langley Research Center. The test cases are zero pressure gradient flat plate, planar shear, and bump-inchannel. The effect of cell topologies on the flow solution is also investigated using the planar shear case. Finally, the assessment of various cell and face gradient options is performed on the zero pressure gradient flat plate case.

Prediction of asymmetric vortical flows around slender bodies using Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Liu, C. H.; Wong, Tin-Chee; Kandil, Osama A.

1992-01-01

Steady and unsteady asymmetric vortical flows around slender bodies at high angles of attack are solved using the unsteady, compressible, thin-layer Navier-Stokes equations. An implicit, upwind-biased, flux-difference splitting, finite-volume scheme is used for the numerical computations. For supersonic flows past point cones, the locally conical flow assumption have been used for efficient computational studies of this phenomenon. Asymmetric flows past a 5-deg semiapex-angle circular cone at different angles of attack, free-stream Mach numbers, and Reynolds numbers have been studied in responses to different sources of disturbances. The effects of grid fineness and computational domain size have also been investigated. Next, the responses of three-dimensional supersonic asymmetric flow around a 5-deg circular cone at different angles of attack and Reynolds numbers to short-duration sideslip disturbances are presented. The results show that flow asymmetry becomes stronger as the Reynolds number and angles of attack are increased. One of the cases of flow over a cone-cylinder configuration is validated fairly well by experimental data.

Workshop 5: Design of a photovoltaic generator for a refuge in the Alps

NASA Astrophysics Data System (ADS)

Roger, J. A.

1982-11-01

The design of a photovoltaic (PV) generator for a refuge located in the mountains (+5 deg north, 4 deg east) at an altitude of 2600 m is discussed. This refuge has a capacity of 90 persons and is not connected to the grid. it is at present equipped with a 14 kVa diesel generator operating in a three phase plus neutral mode. This group provides electricity to various domestic appliances: lighting, heat (in the keeper's room), refrigeration, water pumping, etc. Starting from available documents and data, the task was to design the PV generator to be substituted for this diesel engine. The work was divided in several steps: analysis of the existing loads and of the corresponding consumptions; estimation of the solar energy available on the site; choice of the PV chain necessitating as few modifications as possible in the existing installation; sizing of the elements of the PV chain and scheme of the various parts; and modifications that can be done regarding the loads, and related changes in the design of the system.

PRISM3/GISS Topographic Reconstruction

USGS Publications Warehouse

Sohl, Linda E.; Chandler, Mark A.; Schmunk, Robert B.; Mankoff, Ken; Jonas, Jeffrey A.; Foley, Kevin M.; Dowsett, Harry J.

2009-01-01

The PRISM3/GISS topographic reconstruction is one of the global data sets incorporated into a new reconstruction for the mid-Piacenzian warm interval of the Pliocene, at about 3.3 to 3.0 Ma. The PRISM3/GISS topography-gridded data set is a digitization of a graphical reconstruction, provided at 2 deg x 2 deg resolution and based on updated paleoaltimetry data and a refined land/ocean mask. Mid-Piacenzian topography as shown in this data set is generally quite similar to modern topography, with three notable differences: (1) the coastline as shown is 25 meters higher than modern sea level, reflecting the hypothesized reduction in ice sheet volume; (2) Hudson Bay is filled in to low elevation, in the absence of evidence for submergence at that time; and (3) the West Antarctic ice sheet is absent, permitting open seaways to exist in Ellsworth and Marie Byrd Lands. Two alternate ice sheet configurations with corresponding vegetation schemes are available; one is a minor modification of the PRISM2 ice reconstruction, and one is derived from the British Antarctic Survey Ice Sheet Model (BAS ISM).

PAB3D Simulations for the CAWAPI F-16XL

NASA Technical Reports Server (NTRS)

Elmiligui, Alaa; Abdol-Hamid, K. S.; Massey, Steven J.

2007-01-01

Numerical simulations of the flow around F-16XL are performed as a contribution to the Cranked Arrow Wing Aerodynamic Project International (CAWAPI) using the PAB3D CFD code. Two turbulence models are used in the calculations: a standard k-! model, and the Shih-Zhu-Lumley (SZL) algebraic stress model. Seven flight conditions are simulated for the flow around the F-16XL where the free stream Mach number varies from 0.242 to 0.97. The range of angles of attack varies from 0deg to 20deg. Computational results, surface static pressure, boundary layer velocity profiles, and skin friction are presented and compared with flight data. Numerical results are generally in good agreement with flight data, considering that only one grid resolution is utilized for the different flight conditions simulated in this study. The ASM results are closer to the flight data than the k-! model results. The ASM predicted a stronger primary vortex, however, the origin of the vortex and footprint is approximately the same as in the k-! predictions.

Durability and reliability of electric vehicle batteries under electric utility grid operations: Bidirectional charging impact analysis

NASA Astrophysics Data System (ADS)

Dubarry, Matthieu; Devie, Arnaud; McKenzie, Katherine

2017-08-01

Vehicle-to-grid and Grid-to-vehicle strategies are often cited as promising to mitigate the intermittency of renewable energy on electric power grids. However, their impact on the vehicle battery degradation has not been investigated in detail. The aim of this work is to understand the impact of bidirectional charging on commercial Li-ion cells used in electric vehicles today. Results show that additional cycling to discharge vehicle batteries to the power grid, even at constant power, is detrimental to cell performance. This additional use of the battery packs could shorten the lifetime for vehicle use to less than five years. By contrast, the impact of delaying the charge in order to reduce the impact on the power grid is found to be negligible at room temperature, but could be significant in warmer climates.

Tomography of Pg and Sg Across the Western United States Using USArray Data

NASA Astrophysics Data System (ADS)

Steck, L.; Phillips, W. S.; Begnaud, M. L.; Stead, R.

2009-12-01

In this paper we explore the use of Pg and Sg for determining crustal structure in the western United States. Seismic data used in the study come from USArray, along with local and regional networks in the region. To invert the travel times for velocity structure we use the LSQR algorithm assuming a great circle arc path between source and receiver. First difference smoothing is used to regularize the model and we calculate station and event terms. For Pg we have about 160,000 arrivals from 30,000 events reporting at 1500 stations. If we trim data based on an epicentral ground truth level of 25 km or better, we have 53000 arrivals, 5000 events and 1300 stations. Data density is such that grids of 0.5 deg or better are possible. Velocity results show good correlation with tectonic provinces. We find fast velocities beneath the Snake River Plain, coastal Washington State, and for the coast ranges of California south of Point Reyes. Low velocities are observed on the border between Idaho and Montana, and in the Basin and Range of eastern Nevada, southeastern California, and southern Arizona. For Sg we have 48,813 arrivals for 13,548 events at 1052 stations, not filtering by ground truth level. Excellent coverage allows grids to 0.5 deg or lower. Prominent features of this model include high velocities in the Snake River Plain, Colorado Plateau, and the Cascades and Sierra Nevada. Low velocities are found in Southern California, the Basin and Range, and the Columbia Plateau. Root-mean-square residual reductions are 34% for Pg and 41% for Sg.

Equatorial ozone characteristics as measured at Natal (5.9 deg S, 35.2 deg W)

NASA Technical Reports Server (NTRS)

Kirchhoff, V. W. J. H.; Hilsenrath, E.; Motta, A. G.; Sahai, Y.; Medrano-B, R. A.

1982-01-01

Ozone density profiles obtained through electrochemical concentration cell (ECC) sonde measurements at Natal were analyzed. Time variations, as expected, are small. Outstanding features of the data are tropospheric densities substantially higher than those measured at other stations, and also a total ozone content that is higher than the averages given by satellite measurements.

The Impact of Sika Deer on Vegetation in Japan: Setting Management Priorities on a National Scale

NASA Astrophysics Data System (ADS)

Ohashi, Haruka; Yoshikawa, Masato; Oono, Keiichi; Tanaka, Norihisa; Hatase, Yoriko; Murakami, Yuhide

2014-09-01

Irreversible shifts in ecosystems caused by large herbivores are becoming widespread around the world. We analyzed data derived from the 2009-2010 Sika Deer Impact Survey, which assessed the geographical distribution of deer impacts on vegetation through a questionnaire, on a scale of 5-km grid-cells. Our aim was to identify areas facing irreversible ecosystem shifts caused by deer overpopulation and in need of management prioritization. Our results demonstrated that the areas with heavy impacts on vegetation were widely distributed across Japan from north to south and from the coastal to the alpine areas. Grid-cells with heavy impacts are especially expanding in the southwestern part of the Pacific side of Japan. The intensity of deer impacts was explained by four factors: (1) the number of 5-km grid-cells with sika deer in neighboring 5 km-grid-cells in 1978 and 2003, (2) the year sika deer were first recorded in a grid-cell, (3) the number of months in which maximum snow depth exceeded 50 cm, and (4) the proportion of urban areas in a particular grid-cell. Based on our model, areas with long-persistent deer populations, short snow periods, and fewer urban areas were predicted to be the most vulnerable to deer impact. Although many areas matching these criteria already have heavy deer impact, there are some areas that remain only slightly impacted. These areas may need to be designated as having high management priority because of the possibility of a rapid intensification of deer impact.

The impact of Sika deer on vegetation in Japan: setting management priorities on a national scale.

PubMed

Ohashi, Haruka; Yoshikawa, Masato; Oono, Keiichi; Tanaka, Norihisa; Hatase, Yoriko; Murakami, Yuhide

2014-09-01

Irreversible shifts in ecosystems caused by large herbivores are becoming widespread around the world. We analyzed data derived from the 2009-2010 Sika Deer Impact Survey, which assessed the geographical distribution of deer impacts on vegetation through a questionnaire, on a scale of 5-km grid-cells. Our aim was to identify areas facing irreversible ecosystem shifts caused by deer overpopulation and in need of management prioritization. Our results demonstrated that the areas with heavy impacts on vegetation were widely distributed across Japan from north to south and from the coastal to the alpine areas. Grid-cells with heavy impacts are especially expanding in the southwestern part of the Pacific side of Japan. The intensity of deer impacts was explained by four factors: (1) the number of 5-km grid-cells with sika deer in neighboring 5 km-grid-cells in 1978 and 2003, (2) the year sika deer were first recorded in a grid-cell, (3) the number of months in which maximum snow depth exceeded 50 cm, and (4) the proportion of urban areas in a particular grid-cell. Based on our model, areas with long-persistent deer populations, short snow periods, and fewer urban areas were predicted to be the most vulnerable to deer impact. Although many areas matching these criteria already have heavy deer impact, there are some areas that remain only slightly impacted. These areas may need to be designated as having high management priority because of the possibility of a rapid intensification of deer impact.

Compact cell-centered discretization stencils at fine-coarse block structured grid interfaces

NASA Astrophysics Data System (ADS)

Pletzer, Alexander; Jamroz, Ben; Crockett, Robert; Sides, Scott

2014-03-01

Different strategies for coupling fine-coarse grid patches are explored in the context of the adaptive mesh refinement (AMR) method. We show that applying linear interpolation to fill in the fine grid ghost values can produce a finite volume stencil of comparable accuracy to quadratic interpolation provided the cell volumes are adjusted. The volume of fine cells expands whereas the volume of neighboring coarse cells contracts. The amount by which the cells contract/expand depends on whether the interface is a face, an edge, or a corner. It is shown that quadratic or better interpolation is required when the conductivity is spatially varying, anisotropic, the refinement ratio is other than two, or when the fine-coarse interface is concave.

Crystal structures of complexes of the cys-syn-cys isomer of dicyclohexano-18-crown-6 with oxonium hexafluorotantalate and oxonium hexafluoroniobate

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

Fonari, M. S.; Alekseeva, O. A.; Furmanova, N. G.

2007-03-15

The crystal structures of [(cys-syn-cys-dicyclohexano-18-crown-6 . H{sub 3}O)][TaF{sub 6}] and [(cys-syn-cys-dicyclohexano-18-crown-6 . H{sub 3}O)][NbF{sub 6}] complex compounds are determined using X-ray diffraction analysis. The tantalum complex has two polymorphic modifications, namely, the monoclinic (I) and triclinic (II) modifications. The unit cell parameters of these compounds are as follows: a = 8.507(4) A, b = 11.947(5) A, c = 27.392(12) A, {beta} = 93.11(1) deg., Z = 4, and space group P2{sub 1}/n for modification I; and a = 10.828(1) A, b = 11.204(1) A, c = 12.378(1) A, {alpha} = 72.12(1) deg., {beta} = 79.40(1) deg., {gamma} = 73.70(1) deg.,more » Z = 2, and space group P-1 for modification II. The triclinic niobium complex [(cys-syn-cys-dicyclohexano-18-crown-6 . H{sub 3}O)][NbF{sub 6}] (III) with the unit cell parameters a = 10.796(3) A, b = 11.183(3) A, c = 12.352(3) A, {alpha} = 72.364(5) deg., {beta} = 79.577(5) deg., {gamma} = 73.773(4) deg., Z = 2, and space group P-1 is isostructural with tantalum complex II. The structures of all three complexes are ionic in character. The oxonium cation in complexes I-III is encapsulated by the crown ether and thus forms one ordinary and two bifurcated hydrogen bonds with the oxygen atoms of the crown ether. This macrocyclic cation is bound to the anions through the C-H...F contacts (H...F, 2.48-2.58 A). The conformation of the macrocycle in complex I differs substantially from that in complex II (III)« less

New synthesis of nanopowders of proton conducting materials. A route to densified proton ceramics

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

Khani, Zohreh; Taillades-Jacquin, Melanie; Taillades, Gilles

2009-04-15

Low temperature routes have been developed for the preparation of BaCe{sub 0.9}Y{sub 0.1}O{sub 2.95} (BCY10) and BaZr{sub 0.9}Y{sub 0.1}O{sub 2.95} (BZY10) in the form of nanoparticulate powders for use after densification as ceramic membranes for a proton ceramic fuel cell. These methods make use on the one hand of the chelation of metal (II), (III) and (IV) ions by acrylates (hydrogelation route) and on the other of the destabilisation and precipitation of micro-emulsions. Both routes lead to single phase yttrium doped barium cerate or zirconate perovskites, as observed by X-ray diffraction, after thermal treatment at 900 deg. C for 4more » h for BCY10 and 800 deg. C for BZY10. These temperatures, lower than those usually used for preparation of barium cerate or zirconate, lead to oxide nanoparticles of size <40 nm. Dense ceramics (>=95%) are obtained by sintering BCY10 pellets at 1350 deg. C and BZY10 pellets at 1500 deg. C for 10 h. The water uptake of compacted samples at 500 deg. C is 0.14 wt% for BCY10 and 0.26 wt% for BZY10. Total conductivities in the range 300-600 deg. C were determined using impedance spectroscopy in a humidified nitrogen atmosphere. The total conductivity was 1.8x10{sup -2} S/cm for BCY10 and 2x10{sup -3} S/cm for BZY10 at 600 deg. C. The smallest perovskite nanoparticles and highest conductivities were obtained by hydrogelation of precursor barium, zirconium, cerium and yttrium acrylates. - Graphical Abstract: Low temperature hydrogelation and micro-emulsion routes have been developed for the preparation of rare earth doped barium and zirconium cerates in the form of nanoparticulate powders for use after densification as ceramic membranes for a proton ceramic fuel cell.« less

Hippocampal Remapping Is Constrained by Sparseness rather than Capacity

PubMed Central

Kammerer, Axel; Leibold, Christian

2014-01-01

Grid cells in the medial entorhinal cortex encode space with firing fields that are arranged on the nodes of spatial hexagonal lattices. Potential candidates to read out the space information of this grid code and to combine it with other sensory cues are hippocampal place cells. In this paper, we investigate a population of grid cells providing feed-forward input to place cells. The capacity of the underlying synaptic transformation is determined by both spatial acuity and the number of different spatial environments that can be represented. The codes for different environments arise from phase shifts of the periodical entorhinal cortex patterns that induce a global remapping of hippocampal place fields, i.e., a new random assignment of place fields for each environment. If only a single environment is encoded, the grid code can be read out at high acuity with only few place cells. A surplus in place cells can be used to store a space code for more environments via remapping. The number of stored environments can be increased even more efficiently by stronger recurrent inhibition and by partitioning the place cell population such that learning affects only a small fraction of them in each environment. We find that the spatial decoding acuity is much more resilient to multiple remappings than the sparseness of the place code. Since the hippocampal place code is sparse, we thus conclude that the projection from grid cells to the place cells is not using its full capacity to transfer space information. Both populations may encode different aspects of space. PMID:25474570

Unstructured Cartesian/prismatic grid generation for complex geometries

NASA Technical Reports Server (NTRS)

Karman, Steve L., Jr.

1995-01-01

The generation of a hybrid grid system for discretizing complex three dimensional (3D) geometries is described. The primary grid system is an unstructured Cartesian grid automatically generated using recursive cell subdivision. This grid system is sufficient for computing Euler solutions about extremely complex 3D geometries. A secondary grid system, using triangular-prismatic elements, may be added for resolving the boundary layer region of viscous flows near surfaces of solid bodies. This paper describes the grid generation processes used to generate each grid type. Several example grids are shown, demonstrating the ability of the method to discretize complex geometries, with very little pre-processing required by the user.

Screening for genes and subnetworks associated with pancreatic cancer based on the gene expression profile.

PubMed

Long, Jin; Liu, Zhe; Wu, Xingda; Xu, Yuanhong; Ge, Chunlin

2016-05-01

The present study aimed to screen for potential genes and subnetworks associated with pancreatic cancer (PC) using the gene expression profile. The expression profile GSE 16515 was downloaded from the Gene Expression Omnibus database, which included 36 PC tissue samples and 16 normal samples. Limma package in R language was used to screen differentially expressed genes (DEGs), which were grouped as up‑ and downregulated genes. Then, PFSNet was applied to perform subnetwork analysis for all the DEGs. Moreover, Gene Ontology (GO) and REACTOME pathway enrichment analysis of up‑ and downregulated genes was performed, followed by protein‑protein interaction (PPI) network construction using Search Tool for the Retrieval of Interacting Genes Search Tool for the Retrieval of Interacting Genes. In total, 1,989 DEGs including 1,461 up‑ and 528 downregulated genes were screened out. Subnetworks including pancreatic cancer in PC tissue samples and intercellular adhesion in normal samples were identified, respectively. A total of 8 significant REACTOME pathways for upregulated DEGs, such as hemostasis and cell cycle, mitotic were identified. Moreover, 4 significant REACTOME pathways for downregulated DEGs, including regulation of β‑cell development and transmembrane transport of small molecules were screened out. Additionally, DEGs with high connectivity degrees, such as CCNA2 (cyclin A2) and PBK (PDZ binding kinase), of the module in the protein‑protein interaction network were mainly enriched with cell‑division cycle. CCNA2 and PBK of the module and their relative pathway cell‑division cycle, and two subnetworks (pancreatic cancer and intercellular adhesion subnetworks) may be pivotal for further understanding of the molecular mechanism of PC.

Novel statistical framework to identify differentially expressed genes allowing transcriptomic background differences.

PubMed

Ling, Zhi-Qiang; Wang, Yi; Mukaisho, Kenichi; Hattori, Takanori; Tatsuta, Takeshi; Ge, Ming-Hua; Jin, Li; Mao, Wei-Min; Sugihara, Hiroyuki

2010-06-01

Tests of differentially expressed genes (DEGs) from microarray experiments are based on the null hypothesis that genes that are irrelevant to the phenotype/stimulus are expressed equally in the target and control samples. However, this strict hypothesis is not always true, as there can be several transcriptomic background differences between target and control samples, including different cell/tissue types, different cell cycle stages and different biological donors. These differences lead to increased false positives, which have little biological/medical significance. In this article, we propose a statistical framework to identify DEGs between target and control samples from expression microarray data allowing transcriptomic background differences between these samples by introducing a modified null hypothesis that the gene expression background difference is normally distributed. We use an iterative procedure to perform robust estimation of the null hypothesis and identify DEGs as outliers. We evaluated our method using our own triplicate microarray experiment, followed by validations with reverse transcription-polymerase chain reaction (RT-PCR) and on the MicroArray Quality Control dataset. The evaluations suggest that our technique (i) results in less false positive and false negative results, as measured by the degree of agreement with RT-PCR of the same samples, (ii) can be applied to different microarray platforms and results in better reproducibility as measured by the degree of DEG identification concordance both intra- and inter-platforms and (iii) can be applied efficiently with only a few microarray replicates. Based on these evaluations, we propose that this method not only identifies more reliable and biologically/medically significant DEG, but also reduces the power-cost tradeoff problem in the microarray field. Source code and binaries freely available for download at http://comonca.org.cn/fdca/resources/softwares/deg.zip.

Revealing the potential pathogenesis of glioma by utilizing a glioma associated protein-protein interaction network.

PubMed

Pan, Weiran; Li, Gang; Yang, Xiaoxiao; Miao, Jinming

2015-04-01

This study aims to explore the potential mechanism of glioma through bioinformatic approaches. The gene expression profile (GSE4290) of glioma tumor and non-tumor samples was downloaded from Gene Expression Omnibus database. A total of 180 samples were available, including 23 non-tumor and 157 tumor samples. Then the raw data were preprocessed using robust multiarray analysis, and 8,890 differentially expressed genes (DEGs) were identified by using t-test (false discovery rate < 0.0005). Furthermore, 16 known glioma related genes were abstracted from Genetic Association Database. After mapping 8,890 DEGs and 16 known glioma related genes to Human Protein Reference Database, a glioma associated protein-protein interaction network (GAPN) was constructed. In addition, 51 sub-networks in GAPN were screened out through Molecular Complex Detection (score ≥ 1), and sub-network 1 was found to have the closest interaction (score = 3). What' more, for the top 10 sub-networks, Gene Ontology (GO) enrichment analysis (p value < 0.05) was performed, and DEGs involved in sub-network 1 and 2, such as BRMS1L and CCNA1, were predicted to regulate cell growth, cell cycle, and DNA replication via interacting with known glioma related genes. Finally, the overlaps of DEGs and human essential, housekeeping, tissue-specific genes were calculated (p value = 1.0, 1.0, and 0.00014, respectively) and visualized by Venn Diagram package in R. About 61% of human tissue-specific genes were DEGs as well. This research shed new light on the pathogenesis of glioma based on DEGs and GAPN, and our findings might provide potential targets for clinical glioma treatment.

InGaN High-Temperature Photovoltaic Cells

NASA Technical Reports Server (NTRS)

Starikov, David

2015-01-01

This Phase II project developed Indium-Gallium-Nitride (InGaN) photovoltaic cells for high-temperature and high-radiation environments. The project included theoretical and experimental refinement of device structures produced in Phase I as well as modeling and optimization of solar cell device processing. The devices have been tested under concentrated air mass zero (AM0) sunlight, at temperatures from 100 degC to 250 degC, and after exposure to ionizing radiation. The results are expected to further verify that InGaN can be used for high-temperature and high-radiation solar cells. The large commercial solar cell market could benefit from the hybridization of InGaN materials to existing solar cell technology, which would significantly increase cell efficiency without relying on highly toxic compounds. In addition, further development of this technology to even lower bandgap materials for space applications would extend lifetimes of satellite solar cell arrays due to increased radiation hardness. This could be of importance to the Departmentof Defense (DoD) and commercial satellite manufacturers.

Electrical performance comparison BSFR-/bifacial solar cell array

NASA Astrophysics Data System (ADS)

Hoffmann, U.; Reissmann, F.

1986-11-01

Conventional and bifacial solar arrays were compared on subsystem level using the Space Telescope-solar array mission as reference. Calculations show that the bifacial solar cell has a performance advantage of 18 to 21 percent. This is due to a 5 C average lower temperature of the bifacial cell at the same orbit conditions; the rearside albedo irradiation of 86 to 170 W/sqm (average of 180 deg and 0 deg orbit orientation respectively); and the fact that the temperature difference between the hot case (satellite between Earth and Sun) and the cold case (before eclipse) is lower for the bifacial cell than for the BSFR cell. This lower difference has the advantage that the operation point for the bifacial cells is closer to maximum voltage point over the orbit. Resistivity of the bifacial solar cells against particle radiation, and absorptivity of front and rearside of the bifacial cell for infrared radiation must be verified. Statistical deviations of the albedo intensity and spectrum are not known.

Standardized UXO Technology Demonstration Site, Scoring Record No. 943

DTIC Science & Technology

2014-08-01

COLLERAN ROAD ABERDEEN PROVING GROUND, MARYLAND 21005-5059 Printed on Recycled Paper TEDT-AT-SL-M MEMORANDUM FOR Program Manager – SERDP...equipment. Small munitions grid Contains 300 grid cells . The center of each grid cell contains either munitions, clutter, or nothing with a portion...weather was warm and the field dry throughout the survey period for Battelle. 12 3.3.3 Soil Moisture Three soil probes were placed at various

Schnek: A C++ library for the development of parallel simulation codes on regular grids

NASA Astrophysics Data System (ADS)

Schmitz, Holger

2018-05-01

A large number of algorithms across the field of computational physics are formulated on grids with a regular topology. We present Schnek, a library that enables fast development of parallel simulations on regular grids. Schnek contains a number of easy-to-use modules that greatly reduce the amount of administrative code for large-scale simulation codes. The library provides an interface for reading simulation setup files with a hierarchical structure. The structure of the setup file is translated into a hierarchy of simulation modules that the developer can specify. The reader parses and evaluates mathematical expressions and initialises variables or grid data. This enables developers to write modular and flexible simulation codes with minimal effort. Regular grids of arbitrary dimension are defined as well as mechanisms for defining physical domain sizes, grid staggering, and ghost cells on these grids. Ghost cells can be exchanged between neighbouring processes using MPI with a simple interface. The grid data can easily be written into HDF5 files using serial or parallel I/O.

Efficient Unstructured Grid Adaptation Methods for Sonic Boom Prediction

NASA Technical Reports Server (NTRS)

Campbell, Richard L.; Carter, Melissa B.; Deere, Karen A.; Waithe, Kenrick A.

2008-01-01

This paper examines the use of two grid adaptation methods to improve the accuracy of the near-to-mid field pressure signature prediction of supersonic aircraft computed using the USM3D unstructured grid flow solver. The first method (ADV) is an interactive adaptation process that uses grid movement rather than enrichment to more accurately resolve the expansion and compression waves. The second method (SSGRID) uses an a priori adaptation approach to stretch and shear the original unstructured grid to align the grid with the pressure waves and reduce the cell count required to achieve an accurate signature prediction at a given distance from the vehicle. Both methods initially create negative volume cells that are repaired in a module in the ADV code. While both approaches provide significant improvements in the near field signature (< 3 body lengths) relative to a baseline grid without increasing the number of grid points, only the SSGRID approach allows the details of the signature to be accurately computed at mid-field distances (3-10 body lengths) for direct use with mid-field-to-ground boom propagation codes.

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

Ma, Zhiwen; Eichman, Josh; Kurtz, Jennifer

This National Renewable Energy Laboratory industry-inspired Laboratory Directed Research and Development project evaluates the feasibility and economics of using fuel cell backup power systems in cell towers to provide grid services (e.g., balancing, ancillary services, demand response). The work is intended to evaluate the integration of thousands of under-utilized, clean, efficient, and reliable fuel cell systems that are already installed in cell towers for potential grid and ancillary services.

Mesenchymal change and drug resistance in neuroblastoma.

PubMed

Naiditch, Jessica A; Jie, Chunfa; Lautz, Timothy B; Yu, Songtao; Clark, Sandra; Voronov, Dimitry; Chu, Fei; Madonna, Mary Beth

2015-01-01

Metastatic initiation has many phenotypic similarities to epithelial-to-mesenchymal transition, including loss of cell-cell adhesion, increased invasiveness, and increased cell mobility. We have previously demonstrated that drug resistance is associated with a metastatic phenotype in neuroblastoma (NB). The purpose of this project was to determine if the development of doxorubicin resistance is associated with characteristics of mesenchymal change in human NB cells. Total RNA was isolated from wild type (WT) and doxorubicin-resistant (DoxR) human NB cell lines (SK-N-SH and SK-N-BE(2)C) and analyzed using the Illumina Human HT-12 version 4 Expression BeadChip. Differentially expressed genes (DEGs) were identified. Volcano plots and heat maps were generated. Genes of interest with a fold change in expression >1.5 and an adjusted P < 0.1 were analyzed. Immunofluorescence (IF) and Western blot analysis confirmed microarray results of interest. Matrigel invasion assay and migration wounding assays were performed. Volcano plots and heat maps visually demonstrated a similar pattern of DEGs in the SK-N-SH and SK-N-BE(2)C DoxR cell lines relative to their parental WT lines. Venn diagramming revealed 1594 DEGs common to both DoxR cell lines relative to their parental cell lines. Network analysis pointed to several significantly upregulated epithelial-to-mesenchymal transition pathways, through TGF-beta pathways via RhoA, PI3K, and ILK and via SMADs, as well as via notch signaling pathways. DoxR cell lines displayed a more invasive phenotype than respective WT cell lines. Human SK-N-SH and SK-N-BE(2)C NB cells display characteristics of mesenchymal change via multiple pathways in the transition to a drug-resistant state. Copyright © 2015 Elsevier Inc. All rights reserved.

Variability of drought characteristics in Europe over the last 250 years

NASA Astrophysics Data System (ADS)

Hanel, Martin; Rakovec, Oldrich; Máca, Petr; Markonis, Yannis; Samaniego, Luis; Kumar, Rohini

2017-04-01

The mesoscale hydrological model (mHM) with spatial resolution 0.5deg is applied to simulate water balance across large part of continental Europe (excluding Scandinavia and Russia) for the period 1766-2015. The model is driven by available European gridded monthly temperature and precipitation reconstructions (Casty et al, 2007), which are disaggregated into daily time step using k-nearest neighbour resampling (Lall and Sharma, 1996). To quantify the uncertainty due to temporal disaggregation, several replicates of precipitation and temperature fields for the whole period are considered. In parallel, model parameter uncertainty is addressed by an ensemble of parameter realizations provided by Rakovec et al (2016). Deficit periods with respect to total runoff and soil moisture are identified at each grid cell using the variable threshold method. We assess the severity and intensity of drought, spatial extent of area under drought as well as the length of deficit periods. In addition, we also determine the occurrence of multi-year droughts during the period and evaluate the extremity of recent droughts in Europe (i.e., 2003, 2015) in the context of the whole multi-decadal record. References: Casty, C., Raible, C.C., Stocker, T.F., Luterbacher, J. and H. Wanner (2007), A European pattern climatology 1766-2000, Climate Dynamics, 29(7), DOI:10.1007/s00382-007-0257-6. Lall, U., and A. Sharma (1996), A Nearest neighbor bootstrap for resampling hydrologic time series, Water Resour. Res., 32(3), 679-693, DOI:10.1029/95WR02966. Rakovec, O., Kumar, R., Attinger, S. and Samaniego, L. (2016), Improving the realism of hydrologic model functioning through multivariate parameter estimation, Water Resour. Res., 52, DOI:10.1002/2016WR019430

A high-order spatial filter for a cubed-sphere spectral element model

NASA Astrophysics Data System (ADS)

Kang, Hyun-Gyu; Cheong, Hyeong-Bin

2017-04-01

A high-order spatial filter is developed for the spectral-element-method dynamical core on the cubed-sphere grid which employs the Gauss-Lobatto Lagrange interpolating polynomials (GLLIP) as orthogonal basis functions. The filter equation is the high-order Helmholtz equation which corresponds to the implicit time-differencing of a diffusion equation employing the high-order Laplacian. The Laplacian operator is discretized within a cell which is a building block of the cubed sphere grid and consists of the Gauss-Lobatto grid. When discretizing a high-order Laplacian, due to the requirement of C0 continuity along the cell boundaries the grid-points in neighboring cells should be used for the target cell: The number of neighboring cells is nearly quadratically proportional to the filter order. Discrete Helmholtz equation yields a huge-sized and highly sparse matrix equation whose size is N*N with N the number of total grid points on the globe. The number of nonzero entries is also almost in quadratic proportion to the filter order. Filtering is accomplished by solving the huge-matrix equation. While requiring a significant computing time, the solution of global matrix provides the filtered field free of discontinuity along the cell boundaries. To achieve the computational efficiency and the accuracy at the same time, the solution of the matrix equation was obtained by only accounting for the finite number of adjacent cells. This is called as a local-domain filter. It was shown that to remove the numerical noise near the grid-scale, inclusion of 5*5 cells for the local-domain filter was found sufficient, giving the same accuracy as that obtained by global domain solution while reducing the computing time to a considerably lower level. The high-order filter was evaluated using the standard test cases including the baroclinic instability of the zonal flow. Results indicated that the filter performs better on the removal of grid-scale numerical noises than the explicit high-order viscosity. It was also presented that the filter can be easily implemented on the distributed-memory parallel computers with a desirable scalability.

Glaucoma Diagnostic Capability of Global and Regional Measurements of Isolated Ganglion Cell Layer and Inner Plexiform Layer.

PubMed

Chien, Jason L; Ghassibi, Mark P; Patthanathamrongkasem, Thipnapa; Abumasmah, Ramiz; Rosman, Michael S; Skaat, Alon; Tello, Celso; Liebmann, Jeffrey M; Ritch, Robert; Park, Sung Chul

2017-03-01

To compare glaucoma diagnostic capability of global/regional macular layer parameters in different-sized grids. Serial horizontal spectral-domain optical coherence tomography scans of macula were obtained. Automated macular grids with diameters of 3, 3.45, and 6 mm were used. For each grid, 10 parameters (total volume; average thicknesses in 9 regions) were obtained for 5 layers: macular retinal nerve fiber layer (mRNFL), ganglion cell layer (GCL), inner plexiform layer (IPL), ganglion cell-inner plexiform layer (GCIPL; GCL+IPL), and ganglion cell complex (GCC; mRNFL+GCL+IPL). Sixty-nine normal eyes (69 subjects) and 87 glaucomatous eyes (87 patients) were included. For the total volume parameter, the area under the receiver operating characteristic curves (AUCs) in 6-mm grid were larger than the AUCs in 3- and 3.45-mm grids for GCL, GCC, GCIPL, and mRNFL (all P<0.020). For the average thickness parameters, the best AUC in 6-mm grid (T2 region for GCL, IPL, and GCIPL; I2 region for mRNFL and GCC) was greater than the best AUC in 3-mm grid for GCL, GCC, and mRNFL (P<0.045). The AUC of GCL volume (0.920) was similar to those of GCC (0.920) and GCIPL (0.909) volume. The AUC of GCL T2 region thickness (0.942) was similar to those of GCC I2 region (0.942) and GCIPL T2 region (0.934) thickness. Isolated macular GCL appears to be as good as GCC and GCIPL in glaucoma diagnosis, while IPL does not. Larger macular grids may be better at detecting glaucoma. Each layer has a characteristic region with the best glaucoma diagnostic capability.

New multigrid approach for three-dimensional unstructured, adaptive grids

NASA Technical Reports Server (NTRS)

Parthasarathy, Vijayan; Kallinderis, Y.

1994-01-01

A new multigrid method with adaptive unstructured grids is presented. The three-dimensional Euler equations are solved on tetrahedral grids that are adaptively refined or coarsened locally. The multigrid method is employed to propagate the fine grid corrections more rapidly by redistributing the changes-in-time of the solution from the fine grid to the coarser grids to accelerate convergence. A new approach is employed that uses the parent cells of the fine grid cells in an adapted mesh to generate successively coaser levels of multigrid. This obviates the need for the generation of a sequence of independent, nonoverlapping grids as well as the relatively complicated operations that need to be performed to interpolate the solution and the residuals between the independent grids. The solver is an explicit, vertex-based, finite volume scheme that employs edge-based data structures and operations. Spatial discretization is of central-differencing type combined with a special upwind-like smoothing operators. Application cases include adaptive solutions obtained with multigrid acceleration for supersonic and subsonic flow over a bump in a channel, as well as transonic flow around the ONERA M6 wing. Two levels of multigrid resulted in reduction in the number of iterations by a factor of 5.

Diffraction Analysis of Antennas With Mesh Surfaces

NASA Technical Reports Server (NTRS)

Rahmat-Samii, Yahya

1987-01-01

Strip-aperture model replaces wire-grid model. Far-field radiation pattern of antenna with mesh reflector calculated more accurately with new strip-aperture model than with wire-grid model of reflector surface. More adaptable than wire-grid model to variety of practical configurations and decidedly superior for reflectors in which mesh-cell width exceeds mesh thickness. Satisfies reciprocity theorem. Applied where mesh cells are no larger than tenth of wavelength. Small cell size permits use of simplifying approximation that reflector-surface current induced by electromagnetic field is present even in apertures. Approximation useful in calculating far field.

Simulating fluxes from heterogeneous land surfaces: Explicit subgrid method employing the biosphere-atmosphere transfer scheme (BATS)

NASA Technical Reports Server (NTRS)

Seth, Anji; Giorgi, Filippo; Dickinson, Robert E.

1994-01-01

A vectorized version of the biosphere-atmosphere transfer scheme (VBATS) is used to study moisture, energy, and momentum fluxes from heterogeneous land surfaces st the scale of an atmospheric model (AM) grid cells. To incorporate subgrid scale inhomogeneity, VBATS includes two important features: (1) characterization of the land surface (vegetation and soil parameters) at N subgrid points within an AM grid cell and (2) explicit distribution of climate forcing (precipitation, clouds, etc.) over the subgrid. In this study, VBATS is used in stand-alone mode to simulate a single AM grid cell and to evaluate the effects of subgrid scale vegetation and climate specification on the surface fluxes and hydrology. It is found that the partitioning of energy can be affected by up to 30%, runoff by 50%, and surface stress in excess of 60%. Distributing climate forcing over the AM grid cell increases the Bowen ratio, as a result of enhanced sensible heat flux and reduced latent heat flux. The combined effect of heterogeneous vegetation and distribution of climate is found to be dependent on the dominat vegetation class in the AM grid cell. Development of this method is part of a larger program to explore the importance of subgrid scale processes in regional and global climate simulations.

Environmental boundaries as a mechanism for correcting and anchoring spatial maps

PubMed Central

2016-01-01

Abstract Ubiquitous throughout the animal kingdom, path integration‐based navigation allows an animal to take a circuitous route out from a home base and using only self‐motion cues, calculate a direct vector back. Despite variation in an animal's running speed and direction, medial entorhinal grid cells fire in repeating place‐specific locations, pointing to the medial entorhinal circuit as a potential neural substrate for path integration‐based spatial navigation. Supporting this idea, grid cells appear to provide an environment‐independent metric representation of the animal's location in space and preserve their periodic firing structure even in complete darkness. However, a series of recent experiments indicate that spatially responsive medial entorhinal neurons depend on environmental cues in a more complex manner than previously proposed. While multiple types of landmarks may influence entorhinal spatial codes, environmental boundaries have emerged as salient landmarks that both correct error in entorhinal grid cells and bind internal spatial representations to the geometry of the external spatial world. The influence of boundaries on error correction and grid symmetry points to medial entorhinal border cells, which fire at a high rate only near environmental boundaries, as a potential neural substrate for landmark‐driven control of spatial codes. The influence of border cells on other entorhinal cell populations, such as grid cells, could depend on plasticity, raising the possibility that experience plays a critical role in determining how external cues influence internal spatial representations. PMID:26563618

High-order central ENO finite-volume scheme for hyperbolic conservation laws on three-dimensional cubed-sphere grids

NASA Astrophysics Data System (ADS)

Ivan, L.; De Sterck, H.; Susanto, A.; Groth, C. P. T.

2015-02-01

A fourth-order accurate finite-volume scheme for hyperbolic conservation laws on three-dimensional (3D) cubed-sphere grids is described. The approach is based on a central essentially non-oscillatory (CENO) finite-volume method that was recently introduced for two-dimensional compressible flows and is extended to 3D geometries with structured hexahedral grids. Cubed-sphere grids feature hexahedral cells with nonplanar cell surfaces, which are handled with high-order accuracy using trilinear geometry representations in the proposed approach. Varying stencil sizes and slope discontinuities in grid lines occur at the boundaries and corners of the six sectors of the cubed-sphere grid where the grid topology is unstructured, and these difficulties are handled naturally with high-order accuracy by the multidimensional least-squares based 3D CENO reconstruction with overdetermined stencils. A rotation-based mechanism is introduced to automatically select appropriate smaller stencils at degenerate block boundaries, where fewer ghost cells are available and the grid topology changes, requiring stencils to be modified. Combining these building blocks results in a finite-volume discretization for conservation laws on 3D cubed-sphere grids that is uniformly high-order accurate in all three grid directions. While solution-adaptivity is natural in the multi-block setting of our code, high-order accurate adaptive refinement on cubed-sphere grids is not pursued in this paper. The 3D CENO scheme is an accurate and robust solution method for hyperbolic conservation laws on general hexahedral grids that is attractive because it is inherently multidimensional by employing a K-exact overdetermined reconstruction scheme, and it avoids the complexity of considering multiple non-central stencil configurations that characterizes traditional ENO schemes. Extensive numerical tests demonstrate fourth-order convergence for stationary and time-dependent Euler and magnetohydrodynamic flows on cubed-sphere grids, and robustness against spurious oscillations at 3D shocks. Performance tests illustrate efficiency gains that can be potentially achieved using fourth-order schemes as compared to second-order methods for the same error level. Applications on extended cubed-sphere grids incorporating a seventh root block that discretizes the interior of the inner sphere demonstrate the versatility of the spatial discretization method.

New ghost-node method for linking different models with varied grid refinement

USGS Publications Warehouse

James, S.C.; Dickinson, J.E.; Mehl, S.W.; Hill, M.C.; Leake, S.A.; Zyvoloski, G.A.; Eddebbarh, A.-A.

2006-01-01

A flexible, robust method for linking grids of locally refined ground-water flow models constructed with different numerical methods is needed to address a variety of hydrologic problems. This work outlines and tests a new ghost-node model-linking method for a refined "child" model that is contained within a larger and coarser "parent" model that is based on the iterative method of Steffen W. Mehl and Mary C. Hill (2002, Advances in Water Res., 25, p. 497-511; 2004, Advances in Water Res., 27, p. 899-912). The method is applicable to steady-state solutions for ground-water flow. Tests are presented for a homogeneous two-dimensional system that has matching grids (parent cells border an integer number of child cells) or nonmatching grids. The coupled grids are simulated by using the finite-difference and finite-element models MODFLOW and FEHM, respectively. The simulations require no alteration of the MODFLOW or FEHM models and are executed using a batch file on Windows operating systems. Results indicate that when the grids are matched spatially so that nodes and child-cell boundaries are aligned, the new coupling technique has error nearly equal to that when coupling two MODFLOW models. When the grids are nonmatching, model accuracy is slightly increased compared to that for matching-grid cases. Overall, results indicate that the ghost-node technique is a viable means to couple distinct models because the overall head and flow errors relative to the analytical solution are less than if only the regional coarse-grid model was used to simulate flow in the child model's domain.

DIRECT AND INDIRECT BIOLOGICAL EFFECTS OF RADIATION

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

Hobitz, H.

1961-01-01

The primary physical processes, ionization and excitation, induced by radiation in biological materials are discussed. Their effects in causing reduction, decarboxylation, and depolymerization in proteins and deoxyribonucleic acid of the cell nucleus are examined. The action of radiation doses of 100,000- 600,000 r on pollen of Digitalis purpurea maintained at room temperature and at approximates 190 deg C showed that biological activity was destroyed by doses >200,000 r at room temperature, but at approximates 190 deg the pollen retained some activity even after the highest dose. A similar effect was seen with Bacterium cadaveris cells, about 0.5% of which survivedmore » 50000 r given at l8O deg whereas no cells survived 20000 r given at 4 deg . The presence of 1% cysteamine at the higher temperature increased survival 20-fold. Cytochrome c showed markedly different responses to radiation in dry form as compared with aqueous solution. The anhydrous enzyme showed a linear decline in log activity with radiation dose but in aqueous solution the activity declined more slowly at higher doses. The radiation dose to-produce 50% inactivation was 4 x 10/sup 7/ r in dry form and 6 x 10/sup 5/ r in solution, a 67-fold difference. The results suggest that diffusion of the free radicals (H: or OH:) produced in the primary process is considerably hindered at low temperature and by the absence of water. (H.H.D.)« less

Interlocking egg-crate type grid assembly

DOEpatents

Kast, Steven J.

1987-01-01

Disclosed is an interlocking egg-crate hexagonal grid for supporting a nuclear fuel pin in a hexagonal array. The grid is formed from strips bent at an angle of about 120.degree. at each vertex. Over some faces of each hexagonal cell the strips are coplanar but are arranged, by stacking and interlocking, to avoid any double thickness of metal in that plane. Springs and dimples are formed in the faces of each cell to hold the fuel pin substantially centered.

Interlocking egg-crate type grid assembly

DOEpatents

Kast, S.J.

1985-03-15

Disclosed is an interlocking egg-crate hexagonal grid for supporting a nuclear fuel pin in a hexagonal array. The grid is formed from strips bent at an angle of about 120/sup 0/ at each vertex. Over some faces of each hexagonal cell the strips are coplanar but are arranged, by stacking interlocking, to avoid any double thickness of metal in that plane. Springs and dimples are formed in the faces of each cell to hold the fuel pin substantially centered.

Continuous attractor network models of grid cell firing based on excitatory–inhibitory interactions

PubMed Central

Shipston‐Sharman, Oliver; Solanka, Lukas

2016-01-01

Abstract Neurons in the medial entorhinal cortex encode location through spatial firing fields that have a grid‐like organisation. The challenge of identifying mechanisms for grid firing has been addressed through experimental and theoretical investigations of medial entorhinal circuits. Here, we discuss evidence for continuous attractor network models that account for grid firing by synaptic interactions between excitatory and inhibitory cells. These models assume that grid‐like firing patterns are the result of computation of location from velocity inputs, with additional spatial input required to oppose drift in the attractor state. We focus on properties of continuous attractor networks that are revealed by explicitly considering excitatory and inhibitory neurons, their connectivity and their membrane potential dynamics. Models at this level of detail can account for theta‐nested gamma oscillations as well as grid firing, predict spatial firing of interneurons as well as excitatory cells, show how gamma oscillations can be modulated independently from spatial computations, reveal critical roles for neuronal noise, and demonstrate that only a subset of excitatory cells in a network need have grid‐like firing fields. Evaluating experimental data against predictions from detailed network models will be important for establishing the mechanisms mediating grid firing. PMID:27870120

Transcriptome analysis of PCOS arrested 2-cell embryos.

PubMed

Lu, Cuiling; Chi, Hongbin; Wang, Yapeng; Feng, Xue; Wang, Lina; Huang, Shuo; Yan, Liying; Lin, Shengli; Liu, Ping; Qiao, Jie

2018-06-18

In an attempt to explore the early developmental arrest in embryos from polycystic ovarian syndrome (PCOS) patients, we sequenced the transcriptome profiles of PCOS arrested 2-cell embryos, non-PCOS arrested 2-cell embryos and non-arrested 2-cell embryos using single-cell RNA-Seq technique. Differential expression analysis was performed using the DEGSeq R package. Gene Ontology (GO) enrichment was analyzed using the GOseq R package. Data revealed 62 differentially expressed genes between non-PCOS arrested and PCOS arrested embryos and 2217 differentially expressed genes between PCOS arrested and non-arrested 2-cell embryos. A total of 49 differently expressed genes (DEGs) were annotated with GO terms in the up-regulated genes between PCOS arrested and non-PCOS arrested embryos after GO enrichment. A total of 29 DEGs were annotated with GO terms in the down-regulated genes between PCOS arrested and non-arrested 2-cell embryos after GO enrichment. These data can provide a reference for screening specific genes involved in the arrest of PCOS embryos.

Elliptical storm cell modeling of digital radar data

NASA Technical Reports Server (NTRS)

Altman, F. J.

1972-01-01

A model for spatial distributions of reflectivity in storm cells was fitted to digital radar data. The data were taken with a modified WSR-57 weather radar with 2.6-km resolution. The data consisted of modified B-scan records on magnetic tape of storm cells tracked at 0 deg elevation for several hours. The MIT L-band radar with 0.8-km resolution produced cross-section data on several cells at 1/2 deg elevation intervals. The model developed uses ellipses for contours of constant effective-reflectivity factor Z with constant orientation and eccentricity within a horizontal cell cross section at a given time and elevation. The centers of the ellipses are assumed to be uniformly spaced on a straight line, with areas linearly related to log Z. All cross sections are similar at different heights (except for cell tops, bottoms, and splitting cells), especially for the highest reflectivities; wind shear causes some translation and rotation between levels. Goodness-of-fit measures and parameters of interest for 204 ellipses are considered.

CdS thin film solar cells for terrestrial power

NASA Technical Reports Server (NTRS)

Shirland, F. A.

1975-01-01

The development of very low cost long lived Cu2S/CdS thin film solar cells for large scale energy conversion is reported. Excellent evaporated metal grid patterns were obtained using a specially designed aperture mask. Vacuum evaporated gold and copper grids of 50 lines per inch and 1 micron thickness were adequate electrically for the fine mesh contacting grid. Real time roof top sunlight exposure tests of encapsulated CdS cells showed no loss in output after 5 months. Accelerated life testing of encapsulated cells showed no loss of output power after 6 months of 12 hour dark-12 hour AMI illumination cycles at 40 C, 60 C, 80 C and 100 C temperatures. However, the cells changed their basic parameters, such as series and shunt resistance and junction capacitance.

Microarray-based gene expression profiling in patients with cryopyrin-associated periodic syndromes defines a disease-related signature and IL-1-responsive transcripts.

PubMed

Balow, James E; Ryan, John G; Chae, Jae Jin; Booty, Matthew G; Bulua, Ariel; Stone, Deborah; Sun, Hong-Wei; Greene, James; Barham, Beverly; Goldbach-Mansky, Raphaela; Kastner, Daniel L; Aksentijevich, Ivona

2013-06-01

To analyse gene expression patterns and to define a specific gene expression signature in patients with the severe end of the spectrum of cryopyrin-associated periodic syndromes (CAPS). The molecular consequences of interleukin 1 inhibition were examined by comparing gene expression patterns in 16 CAPS patients before and after treatment with anakinra. We collected peripheral blood mononuclear cells from 22 CAPS patients with active disease and from 14 healthy children. Transcripts that passed stringent filtering criteria (p values≤false discovery rate 1%) were considered as differentially expressed genes (DEG). A set of DEG was validated by quantitative reverse transcription PCR and functional studies with primary cells from CAPS patients and healthy controls. We used 17 CAPS and 66 non-CAPS patient samples to create a set of gene expression models that differentiates CAPS patients from controls and from patients with other autoinflammatory conditions. Many DEG include transcripts related to the regulation of innate and adaptive immune responses, oxidative stress, cell death, cell adhesion and motility. A set of gene expression-based models comprising the CAPS-specific gene expression signature correctly classified all 17 samples from an independent dataset. This classifier also correctly identified 15 of 16 post-anakinra CAPS samples despite the fact that these CAPS patients were in clinical remission. We identified a gene expression signature that clearly distinguished CAPS patients from controls. A number of DEG were in common with other systemic inflammatory diseases such as systemic onset juvenile idiopathic arthritis. The CAPS-specific gene expression classifiers also suggest incomplete suppression of inflammation at low doses of anakinra.

Microarray-based gene expression profiling in patients with cryopyrin-associated periodic syndromes defines a disease-related signature and IL-1-responsive transcripts

PubMed Central

Balow, James E; Ryan, John G; Chae, Jae Jin; Booty, Matthew G; Bulua, Ariel; Stone, Deborah; Sun, Hong-Wei; Greene, James; Barham, Beverly; Goldbach-Mansky, Raphaela; Kastner, Daniel L; Aksentijevich, Ivona

2014-01-01

Objective To analyse gene expression patterns and to define a specific gene expression signature in patients with the severe end of the spectrum of cryopyrin-associated periodic syndromes (CAPS). The molecular consequences of interleukin 1 inhibition were examined by comparing gene expression patterns in 16 CAPS patients before and after treatment with anakinra. Methods We collected peripheral blood mononuclear cells from 22 CAPS patients with active disease and from 14 healthy children. Transcripts that passed stringent filtering criteria (p values ≤ false discovery rate 1%) were considered as differentially expressed genes (DEG). A set of DEG was validated by quantitative reverse transcription PCR and functional studies with primary cells from CAPS patients and healthy controls. We used 17 CAPS and 66 non-CAPS patient samples to create a set of gene expression models that differentiates CAPS patients from controls and from patients with other autoinflammatory conditions. Results Many DEG include transcripts related to the regulation of innate and adaptive immune responses, oxidative stress, cell death, cell adhesion and motility. A set of gene expression-based models comprising the CAPS-specific gene expression signature correctly classified all 17 samples from an independent dataset. This classifier also correctly identified 15 of 16 postanakinra CAPS samples despite the fact that these CAPS patients were in clinical remission. Conclusions We identified a gene expression signature that clearly distinguished CAPS patients from controls. A number of DEG were in common with other systemic inflammatory diseases such as systemic onset juvenile idiopathic arthritis. The CAPS-specific gene expression classifiers also suggest incomplete suppression of inflammation at low doses of anakinra. PMID:23223423

Performance of Wide Operating Temperature Range Electrolytes in Quallion Prototype Li-Ion Cells

NASA Technical Reports Server (NTRS)

Smart, M. C.; Ratnakumar, B. V.; Tomcsi, M. R.; Nagata, M.; Visco, V.; Tsukamoto, H.

2010-01-01

For a number of applications, there is a continued interest in the development of rechargeable lithium-based batteries that can effectively operate over a wide temperature range (i.e., -40 to +70 deg C). These applications include powering future planetary rovers for NASA, enabling the next generation of automotive batteries for DOE, and supporting many DOD applications. Li-ion technology has been demonstrated to have good performance over a reasonably wide temperature range with many systems; however, there is still a desire to improve the low temperature rate capacity as well as the high temperature resilience. In the current study, we would like to present recent results obtained with prototype Li-Ion cells (manufactured by Quallion, LLC) which include various wide operating temperature range electrolytes developed by both JPL and Quallion. To demonstrate the viability of the technology, a number of performance tests were carried out, including: (a) discharge rate characterization over a wide temperature range (down to -60 deg C) using various rates (up to 20C rates), (b) discharge rate characterization at low temperatures with low temperature charging, (c) variable temperature cycling over a wide temperature range (-40 to +70 deg C), and (d) cycling at high temperature (50 deg C). As will be discussed, impressive rate capability was observed at low temperatures with many systems, as well as good resilience to high temperature cycling. To augment the performance testing on the prototype cells, a number of experimental three electrodes cells were fabricated (including Li reference electrodes) to allow the determination of the lithium kinetics of the respective electrodes and interfacial properties as a function of temperatures.

RNA Seq analysis for transcriptome profiling in response to classical swine fever vaccination in indigenous and crossbred pigs.

PubMed

Pathak, Shalu Kumari; Kumar, Amit; Bhuwana, G; Sah, Vaishali; Upmanyu, Vikramadiya; Tiwari, A K; Sahoo, A P; Sahoo, A R; Wani, Sajjad A; Panigrahi, Manjit; Sahoo, N R; Kumar, Ravi

2017-09-01

In present investigation, differential expression of transcriptome after classical swine fever (CSF) vaccination has been explored at the cellular level in crossbred and indigenous (desi) piglets. RNA Sequencing by Expectation-Maximization (RSEM) package was used to quantify gene expression from RNA Sequencing data, and differentially expressed genes (DEGs) were identified using EBSeq, DESeq2, and edgeR softwares. After analysis, 5222, 6037, and 6210 common DEGs were identified in indigenous post-vaccinated verses pre-vaccinated, crossbred post-vaccinated verses pre-vaccinated, and post-vaccinated crossbred verses indigenous pigs, respectively. Functional annotation of these DEGs showed enrichment of antigen processing-cross presentation, B cell receptor signaling, T cell receptor signaling, NF-κB signaling, and TNF signaling pathways. The interaction network among the immune genes included more number of genes with greater connectivity in vaccinated crossbred than the indigenous piglets. Higher expression of IRF3, IL1β, TAP1, CSK, SLA2, SLADM, and NF-kB in crossbred piglets in comparison to indigenous explains the better humoral response observed in crossbred piglets. Here, we predicted that the processed CSFV antigen through the T cell receptor signaling cascade triggers the B cell receptor-signaling pathway to finally activate MAPK kinase and NF-κB signaling pathways in B cell. This activation results in expression of genes/transcription factors that lead to B cell ontogeny, auto immunity and immune response through antibody production. Further, immunologically important genes were validated by qRT-PCR.

Angular and Polarization Response of Multimode Sensors with Resistive-Grid Absorbers

NASA Technical Reports Server (NTRS)

Kusaka, Akito; Wollack, Edward J.; Stevenson, Thomas R.

2014-01-01

High sensitivity receiver systems with near ideal polarization sensitivity are highly desirable for development of millimeter and sub-millimeter radio astronomy. Multimoded bolometers provide a unique solution to achieve such sensitivity, for which hundreds of single-mode sensors would otherwise be required. The primary concern in employing such multimoded sensors for polarimetery is the control of the polarization systematics. In this paper, we examine the angular- and polarization- dependent absorption pattern of a thin resistive grid or membrane, which models an absorber used for a multimoded bolometer. The result shows that a freestanding thin resistive absorber with a surface resistivity of eta/2, where eta is the impedance of free space, attains a beam pattern with equal E- and H-plane responses, leading to zero cross polarization. For a resistive-grid absorber, the condition is met when a pair of grids is positioned orthogonal to each other and both have a resistivity of eta/2. When a reflective backshort termination is employed to improve absorption efficiency, the cross-polar level can be suppressed below -30 dB if acceptance angle of the sensor is limited to < or approx. 60deg. The small cross-polar systematics have even-parity patterns and do not contaminate the measurements of odd-parity polarization patterns, for which many of recent instruments for cosmic microwave background are designed. Underlying symmetry that suppresses these cross-polar systematics is discussed in detail. The estimates and formalism provided in this paper offer key tools in the design consideration of the instruments using the multimoded polarimeters.

Simulation of Runoff Hydrograph on Soil Surfaces with Different Microtopography Using a Travel Time Method at the Plot Scale

PubMed Central

Zhao, Longshan; Wu, Faqi

2015-01-01

In this study, a simple travel time-based runoff model was proposed to simulate a runoff hydrograph on soil surfaces with different microtopographies. Three main parameters, i.e., rainfall intensity (I), mean flow velocity (v m) and ponding time of depression (t p), were inputted into this model. The soil surface was divided into numerous grid cells, and the flow length of each grid cell (l i) was then calculated from a digital elevation model (DEM). The flow velocity in each grid cell (v i) was derived from the upstream flow accumulation area using v m. The total flow travel time through each grid cell to the surface outlet was the sum of the sum of flow travel times along the flow path (i.e., the sum of l i/v i) and t p. The runoff rate at the slope outlet for each respective travel time was estimated by finding the sum of the rain rate from all contributing cells for all time intervals. The results show positive agreement between the measured and predicted runoff hydrographs. PMID:26103635

Simulation of Runoff Hydrograph on Soil Surfaces with Different Microtopography Using a Travel Time Method at the Plot Scale.

PubMed

Zhao, Longshan; Wu, Faqi

2015-01-01

In this study, a simple travel time-based runoff model was proposed to simulate a runoff hydrograph on soil surfaces with different microtopographies. Three main parameters, i.e., rainfall intensity (I), mean flow velocity (vm) and ponding time of depression (tp), were inputted into this model. The soil surface was divided into numerous grid cells, and the flow length of each grid cell (li) was then calculated from a digital elevation model (DEM). The flow velocity in each grid cell (vi) was derived from the upstream flow accumulation area using vm. The total flow travel time through each grid cell to the surface outlet was the sum of the sum of flow travel times along the flow path (i.e., the sum of li/vi) and tp. The runoff rate at the slope outlet for each respective travel time was estimated by finding the sum of the rain rate from all contributing cells for all time intervals. The results show positive agreement between the measured and predicted runoff hydrographs.

Genome-wide expression profiling analysis to identify key genes in the anti-HIV mechanism of CD4+ and CD8+ T cells.

PubMed

Gao, Lijie; Wang, Yunqi; Li, Yi; Dong, Ya; Yang, Aimin; Zhang, Jie; Li, Fengying; Zhang, Rongqiang

2018-07-01

Comprehensive bioinformatics analyses were performed to explore the key biomarkers in response to HIV infection of CD4 + and CD8 + T cells. The numbers of CD4 + and CD8 + T cells of HIV infected individuals were analyzed and the GEO database (GSE6740) was screened for differentially expressed genes (DEGs) in HIV infected CD4 + and CD8 + T cells. Gene Ontology enrichment, KEGG pathway analyses, and protein-protein interaction (PPI) network were performed to identify the key pathway and core proteins in anti-HIV virus process of CD4 + and CD8 + T cells. Finally, we analyzed the expressions of key proteins in HIV-infected T cells (GSE6740 dataset) and peripheral blood mononuclear cells(PBMCs) (GSE511 dataset). 1) CD4 + T cells counts and ratio of CD4 + /CD8 + T cells decreased while CD8 + T cells counts increased in HIV positive individuals; 2) 517 DEGs were found in HIV infected CD4 + and CD8 + T cells at acute and chronic stage with the criterial of P-value <0.05 and fold change (FC) ≥2; 3) In acute HIV infection, type 1 interferon (IFN-1) pathway might played a critical role in response to HIV infection of T cells. The main biological processes of the DEGs were response to virus and defense response to virus. At chronic stage, ISG15 protein, in conjunction with IFN-1 pathway might play key roles in anti-HIV responses of CD4 + T cells; and 4) The expression of ISG15 increased in both T cells and PBMCs after HIV infection. Gene expression profile of CD4 + and CD8 + T cells changed significantly in HIV infection, in which ISG15 gene may play a central role in activating the natural antiviral process of immune cells. © 2018 Wiley Periodicals, Inc.

Analysis and comparison of oxygen consumption of HepG2 cells in a monolayer and three-dimensional high density cell culture by use of a matrigrid®.

PubMed

Weise, Frank; Fernekorn, Uta; Hampl, Jörg; Klett, Maren; Schober, Andreas

2013-09-01

By the use of a MatriGrid® we have established a three-dimensional high density cell culture. The MatriGrid® is a culture medium permeable, polymeric scaffold with 187 microcavities. In these cavities (300 μm diameter and 207 μm deep) the cells can growth three-dimensionally. For these experiments we measured the oxygen consumption of HepG2 cell cultures in order to optimize cultivation conditions. We measured and compared the oxygen consumption, growth rate and vitality under three different cultivation conditions: monolayer, three-dimensional static and three-dimensional actively perfused. The results show that the cells in a three-dimensional cell culture consume less oxygen as in a monolayer cell culture and that the actively perfused three-dimensional cell culture in the MatriGrid® has a similar growth rate and vitality as the monolayer culture. Copyright © 2013 Wiley Periodicals, Inc.

The Design of Connection Solid Oxide Fuel Cell (SOFC) Integrated Grid with Three-Phase Inverter

NASA Astrophysics Data System (ADS)

Darjat; Sulistyo; Triwiyatno, Aris; Thalib, Humaid

2018-03-01

Fuel cell technology is a relatively new energy-saving technology that has the potential to replace conventional energy technologies. Among the different types of generation technologies, fuel cells is the generation technologies considered as a potential source of power generation because it is flexible and can be placed anywhere based distribution system. Modeling of SOFC is done by using Nernst equation. The output power of the fuel cell can be controlled by controlling the flow rate of the fuels used in the process. Three-phase PWM inverter is used to get the form of three-phase voltage which same with the grid. In this paper, the planning and design of the SOFC are connected to the grid.

Transcriptome profiling analysis of senescent gingival fibroblasts in response to Fusobacterium nucleatum infection

PubMed Central

Ahn, Sun-Hee; Chun, Sung-Min; Park, Chungoo; Lee, Jong-Hee; Lee, Seok-Woo

2017-01-01

Periodontal disease is caused by dental plaque biofilms. Fusobacterium nucleatum is an important periodontal pathogen involved in the development of bacterial complexity in dental plaque biofilms. Human gingival fibroblasts (GFs) act as the first line of defense against oral microorganisms and locally orchestrate immune responses by triggering the production of reactive oxygen species and pro-inflammatory cytokines (IL-6 and IL-8). The frequency and severity of periodontal diseases is known to increase in elderly subjects. However, despite several studies exploring the effects of aging in periodontal disease, the underlying mechanisms through which aging affects the interaction between F. nucleatum and human GFs remain unclear. To identify genes affected by infection, aging, or both, we performed an RNA-Seq analysis using GFs isolated from a single healthy donor that were passaged for a short period of time (P4) ‘young GFs’ or for longer period of time (P22) ‘old GFs’, and infected or not with F. nucleatum. Comparing F. nucleatum-infected and uninfected GF(P4) cells the differentially expressed genes (DEGs) were involved in host defense mechanisms (i.e., immune responses and defense responses), whereas comparing F. nucleatum-infected and uninfected GF(P22) cells the DEGs were involved in cell maintenance (i.e., TGF-β signaling, skeletal development). Most DEGs in F. nucleatum-infected GF(P22) cells were downregulated (85%) and were significantly associated with host defense responses such as inflammatory responses, when compared to the DEGs in F. nucleatum-infected GF(P4) cells. Five genes (GADD45b, KLF10, CSRNP1, ID1, and TM4SF1) were upregulated in response to F. nucleatum infection; however, this effect was only seen in GF(P22) cells. The genes identified here appear to interact with each other in a network associated with free radical scavenging, cell cycle, and cancer; therefore, they could be potential candidates involved in the aged GF’s response to F. nucleatum infection. Further studies are needed to confirm these observations. PMID:29190775

Silicon solar cells made by a self-aligned, selective-emitter, plasma-etchback process

DOEpatents

Ruby, Douglas S.; Schubert, William K.; Gee, James M.

1999-01-01

A potentially low-cost process for forming and passivating a selective emitter. The process uses a plasma etch of the heavily doped emitter to improve its performance. The grids of the solar cell are used to mask the plasma etch so that only the emitter in the region between the grids is etched, while the region beneath the grids remains heavily doped for low contact resistance. This process is potentially low-cost because it requires no alignment. After the emitter etch, a silicon nitride layer is deposited by plasma-enhanced, chemical vapor deposition, and the solar cell is annealed in a forming gas.

Silicon solar cells made by a self-aligned, selective-emitter, plasma-etchback process

DOEpatents

Ruby, D.S.; Schubert, W.K.; Gee, J.M.

1999-02-16

A potentially low-cost process for forming and passivating a selective emitter. The process uses a plasma etch of the heavily doped emitter to improve its performance. The grids of the solar cell are used to mask the plasma etch so that only the emitter in the region between the grids is etched, while the region beneath the grids remains heavily doped for low contact resistance. This process is potentially low-cost because it requires no alignment. After the emitter etch, a silicon nitride layer is deposited by plasma-enhanced, chemical vapor deposition, and the solar cell is annealed in a forming gas. 5 figs.

Comparison of properties of medial entorhinal cortex layer II neurons in two anatomical dimensions with and without cholinergic activation.

PubMed

Yoshida, Motoharu; Jochems, Arthur; Hasselmo, Michael E

2013-01-01

Mechanisms underlying grid cell firing in the medial entorhinal cortex (MEC) still remain unknown. Computational modeling studies have suggested that cellular properties such as spike frequency adaptation and persistent firing might underlie the grid cell firing. Recent in vivo studies also suggest that cholinergic activation influences grid cell firing. Here we investigated the anatomical distribution of firing frequency adaptation, the medium spike after hyperpolarization potential (mAHP), subthreshold membrane potential oscillations, sag potential, input resistance and persistent firing, in MEC layer II principal cells using in vitro whole-cell patch clamp recordings in rats. Anatomical distributions of these properties were compared along both the dorso-ventral and medio-lateral axes, both with and without the cholinergic receptor agonist carbachol. We found that spike frequency adaptation is significantly stronger in ventral than in dorsal neurons both with and without carbachol. Spike frequency adaptation was significantly correlated with the duration of the mAHP, which also showed a gradient along the dorso-ventral axis. In carbachol, we found that about 50% of MEC layer II neurons show persistent firing which lasted more than 30 seconds. Persistent firing of MEC layer II neurons might contribute to grid cell firing by providing the excitatory drive. Dorso-ventral differences in spike frequency adaptation we report here are opposite from previous predictions by a computational model. We discuss an alternative mechanism as to how dorso-ventral differences in spike frequency adaptation could contribute to different scales of grid spacing.

Accuracy of Gradient Reconstruction on Grids with High Aspect Ratio

NASA Technical Reports Server (NTRS)

Thomas, James

2008-01-01

Gradient approximation methods commonly used in unstructured-grid finite-volume schemes intended for solutions of high Reynolds number flow equations are studied comprehensively. The accuracy of gradients within cells and within faces is evaluated systematically for both node-centered and cell-centered formulations. Computational and analytical evaluations are made on a series of high-aspect-ratio grids with different primal elements, including quadrilateral, triangular, and mixed element grids, with and without random perturbations to the mesh. Both rectangular and cylindrical geometries are considered; the latter serves to study the effects of geometric curvature. The study shows that the accuracy of gradient reconstruction on high-aspect-ratio grids is determined by a combination of the grid and the solution. The contributors to the error are identified and approaches to reduce errors are given, including the addition of higher-order terms in the direction of larger mesh spacing. A parameter GAMMA characterizing accuracy on curved high-aspect-ratio grids is discussed and an approximate-mapped-least-square method using a commonly-available distance function is presented; the method provides accurate gradient reconstruction on general grids. The study is intended to be a reference guide accompanying the construction of accurate and efficient methods for high Reynolds number applications

Comparative effects of inhaled diesel exhaust and ambient fine particles on inflammation, atherosclerosis, and vascular dysfunction

PubMed Central

Quan, Chunli; Sun, Qinghua; Lippmann, Morton; Chen, Lung-Chi

2011-01-01

Ambient air PM2.5 (particulate matter less than 2.5 μm in diameter) has been associated with cardiovascular diseases (CVDs), but the underlying mechanisms affecting CVDs are unknown. The authors investigated whether subchronic inhalation of concentrated ambient PM2.5 (CAPs), whole diesel exhaust (WDE), or diesel exhaust gases (DEGs) led to exacerbation of atherosclerosis, pulmonary and systemic inflammation, and vascular dysfunction; and whether DEG interactions with CAPs alter cardiovascular effects. ApoE−/− mice were simultaneously exposed via inhalation for 5 hours/day, 4 days/week, for up to 5 months to one of five different exposure atmospheres: (1) filtered air (FA); (2) CAPs (105 μg/m3); (3) WDE (DEP = 436 μg/m3); (4) DEG (equivalent to gas levels in WDE group); and (5) CAPs+DEG (PM2.5: 113 μg/m3; with DEG equivalent to WDE group). After 3 and 5 months, lung lavage fluid and blood sera were analyzed, and atherosclerotic plaques were quantified by ultrasound imaging, hematoxylin and eosin (H&E stain), and en face Sudan IV stain. Vascular functions were assessed after 5 months of exposure. The authors showed that (1) subchronic CAPs, WDE, and DEG inhalations increased serum vascular cell adhesion molecule (VCAM)-1 levels and enhanced phenylephrine (PE)-induced vasoconstriction; (2) for plaque exacerbation, CAPs > WDE > DEG = FA, thus PM components (not present in WDE) were responsible for plaque development; (3) atherosclerosis can exacerbated through mechanistic pathways other than inflammation and vascular dysfunction; and (4) although there were no significant interactions between CAPs and DEG on plaque exacerbation, it is less clear whether the effects of CAPs on vasomotor dysfunction and pulmonary/systemic inflammation were enhanced by the DEG coexposure. PMID:20462391

Development and evaluation of a local grid refinement method for block-centered finite-difference groundwater models using shared nodes

USGS Publications Warehouse

Mehl, S.; Hill, M.C.

2002-01-01

A new method of local grid refinement for two-dimensional block-centered finite-difference meshes is presented in the context of steady-state groundwater-flow modeling. The method uses an iteration-based feedback with shared nodes to couple two separate grids. The new method is evaluated by comparison with results using a uniform fine mesh, a variably spaced mesh, and a traditional method of local grid refinement without a feedback. Results indicate: (1) The new method exhibits quadratic convergence for homogeneous systems and convergence equivalent to uniform-grid refinement for heterogeneous systems. (2) Coupling the coarse grid with the refined grid in a numerically rigorous way allowed for improvement in the coarse-grid results. (3) For heterogeneous systems, commonly used linear interpolation of heads from the large model onto the boundary of the refined model produced heads that are inconsistent with the physics of the flow field. (4) The traditional method works well in situations where the better resolution of the locally refined grid has little influence on the overall flow-system dynamics, but if this is not true, lack of a feedback mechanism produced errors in head up to 3.6% and errors in cell-to-cell flows up to 25%. ?? 2002 Elsevier Science Ltd. All rights reserved.

Identification of upstream transcription factors (TFs) for expression signature genes in breast cancer.

PubMed

Zang, Hongyan; Li, Ning; Pan, Yuling; Hao, Jingguang

2017-03-01

Breast cancer is a common malignancy among women with a rising incidence. Our intention was to detect transcription factors (TFs) for deeper understanding of the underlying mechanisms of breast cancer. Integrated analysis of gene expression datasets of breast cancer was performed. Then, functional annotation of differentially expressed genes (DEGs) was conducted, including Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Furthermore, TFs were identified and a global transcriptional regulatory network was constructed. Seven publically available GEO datasets were obtained, and a set of 1196 DEGs were identified (460 up-regulated and 736 down-regulated). Functional annotation results showed that cell cycle was the most significantly enriched pathway, which was consistent with the fact that cell cycle is closely related to various tumors. Fifty-three differentially expressed TFs were identified, and the regulatory networks consisted of 817 TF-target interactions between 46 TFs and 602 DEGs in the context of breast cancer. Top 10 TFs covering the most downstream DEGs were SOX10, NFATC2, ZNF354C, ARID3A, BRCA1, FOXO3, GATA3, ZEB1, HOXA5 and EGR1. The transcriptional regulatory networks could enable a better understanding of regulatory mechanisms of breast cancer pathology and provide an opportunity for the development of potential therapy.

Injection of Spin-Polarized Electrons into a AlGaN/GaN Device from an Electrochemical Cell: Evidence for an Extremely Long Spin Lifetime.

PubMed

Kumar, Anup; Capua, Eyal; Fontanesi, Claudio; Carmieli, Raanan; Naaman, Ron

2018-04-24

Spin-polarized electrons are injected from an electrochemical cell through a chiral self-assembled organic monolayer into a AlGaN/GaN device in which a shallow two-dimensional electron gas (2DEG) layer is formed. The injection is monitored by a microwave signal that indicates a coherent spin lifetime that exceeds 10 ms at room temperature. The signal was found to be magnetic field independent; however, it depends on the current of the injected electrons, on the length of the chiral molecules, and on the existence of 2DEG.

De novo Transcriptome Profiling of Flowers, Flower Pedicels and Pods of Lupinus luteus (Yellow Lupine) Reveals Complex Expression Changes during Organ Abscission.

PubMed

Glazinska, Paulina; Wojciechowski, Waldemar; Kulasek, Milena; Glinkowski, Wojciech; Marciniak, Katarzyna; Klajn, Natalia; Kesy, Jacek; Kopcewicz, Jan

2017-01-01

Yellow lupine ( Lupinus luteus L., Taper c.), a member of the legume family ( Fabaceae L.), has an enormous practical importance. Its excessive flower and pod abscission represents an economic drawback, as proper flower and seed formation and development is crucial for the plant's productivity. Generative organ detachment takes place at the basis of the pedicels, within a specialized group of cells collectively known as the abscission zone (AZ). During plant growth these cells become competent to respond to specific signals that trigger separation and lead to the abolition of cell wall adhesion. Little is known about the molecular network controlling the yellow lupine organ abscission. The aim of our study was to establish the divergences and similarities in transcriptional networks in the pods, flowers and flower pedicels abscised or maintained on the plant, and to identify genes playing key roles in generative organ abscission in yellow lupine. Based on de novo transcriptome assembly, we identified 166,473 unigenes representing 219,514 assembled unique transcripts from flowers, flower pedicels and pods undergoing abscission and from control organs. Comparison of the cDNA libraries from dropped and control organs helped in identifying 1,343, 2,933 and 1,491 differentially expressed genes (DEGs) in the flowers, flower pedicels and pods, respectively. In DEG analyses, we focused on genes involved in phytohormonal regulation, cell wall functioning and metabolic pathways. Our results indicate that auxin, ethylene and gibberellins are some of the main factors engaged in generative organ abscission. Identified 28 DEGs common for all library comparisons are involved in cell wall functioning, protein metabolism, water homeostasis and stress response. Interestingly, among the common DEGs we also found an miR169 precursor, which is the first evidence of micro RNA engaged in abscission. A KEGG pathway enrichment analysis revealed that the identified DEGs were predominantly involved in carbohydrate and amino acid metabolism, but some other pathways were also targeted. This study represents the first comprehensive transcriptome-based characterization of organ abscission in L. luteus and provides a valuable data source not only for understanding the abscission signaling pathway in yellow lupine, but also for further research aimed at improving crop yields.

De novo Transcriptome Profiling of Flowers, Flower Pedicels and Pods of Lupinus luteus (Yellow Lupine) Reveals Complex Expression Changes during Organ Abscission

PubMed Central

Glazinska, Paulina; Wojciechowski, Waldemar; Kulasek, Milena; Glinkowski, Wojciech; Marciniak, Katarzyna; Klajn, Natalia; Kesy, Jacek; Kopcewicz, Jan

2017-01-01

Yellow lupine (Lupinus luteus L., Taper c.), a member of the legume family (Fabaceae L.), has an enormous practical importance. Its excessive flower and pod abscission represents an economic drawback, as proper flower and seed formation and development is crucial for the plant's productivity. Generative organ detachment takes place at the basis of the pedicels, within a specialized group of cells collectively known as the abscission zone (AZ). During plant growth these cells become competent to respond to specific signals that trigger separation and lead to the abolition of cell wall adhesion. Little is known about the molecular network controlling the yellow lupine organ abscission. The aim of our study was to establish the divergences and similarities in transcriptional networks in the pods, flowers and flower pedicels abscised or maintained on the plant, and to identify genes playing key roles in generative organ abscission in yellow lupine. Based on de novo transcriptome assembly, we identified 166,473 unigenes representing 219,514 assembled unique transcripts from flowers, flower pedicels and pods undergoing abscission and from control organs. Comparison of the cDNA libraries from dropped and control organs helped in identifying 1,343, 2,933 and 1,491 differentially expressed genes (DEGs) in the flowers, flower pedicels and pods, respectively. In DEG analyses, we focused on genes involved in phytohormonal regulation, cell wall functioning and metabolic pathways. Our results indicate that auxin, ethylene and gibberellins are some of the main factors engaged in generative organ abscission. Identified 28 DEGs common for all library comparisons are involved in cell wall functioning, protein metabolism, water homeostasis and stress response. Interestingly, among the common DEGs we also found an miR169 precursor, which is the first evidence of micro RNA engaged in abscission. A KEGG pathway enrichment analysis revealed that the identified DEGs were predominantly involved in carbohydrate and amino acid metabolism, but some other pathways were also targeted. This study represents the first comprehensive transcriptome-based characterization of organ abscission in L. luteus and provides a valuable data source not only for understanding the abscission signaling pathway in yellow lupine, but also for further research aimed at improving crop yields. PMID:28512462

Mathematical modeling of polymer flooding using the unstructured Voronoi grid

NASA Astrophysics Data System (ADS)

Kireev, T. F.; Bulgakova, G. T.; Khatmullin, I. F.

2017-12-01

Effective recovery of unconventional oil reserves necessitates development of enhanced oil recovery techniques such as polymer flooding. The study investigated the model of polymer flooding with effects of adsorption and water salinity. The model takes into account six components that include elements of the classic black oil model. These components are polymer, salt, water, dead oil, dry gas and dissolved gas. Solution of the problem is obtained by finite volume method on unstructured Voronoi grid using fully implicit scheme and the Newton’s method. To compare several different grid configurations numerical simulation of polymer flooding is performed. The oil rates obtained by a hexagonal locally refined Voronoi grid are shown to be more accurate than the oil rates obtained by a rectangular grid with the same number of cells. The latter effect is caused by high solution accuracy near the wells due to the local grid refinement. Minimization of the grid orientation effect caused by the hexagonal pattern is also demonstrated. However, in the inter-well regions with large Voronoi cells flood front tends to flatten and the water breakthrough moment is smoothed.

Interdigitated photovoltaic power conversion device

DOEpatents

Ward, James Scott; Wanlass, Mark Woodbury; Gessert, Timothy Arthur

1999-01-01

A photovoltaic power conversion device has a top surface adapted to receive impinging radiation. The device includes at least two adjacent, serially connected cells. Each cell includes a semi-insulating substrate and a lateral conductivity layer of a first doped electrical conductivity disposed on the substrate. A base layer is disposed on the lateral conductivity layer and has the same electrical charge conductivity thereof. An emitter layer of a second doped electrical conductivity of opposite electrical charge is disposed on the base layer and forms a p-n junction therebetween. A plurality of spaced channels are formed in the emitter and base layers to expose the lateral conductivity layer at the bottoms thereof. A front contact grid is positioned on the top surface of the emitter layer of each cell. A first current collector is positioned along one outside edge of at least one first cell. A back contact grid is positioned in the channels at the top surface of the device for engagement with the lateral conductivity layer. A second current collector is positioned along at least one outside edge of at least one oppositely disposed second cell. Finally, an interdigitation mechanism is provided for serially connecting the front contact grid of one cell to the back contact grid of an adjacent cell at the top surface of the device.

Interdigitated photovoltaic power conversion device

DOEpatents

Ward, J.S.; Wanlass, M.W.; Gessert, T.A.

1999-04-27

A photovoltaic power conversion device has a top surface adapted to receive impinging radiation. The device includes at least two adjacent, serially connected cells. Each cell includes a semi-insulating substrate and a lateral conductivity layer of a first doped electrical conductivity disposed on the substrate. A base layer is disposed on the lateral conductivity layer and has the same electrical charge conductivity thereof. An emitter layer of a second doped electrical conductivity of opposite electrical charge is disposed on the base layer and forms a p-n junction therebetween. A plurality of spaced channels are formed in the emitter and base layers to expose the lateral conductivity layer at the bottoms thereof. A front contact grid is positioned on the top surface of the emitter layer of each cell. A first current collector is positioned along one outside edge of at least one first cell. A back contact grid is positioned in the channels at the top surface of the device for engagement with the lateral conductivity layer. A second current collector is positioned along at least one outside edge of at least one oppositely disposed second cell. Finally, an interdigitation mechanism is provided for serially connecting the front contact grid of one cell to the back contact grid of an adjacent cell at the top surface of the device. 15 figs.

Hyperbolic Prismatic Grid Generation and Solution of Euler Equations on Prismatic Grids

NASA Technical Reports Server (NTRS)

Pandya, S. A.; Chattot, JJ; Hafez, M. M.; Kutler, Paul (Technical Monitor)

1994-01-01

A hyperbolic grid generation method is used to generate prismatic grids and an approach using prismatic grids to solve the Euler equations is presented. The theory of the stability and feasibility of the hyperbolic grid generation method is presented. The hyperbolic grid generation method of Steger et al for structured grids is applied to a three dimensional triangularized surface definition to generate a grid that is unstructured on each successive layer. The grid, however, retains structure in the body-normal direction and has a computational cell shaped like a triangular prism. In order to take advantage of the structure in the normal direction, a finite-volume scheme that treats the unknowns along the normal direction implicitly is introduced and the flow over a sphere is simulated.

Method of grid generation

DOEpatents

Barnette, Daniel W.

2002-01-01

The present invention provides a method of grid generation that uses the geometry of the problem space and the governing relations to generate a grid. The method can generate a grid with minimized discretization errors, and with minimal user interaction. The method of the present invention comprises assigning grid cell locations so that, when the governing relations are discretized using the grid, at least some of the discretization errors are substantially zero. Conventional grid generation is driven by the problem space geometry; grid generation according to the present invention is driven by problem space geometry and by governing relations. The present invention accordingly can provide two significant benefits: more efficient and accurate modeling since discretization errors are minimized, and reduced cost grid generation since less human interaction is required.

Bioinformatic analysis of the effects and mechanisms of decitabine and cytarabine on acute myeloid leukemia

PubMed Central

Zhou, Shiyong; Liu, Pengfei; Zhang, Huilai

2017-01-01

Acute myeloid leukemia (AML) is a frequently occurring malignant disease of the blood and may result from a variety of genetic disorders. The present study aimed to identify the underlying mechanisms associated with the therapeutic effects of decitabine and cytarabine on AML, using microarray analysis. The microarray datasets GSE40442 and GSE40870 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and differentially methylated sites were identified in AML cells treated with decitabine compared with those treated with cytarabine via the Linear Models for Microarray Data package, following data pre-processing. Gene Ontology (GO) analysis of DEGs was performed using the Database for Annotation, Visualization and Integrated Analysis Discovery. Genes corresponding to the differentially methylated sites were obtained using the annotation package of the methylation microarray platform. The overlapping genes were identified, which exhibited the opposite variation trend between gene expression and DNA methylation. Important transcription factor (TF)-gene pairs were screened out, and a regulated network subsequently constructed. A total of 190 DEGs and 540 differentially methylated sites were identified in AML cells treated with decitabine compared with those treated with cytarabine. A total of 36 GO terms of DEGs were enriched, including nucleosomes, protein-DNA complexes and the nucleosome assembly. The 540 differentially methylated sites were located on 240 genes, including the acid-repeat containing protein (ACRC) gene that was additionally differentially expressed. In addition, 60 TF pairs and overlapped methylated sites, and 140 TF-pairs and DEGs were screened out. The regulated network included 68 nodes and 140 TF-gene pairs. The present study identified various genes including ACRC and proliferating cell nuclear antigen, in addition to various TFs, including TATA-box binding protein associated factor 1 and CCCTC-binding factor, which may be potential therapeutic targets of AML. PMID:28498449

Bioinformatic analysis of the effects and mechanisms of decitabine and cytarabine on acute myeloid leukemia.

PubMed

Zhou, Shiyong; Liu, Pengfei; Zhang, Huilai

2017-07-01

Acute myeloid leukemia (AML) is a frequently occurring malignant disease of the blood and may result from a variety of genetic disorders. The present study aimed to identify the underlying mechanisms associated with the therapeutic effects of decitabine and cytarabine on AML, using microarray analysis. The microarray datasets GSE40442 and GSE40870 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and differentially methylated sites were identified in AML cells treated with decitabine compared with those treated with cytarabine via the Linear Models for Microarray Data package, following data pre‑processing. Gene Ontology (GO) analysis of DEGs was performed using the Database for Annotation, Visualization and Integrated Analysis Discovery. Genes corresponding to the differentially methylated sites were obtained using the annotation package of the methylation microarray platform. The overlapping genes were identified, which exhibited the opposite variation trend between gene expression and DNA methylation. Important transcription factor (TF)‑gene pairs were screened out, and a regulated network subsequently constructed. A total of 190 DEGs and 540 differentially methylated sites were identified in AML cells treated with decitabine compared with those treated with cytarabine. A total of 36 GO terms of DEGs were enriched, including nucleosomes, protein‑DNA complexes and the nucleosome assembly. The 540 differentially methylated sites were located on 240 genes, including the acid‑repeat containing protein (ACRC) gene that was additionally differentially expressed. In addition, 60 TF pairs and overlapped methylated sites, and 140 TF‑pairs and DEGs were screened out. The regulated network included 68 nodes and 140 TF‑gene pairs. The present study identified various genes including ACRC and proliferating cell nuclear antigen, in addition to various TFs, including TATA‑box binding protein associated factor 1 and CCCTC‑binding factor, which may be potential therapeutic targets of AML.

Monthly fractional green vegetation cover associated with land cover classes of the conterminous USA

USGS Publications Warehouse

Gallo, Kevin P.; Tarpley, Dan; Mitchell, Ken; Csiszar, Ivan; Owen, Timothy W.; Reed, Bradley C.

2001-01-01

The land cover classes developed under the coordination of the International Geosphere-Biosphere Programme Data and Information System (IGBP-DIS) have been analyzed for a study area that includes the Conterminous United States and portions of Mexico and Canada. The 1-km resolution data have been analyzed to produce a gridded data set that includes within each 20-km grid cell: 1) the three most dominant land cover classes, 2) the fractional area associated with each of the three dominant classes, and 3) the fractional area covered by water. Additionally, the monthly fraction of green vegetation cover (fgreen) associated with each of the three dominant land cover classes per grid cell was derived from a 5-year climatology of 1-km resolution NOAA-AVHRR data. The variables derived in this study provide a potential improvement over the use of monthly fgreen linked to a single land cover class per model grid cell.

Draft reference grid cells for emergency response reconnaissance developed for use by the US Environmental Protection Agency [ER.QUADS6K_EPA

EPA Pesticide Factsheets

Draft reference grid cells for emergency response reconnaissance developed for use by the US Environmental Protection Agency. Grid cells are based on densification of the USGS Quarterquad (1:12,000 scale or 12K) grids for the continental United States, Alaska, Hawaii and Puerto Rico and are roughly equivalent to 1:6000 scale (6K) quadrangles approximately 2 miles long on each side. Note: This file is >80MB in size. Regional subsets have been created from this national file that include a 20 mile buffer of tiles around each EPA Region. To access the regional subsets, go to http://geodata.epa.gov/OSWER/6kquads_epa.zip and select the name of the file that corresponds to your region of interest (e.g. 6kquadr1.zip is the name of the file created for EPA Region 1).

Using Grid Cells for Navigation

PubMed Central

Bush, Daniel; Barry, Caswell; Manson, Daniel; Burgess, Neil

2015-01-01

Summary Mammals are able to navigate to hidden goal locations by direct routes that may traverse previously unvisited terrain. Empirical evidence suggests that this “vector navigation” relies on an internal representation of space provided by the hippocampal formation. The periodic spatial firing patterns of grid cells in the hippocampal formation offer a compact combinatorial code for location within large-scale space. Here, we consider the computational problem of how to determine the vector between start and goal locations encoded by the firing of grid cells when this vector may be much longer than the largest grid scale. First, we present an algorithmic solution to the problem, inspired by the Fourier shift theorem. Second, we describe several potential neural network implementations of this solution that combine efficiency of search and biological plausibility. Finally, we discuss the empirical predictions of these implementations and their relationship to the anatomy and electrophysiology of the hippocampal formation. PMID:26247860

Fast and accurate Voronoi density gridding from Lagrangian hydrodynamics data

NASA Astrophysics Data System (ADS)

Petkova, Maya A.; Laibe, Guillaume; Bonnell, Ian A.

2018-01-01

Voronoi grids have been successfully used to represent density structures of gas in astronomical hydrodynamics simulations. While some codes are explicitly built around using a Voronoi grid, others, such as Smoothed Particle Hydrodynamics (SPH), use particle-based representations and can benefit from constructing a Voronoi grid for post-processing their output. So far, calculating the density of each Voronoi cell from SPH data has been done numerically, which is both slow and potentially inaccurate. This paper proposes an alternative analytic method, which is fast and accurate. We derive an expression for the integral of a cubic spline kernel over the volume of a Voronoi cell and link it to the density of the cell. Mass conservation is ensured rigorously by the procedure. The method can be applied more broadly to integrate a spherically symmetric polynomial function over the volume of a random polyhedron.

A New Family of Multilevel Grid Connected Inverters Based on Packed U Cell Topology.

PubMed

Pakdel, Majid; Jalilzadeh, Saeid

2017-09-29

In this paper a novel packed U cell (PUC) based multilevel grid connected inverter is proposed. Unlike the U cell arrangement which consists of two power switches and one capacitor, in the proposed converter topology a lower DC power supply from renewable energy resources such as photovoltaic arrays (PV) is used as a base power source. The proposed topology offers higher efficiency and lower cost using a small number of power switches and a lower DC power source which is supplied from renewable energy resources. Other capacitor voltages are extracted from the base lower DC power source using isolated DC-DC power converters. The operation principle of proposed transformerless multilevel grid connected inverter is analyzed theoretically. Operation of the proposed multilevel grid connected inverter is verified through simulation studies. An experimental prototype using STM32F407 discovery controller board is performed to verify the simulation results.

Thermal stress cycling of GaAs solar cells

NASA Technical Reports Server (NTRS)

Francis, Robert W.

1987-01-01

Thermal stress cycling was performed on gallium arsenide solar cells to investigate their electrical, mechanical, and structural integrity. Cells were cycled under low Earth orbit (LEO) simulated temperature conditions in vacuum. Cell evaluations consisted of power output values, spectral response, optical microscopy and ion microprobe mass analysis, and depth profiles on both front surface inter-grid areas and metallization contact grid lines. Cells were examined for degradation after 500, 5,000, 10,000 and 15,245 thermal cycles. No indication of performance degradation was found for any vendor's cell lot.

VizieR Online Data Catalog: Spectropolarimetric survey of radio sources (Anderson+, 2015)

NASA Astrophysics Data System (ADS)

Anderson, C. S.; Gaensler, B. M.; Feain, I. J.; Franzen, T. M. O.

2017-10-01

We obtained mosaicked observations of a 30 deg2 region of sky the CABB correlator on the Australia Telescope Compact Array (ATCA; Wilson et al. 2011MNRAS.416..832W). Our observations were performed using the "CFB 1M" mode, which generates all polarization products from 1.1 to 3.1 GHz with 1 MHz channel widths. The mosaic consisted of 342 pointings laid out in a hexagonal grid. This grid spanned 7.5° in RA and 5.5° in DE and was centered on RA=03h29m40s and DE=-36°16'30" (J2000) in Fornax. The angular separation of the mosaic pointings was 0.323° and therefore spatially Nyquist-sampled at 1.4 GHz. To obtain adequate uv coverage, we broke the full mosaic up into seven submosaics and observed each submosaic on consecutive days. We completed the full seven-day observing run twice-once in each of the 1.5B and 750B array configurations, from 2011 May 5-11 and 2011 June 10-16, respectively. (1 data file).

Afterbody Heating Predictions for a Mars Science Laboratory Entry Vehicle

NASA Technical Reports Server (NTRS)

Edquist, Karl T.

2005-01-01

The Mars Science Laboratory mission intends to deliver a large rover to the Martian surface within 10 km of its target site. One candidate entry vehicle aeroshell consists of a 3.75-m diameter, 70-deg sphere-cone forebody and a biconic afterbody similar to that of Viking. This paper presents computational fluid dynamics predictions of laminar afterbody heating rates for this configuration and a 2010 arrival at Mars. Computational solutions at flight conditions used an 8-species Mars gas model in chemical and thermal non-equilibrium. A grid resolution study examined the effects of mesh spacing on afterbody heating rates and resulted in grids used for heating predictions on a reference entry trajectory. Afterbody heating rate reaches its maximum value near 0.6 W/sq cm on the first windward afterbody cone at the time of peak freestream dynamic pressure. Predicted afterbody heating rates generally are below 3% of the forebody laminar nose cap heating rate throughout the design trajectory. The heating rates integrated over time provide total heat load during entry, which drives thermal protection material thickness.

Selective heterogeneity in exoprotease production by Bacillus subtilis.

PubMed

Davidson, Fordyce A; Seon-Yi, Chung; Stanley-Wall, Nicola R

2012-01-01

Bacteria have elaborate signalling mechanisms to ensure a behavioural response that is most likely to enhance survival in a changing environment. It is becoming increasingly apparent that as part of this response, bacteria are capable of cell differentiation and can generate multiple, mutually exclusive co-existing cell states. These cell states are often associated with multicellular processes that bring benefit to the community as a whole but which may be, paradoxically, disadvantageous to an individual subpopulation. How this process of cell differentiation is controlled is intriguing and remains a largely open question. In this paper, we consider an important aspect of cell differentiation that is known to occur in the gram-positive bacterium Bacillus subtilis: we investigate the role of two master regulators DegU and Spo0A in the control of extra-cellular protease production. Recent work in this area focussed the on role of DegU in this process and suggested that transient effects in protein production were the drivers of cell-response heterogeneity. Here, using a combination of mathematical modelling, analysis and stochastic simulations, we provide a complementary analysis of this regulatory system that investigates the roles of both DegU and Spo0A in extra-cellular protease production. In doing so, we present a mechanism for bimodality, or system heterogeneity, without the need for a bistable switch in the underlying regulatory network. Moreover, our analysis leads us to conclude that this heterogeneity is in fact a persistent, stable feature. Our results suggest that system response is divided into three zones: low and high signal levels induce a unimodal or undifferentiated response from the cell population with all cells OFF and ON, respectively for exoprotease production. However, for intermediate levels of signal, a heterogeneous response is predicted with a spread of activity levels, representing typical "bet-hedging" behaviour.

On the Quality of Velocity Interpolation Schemes for Marker-in-Cell Method and Staggered Grids

NASA Astrophysics Data System (ADS)

Pusok, Adina E.; Kaus, Boris J. P.; Popov, Anton A.

2017-03-01

The marker-in-cell method is generally considered a flexible and robust method to model the advection of heterogenous non-diffusive properties (i.e., rock type or composition) in geodynamic problems. In this method, Lagrangian points carrying compositional information are advected with the ambient velocity field on an Eulerian grid. However, velocity interpolation from grid points to marker locations is often performed without considering the divergence of the velocity field at the interpolated locations (i.e., non-conservative). Such interpolation schemes can induce non-physical clustering of markers when strong velocity gradients are present (Journal of Computational Physics 166:218-252, 2001) and this may, eventually, result in empty grid cells, a serious numerical violation of the marker-in-cell method. To remedy this at low computational costs, Jenny et al. (Journal of Computational Physics 166:218-252, 2001) and Meyer and Jenny (Proceedings in Applied Mathematics and Mechanics 4:466-467, 2004) proposed a simple, conservative velocity interpolation scheme for 2-D staggered grid, while Wang et al. (Geochemistry, Geophysics, Geosystems 16(6):2015-2023, 2015) extended the formulation to 3-D finite element methods. Here, we adapt this formulation for 3-D staggered grids (correction interpolation) and we report on the quality of various velocity interpolation methods for 2-D and 3-D staggered grids. We test the interpolation schemes in combination with different advection schemes on incompressible Stokes problems with strong velocity gradients, which are discretized using a finite difference method. Our results suggest that a conservative formulation reduces the dispersion and clustering of markers, minimizing the need of unphysical marker control in geodynamic models.

Ocular anatomy, ganglion cell distribution and retinal resolution of a killer whale (Orcinus orca).

PubMed

Mass, Alla M; Supin, Alexander Y; Abramov, Andrey V; Mukhametov, Lev M; Rozanova, Elena I

2013-01-01

Retinal topography, cell density and sizes of ganglion cells in the killer whale (Orcinus orca) were analyzed in retinal whole mounts stained with cresyl violet. A distinctive feature of the killer whale's retina is the large size of ganglion cells and low cell density compared to terrestrial mammals. The ganglion cell diameter ranged from 8 to 100 µm, with the majority of cells within a range of 20-40 µm. The topographic distribution of ganglion cells displayed two spots of high cell density located in the temporal and nasal quadrants, 20 mm from the optic disk. The high-density areas were connected by a horizontal belt-like area passing below the optic disk of the retina. Peak cell densities in these areas were evaluated. Mean peak cell densities were 334 and 288 cells/mm(2) in the temporal and nasal high-density areas, respectively. With a posterior nodal distance of 19.5 mm, these high-density data predict a retinal resolution of 9.6' (3.1 cycles/deg.) and 12.6' (2.4 cycles/deg.) in the temporal and nasal areas, respectively, in water. Copyright © 2012 S. Karger AG, Basel.

A three-dimensional electrostatic particle-in-cell methodology on unstructured Delaunay-Voronoi grids

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

Gatsonis, Nikolaos A.; Spirkin, Anton

2009-06-01

The mathematical formulation and computational implementation of a three-dimensional particle-in-cell methodology on unstructured Delaunay-Voronoi tetrahedral grids is presented. The method allows simulation of plasmas in complex domains and incorporates the duality of the Delaunay-Voronoi in all aspects of the particle-in-cell cycle. Charge assignment and field interpolation weighting schemes of zero- and first-order are formulated based on the theory of long-range constraints. Electric potential and fields are derived from a finite-volume formulation of Gauss' law using the Voronoi-Delaunay dual. Boundary conditions and the algorithms for injection, particle loading, particle motion, and particle tracking are implemented for unstructured Delaunay grids. Error andmore » sensitivity analysis examines the effects of particles/cell, grid scaling, and timestep on the numerical heating, the slowing-down time, and the deflection times. The problem of current collection by cylindrical Langmuir probes in collisionless plasmas is used for validation. Numerical results compare favorably with previous numerical and analytical solutions for a wide range of probe radius to Debye length ratios, probe potentials, and electron to ion temperature ratios. The versatility of the methodology is demonstrated with the simulation of a complex plasma microsensor, a directional micro-retarding potential analyzer that includes a low transparency micro-grid.« less

Hebbian Plasticity Realigns Grid Cell Activity with External Sensory Cues in Continuous Attractor Models

PubMed Central

Mulas, Marcello; Waniek, Nicolai; Conradt, Jörg

2016-01-01

After the discovery of grid cells, which are an essential component to understand how the mammalian brain encodes spatial information, three main classes of computational models were proposed in order to explain their working principles. Amongst them, the one based on continuous attractor networks (CAN), is promising in terms of biological plausibility and suitable for robotic applications. However, in its current formulation, it is unable to reproduce important electrophysiological findings and cannot be used to perform path integration for long periods of time. In fact, in absence of an appropriate resetting mechanism, the accumulation of errors over time due to the noise intrinsic in velocity estimation and neural computation prevents CAN models to reproduce stable spatial grid patterns. In this paper, we propose an extension of the CAN model using Hebbian plasticity to anchor grid cell activity to environmental landmarks. To validate our approach we used as input to the neural simulations both artificial data and real data recorded from a robotic setup. The additional neural mechanism can not only anchor grid patterns to external sensory cues but also recall grid patterns generated in previously explored environments. These results might be instrumental for next generation bio-inspired robotic navigation algorithms that take advantage of neural computation in order to cope with complex and dynamic environments. PMID:26924979

High-throughput transcriptome sequencing analysis provides preliminary insights into the biotransformation mechanism of Rhodopseudomonas palustris treated with alpha-rhamnetin-3-rhamnoside.

PubMed

Bi, Lei; Guan, Chun-jie; Yang, Guan-e; Yang, Fei; Yan, Hong-yu; Li, Qing-shan

2016-04-01

The purple photosynthetic bacterium Rhodopseudomonas palustris has been widely applied to enhance the therapeutic effects of traditional Chinese medicine using novel biotransformation technology. However, comprehensive studies of the R. palustris biotransformation mechanism are rare. Therefore, investigation of the expression patterns of genes involved in metabolic pathways that are active during the biotransformation process is essential to elucidate this complicated mechanism. To promote further study of the biotransformation of R. palustris, we assembled all R. palustris transcripts using Trinity software and performed differential expression analysis of the resulting unigenes. A total of 9725, 7341 and 10,963 unigenes were obtained by assembling the alpha-rhamnetin-3-rhamnoside-treated R. palustris (RPB) reads, control R. palustris (RPS) reads and combined RPB&RPS reads, respectively. A total of 9971 unigenes assembled from the RPB&RPS reads were mapped to the nr, nt, Swiss-Prot, Gene Ontology (GO), Clusters of Orthologous Groups (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (E-value <0.00001) databases using BLAST software. A total of 3360 unique differentially expressed genes (DEGs) in RPB versus RPS were identified, among which 922 unigenes were up-regulated and 2438 were down-regulated. The unigenes were mapped to the KEGG database, resulting in the identification of 7676 pathways among all annotated unigenes and 2586 pathways among the DEGs. Some sets of functional unigenes annotated to important metabolic pathways and environmental information processing were differentially expressed between the RPS and RPB samples, including those involved in energy metabolism (18.4% of total DEGs), carbohydrate metabolism (36.0% of total DEGs), ABC transport (6.0% of total DEGs), the two-component system (8.6% of total DEGs), cell motility (4.3% of total DEGs) and the cell cycle (1.5% of total DEGs). We also identified 19 transcripts annotated as hydrolytic enzymes and other enzymes involved in ARR catabolism in R. palustris. We present the first comparative transcriptome profiles of RPB and RPS samples to facilitate elucidation of the molecular mechanism of biotransformation in R. palustris. Furthermore, we propose two putative ARR biotransformation mechanisms in R. palustris. These analytical results represent a useful genomic resource for in-depth research into the molecular basis of biotransformation and genetic modification in R. palustris. Copyright © 2016 Elsevier GmbH. All rights reserved.

THE CHANDRA COSMOS SURVEY. I. OVERVIEW AND POINT SOURCE CATALOG

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

Elvis, Martin; Civano, Francesca; Aldcroft, T. L.

2009-09-01

The Chandra COSMOS Survey (C-COSMOS) is a large, 1.8 Ms, Chandra program that has imaged the central 0.5 deg{sup 2} of the COSMOS field (centered at 10 {sup h}, +02 deg.) with an effective exposure of {approx}160 ks, and an outer 0.4 deg{sup 2} area with an effective exposure of {approx}80 ks. The limiting source detection depths are 1.9 x 10{sup -16} erg cm{sup -2} s{sup -1} in the soft (0.5-2 keV) band, 7.3 x 10{sup -16} erg cm{sup -2} s{sup -1} in the hard (2-10 keV) band, and 5.7 x 10{sup -16} erg cm{sup -2} s{sup -1} in themore » full (0.5-10 keV) band. Here we describe the strategy, design, and execution of the C-COSMOS survey, and present the catalog of 1761 point sources detected at a probability of being spurious of <2 x 10{sup -5} (1655 in the full, 1340 in the soft, and 1017 in the hard bands). By using a grid of 36 heavily ({approx}50%) overlapping pointing positions with the ACIS-I imager, a remarkably uniform ({+-}12%) exposure across the inner 0.5 deg{sup 2} field was obtained, leading to a sharply defined lower flux limit. The widely different point-spread functions obtained in each exposure at each point in the field required a novel source detection method, because of the overlapping tiling strategy, which is described in a companion paper. This method produced reliable sources down to a 7-12 counts, as verified by the resulting logN-logS curve, with subarcsecond positions, enabling optical and infrared identifications of virtually all sources, as reported in a second companion paper. The full catalog is described here in detail and is available online.« less

A grid amplifier

NASA Technical Reports Server (NTRS)

Kim, Moonil; Weikle, Robert M., II; Hacker, Jonathan B.; Delisio, Michael P.; Rutledge, David B.; Rosenberg, James J.; Smith, R. P.

1991-01-01

A 50-MESFET grid amplifier is reported that has a gain of 11 dB at 3.3 GHz. The grid isolates the input from the output by using vertical polarization for the input beam and horizontal polarization for the transmitted output beam. The grid unit cell is a two-MESFET differential amplifier. A simple calibration procedure allows the gain to be calculated from a relative power measurement. This grid is a hybrid circuit, but the structure is suitable for fabrication as a monolithic wafer-scale integrated circuit, particularly at millimeter wavelengths.

Efficiency enhancement of silicon nanowire solar cells by using UV/Ozone treatments and micro-grid electrodes

NASA Astrophysics Data System (ADS)

Chen, Junyi; Subramani, Thiyagu; Sun, Yonglie; Jevasuwan, Wipakorn; Fukata, Naoki

2018-05-01

Silicon nanowire solar cells were fabricated by metal catalyzed electroless etching (MCEE) followed by thermal chemical vapor deposition (CVD). In this study, we investigated two effects, a UV/ozone treatment and the use of a micro-grid electrodes, to enhance light absorption and reduce the optic losses in the solar cell device. The UV/ozone treatment successfully improved the conversion efficiency. The micro-grid electrodes were then applied in solar cell devices subjected to a back surface field (BSF) treatment and rapid thermal annealing (RTA). These effects improved the conversion efficiency from 9.4% to 10.9%. Moreover, to reduce surface recombination and improve the continuity of front electrodes, we optimized the etching time of the MCEE process, giving a high efficiency of 12.3%.

Coarse-grained hydrodynamics from correlation functions

NASA Astrophysics Data System (ADS)

Palmer, Bruce

2018-02-01

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configurations from a molecular dynamics simulation or other atomistic simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilibrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is demonstrated on a discrete particle simulation of diffusion with a spatially dependent diffusion coefficient. Correlation functions are calculated from the particle simulation and the spatially varying diffusion coefficient is recovered using a fitting procedure.

A New Sensor for Measurement of Dynamic Contact Stress in the Hip

PubMed Central

Rudert, M. J.; Ellis, B. J.; Henak, C. R.; Stroud, N. J.; Pederson, D. R.; Weiss, J. A.; Brown, T. D.

2014-01-01

Various techniques exist for quantifying articular contact stress distributions, an important class of measurements in the field of orthopaedic biomechanics. In situations where the need for dynamic recording has been paramount, the approach of preference has involved thin-sheet multiplexed grid-array transducers. To date, these sensors have been used to study contact stresses in the knee, shoulder, ankle, wrist, and spinal facet joints. Until now, however, no such sensor had been available for the human hip joint due to difficulties posed by the deep, bi-curvilinear geometry of the acetabulum. We report here the design and development of a novel sensor capable of measuring dynamic contact stress in human cadaveric hip joints (maximum contact stress of 20 MPa and maximum sampling rate 100 readings/s). Particular emphasis is placed on issues concerning calibration, and on the effect of joint curvature on the sensor's performance. The active pressure-sensing regions of the sensors have the shape of a segment of an annulus with a 150-deg circumferential span, and employ a polar/circumferential “ring-and-spoke” sensel grid layout. There are two sensor sizes, having outside radii of 44 and 48 mm, respectively. The new design was evaluated in human cadaver hip joints using two methods. The stress magnitudes and spatial distribution measured by the sensor were compared to contact stresses measured by pressure sensitive film during static loading conditions that simulated heel strike during walking and stair climbing. Additionally, the forces obtained by spatial integration of the sensor contact stresses were compared to the forces measured by load cells during the static simulations and for loading applied by a dynamic hip simulator. Stress magnitudes and spatial distribution patterns obtained from the sensor versus from pressure sensitive film exhibited good agreement. The joint forces obtained during both static and dynamic loading were within ±10% and ±26%, respectively, of the forces measured by the load cells. These results provide confidence in the measurements obtained by the sensor. The new sensor's real-time output and dynamic measurement capabilities hold significant advantages over static measurements from pressure sensitive film. PMID:24763632

A new sensor for measurement of dynamic contact stress in the hip.

PubMed

Rudert, M J; Ellis, B J; Henak, C R; Stroud, N J; Pederson, D R; Weiss, J A; Brown, T D

2014-03-01

Various techniques exist for quantifying articular contact stress distributions, an important class of measurements in the field of orthopaedic biomechanics. In situations where the need for dynamic recording has been paramount, the approach of preference has involved thin-sheet multiplexed grid-array transducers. To date, these sensors have been used to study contact stresses in the knee, shoulder, ankle, wrist, and spinal facet joints. Until now, however, no such sensor had been available for the human hip joint due to difficulties posed by the deep, bi-curvilinear geometry of the acetabulum. We report here the design and development of a novel sensor capable of measuring dynamic contact stress in human cadaveric hip joints (maximum contact stress of 20 MPa and maximum sampling rate 100 readings/s). Particular emphasis is placed on issues concerning calibration, and on the effect of joint curvature on the sensor's performance. The active pressure-sensing regions of the sensors have the shape of a segment of an annulus with a 150-deg circumferential span, and employ a polar/circumferential "ring-and-spoke" sensel grid layout. There are two sensor sizes, having outside radii of 44 and 48 mm, respectively. The new design was evaluated in human cadaver hip joints using two methods. The stress magnitudes and spatial distribution measured by the sensor were compared to contact stresses measured by pressure sensitive film during static loading conditions that simulated heel strike during walking and stair climbing. Additionally, the forces obtained by spatial integration of the sensor contact stresses were compared to the forces measured by load cells during the static simulations and for loading applied by a dynamic hip simulator. Stress magnitudes and spatial distribution patterns obtained from the sensor versus from pressure sensitive film exhibited good agreement. The joint forces obtained during both static and dynamic loading were within ±10% and ±26%, respectively, of the forces measured by the load cells. These results provide confidence in the measurements obtained by the sensor. The new sensor's real-time output and dynamic measurement capabilities hold significant advantages over static measurements from pressure sensitive film.

Validation and Development of the GPCP Experimental One-Degree Daily (1DD) Global Precipitation Product

NASA Technical Reports Server (NTRS)

Huffman, George J.; Adler, Robert F.; Bolvin, David T.; Einaud, Franco (Technical Monitor)

2000-01-01

The One-Degree Daily (1DD) precipitation dataset has been developed for the Global Precipitation Climatology Project (GPCP) and is currently in beta test preparatory to release as an official GPCP product. The 1DD provides a globally-complete, observation-only estimate of precipitation on a daily 1 deg. x 1 deg. grid for the period 1997 through early 2000 (by the time of the conference). In the latitude band 40N-40S the 1DD uses the Threshold-Matched Precipitation Index (TMPI), a GPI-like IR product with the pixel-level T(sub b) threshold and (single) conditional rain rate determined locally for each month by the frequency of precipitation in the GPROF SSM/I product and by, the precipitation amount in the GPCP monthly satellite-gauge (SG) combination. Outside 40N-40S the 1DD uses a scaled TOVS precipitation estimate that has month-by-month adjustments based on the TMPI and the SG. Early validation results are encouraging. The 1DD shows relatively large scatter about the daily validation values in individual grid boxes, as expected for a technique that depends on cloud-sensing schemes such as the TMPI and TOVS. On the other hand, the time series of 1DD shows good correlation with validation in individual boxes. For example, the 1997-1998 time series of 1DD and Oklahoma Mesonet values in a grid box in northeastern Oklahoma have the correlation coefficient = 0.73. Looking more carefully at these two time series, the number of raining days for the 1DD is within 7% of the Mesonet value, while the distribution of daily rain values is very similar. Other tests indicate that area- or time-averaging improve the error characteristics, making the data set highly attractive to users interested in stream flow, short-term regional climatology, and model comparisons. The second generation of the 1DD product is currently under development; it is designed to directly incorporate TRMM and other high-quality precipitation estimates. These data are generally sparse because they are observed by low-orbit satellites, so a fair amount of work must be devoted to analyzing the effect of data boundaries. This work is laying, the groundwork for effective use of the NASA Global Precipitation Mission, which will have full Global coverage by low-orbit passive microwave satellites every three hours.

Comparison of Cartesian grid configurations for application of the finite-difference time-domain method to electromagnetic scattering by dielectric particles.

PubMed

Yang, Ping; Kattawar, George W; Liou, Kuo-Nan; Lu, Jun Q

2004-08-10

Two grid configurations can be employed to implement the finite-difference time-domain (FDTD) technique in a Cartesian system. One configuration defines the electric and magnetic field components at the cell edges and cell-face centers, respectively, whereas the other reverses these definitions. These two grid configurations differ in terms of implication on the electromagnetic boundary conditions if the scatterer in the FDTD computation is a dielectric particle. The permittivity has an abrupt transition at the cell interface if the dielectric properties of two adjacent cells are not identical. Similarly, the discontinuity of permittivity is also observed at the edges of neighboring cells that are different in terms of their dielectric constants. We present two FDTD schemes for light scattering by dielectric particles to overcome the above-mentioned discontinuity on the basis of the electromagnetic boundary conditions for the two Cartesian grid configurations. We also present an empirical approach to accelerate the convergence of the discrete Fourier transform to obtain the field values in the frequency domain. As a new application of the FDTD method, we investigate the scattering properties of multibranched bullet-rosette ice crystals at both visible and thermal infrared wavelengths.

Impact of GPM Rainrate Data Assimilation on Simulation of Hurricane Harvey (2017)

NASA Technical Reports Server (NTRS)

Li, Xuanli; Srikishen, Jayanthi; Zavodsky, Bradley; Mecikalski, John

2018-01-01

Built upon Tropical Rainfall Measuring Mission (TRMM) legacy for next-generation global observation of rain and snow. The GPM was launched in February 2014 with Dual-frequency Precipitation Radar (DPR) and GPM Microwave Imager (GMI) onboard. The GPM has a broad global coverage approximately 70deg S -70deg N with a swath of 245/125-km for the Ka (35.5 GHz)/Ku (13.6 GHz) band radar, and 850-km for the 13-channel GMI. GPM also features better retrievals for heavy, moderate, and light rain and snowfall To develop methodology to assimilate GPM surface precipitation data with Grid-point Statistical Interpolation (GSI) data assimilation system and WRF ARW model To investigate the potential and the value of utilizing GPM observation into NWP for operational environment The GPM rain rate data has been successfully assimilated using the GSI rain data assimilation package. Impacts of rain rate data have been found in temperature and moisture fields of initial conditions. 2.Assimilation of either GPM IMERG or GPROF rain product produces significant improvement in precipitation amount and structure for Hurricane Harvey (2017) forecast. Since IMERG data is available half-hourly, further forecast improvement is expected with continuous assimilation of IMERG data

Breaking down the delta wing vortex: The role of vorticity in the breakdown process. Ph.D. Thesis Final Report

NASA Technical Reports Server (NTRS)

Nelson, Robert C.; Visser, Kenneth D.

1990-01-01

Experimental x-wire measurements of the flowfield above a 70 and 75 deg flat plate delta wing were performed at a Reynolds number of 250,000. Grids were taken normal to the wing at various chordwise locations for angles of attack of 20 and 30 deg. Axial and azimuthal vorticity distributions were derived from the velocity fields. The dependence of circulation on distance from the vortex core and on chordwise location was also examined. The effects of nondimensionalization in comparison with other experimental data is made. The results indicate that the circulation distribution scales with the local semispan and grows in a nearly linear fashion in the chordwise direction. The spanwise distribution of axial vorticity is severely altered through the breakdown. The axial vorticity components with a negative sense, such as that found in the secondary vortex, seem to remain unaffected by changes in wind sweep or angle of attack, in direct contrast to the positive components. In addition, the inclusion of the local wing geometry into a previously derived correlation parameter allows the circulation of growing leading edge vortex flows to be reduced into a single curve.

ERS-1 scatterometer calibration and validation activities at ECMWF. B: From radar backscatter characteristics to wind vector solutions

NASA Technical Reports Server (NTRS)

Stoffelen, AD; Anderson, David L. T.; Woiceshyn, Peter M.

1992-01-01

Calibration and validation activities for the ERS-1 scatterometer were carried out at ECMWF (European Center for Medium range Weather Forecast) complementary to the 'Haltenbanken' field campaign off the coast of Norway. At a Numerical Weather Prediction (NWP) center a wealth of verifying data is available both in time and space. This data is used to redefine the wind retrieval procedure given the instrumental characteristics. It was found that a maximum likelihood estimation procedure to obtain the coefficients of a reformulated sigma deg to wind relationship should use radar measurements in logarithmic rather than physical space, and use winds as the wind components rather than wind speed and direction. Doing this, a much more accurate transfer function than the one currently operated by ESA was derived. Sigma deg measurement space shows no signature of a separation in an upwind solution cone and a downwind solution cone. As such signature was anticipated in ESA's wind direction ambiguity removal algorithm, reconsideration of the procedure is necessary. Despite the fact that revisions have to be made in the process of wind retrieval; a grid potential is shown for scatterometry in meteorology and climatology.

GRID-BASED EXPLORATION OF COSMOLOGICAL PARAMETER SPACE WITH SNAKE

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

Mikkelsen, K.; Næss, S. K.; Eriksen, H. K., E-mail: kristin.mikkelsen@astro.uio.no

2013-11-10

We present a fully parallelized grid-based parameter estimation algorithm for investigating multidimensional likelihoods called Snake, and apply it to cosmological parameter estimation. The basic idea is to map out the likelihood grid-cell by grid-cell according to decreasing likelihood, and stop when a certain threshold has been reached. This approach improves vastly on the 'curse of dimensionality' problem plaguing standard grid-based parameter estimation simply by disregarding grid cells with negligible likelihood. The main advantages of this method compared to standard Metropolis-Hastings Markov Chain Monte Carlo methods include (1) trivial extraction of arbitrary conditional distributions; (2) direct access to Bayesian evidences; (3)more » better sampling of the tails of the distribution; and (4) nearly perfect parallelization scaling. The main disadvantage is, as in the case of brute-force grid-based evaluation, a dependency on the number of parameters, N{sub par}. One of the main goals of the present paper is to determine how large N{sub par} can be, while still maintaining reasonable computational efficiency; we find that N{sub par} = 12 is well within the capabilities of the method. The performance of the code is tested by comparing cosmological parameters estimated using Snake and the WMAP-7 data with those obtained using CosmoMC, the current standard code in the field. We find fully consistent results, with similar computational expenses, but shorter wall time due to the perfect parallelization scheme.« less

Woven-grid sealed quasi-bipolar lead-acid battery construction and fabricating method

NASA Technical Reports Server (NTRS)

Rippel, Wally E. (Inventor)

1989-01-01

A quasi-bipolar lead-acid battery construction includes a plurality of bipolar cells disposed in side-by-side relation to form a stack, and a pair of monoplanar plates at opposite ends of the stack, the cell stack and monopolar plates being contained within a housing of the battery. Each bipolar cell is loaded with an electrolyte and composed of a bipolar electrode plate and a pair of separator plates disposed on opposite sides of the electrode plate and peripherally sealed thereto. Each bipolar electrode plate is composed of a partition sheet and two bipolar electrode elements folded into a hairpin configuration and applied over opposite edges of the partition sheet so as to cover the opposite surfaces of the opposite halves thereof. Each bipolar electrode element is comprised of a woven grid with a hot-melt strip applied to a central longitudinal region of the grid along which the grid is folded into the hairpin configuration, and layers of negative and positive active material pastes applied to opposite halves of the grid on opposite sides of the central hot-melt strip. The grid is made up of strands of conductive and non-conductive yarns composing the respective transverse and longitudinal weaves of the grid. The conductive yarn has a multi-stranded glass core surrounded and covered by a lead sheath, whereas the non-conductive yarn has a multi-stranded glass core surrounded and covered by a thermally activated sizing.

Efficient Fluid Dynamic Design Optimization Using Cartesian Grids

NASA Technical Reports Server (NTRS)

Dadone, A.; Grossman, B.; Sellers, Bill (Technical Monitor)

2004-01-01

This report is subdivided in three parts. The first one reviews a new approach to the computation of inviscid flows using Cartesian grid methods. The crux of the method is the curvature-corrected symmetry technique (CCST) developed by the present authors for body-fitted grids. The method introduces ghost cells near the boundaries whose values are developed from an assumed flow-field model in vicinity of the wall consisting of a vortex flow, which satisfies the normal momentum equation and the non-penetration condition. The CCST boundary condition was shown to be substantially more accurate than traditional boundary condition approaches. This improved boundary condition is adapted to a Cartesian mesh formulation, which we call the Ghost Body-Cell Method (GBCM). In this approach, all cell centers exterior to the body are computed with fluxes at the four surrounding cell edges. There is no need for special treatment corresponding to cut cells which complicate other Cartesian mesh methods.

MESH2D Grid generator design and use

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

Flach, G. P.

Mesh2d is a Fortran90 program originally designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). x-coordinates depending only on index i implies strictly vertical x-grid lines, whereas the y-grid lines can undulate. Mesh2d also assigns an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations. Since the original development effort, Mesh2d has been extended to more general two-dimensional structured grids of the form [x(i,j),(i,j)].

Identification of key microRNAs and genes in preeclampsia by bioinformatics analysis

PubMed Central

Luo, Shouling; Cao, Nannan; Tang, Yao; Gu, Weirong

2017-01-01

Preeclampsia is a leading cause of perinatal maternal–foetal mortality and morbidity. The aim of this study is to identify the key microRNAs and genes in preeclampsia and uncover their potential functions. We downloaded the miRNA expression profile of GSE84260 and the gene expression profile of GSE73374 from the Gene Expression Omnibus database. Differentially expressed miRNAs and genes were identified and compared to miRNA-target information from MiRWalk 2.0, and a total of 65 differentially expressed miRNAs (DEMIs), including 32 up-regulated miRNAs and 33 down-regulated miRNAs, and 91 differentially expressed genes (DEGs), including 83 up-regulated genes and 8 down-regulated genes, were identified. The pathway enrichment analyses of the DEMIs showed that the up-regulated DEMIs were enriched in the Hippo signalling pathway and MAPK signalling pathway, and the down-regulated DEMIs were enriched in HTLV-I infection and miRNAs in cancers. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses of the DEGs were performed using Multifaceted Analysis Tool for Human Transcriptome. The up-regulated DEGs were enriched in biological processes (BPs), including the response to cAMP, response to hydrogen peroxide and cell-cell adhesion mediated by integrin; no enrichment of down-regulated DEGs was identified. KEGG analysis showed that the up-regulated DEGs were enriched in the Hippo signalling pathway and pathways in cancer. A PPI network of the DEGs was constructed by using Cytoscape software, and FOS, STAT1, MMP14, ITGB1, VCAN, DUSP1, LDHA, MCL1, MET, and ZFP36 were identified as the hub genes. The current study illustrates a characteristic microRNA profile and gene profile in preeclampsia, which may contribute to the interpretation of the progression of preeclampsia and provide novel biomarkers and therapeutic targets for preeclampsia. PMID:28594854

Shock-Wave/Boundary-Layer Interactions in Hypersonic Low Density Flows

NASA Technical Reports Server (NTRS)

Moss, James N.; Olejniczak, Joseph

2004-01-01

Results of numerical simulations of Mach 10 air flow over a hollow cylinder-flare and a double-cone are presented where viscous effects are significant. The flow phenomena include shock-shock and shock- boundary-layer interactions with accompanying flow separation, recirculation, and reattachment. The purpose of this study is to promote an understanding of the fundamental gas dynamics resulting from such complex interactions and to clarify the requirements for meaningful simulations of such flows when using the direct simulation Monte Carlo (DSMC) method. Particular emphasis is placed on the sensitivity of computed results to grid resolution. Comparisons of the DSMC results for the hollow cylinder-flare (30 deg.) configuration are made with the results of experimental measurements conducted in the ONERA RSCh wind tunnel for heating, pressure, and the extent of separation. Agreement between computations and measurements for various quantities is good except that for pressure. For the same flow conditions, the double- cone geometry (25 deg.- 65 deg.) produces much stronger interactions, and these interactions are investigated numerically using both DSMC and Navier-Stokes codes. For the double-cone computations, a two orders of magnitude variation in free-stream density (with Reynolds numbers from 247 to 24,7 19) is investigated using both computational methods. For this range of flow conditions, the computational results are in qualitative agreement for the extent of separation with the DSMC method always predicting a smaller separation region. Results from the Navier-Stokes calculations suggest that the flow for the highest density double-cone case may be unsteady; however, the DSMC solution does not show evidence of unsteadiness.

A 3-month long operational implementation of an ensemble prediction system of storm surge for the city of Venice

NASA Astrophysics Data System (ADS)

Mel, Riccardo; Lionello, Piero

2014-05-01

Advantages of an ensemble prediction forecast (EPF) technique that has been used for sea level (SL) prediction at the Northern Adriatic coast are investigated. The aims is to explore whether EPF is more precise than the traditional Deterministic Forecast (DF) and the value of the added information, mainly on forecast uncertainty. Improving the SL forecast for the city of Venice is of paramount importance for the management and maintenance of this historical city and for operating the movable barriers that are presently being built for its protection. The operational practice is simulated for three months from 1st October to 31st December 2010. The EPF is based on the HYPSE model, which is a standard single-layer nonlinear shallow water model, whose equations are derived from the depth averaged momentum equations and predicts the SL. A description of the model is available in the scientific literature. Forcing of HYPSE are provided by three different sets of 3-hourly ECMWF 10m-wind and MSLP fields: the high resolution meteorological forecast (which is used for the deterministic SL forecast, DF), the control run forecast (CRF, that differs from the DF forecast only for it lower meteorological fields resolution) and the 50 ensemble members of the ECMWF EPS (which are used for the SL-EPS. The resolution of DF fields is T1279 and resolution of both CRF and ECMWF EPS fields is T639 resolution. The 10m wind and MSLP fields have been downloaded at 0.125degs (DF) and 0.25degs(CRF and EPS) and linearly interpolated to the HYPSE grid (which is the same for all simulations). The version of HYPSE used in the SR EPS uses a rectangular mesh grid of variable size, which has the minimum grid step (0.03 degrees) in the northern part of the Adriatic Sea, from where grid step increases with a 1.01 factor in both latitude and longitude (In practice, resolution varies in the range from 3.3 to 7km). Results are analyzed considering the EPS spread, the rms of the simulations, the Brier Skill Score and are compared to observations at tide gauges distributed along the Croatian and Italian coast of the Adriatic Sea. It is shown that the ensemble spread is indeed a reliable indicator of the uncertainty of the storm surge prediction. Further, results show how uncertainty depends on the predicted value of sea level and how it increases with the forecast time range. The accuracy of the ensemble mean forecast is actually larger than that of the deterministic forecast, though the latter is produced by meteorological forcings at higher resolution

A Computational Fluid Dynamics Study of Swirling Flow Reduction by Using Anti-Vortex Baffle

NASA Technical Reports Server (NTRS)

Yang, H. Q.; West, Jeff; Peugeot, John W.

2017-01-01

OBJECTIVES: To evaluate proposed anti-vortex design in suppressing swirling flow during US burn. APPROACH: Include two major body forces in the analysis a)Vehicle acceleration (all three components); b)Vehicle maneuvers (roll, pitch, and yaw). Perform two drainage analyses of Ares I LOX tank using 6 DOF body forces predicted by GN&C analysis (Guidance Navigation and Control) during vehicle ascent: one with baffle, one without baffle. MODEL: Use Ares I defined geometry. O-Grid for easy fitting of baffle. In this preliminary analysis the holes are sealed. Use whole 360 deg. model with no assumption of symmetry or cyclic boundary conditions. Read in 6DOF data vs time from a file.

Apollo 16 far-ultraviolet imagery and spectra of the Large Magellanic Cloud

NASA Technical Reports Server (NTRS)

Page, T.; Carruthers, G. R.

1976-01-01

The Large Magellanic Cloud was observed by the far ultraviolet camera spectrograph from the lunar surface during the Apollo 16 mission 22 April 1972. Images were obtained with about 3 arc min resolution, in the 1,050 to 1,600 and 1,250 to 1,600 A wavelength ranges, of nearly the entire LMC. Spectra were also obtained in the 1,050 to 1,600 and 900 to 1,600 A ranges along a strip 1/4 deg wide (determined by the instrument's grid collimator) passing across the LMC. The images and spectra have been scanned with a PDS microdensitometer, and isodensity contour plots have been prepared using the Univac 1108 computer.

Solution strategies and heat transfer calculations for three-dimensional configurations at hypersonic speeds

NASA Technical Reports Server (NTRS)

Weilmuenster, K. J.; Gnoffo, Peter A.

1992-01-01

A procedure which reduces the memory requirements for computing the viscous flow over a modified Orbiter geometry at a hypersonic flight condition is presented. The Langley Aerothermodynamic Upwind Relaxation Algorithm (LAURA) code which incorporates a thermochemical nonequilibrium chemistry model, a finite rate catalytic wall boundary condition and wall temperature distribution based on radiation equilibrium is used in this study. In addition, the effect of choice of 'min mod' function, eigenvalue limiter and grid density on surface heating is investigated. The surface heating from a flowfield calculation at Mach number 22, altitude of 230,000 ft and 40 deg angle of attack is compared with flight data from three Orbiter flights.

Enhancement of photovoltaic cell performance using periodic triangular gratings

NASA Astrophysics Data System (ADS)

Bordatchev, Evgueni; Tauhiduzzaman, Mohammed; Dey, Rajat

2014-01-01

The solar energy industry strives to produce more efficient and yet cost effective solar panels each consisting of an array of photovoltaic (PV) cells. The goal of this study was to enhance the performance of PV cells through increasing the cells' optical efficiency defined as a percentage of surface incident light that reaches the PV material. This was achieved through the reduction of waveguide decoupling loss and Fresnel reflection losses by integrating specific nonimaging micro-optical structures on the top surface of existing PV cells. Due to this integration, optical efficiency and performance were increased through the enhancement of light trapping, light guiding, and in-coupling functionalities. Periodic triangular gratings (PTGs) were designed, nonsequentially modeled, optimized, and fabricated in polydimethylsiloxane as proposed micro-optical structures. Then the performance of PV cells with and without integrated PTGs was evaluated and compared. Initial optical simulation results show that an original PV cell (without PTG) exhibits an average optical efficiency of 32.7% over a range of incident light angles between 15 and 90 deg. Integration of the PTG allows the capture of incoming sunlight by total internal reflection (TIR), whence it is reflected back onto the PV cell for multiple consecutive chances for absorption and PV conversion. Geometry of the PTG was optimized with respect to an angle of light incidence of {15, 30, 45, 60, 75, 90} deg. Optical efficiency of the geometrically optimized PTGs was then analyzed under the same set of incident light angles and a maximum optical efficiency of 54.1% was observed for a PV cell with integrated PTG optimized at 90 deg. This is a 53.3% relative improvement in optical performance when compared to an original PV cell. Functional PTG prototypes were then fabricated with optical surface quality (below 10 nm Ra) and integrated with PV cells demonstrating an increase in maximum power by 1.08 mW/cm (7.6% improvement in PV performance) and in short circuit current by 2.39 mA/cm (6.4% improvement).

Grid cell mechanisms and function: Contributions of entorhinal persistent spiking and phase resetting

PubMed Central

Hasselmo, Michael E.

2008-01-01

This article presents a model of grid cell firing based on the intrinsic persistent firing shown experimentally in neurons of entorhinal cortex. In this model, the mechanism of persistent firing allows individual neurons to hold a stable baseline firing frequency. Depolarizing input from speed modulated head direction cells transiently shifts the frequency of firing from baseline, resulting in a shift in spiking phase in proportion to the integral of velocity. The convergence of input from different persistent firing neurons causes spiking in a grid cell only when the persistent firing neurons are within similar phase ranges. This model effectively simulates the two-dimensional firing of grid cells in open field environments, as well as the properties of theta phase precession. This model provides an alternate implementation of oscillatory interference models. The persistent firing could also interact on a circuit level with rhythmic inhibition and neurons showing membrane potential oscillations to code position with spiking phase. These mechanisms could operate in parallel with computation of position from visual angle and distance of stimuli. In addition to simulating two-dimensional grid patterns, models of phase interference can account for context-dependent firing in other tasks. In network simulations of entorhinal cortex, hippocampus and postsubiculum, the reset of phase effectively replicates context-dependent firing by entorhinal and hippocampal neurons during performance of a continuous spatial alternation task, a delayed spatial alternation task with running in a wheel during the delay period, and a hairpin maze task. PMID:19021258

Inflammatory and Repair Pathways Induced in Human Bronchoalveolar Lavage Cells with Ozone Inhalation

PubMed Central

Wong, Hofer; Tenney, Rachel; Chen, Chun; Stiner, Rachel; Balmes, John R.; Paquet, Agnès C.; Arjomandi, Mehrdad

2015-01-01

Background Inhalation of ambient levels of ozone causes airway inflammation and epithelial injury. Methods To examine the responses of airway cells to ozone-induced oxidative injury, 19 subjects (7 with asthma) were exposed to clean air (0ppb), medium (100ppb), and high (200ppb) ambient levels of ozone for 4h on three separate occasions in a climate-controlled chamber followed by bronchoscopy with bronchoalveolar lavage (BAL) 24h later. BAL cell mRNA expression was examined using Affymetrix GeneChip Microarray. The role of a differentially expressed gene (DEG) in epithelial injury was evaluated in an in vitro model of injury [16HBE14o- cell line scratch assay]. Results Ozone exposure caused a dose-dependent up-regulation of several biologic pathways involved in inflammation and repair including chemokine and cytokine secretion, activity, and receptor binding; metalloproteinase and endopeptidase activity; adhesion, locomotion, and migration; and cell growth and tumorigenesis regulation. Asthmatic subjects had 1.7- to 3.8-fold higher expression of many DEGs suggestive of increased proinflammatory and matrix degradation and remodeling signals. The most highly up-regulated gene was osteopontin, the protein level of which in BAL fluid increased in a dose-dependent manner after ozone exposure. Asthmatic subjects had a disproportionate increase in non-polymerized osteopontin with increasing exposure to ozone. Treatment with polymeric, but not monomeric, osteopontin enhanced the migration of epithelial cells and wound closure in an α9β1 integrin-dependent manner. Conclusions Expression profiling of BAL cells after ozone exposure reveals potential regulatory genes and pathways activated by oxidative stress. One DEG, osteopontin, promotes epithelial wound healing in an in vitro model of injury. PMID:26035830

Theta phase precession of grid and place cell firing in open environments

PubMed Central

Jeewajee, A.; Barry, C.; Douchamps, V.; Manson, D.; Lever, C.; Burgess, N.

2014-01-01

Place and grid cells in the rodent hippocampal formation tend to fire spikes at successively earlier phases relative to the local field potential theta rhythm as the animal runs through the cell's firing field on a linear track. However, this ‘phase precession’ effect is less well characterized during foraging in two-dimensional open field environments. Here, we mapped runs through the firing fields onto a unit circle to pool data from multiple runs. We asked which of seven behavioural and physiological variables show the best circular–linear correlation with the theta phase of spikes from place cells in hippocampal area CA1 and from grid cells from superficial layers of medial entorhinal cortex. The best correlate was the distance to the firing field peak projected onto the animal's current running direction. This was significantly stronger than other correlates, such as instantaneous firing rate and time-in-field, but similar in strength to correlates with other measures of distance travelled through the firing field. Phase precession was stronger in place cells than grid cells overall, and robust phase precession was seen in traversals through firing field peripheries (although somewhat less than in traversals through the centre), consistent with phase coding of displacement along the current direction. This type of phase coding, of place field distance ahead of or behind the animal, may be useful for allowing calculation of goal directions during navigation. PMID:24366140

Lunar Observer Laser Altimeter observations for lunar base site selection

NASA Technical Reports Server (NTRS)

Garvin, James B.; Bufton, Jack L.

1992-01-01

One of the critical datasets for optimal selection of future lunar landing sites is local- to regional-scale topography. Lunar base site selection will require such data for both engineering and scientific operations purposes. The Lunar Geoscience Orbiter or Lunar Observer is the ideal precursory science mission from which to obtain this required information. We suggest that a simple laser altimeter instrument could be employed to measure local-scale slopes, heights, and depths of lunar surface features important to lunar base planning and design. For this reason, we have designed and are currently constructing a breadboard of a Lunar Observer Laser Altimeter (LOLA) instrument capable of acquiring contiguous-footprint topographic profiles with both 30-m and 300-m along-track resolution. This instrument meets all the severe weight, power, size, and data rate limitations imposed by Observer-class spacecraft. In addition, LOLA would be capable of measuring the within-footprint vertical roughness of the lunar surface, and the 1.06-micron relative surface reflectivity at normal incidence. We have used airborne laser altimeter data for a few representative lunar analog landforms to simulate and analyze LOLA performance in a 100-km lunar orbit. We demonstrate that this system in its highest resolution mode (30-m diameter footprints) would quantify the topography of all but the very smallest lunar landforms. At its global mapping resolution (300-m diameter footprints), LOLA would establish the topographic context for lunar landing site selection by providing the basis for constructing a 1-2 km spatial resolution global, geodetic topographic grid that would contain a high density of observations (e.g., approximately 1000 observations per each 1 deg by 1 deg cell at the lunar equator). The high spatial and vertical resolution measurements made with a LOLA-class instrument on a precursory Lunar Observer would be highly synergistic with high-resolution imaging datasets, and will allow for direct quantification of critical slopes, heights, and depths of features visible in images of potential lunar base sites.

The R package 'icosa' for coarse resolution global triangular and penta-hexagonal gridding

NASA Astrophysics Data System (ADS)

Kocsis, Adam T.

2017-04-01

With the development of the internet and the computational power of personal computers, open source programming environments have become indispensable for science in the past decade. This includes the increase of the GIS capacity of the free R environment, which was originally developed for statistical analyses. The flexibility of R made it a preferred programming tool in a multitude of disciplines from the area of the biological and geological sciences. Many of these subdisciplines operate with incidence (occurrence) data that are in a large number of cases to be grained before further analyses can be conducted. This graining is executed mostly by gridding data to cells of a Gaussian grid of various resolutions to increase the density of data in a single unit of the analyses. This method has obvious shortcomings despite the ease of its application: well-known systematic biases are induced to cell sizes and shapes that can interfere with the results of statistical procedures, especially if the number of incidence points influences the metrics in question. The 'icosa' package employs a common method to overcome this obstacle by implementing grids with roughly equal cell sizes and shapes that are based on tessellated icosahedra. These grid objects are essentially polyhedra with xyz Cartesian vertex data that are linked to tables of faces and edges. At its current developmental stage, the package uses a single method of tessellation which balances grid cell size and shape distortions, but its structure allows the implementation of various other types of tessellation algorithms. The resolution of the grids can be set by the number of breakpoints inserted into a segment forming an edge of the original icosahedron. Both the triangular and their inverted penta-hexagonal grids are available for creation with the package. The package also incorporates functions to look up coordinates in the grid very effectively and data containers to link data to the grid structure. The classes defined in the package are communicating with classes of the 'sp' and 'raster' packages and functions are supplied that allow resolution change and type conversions. Three-dimensional rendering is made available with the 'rgl' package and two-dimensional projections can be calculated using 'sp' and 'rgdal'. The package was developed as part of a project funded by the Deutsche Forschungsgemeinschaft (KO - 5382/1-1).

CVD-MPFA full pressure support, coupled unstructured discrete fracture-matrix Darcy-flux approximations

NASA Astrophysics Data System (ADS)

Ahmed, Raheel; Edwards, Michael G.; Lamine, Sadok; Huisman, Bastiaan A. H.; Pal, Mayur

2017-11-01

Two novel control-volume methods are presented for flow in fractured media, and involve coupling the control-volume distributed multi-point flux approximation (CVD-MPFA) constructed with full pressure support (FPS), to two types of discrete fracture-matrix approximation for simulation on unstructured grids; (i) involving hybrid grids and (ii) a lower dimensional fracture model. Flow is governed by Darcy's law together with mass conservation both in the matrix and the fractures, where large discontinuities in permeability tensors can occur. Finite-volume FPS schemes are more robust than the earlier CVD-MPFA triangular pressure support (TPS) schemes for problems involving highly anisotropic homogeneous and heterogeneous full-tensor permeability fields. We use a cell-centred hybrid-grid method, where fractures are modelled by lower-dimensional interfaces between matrix cells in the physical mesh but expanded to equi-dimensional cells in the computational domain. We present a simple procedure to form a consistent hybrid-grid locally for a dual-cell. We also propose a novel hybrid-grid for intersecting fractures, for the FPS method, which reduces the condition number of the global linear system and leads to larger time steps for tracer transport. The transport equation for tracer flow is coupled with the pressure equation and provides flow parameter assessment of the fracture models. Transport results obtained via TPS and FPS hybrid-grid formulations are compared with the corresponding results of fine-scale explicit equi-dimensional formulations. The results show that the hybrid-grid FPS method applies to general full-tensor fields and provides improved robust approximations compared to the hybrid-grid TPS method for fractured domains, for both weakly anisotropic permeability fields and very strong anisotropic full-tensor permeability fields where the TPS scheme exhibits spurious oscillations. The hybrid-grid FPS formulation is extended to compressible flow and the results demonstrate the method is also robust for transient flow. Furthermore, we present FPS coupled with a lower-dimensional fracture model, where fractures are strictly lower-dimensional in the physical mesh as well as in the computational domain. We present a comparison of the hybrid-grid FPS method and the lower-dimensional fracture model for several cases of isotropic and anisotropic fractured media which illustrate the benefits of the respective methods.

Motor coordination in mice with hotfoot, Lurcher, and double mutations of the Grid2 gene encoding the delta-2 excitatory amino acid receptor.

PubMed

Lalonde, R; Hayzoun, K; Selimi, F; Mariani, J; Strazielle, C

2003-11-01

Grid2(ho/ho) is a loss of function gene mutation resulting in abnormal dendritic arborizations of Purkinje cells. These mutants were compared in a series of motor coordination tests requiring balance and equilibrium to nonataxic controls (Grid2(ho/+)) and to a double mutant (Grid2(ho/Lc)) with an inserted Lc mutation. The performance of Grid2(ho/ho) mutant mice was poorer than that of controls on stationary beam, coat hanger, unsteady platform, and rotorod tests. Grid2(ho/Lc) did not differ from Grid2(Lc/+) mice. However, the insertion of the Lc mutation in Grid2(ho/Lc) potentiated the deficits found in Grid2(ho/ho) in stationary beam, unsteady platform, and rotorod tests. These results indicate a deleterious effect of the Lc mutation on Grid2-deficient mice.

A Co-Drug of Butyric Acid Derived from Fermentation Metabolites of the Human Skin Microbiome Stimulates Adipogenic Differentiation of Adipose-Derived Stem Cells: Implications in Tissue Augmentation.

PubMed

Wang, Yanhan; Zhang, Lingjuan; Yu, Jinghua; Huang, Stephen; Wang, Zhenping; Chun, Kimberly Ann; Lee, Tammy Ling; Chen, Ying-Tung; Gallo, Richard L; Huang, Chun-Ming

2017-01-01

We show that Staphylococcus epidermidis, a commensal bacterium in the human skin microbiome, produces short-chain fatty acids by glycerol fermentation that can induce adipogenesis. Although the antimicrobial and anti-inflammatory activities of short-chain fatty acids have been previously well characterized, little is known about the contribution of short-chain fatty acids to the adipogenic differentiation of adipose-derived stem cells (ADSCs). We show that ADSCs differentiated into adipocytes and accumulated lipids in the cytoplasm when cultured with butyric acid, a principal short-chain fatty acid in the fermentation metabolites of S. epidermidis. Additionally, a co-drug, butyric acid 2-(2-butyryloxyethoxy) ethyl ester (BA-DEG-BA), released active butyric acid when it was intradermally injected into mouse ears and induced ADSC differentiation, characterized by an increased expression of cytoplasmic lipids and perilipin A. The BA-DEG-BA-induced adipogenic differentiation was mediated via peroxisome proliferator-activated receptor gamma. Furthermore, intradermal injection of ADSCs along with BA-DEG-BA into mouse ears markedly enhanced the adipogenic differentiation of ADSCs, leading to dermal augmentation. Our study introduces BA-DEG-BA as an enhancer of ADSC adipogenesis and suggests an integral interaction between the human skin microbiome and ADSCs. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

A Cell-Centered Multigrid Algorithm for All Grid Sizes

NASA Technical Reports Server (NTRS)

Gjesdal, Thor

1996-01-01

Multigrid methods are optimal; that is, their rate of convergence is independent of the number of grid points, because they use a nested sequence of coarse grids to represent different scales of the solution. This nesting does, however, usually lead to certain restrictions of the permissible size of the discretised problem. In cases where the modeler is free to specify the whole problem, such constraints are of little importance because they can be taken into consideration from the outset. We consider the situation in which there are other competing constraints on the resolution. These restrictions may stem from the physical problem (e.g., if the discretised operator contains experimental data measured on a fixed grid) or from the need to avoid limitations set by the hardware. In this paper we discuss a modification to the cell-centered multigrid algorithm, so that it can be used br problems with any resolution. We discuss in particular a coarsening strategy and choice of intergrid transfer operators that can handle grids with both an even or odd number of cells. The method is described and applied to linear equations obtained by discretization of two- and three-dimensional second-order elliptic PDEs.

The Impacts of Bowtie Effect and View Angle Discontinuity on MODIS Swath Data Gridding

NASA Technical Reports Server (NTRS)

Wang, Yujie; Lyapustin, Alexei

2007-01-01

We have analyzed two effects of the MODIS viewing geometry on the quality of gridded imagery. First, the fact that the MODIS scans a swath of the Earth 10 km wide at nadir, causes abrupt change of the view azimuth angle at the boundary of adjacent scans. This discontinuity appears as striping of the image clearly visible in certain cases with viewing geometry close to principle plane over the snow of the glint area of water. The striping is a true surface Bi-directional Reflectance Factor (BRF) effect and should be preserved during gridding. Second, due to bowtie effect, the observations in adjacent scans overlap each other. Commonly used method of calculating grid cell value by averaging all overlapping observations may result in smearing of the image. This paper describes a refined gridding algorithm that takes the above two effects into account. By calculating the grid cell value by averaging the overlapping observations from a single scan, the new algorithm preserves the measured BRF signal and enhances sharpness of the image.

Physiological and transcriptome response to cadmium in cosmos (Cosmos bipinnatus Cav.) seedlings.

PubMed

Liu, Yujing; Yu, Xiaofang; Feng, Yimei; Zhang, Chao; Wang, Chao; Zeng, Jian; Huang, Zhuo; Kang, Houyang; Fan, Xing; Sha, Lina; Zhang, Haiqin; Zhou, Yonghong; Gao, Suping; Chen, Qibing

2017-10-31

To date, several species of Asteraceae have been considered as Cd-accumulators. However, little information on the Cd tolerance and associated mechanisms of Asteraceae species Cosmos bipinnatus, is known. Presently, several physiological indexes and transcriptome profiling under Cd stress were investigated. C. bipinnatus exhibited strong Cd tolerance and recommended as a Cd-accumulator, although the biomasses were reduced by Cd. Meanwhile, Cd stresses reduced Zn and Ca uptake, but increased Fe uptake. Subcellular distribution indicated that the vacuole sequestration in root mainly detoxified Cd under lower Cd stress. Whilst, cell wall binding and vacuole sequestration in root co-detoxified Cd under high Cd exposure. Meanwhile, 66,407 unigenes were assembled and 41,674 (62.75%) unigenes were annotated in at least one database. 2,658 DEGs including 1,292 up-regulated unigenes and 1,366 down-regulated unigenes were identified under 40 μmol/L Cd stress. Among of these DEGs, ZIPs, HMAs, NRAMPs and ABC transporters might participate in Cd uptake, translocation and accumulation. Many DEGs participating in several processes such as cell wall biosynthesis, GSH metabolism, TCA cycle and antioxidant system probably play critical roles in cell wall binding, vacuole sequestration and detoxification. These results provided a novel insight into the physiological and transcriptome response to Cd in C. bipinnatus seedlings.

Solar Maps Development: How the Maps Were Made | Geospatial Data Science |

Science.gov Websites

10% of a true measured value within the grid cell. Due to terrain effects and other microclimate effects and other microclimate influences, the local cloud cover can vary significantly even within a approximately 10% of a true measured value within the grid cell. Due to terrain effects and other microclimate

Documentation and analysis of a geographic information system application for combining data layers, using nonpoint-source pollution as an example

USGS Publications Warehouse

Kiesler, James L.

2002-01-01

An analysis of the application indicates that the selected data layers to be combined should be at the greatest spatial resolution possible; however, all data layers do not have to be at the same spatial resolution. The spatial variation of the data layers should be adequately defined. The size of each grid cell should be small enough to maintain the spatial definition of smaller features within the data layers. The most accurate results are shown to occur when the values for the grid cells representing the individual data layers are summed and the mean of the summed grid-cell values is used to describe the watershed of interest.

Semitransparent organic solar cells with hybrid monolayer graphene/metal grid as top electrodes

NASA Astrophysics Data System (ADS)

Lin, Peng; Choy, Wallace C. H.; Zhang, Di; Xie, Fengxian; Xin, Jianzhuo; Leung, C. W.

2013-03-01

Hybrid transparent monolayer graphene/metal grid is proposed as top electrode of semitransparent organic solar cells. The hybrid electrode using gold grid on flexible polyethylene terephthalate substrate shows very low sheet resistance of 22 ± 3 Ω/□ and high optical transmittance of 81.4%, which is comparable to conventional indium tin oxide/glass electrode. Using lamination process, the layer of poly(3,4-ethylenedioythiophene):poly(styrenesulfonate) doped with D-sorbitol plays an important role in the electrical performance of the laminated devices. In addition, the devices show best power convention efficiency of 3.1% and fill factor of 55.0%, which are much better than those of similar graphene-based semitransparent organic solar cells.

Using Grid Cells for Navigation.

PubMed

Bush, Daniel; Barry, Caswell; Manson, Daniel; Burgess, Neil

2015-08-05

Mammals are able to navigate to hidden goal locations by direct routes that may traverse previously unvisited terrain. Empirical evidence suggests that this "vector navigation" relies on an internal representation of space provided by the hippocampal formation. The periodic spatial firing patterns of grid cells in the hippocampal formation offer a compact combinatorial code for location within large-scale space. Here, we consider the computational problem of how to determine the vector between start and goal locations encoded by the firing of grid cells when this vector may be much longer than the largest grid scale. First, we present an algorithmic solution to the problem, inspired by the Fourier shift theorem. Second, we describe several potential neural network implementations of this solution that combine efficiency of search and biological plausibility. Finally, we discuss the empirical predictions of these implementations and their relationship to the anatomy and electrophysiology of the hippocampal formation. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

APORT: a program for the area-based apportionment of county variables to cells of a polar grid. [Airborne pollutant transport models

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

Fields, D.E.; Little, C.A.

1978-11-01

The APORT computer code was developed to apportion variables tabulated for polygon-structured civil districts onto cells of a polar grid. The apportionment is based on fractional overlap between the polygon and the grid cells. Centering the origin of the polar system at a pollutant source site yields results that are very useful for assessing and interpreting the effects of airborne pollutant dissemination. The APOPLT graphics code, which uses the same data set as APORT, provides a convenient visual display of the polygon structure and the extent of the polar grid. The APORT/APOPLT methodology was verified by application to county summariesmore » of cattle population for counties surrounding the Oyster Creek, New Jersey, nuclear power plant. These numerical results, which were obtained using approximately 2-min computer time on an IBM System 360/91 computer, compare favorably to results of manual computations in both speed and accuracy.« less

Deriving flow directions for coarse-resolution (1-4 km) gridded hydrologic modeling

NASA Astrophysics Data System (ADS)

Reed, Seann M.

2003-09-01

The National Weather Service Hydrology Laboratory (NWS-HL) is currently testing a grid-based distributed hydrologic model at a resolution (4 km) commensurate with operational, radar-based precipitation products. To implement distributed routing algorithms in this framework, a flow direction must be assigned to each model cell. A new algorithm, referred to as cell outlet tracing with an area threshold (COTAT) has been developed to automatically, accurately, and efficiently assign flow directions to any coarse-resolution grid cells using information from any higher-resolution digital elevation model. Although similar to previously published algorithms, this approach offers some advantages. Use of an area threshold allows more control over the tendency for producing diagonal flow directions. Analyses of results at different output resolutions ranging from 300 m to 4000 m indicate that it is possible to choose an area threshold that will produce minimal differences in average network flow lengths across this range of scales. Flow direction grids at a 4 km resolution have been produced for the conterminous United States.

Local transformations of the hippocampal cognitive map.

PubMed

Krupic, Julija; Bauza, Marius; Burton, Stephen; O'Keefe, John

2018-03-09

Grid cells are neurons active in multiple fields arranged in a hexagonal lattice and are thought to represent the "universal metric for space." However, they become nonhomogeneously distorted in polarized enclosures, which challenges this view. We found that local changes to the configuration of the enclosure induce individual grid fields to shift in a manner inversely related to their distance from the reconfigured boundary. The grid remained primarily anchored to the unchanged stable walls and showed a nonuniform rescaling. Shifts in simultaneously recorded colocalized grid fields were strongly correlated, which suggests that the readout of the animal's position might still be intact. Similar field shifts were also observed in place and boundary cells-albeit of greater magnitude and more pronounced closer to the reconfigured boundary-which suggests that there is no simple one-to-one relationship between these three different cell types. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Protein-protein interaction network of gene expression in the hydrocortisone-treated keloid.

PubMed

Chen, Rui; Zhang, Zhiliang; Xue, Zhujia; Wang, Lin; Fu, Mingang; Lu, Yi; Bai, Ling; Zhang, Ping; Fan, Zhihong

2015-01-01

In order to explore the molecular mechanism of hydrocortisone in keloid tissue, the gene expression profiles of keloid samples treated with hydrocortisone were subjected to bioinformatics analysis. Firstly, the gene expression profiles (GSE7890) of five samples of keloid treated with hydrocortisone and five untreated keloid samples were downloaded from the Gene Expression Omnibus (GEO) database. Secondly, data were preprocessed using packages in R language and differentially expressed genes (DEGs) were screened using a significance analysis of microarrays (SAM) protocol. Thirdly, the DEGs were subjected to gene ontology (GO) function and KEGG pathway enrichment analysis. Finally, the interactions of DEGs in samples of keloid treated with hydrocortisone were explored in a human protein-protein interaction (PPI) network, and sub-modules of the DEGs interaction network were analyzed using Cytoscape software. Based on the analysis, 572 DEGs in the hydrocortisone-treated samples were screened; most of these were involved in the signal transduction and cell cycle. Furthermore, three critical genes in the module, including COL1A1, NID1, and PRELP, were screened in the PPI network analysis. These findings enhance understanding of the pathogenesis of the keloid and provide references for keloid therapy. © 2015 The International Society of Dermatology.

A numerical study of the effect of geometry variation, turbulence models, and dissipation on the flow past control surfaces

NASA Technical Reports Server (NTRS)

Chaussee, Denny S.

1993-01-01

The steady 3D viscous flow past the ONERA M6 wing and a slender delta wing-body with trailing edge control surfaces has been computed. A cell-centered finite-volume Navier-Stokes patched zonal method has been used for the numerical simulation. Both diagonalized and LUSGS schemes have been implemented. Besides the standard nonplanar zonal interfacing techniques, a new virtual zone capability has been employed. For code validation, the transonic flow past the ONERA M5 wing is calculated for angles-of-attack of 3.06 deg and 5.06 deg and compared with the available experiments. The wing-body computational results are compared with experimental data for both trailing-edge flaps deflected. The experimental flow conditions are M subinfinity = 0.4, a turbulent Reynolds number of 5.41 million based on a mean aerodynamic chord of 25.959 inches, adiabatic wall, and angles-of-attack varying from 0 deg to 23.85 deg. The computational results are presented for the 23.85 deg angle-of-attack case. The effects of the base flow due to a model sting, the varying second and fourth order numerical dissipation, and the turbulence model are all considered.

A Cartesian, cell-based approach for adaptively-refined solutions of the Euler and Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Coirier, William J.; Powell, Kenneth G.

1994-01-01

A Cartesian, cell-based approach for adaptively-refined solutions of the Euler and Navier-Stokes equations in two dimensions is developed and tested. Grids about geometrically complicated bodies are generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, N-sided 'cut' cells are created using polygon-clipping algorithms. The grid is stored in a binary-tree structure which provides a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive mesh refinement. The Euler and Navier-Stokes equations are solved on the resulting grids using a finite-volume formulation. The convective terms are upwinded: a gradient-limited, linear reconstruction of the primitive variables is performed, providing input states to an approximate Riemann solver for computing the fluxes between neighboring cells. The more robust of a series of viscous flux functions is used to provide the viscous fluxes at the cell interfaces. Adaptively-refined solutions of the Navier-Stokes equations using the Cartesian, cell-based approach are obtained and compared to theory, experiment, and other accepted computational results for a series of low and moderate Reynolds number flows.

A Cartesian, cell-based approach for adaptively-refined solutions of the Euler and Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Coirier, William J.; Powell, Kenneth G.

1995-01-01

A Cartesian, cell-based approach for adaptively-refined solutions of the Euler and Navier-Stokes equations in two dimensions is developed and tested. Grids about geometrically complicated bodies are generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, N-sided 'cut' cells are created using polygon-clipping algorithms. The grid is stored in a binary-tree data structure which provides a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive mesh refinement. The Euler and Navier-Stokes equations are solved on the resulting grids using a finite-volume formulation. The convective terms are upwinded: A gradient-limited, linear reconstruction of the primitive variables is performed, providing input states to an approximate Riemann solver for computing the fluxes between neighboring cells. The more robust of a series of viscous flux functions is used to provide the viscous fluxes at the cell interfaces. Adaptively-refined solutions of the Navier-Stokes equations using the Cartesian, cell-based approach are obtained and compared to theory, experiment and other accepted computational results for a series of low and moderate Reynolds number flows.

Identification of senescence-associated genes in human bone marrow mesenchymal stem cells

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

Ryu, Eunsook; Hong, Su; Kang, Jaeku

2008-07-04

Human bone marrow mesenchymal stem cells (hBMMSCs) are multipotent stem cells that can differentiate into several specialized cell types, including bone, cartilage, and fat cells. The proliferative capacity of hBMMSCs paves the way for the development of regenerative medicine and tissue engineering. However, long-term in vitro culture of hBMMSCs leads to a reduced life span of the cells due to senescence, which leads eventually to growth arrest. To investigate the molecular mechanism behind the cellular senescence of hBMMSCs, microarray analysis was used to compare the expression profiles of early passage hBMMSCs, late passage hBMMSCs and hBMMSCs ectopically expressing human telomerasemore » reverse transcriptase (hTERT). Using an intersection analysis of 3892 differentially expressed genes (DEGs) out of 27,171 total genes analyzed, we identified 338 senescence-related DEGs. GO term categorization and pathway network analysis revealed that the identified genes are strongly related to known senescence pathways and mechanisms. The genes identified using this approach will facilitate future studies of the mechanisms underlying the cellular senescence of hBMMSCs.« less

Identification of key genes related to high-risk gastrointestinal stromal tumors using bioinformatics analysis.

PubMed

Jin, Shuan; Zhu, Wenhua; Li, Jun

2018-01-01

The purpose of this study was to identify predictive biomarkers used for clinical therapy and prognostic evaluation of high-risk gastrointestinal stromal tumors (GISTs). In this study, microarray data GSE31802 were used to identify differentially expressed genes (DEGs) between high-risk GISTs and low-risk GISTs. Then, enrichment analysis of DEGs was conducted based on the gene ontology and kyoto encyclopedia of genes and genomes pathway database. In addition, the transcription factors and cancer-related genes in DEGs were screened according to the TRANSFAC, TSGene, and TAG database. Finally, protein-protein interaction (PPI) network was constructed and analyzed to look for critical genes involved in high-risk GISTs. A total of forty DEGs were obtained and these genes were mainly involved in four pathways, including melanogenesis, neuroactive ligand-receptor interaction, malaria, and hematopoietic cell lineage. The enriched biological processes were related to the regulation of insulin secretion, integrin activation, and neuropeptide signaling pathway. Transcription factor analysis of DEGs indicated that POU domain, class 2, associating factor 1 (POU2AF1) was significantly downregulated in high-risk GISTs. By constructing the PPI network of DEGs, ten genes with high degrees formed local networks, such as PNOC, P2RY14, and SELP. Four genes as POU2AF1, PNOC, P2RY14, and SELP might be used as biomarkers for prognosis of high-risk GISTs.

Interplay of PDZ and protease domain of DegP ensures efficient elimination of misfolded proteins

PubMed Central

Krojer, Tobias; Pangerl, Karen; Kurt, Juliane; Sawa, Justyna; Stingl, Christoph; Mechtler, Karl; Huber, Robert; Ehrmann, Michael; Clausen, Tim

2008-01-01

Aberrant proteins represent an extreme hazard to cells. Therefore, molecular chaperones and proteases have to carry out protein quality control in each cellular compartment. In contrast to the ATP-dependent cytosolic proteases and chaperones, the molecular mechanisms of extracytosolic factors are largely unknown. To address this question, we studied the protease function of DegP, the central housekeeping protein in the bacterial envelope. Our data reveal that DegP processively degrades misfolded proteins into peptides of defined size by employing a molecular ruler comprised of the PDZ1 domain and the proteolytic site. Furthermore, peptide binding to the PDZ domain transforms the resting protease into its active state. This allosteric activation mechanism ensures the regulated and rapid elimination of misfolded proteins upon folding stress. In comparison to the cytosolic proteases, the regulatory features of DegP are established by entirely different mechanisms reflecting the convergent evolution of an extracytosolic housekeeping protease. PMID:18505836

Unstructured Euler flow solutions using hexahedral cell refinement

NASA Technical Reports Server (NTRS)

Melton, John E.; Cappuccio, Gelsomina; Thomas, Scott D.

1991-01-01

An attempt is made to extend grid refinement into three dimensions by using unstructured hexahedral grids. The flow solver is developed using the TIGER (topologically Independent Grid, Euler Refinement) as the starting point. The program uses an unstructured hexahedral mesh and a modified version of the Jameson four-stage, finite-volume Runge-Kutta algorithm for integration of the Euler equations. The unstructured mesh allows for local refinement appropriate for each freestream condition, thereby concentrating mesh cells in the regions of greatest interest. This increases the computational efficiency because the refinement is not required to extend throughout the entire flow field.

Combined effect of pulse density and grid cell size on predicting and mapping aboveground carbon in fast-growing Eucalyptus forest plantation using airborne LiDAR data.

PubMed

Silva, Carlos Alberto; Hudak, Andrew Thomas; Klauberg, Carine; Vierling, Lee Alexandre; Gonzalez-Benecke, Carlos; de Padua Chaves Carvalho, Samuel; Rodriguez, Luiz Carlos Estraviz; Cardil, Adrián

2017-12-01

LiDAR remote sensing is a rapidly evolving technology for quantifying a variety of forest attributes, including aboveground carbon (AGC). Pulse density influences the acquisition cost of LiDAR, and grid cell size influences AGC prediction using plot-based methods; however, little work has evaluated the effects of LiDAR pulse density and cell size for predicting and mapping AGC in fast-growing Eucalyptus forest plantations. The aim of this study was to evaluate the effect of LiDAR pulse density and grid cell size on AGC prediction accuracy at plot and stand-levels using airborne LiDAR and field data. We used the Random Forest (RF) machine learning algorithm to model AGC using LiDAR-derived metrics from LiDAR collections of 5 and 10 pulses m -2 (RF5 and RF10) and grid cell sizes of 5, 10, 15 and 20 m. The results show that LiDAR pulse density of 5 pulses m -2 provides metrics with similar prediction accuracy for AGC as when using a dataset with 10 pulses m -2 in these fast-growing plantations. Relative root mean square errors (RMSEs) for the RF5 and RF10 were 6.14 and 6.01%, respectively. Equivalence tests showed that the predicted AGC from the training and validation models were equivalent to the observed AGC measurements. The grid cell sizes for mapping ranging from 5 to 20 also did not significantly affect the prediction accuracy of AGC at stand level in this system. LiDAR measurements can be used to predict and map AGC across variable-age Eucalyptus plantations with adequate levels of precision and accuracy using 5 pulses m -2 and a grid cell size of 5 m. The promising results for AGC modeling in this study will allow for greater confidence in comparing AGC estimates with varying LiDAR sampling densities for Eucalyptus plantations and assist in decision making towards more cost effective and efficient forest inventory.

Transfrontier Macroseismic Data Exchange in Europe: Intensity Assessment of M>4 Earthquakes by a Grid Cell Approach

NASA Astrophysics Data System (ADS)

Van Noten, K.; Lecocq, T.; Sira, C.; Hinzen, K. G.; Camelbeeck, T.

2016-12-01

In the US, the USGS is the only institute that gathers macroseismic data through its online "Did You Feel It?" (DYFI) system allowing a homogeneous and consistent intensity assessment. In Europe, however, we face a much more complicated situation. As almost every nation has its own inquiry in their national language(s) and both the EMSC and the USGS run an international DYFI inquiry, responses to European transfrontier-felt seismic events are strongly fragmented across different institutes. To make a realistic ground motion intensity assessment, macroseismic databases need to be merged in a consistent way hereby dealing with duplicated responses, different intensity calculations and legal issues (observer's privacy). In this presentation, we merge macroseismic datasets by a grid cell approach. Instead of using the irregularly-shaped, arbitrary municipal boundaries, we structure the model area into (100 km2) grid cells and assign an intensity value to each grid cell based on all institutional (geocoded) responses in that cell. The resulting macroseismic grid cell distribution shows a less subjective and more homogeneous intensity distribution than the classic community distribution despite less datapoints are used after geocoding the participant's location. The method is demonstrated on the 2011 ML 4.3 (MW 3.7) Goch (Germany) and the 2015 ML 4.2 (MW 3.7) Ramsgate (UK) earthquakes both felt in NW Europe. Integration of data results in a non-circular distribution in which the felt area extends significantly more in E-W than in N-S direction, illustrating a low-pass filtering effect due to the south-to-north increasing thickness of cover sediments above the regional London-Brabant Massif. Ground motions were amplified and attenuated at places with a shallow and deep basement, respectively. To large extend, the shape of the attenuation model derived through the grid cell intensity points is rather similar as the Atkinson and Wald (2007) CEUS prediction. The attenuation only suffers from underreported low intensities and non-reported intensity I at large epicentral distance. Figure: European institutes that provide an online "Did You Feel It?" inquiry. The question mark indicates countries in which an inquiry is absent or has not been found.

Exploration Gap Assessment (FY13 Update)

DOE Data Explorer

Dan Getman

2013-09-30

This submission contains an update to the previous Exploration Gap Assessment funded in 2012, which identify high potential hydrothermal areas where critical data are needed (gap analysis on exploration data). The uploaded data are contained in two data files for each data category: A shape (SHP) file containing the grid, and a data file (CSV) containing the individual layers that intersected with the grid. This CSV can be joined with the map to retrieve a list of datasets that are available at any given site. A grid of the contiguous U.S. was created with 88,000 10-km by 10-km grid cells, and each cell was populated with the status of data availability corresponding to five data types: 1. well data 2. geologic maps 3. fault maps 4. geochemistry data 5. geophysical data

De novo Transcriptome Assembly of Floral Buds of Pineapple and Identification of Differentially Expressed Genes in Response to Ethephon Induction

PubMed Central

Liu, Chuan-He; Fan, Chao

2016-01-01

A remarkable characteristic of pineapple is its ability to undergo floral induction in response to external ethylene stimulation. However, little information is available regarding the molecular mechanism underlying this process. In this study, the differentially expressed genes (DEGs) in plants exposed to 1.80 mL·L−1 (T1) or 2.40 mL·L−1 ethephon (T2) compared with Ct plants (control, cleaning water) were identified using RNA-seq and gene expression profiling. Illumina sequencing generated 65,825,224 high-quality reads that were assembled into 129,594 unigenes with an average sequence length of 1173 bp. Of these unigenes, 24,775 were assigned to specific KEGG pathways, of which metabolic pathways and biosynthesis of secondary metabolites were the most highly represented. Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority were involved in metabolic and cellular processes, cell and cell part, catalytic activity and binding. Gene expression profiling analysis revealed 3788, 3062, and 758 DEGs in the comparisons of T1 with Ct, T2 with Ct, and T2 with T1, respectively. GO analysis indicated that these DEGs were predominantly annotated to metabolic and cellular processes, cell and cell part, catalytic activity, and binding. KEGG pathway analysis revealed the enrichment of several important pathways among the DEGs, including metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Thirteen DEGs were identified as candidate genes associated with the process of floral induction by ethephon, including three ERF-like genes, one ETR-like gene, one LTI-like gene, one FT-like gene, one VRN1-like gene, three FRI-like genes, one AP1-like gene, one CAL-like gene, and one AG-like gene. qPCR analysis indicated that the changes in the expression of these 13 candidate genes were consistent with the alterations in the corresponding RPKM values, confirming the accuracy and credibility of the RNA-seq and gene expression profiling results. Ethephon-mediated induction likely mimics the process of vernalization in the floral transition in pineapple by increasing LTI, FT, and VRN1 expression and promoting the up-regulation of floral meristem identity genes involved in flower development. The candidate genes screened can be used in investigations of the molecular mechanisms of the flowering pathway and of various other biological mechanisms in pineapple. PMID:26955375

Topographic organization, number, and laminar distribution of callosal cells connecting visual cortical areas 17 and 18 of normally pigmented and Siamese cats.

PubMed

Berman, N E; Grant, S

1992-07-01

The callosal connections between visual cortical areas 17 and 18 in adult normally pigmented and "Boston" Siamese cats were studied using degeneration methods, and by transport of WGA-HRP combined with electrophysiological mapping. In normal cats, over 90% of callosal neurons were located in the supragranular layers. The supragranular callosal cell zone spanned the area 17/18 border and extended, on average, some 2-3 mm into both areas to occupy a territory which was roughly co-extensive with the distribution of callosal terminations in these areas. The region of the visual field adjoining the vertical meridian that was represented by neurons in the supragranular callosal cell zone was shown to increase systematically with decreasing visual elevation. Thus, close to the area centralis, receptive-field centers recorded from within this zone extended only up to 5 deg into the contralateral hemifield but at elevations of -10 deg and -40 deg they extended as far as 8 deg and 14 deg, respectively, into this hemifield. This suggests an element of visual non-correspondence in the callosal pathway between these cortical areas, which may be an essential substrate for "coarse" stereopsis at the visual midline. In the Siamese cats, the callosal cell and termination zones in areas 17 and 18 were expanded in width compared to the normal animals, but the major components were less robust. The area 17/18 border was often devoid of callosal axons and, in particular, the number of supragranular layer neurons participating in the pathway were drastically reduced, to only about 25% of those found in the normally pigmented adults. The callosal zones contained representations of the contralateral and ipsilateral hemifields that were roughly mirror-symmetric about the vertical meridian, and both hemifield representations increased with decreasing visual elevation. The extent and severity of the anomalies observed were similar across individual cats, regardless of whether a strabismus was also present. The callosal pathway between these visual cortical areas in the Siamese cat has been considered "silent," since nearly all neurons within its territory are activated only by the contralateral eye. The paucity of supragranular pyramidal neurons involved in the pathway may explain this silence.

Weekly agricultural emissions and ambient concentrations of ammonia: Validation of an emission inventory

NASA Astrophysics Data System (ADS)

Bittman, Shabtai; Jones, Keith; Vingarzan, Roxanne; Hunt, Derek E.; Sheppard, Steve C.; Tait, John; So, Rita; Zhao, Johanna

2015-07-01

Weekly inventories for emissions of agricultural ammonia were calculated for 139 4 × 4 km grid cells over 52 weeks in the intensely farmed Lower Fraser Valley, BC. The grid cells were located both inside and outside an area that had been depopulated of poultry due to an outbreak of Avian Influenza prior to the start of the study. During the study period, ambient ammonia concentrations were measured hourly at two locations outside the cull area and one location inside the cull area. Large emission differences between grid cells and differences in temporal variation between cells were related to farming practices and meteorological factors such as temperature and rainfall. Weekly average ambient concentrations at the three sampling locations were significantly correlated with estimates of weekly emissions for many of the grid cells in the study area. Inside the cull area, ambient concentrations during the cull (week 1) were 37% of the concentrations after the cull (week 52), while outside the cull there was almost no difference between week 1 and week 52, suggesting that in normal (non-cull) conditions, about 60% of the ambient ammonia was due to poultry farms. Estimated emissions in weeks 1 and 52 for grid cells affected by the cull indicated that over 90% of the emissions came from poultry. The discrepancy in difference between week 1 and 52 for emissions and ambient concentrations could be due to atmospheric factors like transport, atmospheric reactions, dispersion or deposition; to errors in the inventory including farming data, emission factors; and omission of some non-poultry emission sources. Overall the study supports the ammonia emission inventory estimates. Detailed emission data helps in modeling ammonia in the atmosphere and is useful for developing abatement policy.

Parallel grid library for rapid and flexible simulation development

NASA Astrophysics Data System (ADS)

Honkonen, I.; von Alfthan, S.; Sandroos, A.; Janhunen, P.; Palmroth, M.

2013-04-01

We present an easy to use and flexible grid library for developing highly scalable parallel simulations. The distributed cartesian cell-refinable grid (dccrg) supports adaptive mesh refinement and allows an arbitrary C++ class to be used as cell data. The amount of data in grid cells can vary both in space and time allowing dccrg to be used in very different types of simulations, for example in fluid and particle codes. Dccrg transfers the data between neighboring cells on different processes transparently and asynchronously allowing one to overlap computation and communication. This enables excellent scalability at least up to 32 k cores in magnetohydrodynamic tests depending on the problem and hardware. In the version of dccrg presented here part of the mesh metadata is replicated between MPI processes reducing the scalability of adaptive mesh refinement (AMR) to between 200 and 600 processes. Dccrg is free software that anyone can use, study and modify and is available at https://gitorious.org/dccrg. Users are also kindly requested to cite this work when publishing results obtained with dccrg. Catalogue identifier: AEOM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOM_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU Lesser General Public License version 3 No. of lines in distributed program, including test data, etc.: 54975 No. of bytes in distributed program, including test data, etc.: 974015 Distribution format: tar.gz Programming language: C++. Computer: PC, cluster, supercomputer. Operating system: POSIX. The code has been parallelized using MPI and tested with 1-32768 processes RAM: 10 MB-10 GB per process Classification: 4.12, 4.14, 6.5, 19.3, 19.10, 20. External routines: MPI-2 [1], boost [2], Zoltan [3], sfc++ [4] Nature of problem: Grid library supporting arbitrary data in grid cells, parallel adaptive mesh refinement, transparent remote neighbor data updates and load balancing. Solution method: The simulation grid is represented by an adjacency list (graph) with vertices stored into a hash table and edges into contiguous arrays. Message Passing Interface standard is used for parallelization. Cell data is given as a template parameter when instantiating the grid. Restrictions: Logically cartesian grid. Running time: Running time depends on the hardware, problem and the solution method. Small problems can be solved in under a minute and very large problems can take weeks. The examples and tests provided with the package take less than about one minute using default options. In the version of dccrg presented here the speed of adaptive mesh refinement is at most of the order of 106 total created cells per second. http://www.mpi-forum.org/. http://www.boost.org/. K. Devine, E. Boman, R. Heaphy, B. Hendrickson, C. Vaughan, Zoltan data management services for parallel dynamic applications, Comput. Sci. Eng. 4 (2002) 90-97. http://dx.doi.org/10.1109/5992.988653. https://gitorious.org/sfc++.

Validation for the Tropical Rainfall Measuring Mission: Lessons Learned and Future Plans

NASA Technical Reports Server (NTRS)

Wolff, David B.; Amitai, E.; Marks, D. A.; Silberstein, D.; Lawrence, R. J.

2005-01-01

The Tropical Rainfall Measuring Mission (TRMM) was launched in November 1997 and is a highly regarded and successful mission. A major component of the TRMM program was its Ground Validation (GV) program. Through dedicated research and hard work by many groups, both the GV and satellite-retrieved rain estimates have shown a convergence at key GV sites, lending credibility to the global TRMM estimates. To be sure, there are some regional differences between the various satellite estimates themselves, which still need to be addressed; however, it can be said with some certainty that TRMM has provided a high-quality, long-term climatological data set for researchers that provides errors on the order of 10-20%, rather than pre-TRMM era error estimates on the order of 50-100%. The TRMM GV program's main operational task is to provide rainfall products for four sites: Darwin, Australia (DARW); Houston, Texas (HSTN); Kwajalein, Republic of the Marshall Islands (KWAJ); and, Melbourne, Florida (MELB). A comparison between TRMM Ground Validation (Version 5) and Satellite (Version 6) rain intensity estimates is presented. The gridded satellite product (3668) will be compared to GV Level II rain-intensity and -type maps (2A53 and 2A54, respectively). The 3G68 product represents a 0.5 deg x 0.5 deg data grid providing estimates of rain intensities from the TRMM Precipitation Radar (PR), Microwave Imager (TMI) and Combined (COM) algorithms. The comparisons will be sub-setted according to geographical type (land, coast and ocean). The convergence of the GV and satellite estimates bodes well for expectations for the proposed Global Precipitation Measurement (GPM) program and this study and others are being leveraged towards planning GV goals for GPM. A discussion of lessons learned and future plans for TRMM GV in planning for GPM will also be provided.

Support grid for fuel elements in a nuclear reactor

DOEpatents

Finch, Lester M.

1977-01-01

A support grid is provided for holding nuclear fuel rods in a rectangular array. Intersecting sheet metal strips are interconnected using opposing slots in the strips to form a rectangular cellular grid structure for engaging the sides of a multiplicity of fuel rods. Spring and dimple supports for engaging fuel and guide rods extending through each cell in the support grid are formed in the metal strips with the springs thus formed being characterized by nonlinear spring rates.

Micro-grid platform based on NODE.JS architecture, implemented in electrical network instrumentation

NASA Astrophysics Data System (ADS)

Duque, M.; Cando, E.; Aguinaga, A.; Llulluna, F.; Jara, N.; Moreno, T.

2016-05-01

In this document, I propose a theory about the impact of systems based on microgrids in non-industrialized countries that have the goal to improve energy exploitation through alternatives methods of a clean and renewable energy generation and the creation of the app to manage the behavior of the micro-grids based on the NodeJS, Django and IOJS technologies. The micro-grids allow the optimal way to manage energy flow by electric injection directly in electric network small urban's cells in a low cost and available way. In difference from conventional systems, micro-grids can communicate between them to carry energy to places that have higher demand in accurate moments. This system does not require energy storage, so, costs are lower than conventional systems like fuel cells, solar panels or else; even though micro-grids are independent systems, they are not isolated. The impact that this analysis will generate, is the improvement of the electrical network without having greater control than an intelligent network (SMART-GRID); this leads to move to a 20% increase in energy use in a specified network; that suggest there are others sources of energy generation; but for today's needs, we need to standardize methods and remain in place to support all future technologies and the best option are the Smart Grids and Micro-Grids.

Analyzing the differentially expressed genes and pathway cross-talk in aggressive breast cancer.

PubMed

Chen, Wen-Yan; Wu, Fang; You, Zhen-Yu; Zhang, Zhan-Min; Guo, Yu-Ling; Zhong, Lu-Xing

2015-01-01

The aim of this study was to explore the genes and pathways involved in the aggressive breast cancer cells. The gene expression profiles of GSE40057, including four aggressive breast cell lines and six less aggressive cell lines, were downloaded from the Gene Expression Omnibus (GEO) database. The gene differential expression analysis was carried out with limma software with the method of Bayes for multiple tests. The gene ontology (GO) term enrichment and pathway cross-talk analysis were performed with the online tool of DAVID and Cytoscape software. A total of 401 differentially expressed genes (DEG), such as pentraxin 3 (PTX3), snail family zinc finger 2 (SNAI2), interleukin-8/6 (IL-8/6), osteonectin (SPARC), matrix metallopeptidase-1 (MMP-1) and Ras-related protein Rab-25 (Rab 25), were identified between aggressive and less aggressive cell lines. They were mainly enriched in the GO terms of response to wounding, negative regulation of cell proliferation and calcium binding. Pathways in cancer dysfunctionally interacted with glyoxylate and dicarboxylate metabolism (P < 0.0001), basal transcription factors (P < 0.0001), tyrosine metabolism (P < 0.0001), calcium signaling pathway (P = 0.0021), FcγR-mediated phagocytosis (P = 0.0022), metabolism of xenobiotics by cytochrome P450 (P = 0.0097) and phagosome (P = 0.0102). The screened aggressive cancer-associated DEG (PTX3, SNAI2, IL-8/6, SPARC, MMP-1 and Rab25) and significant pathways (calcium signaling pathway, tyrosine metabolism, alanine, aspartate and glutamate metabolism) give us new insights into the mechanism of aggressive breast cancer cells, and these DEG may become promising target genes in the treatment of metastatic breast cancer. © 2014 The Authors. Journal of Obstetrics and Gynaecology Research © 2014 Japan Society of Obstetrics and Gynecology.

Sodium metavanadate exhibits carcinogenic tendencies in vitro in immortalized human bronchial epithelial cells.

PubMed

Passantino, Lisa; Muñoz, Alexandra B; Costa, Max

2013-10-01

Pentavalent vanadium compounds induce intracellular changes in vitro that are consistent with those of other carcinogenic substances. While there is no clear evidence that vanadium compounds cause cancer in humans, vanadium pentoxide causes lung cancer in rodents after long-term inhalation exposures and in turn IARC has categorized it as a group 2B possible human carcinogen. The goal of this study was to investigate the carcinogenicity of NaVO3 in the human immortalized bronchial epithelial cell line, Beas-2B. Cells were treated with 10 μM NaVO3 for 5 weeks, with or without recovery time, followed by gene expression microarray analysis. In a separate experiment, cells were exposed to 1-10 μM NaVO3 for 4 weeks and then grown in soft agar to test for anchorage-independent growth. A dose-dependent increase in the number of colonies was observed. In scratch tests, NaVO3-transformed clones could repair a wound faster than controls. In a gene expression microarray analysis of soft agar clones there were 2010 differentially expressed genes (DEG) (adjusted p-value ≤ 0.05) in NaVO3-transformed clones relative to control clones. DEG from this experiment were compared with the DEG of 5 week NaVO3 exposure with or without recovery, all with adjusted p-values < 0.05, and 469 genes were altered in the same direction for transformed clones, 5 week NaVO3-treated cells, and the recovered cells. The data from this study imply that chronic exposure to NaVO3 causes changes that are consistent with cellular transformation including anchorage-independent growth, enhanced migration ability, and gene expression changes that were likely epigenetically inherited.

Solution-Adaptive Cartesian Cell Approach for Viscous and Inviscid Flows

NASA Technical Reports Server (NTRS)

Coirier, William J.; Powell, Kenneth G.

1996-01-01

A Cartesian cell-based approach for adaptively refined solutions of the Euler and Navier-Stokes equations in two dimensions is presented. Grids about geometrically complicated bodies are generated automatically, by the recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, polygonal cut cells are created using modified polygon-clipping algorithms. The grid is stored in a binary tree data structure that provides a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive mesh refinement. The Euler and Navier-Stokes equations are solved on the resulting grids using a finite volume formulation. The convective terms are upwinded: A linear reconstruction of the primitive variables is performed, providing input states to an approximate Riemann solver for computing the fluxes between neighboring cells. The results of a study comparing the accuracy and positivity of two classes of cell-centered, viscous gradient reconstruction procedures is briefly summarized. Adaptively refined solutions of the Navier-Stokes equations are shown using the more robust of these gradient reconstruction procedures, where the results computed by the Cartesian approach are compared to theory, experiment, and other accepted computational results for a series of low and moderate Reynolds number flows.

A new ghost-node method for linking different models and initial investigations of heterogeneity and nonmatching grids

USGS Publications Warehouse

Dickinson, J.E.; James, S.C.; Mehl, S.; Hill, M.C.; Leake, S.A.; Zyvoloski, G.A.; Faunt, C.C.; Eddebbarh, A.-A.

2007-01-01

A flexible, robust method for linking parent (regional-scale) and child (local-scale) grids of locally refined models that use different numerical methods is developed based on a new, iterative ghost-node method. Tests are presented for two-dimensional and three-dimensional pumped systems that are homogeneous or that have simple heterogeneity. The parent and child grids are simulated using the block-centered finite-difference MODFLOW and control-volume finite-element FEHM models, respectively. The models are solved iteratively through head-dependent (child model) and specified-flow (parent model) boundary conditions. Boundary conditions for models with nonmatching grids or zones of different hydraulic conductivity are derived and tested against heads and flows from analytical or globally-refined models. Results indicate that for homogeneous two- and three-dimensional models with matched grids (integer number of child cells per parent cell), the new method is nearly as accurate as the coupling of two MODFLOW models using the shared-node method and, surprisingly, errors are slightly lower for nonmatching grids (noninteger number of child cells per parent cell). For heterogeneous three-dimensional systems, this paper compares two methods for each of the two sets of boundary conditions: external heads at head-dependent boundary conditions for the child model are calculated using bilinear interpolation or a Darcy-weighted interpolation; specified-flow boundary conditions for the parent model are calculated using model-grid or hydrogeologic-unit hydraulic conductivities. Results suggest that significantly more accurate heads and flows are produced when both Darcy-weighted interpolation and hydrogeologic-unit hydraulic conductivities are used, while the other methods produce larger errors at the boundary between the regional and local models. The tests suggest that, if posed correctly, the ghost-node method performs well. Additional testing is needed for highly heterogeneous systems. ?? 2007 Elsevier Ltd. All rights reserved.

Global gene expression profile of peripheral blood mononuclear cells challenged with Theileria annulata in crossbred and indigenous cattle.

PubMed

Kumar, Amod; Gaur, Gyanendra Kumar; Gandham, Ravi Kumar; Panigrahi, Manjit; Ghosh, Shrikant; Saravanan, B C; Bhushan, Bharat; Tiwari, Ashok Kumar; Sulabh, Sourabh; Priya, Bhuvana; V N, Muhasin Asaf; Gupta, Jay Prakash; Wani, Sajad Ahmad; Sahu, Amit Ranjan; Sahoo, Aditya Prasad

2017-01-01

Bovine tropical theileriosis is an important haemoprotozoan disease associated with high rates of morbidity and mortality particularly in exotic and crossbred cattle. It is one of the major constraints of the livestock development programmes in India and Southeast Asia. Indigenous cattle (Bos indicus) are reported to be comparatively less affected than exotic and crossbred cattle. However, genetic basis of resistance to tropical theileriosis in indigenous cattle is not well documented. Recent studies incited an idea that differentially expressed genes in exotic and indigenous cattle play significant role in breed specific resistance to tropical theileriosis. The present study was designed to determine the global gene expression profile in peripheral blood mononuclear cells derived from indigenous (Tharparkar) and cross-bred cattle following in vitro infection of T. annulata (Parbhani strain). Two separate microarray experiments were carried out each for cross-bred and Tharparkar cattle. The cross-bred cattle showed 1082 differentially expressed genes (DEGs). Out of total DEGs, 597 genes were down-regulated and 485 were up-regulated. Their fold change varied from 2283.93 to -4816.02. Tharparkar cattle showed 875 differentially expressed genes including 451 down-regulated and 424 up-regulated. The fold change varied from 94.93 to -19.20. A subset of genes was validated by qRT-PCR and results were correlated well with microarray data indicating that microarray results provided an accurate report of transcript level. Functional annotation study of DEGs confirmed their involvement in various pathways including response to oxidative stress, immune system regulation, cell proliferation, cytoskeletal changes, kinases activity and apoptosis. Gene network analysis of these DEGs plays an important role to understand the interaction among genes. It is therefore, hypothesized that the different susceptibility to tropical theileriosis exhibited by indigenous and crossbred cattle is due to breed-specific differences in the dealing of infected cells with other immune cells, which ultimately influence the immune response responded against T. annulata infection. Copyright © 2016 Elsevier B.V. All rights reserved.

EAULIQ: The Next Generation

NASA Technical Reports Server (NTRS)

Randall, David A.; Fowler, Laura D.

1999-01-01

This report summarizes the design of a new version of the stratiform cloud parameterization called Eauliq; the new version is called Eauliq NG. The key features of Eauliq NG are: (1) a prognostic fractional area covered by stratiform cloudiness, following the approach developed by M. Tiedtke for use in the ECMWF model; (2) separate prognostic thermodynamic variables for the clear and cloudy portions of each grid cell; (3) separate vertical velocities for the clear and cloudy portions of each grid cell, allowing the model to represent some aspects of observed mesoscale circulations; (4) cumulus entrainment from both the clear and cloudy portions of a grid cell, and cumulus detrainment into the cloudy portion only; and (5) the effects of the cumulus-induced subsidence in the cloudy portion of a grid cell on the cloud water and ice there. In this paper we present the mathematical framework of Eauliq NG; a discussion of cumulus effects; a new parameterization of lateral mass exchanges between clear and cloudy regions; and a theory to determine the mesoscale mass circulation, based on the hypothesis that the stratiform clouds remain neutrally buoyant through time and that the mesoscale circulations are the mechanism which makes this possible. An appendix also discusses some time-differencing methods.

Selective Capture of Histidine-tagged Proteins from Cell Lysates Using TEM grids Modified with NTA-Graphene Oxide

NASA Astrophysics Data System (ADS)

Benjamin, Christopher J.; Wright, Kyle J.; Bolton, Scott C.; Hyun, Seok-Hee; Krynski, Kyle; Grover, Mahima; Yu, Guimei; Guo, Fei; Kinzer-Ursem, Tamara L.; Jiang, Wen; Thompson, David H.

2016-10-01

We report the fabrication of transmission electron microscopy (TEM) grids bearing graphene oxide (GO) sheets that have been modified with Nα, Nα-dicarboxymethyllysine (NTA) and deactivating agents to block non-selective binding between GO-NTA sheets and non-target proteins. The resulting GO-NTA-coated grids with these improved antifouling properties were then used to isolate His6-T7 bacteriophage and His6-GroEL directly from cell lysates. To demonstrate the utility and simplified workflow enabled by these grids, we performed cryo-electron microscopy (cryo-EM) of His6-GroEL obtained from clarified E. coli lysates. Single particle analysis produced a 3D map with a gold standard resolution of 8.1 Å. We infer from these findings that TEM grids modified with GO-NTA are a useful tool that reduces background and improves both the speed and simplicity of biological sample preparation for high-resolution structure elucidation by cryo-EM.

Selective Capture of Histidine-tagged Proteins from Cell Lysates Using TEM grids Modified with NTA-Graphene Oxide.

PubMed

Benjamin, Christopher J; Wright, Kyle J; Bolton, Scott C; Hyun, Seok-Hee; Krynski, Kyle; Grover, Mahima; Yu, Guimei; Guo, Fei; Kinzer-Ursem, Tamara L; Jiang, Wen; Thompson, David H

2016-10-17

We report the fabrication of transmission electron microscopy (TEM) grids bearing graphene oxide (GO) sheets that have been modified with N α , N α -dicarboxymethyllysine (NTA) and deactivating agents to block non-selective binding between GO-NTA sheets and non-target proteins. The resulting GO-NTA-coated grids with these improved antifouling properties were then used to isolate His 6 -T7 bacteriophage and His 6 -GroEL directly from cell lysates. To demonstrate the utility and simplified workflow enabled by these grids, we performed cryo-electron microscopy (cryo-EM) of His 6 -GroEL obtained from clarified E. coli lysates. Single particle analysis produced a 3D map with a gold standard resolution of 8.1 Å. We infer from these findings that TEM grids modified with GO-NTA are a useful tool that reduces background and improves both the speed and simplicity of biological sample preparation for high-resolution structure elucidation by cryo-EM.

The Mexican Drought Atlas: Tree-Ring Reconstructions of the Soil Moisture Balance During the Late Pre-Hispanic, Colonial, and Modern Eras

NASA Technical Reports Server (NTRS)

Stahle, David W.; Cook, Edward R.; Burnette, Dorian J.; Villanueva, Jose; Cerano, Julian; Burns, Jordan N.; Griffin, Daniel; Cook, Benjamin I.; Acuna, Rodolfo; Torbenson, Max C. A.;

Optimized design and control of an off grid solar PV/hydrogen fuel cell power system for green buildings

NASA Astrophysics Data System (ADS)

Ghenai, C.; Bettayeb, M.

2017-11-01

Modelling, simulation, optimization and control strategies are used in this study to design a stand-alone solar PV/Fuel Cell/Battery/Generator hybrid power system to serve the electrical load of a commercial building. The main objective is to design an off grid energy system to meet the desired electric load of the commercial building with high renewable fraction, low emissions and low cost of energy. The goal is to manage the energy consumption of the building, reduce the associate cost and to switch from grid-tied fossil fuel power system to an off grid renewable and cleaner power system. Energy audit was performed in this study to determine the energy consumption of the building. Hourly simulations, modelling and optimization were performed to determine the performance and cost of the hybrid power configurations using different control strategies. The results show that the hybrid off grid solar PV/Fuel Cell/Generator/Battery/Inverter power system offers the best performance for the tested system architectures. From the total energy generated from the off grid hybrid power system, 73% is produced from the solar PV, 24% from the fuel cell and 3% from the backup Diesel generator. The produced power is used to meet all the AC load of the building without power shortage (<0.1%). The hybrid power system produces 18.2% excess power that can be used to serve the thermal load of the building. The proposed hybrid power system is sustainable, economically viable and environmentally friendly: High renewable fraction (66.1%), low levelized cost of energy (92 /MWh), and low carbon dioxide emissions (24 kg CO2/MWh) are achieved.

Multi-Material Front Contact for 19% Thin Film Solar Cells.

PubMed

van Deelen, Joop; Tezsevin, Yasemin; Barink, Marco

2016-02-06

The trade-off between transmittance and conductivity of the front contact material poses a bottleneck for thin film solar panels. Normally, the front contact material is a metal oxide and the optimal cell configuration and panel efficiency were determined for various band gap materials, representing Cu(In,Ga)Se₂ (CIGS), CdTe and high band gap perovskites. Supplementing the metal oxide with a metallic copper grid improves the performance of the front contact and aims to increase the efficiency. Various front contact designs with and without a metallic finger grid were calculated with a variation of the transparent conductive oxide (TCO) sheet resistance, scribing area, cell length, and finger dimensions. In addition, the contact resistance and illumination power were also assessed and the optimal thin film solar panel design was determined. Adding a metallic finger grid on a TCO gives a higher solar cell efficiency and this also enables longer cell lengths. However, contact resistance between the metal and the TCO material can reduce the efficiency benefit somewhat.

FAS multigrid calculations of three dimensional flow using non-staggered grids

NASA Technical Reports Server (NTRS)

Matovic, D.; Pollard, A.; Becker, H. A.; Grandmaison, E. W.

1993-01-01

Grid staggering is a well known remedy for the problem of velocity/pressure coupling in incompressible flow calculations. Numerous inconveniences occur, however, when staggered grids are implemented, particularly when a general-purpose code, capable of handling irregular three-dimensional domains, is sought. In several non-staggered grid numerical procedures proposed in the literature, the velocity/pressure coupling is achieved by either pressure or velocity (momentum) averaging. This approach is not convenient for simultaneous (block) solvers that are preferred when using multigrid methods. A new method is introduced in this paper that is based upon non-staggered grid formulation with a set of virtual cell face velocities used for pressure/velocity coupling. Instead of pressure or velocity averaging, a momentum balance at the cell face is used as a link between the momentum and mass balance constraints. The numerical stencil is limited to 9 nodes (in 2D) or 27 nodes (in 3D), both during the smoothing and inter-grid transfer, which is a convenient feature when a block point solver is applied. The results for a lid-driven cavity and a cube in a lid-driven cavity are presented and compared to staggered grid calculations using the same multigrid algorithm. The method is shown to be stable and produce a smooth (wiggle-free) pressure field.

Cystathionine metabolic enzymes play a role in the inflammation resolution of human keratinocytes in response to sub-cytotoxic formaldehyde exposure

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

Lee, Eunyoung

Low-level formaldehyde exposure is inevitable in industrialized countries. Although daily-life formaldehyde exposure level is practically impossible to induce cell death, most of mechanistic studies related to formaldehyde toxicity have been performed in cytotoxic concentrations enough to trigger cell death mechanism. Currently, toxicological mechanisms underlying the sub-cytotoxic exposure to formaldehyde are not clearly elucidated in skin cells. In this study, the genome-scale transcriptional analysis in normal human keratinocytes (NHKs) was performed to investigate cutaneous biological pathways associated with daily life formaldehyde exposure. We selected the 175 upregulated differentially expressed genes (DEGs) and 116 downregulated DEGs in NHKs treated with 200 μMmore » formaldehyde. In the Gene Ontology (GO) enrichment analysis of the 175 upregulated DEGs, the endoplasmic reticulum (ER) unfolded protein response (UPR) was identified as the most significant GO biological process in the formaldeyde-treated NHKs. Interestingly, the sub-cytotoxic formaldehyde affected NHKs to upregulate two enzymes important in the cellular transsulfuration pathway, cystathionine γ-lyase (CTH) and cystathionine-β-synthase (CBS). In the temporal expression analysis, the upregulation of the pro-inflammatory DEGs such as MMP1 and PTGS2 was detected earlier than that of CTH, CBS and other ER UPR genes. The metabolites of CTH and CBS, L-cystathionine and L-cysteine, attenuated the formaldehyde-induced upregulation of pro-inflammatory DEGs, MMP1, PTGS2, and CXCL8, suggesting that CTH and CBS play a role in the negative feedback regulation of formaldehyde-induced pro-inflammatory responses in NHKs. In this regard, the sub-cytotoxic formaldehyde-induced CBS and CTH may regulate inflammation fate decision to resolution by suppressing the early pro-inflammatory response. - Highlights: • Sub-cytotoxic formaldehyde upregulates ER UPR-associated genes in NHKs. • Formaldehyde-induced ER UPR genes includes cystathionine γ-lyase (CTH). • Sub-cytotoxic formaldehyde upregulates cystathionine-β-synthase (CBS) in NHKs. • Cystathionine metabolic enzymes may attenuate formaldehyde-induced inflammation in NHKs. • Cystathionine metabolic enzymes may play a role in the resolution of inflammation in NHKs.« less

Electric Power System for High Altitude UAV Technology Survey

NASA Technical Reports Server (NTRS)

1997-01-01

Electric powertrain technologies with application to high altitude Unmanned Aerial Vehicles (UAV) are assessed. One hundred twenty five solar electric UAV configurations and missions were simulated. Synergistic design opportunities were investigated with the premise that specific benefits may be realized, for example, if a single component can serve multiple functions, such as a battery being used for energy storage as well as for a structural component of the aircraft. For each UAV mission simulation, the airframe structure, powertrain configuration (type of solar cells, energy storage options) and performance baseline (1997 or 2001) were specified. It has been found that the use of the high efficiency (multijunction) solar cells or the use of the synergistic amorphous silicon solar cell configuration yields aircraft that can accomplish the majority of the missions of interest for any latitude between 0 deg and 55 deg, hence, a single versatile aircraft can be constructed and implemented to accomplish these missions.

Ultra-low-mass flexible planar solar arrays using 50-micron-thick solar cells

NASA Technical Reports Server (NTRS)

Costogue, E. N.; Rayl, G.

1978-01-01

A conceptual design study has been completed which has shown the feasibility of ultra-low-mass planar solar arrays with specific power of 200 watts/kilogram. The beginning of life (BOL) power output of the array designs would be 10 kW at 1 astronomical unit (AU) and a 55C deg operating temperature. Two designs were studied: a retractable rollout design and a non-retractable fold-out. The designs employed a flexible low-mass blanket and low-mass structures. The blanket utilized 2 x 2 cm high-efficiency (13.5% at 28C deg AM0), ultra-thin (50 micron), silicon solar cells protected by thin (75 micron) plastic encapsulants. The structural design utilized the 'V'-stiffened approach which allows a lower mass boom to be used. In conjunction with the conceptual design, modules using the thin cells and plastic encapsulant were designed and fabricated.

On the use of Schwarz-Christoffel conformal mappings to the grid generation for global ocean models

NASA Astrophysics Data System (ADS)

Xu, S.; Wang, B.; Liu, J.

2015-10-01

In this article we propose two grid generation methods for global ocean general circulation models. Contrary to conventional dipolar or tripolar grids, the proposed methods are based on Schwarz-Christoffel conformal mappings that map areas with user-prescribed, irregular boundaries to those with regular boundaries (i.e., disks, slits, etc.). The first method aims at improving existing dipolar grids. Compared with existing grids, the sample grid achieves a better trade-off between the enlargement of the latitudinal-longitudinal portion and the overall smooth grid cell size transition. The second method addresses more modern and advanced grid design requirements arising from high-resolution and multi-scale ocean modeling. The generated grids could potentially achieve the alignment of grid lines to the large-scale coastlines, enhanced spatial resolution in coastal regions, and easier computational load balance. Since the grids are orthogonal curvilinear, they can be easily utilized by the majority of ocean general circulation models that are based on finite difference and require grid orthogonality. The proposed grid generation algorithms can also be applied to the grid generation for regional ocean modeling where complex land-sea distribution is present.

Development of an Automatic Grid Generator for Multi-Element High-Lift Wings

NASA Technical Reports Server (NTRS)

Eberhardt, Scott; Wibowo, Pratomo; Tu, Eugene

1996-01-01

The procedure to generate the grid around a complex wing configuration is presented in this report. The automatic grid generation utilizes the Modified Advancing Front Method as a predictor and an elliptic scheme as a corrector. The scheme will advance the surface grid one cell outward and the newly obtained grid is corrected using the Laplace equation. The predictor-corrector step ensures that the grid produced will be smooth for every configuration. The predictor-corrector scheme is extended for a complex wing configuration. A new technique is developed to deal with the grid generation in the wing-gaps and on the flaps. It will create the grids that fill the gap on the wing surface and the gap created by the flaps. The scheme recognizes these configurations automatically so that minimal user input is required. By utilizing an appropriate sequence in advancing the grid points on a wing surface, the automatic grid generation for complex wing configurations is achieved.

Triangle Geometry Processing for Surface Modeling and Cartesian Grid Generation

NASA Technical Reports Server (NTRS)

Aftosmis, Michael J. (Inventor); Melton, John E. (Inventor); Berger, Marsha J. (Inventor)

2002-01-01

Cartesian mesh generation is accomplished for component based geometries, by intersecting components subject to mesh generation to extract wetted surfaces with a geometry engine using adaptive precision arithmetic in a system which automatically breaks ties with respect to geometric degeneracies. During volume mesh generation, intersected surface triangulations are received to enable mesh generation with cell division of an initially coarse grid. The hexagonal cells are resolved, preserving the ability to directionally divide cells which are locally well aligned.

Triangle geometry processing for surface modeling and cartesian grid generation

DOEpatents

Aftosmis, Michael J [San Mateo, CA; Melton, John E [Hollister, CA; Berger, Marsha J [New York, NY

2002-09-03

Cartesian mesh generation is accomplished for component based geometries, by intersecting components subject to mesh generation to extract wetted surfaces with a geometry engine using adaptive precision arithmetic in a system which automatically breaks ties with respect to geometric degeneracies. During volume mesh generation, intersected surface triangulations are received to enable mesh generation with cell division of an initially coarse grid. The hexagonal cells are resolved, preserving the ability to directionally divide cells which are locally well aligned.

Wave Information Studies of US Coastlines: Hindcast Wave Information for the Great Lakes: Lake Erie

DTIC Science & Technology

1991-10-01

total ice cover) for individual grid cells measuring 5 km square. 42. The GLERL analyzed each half-month data set to provide the maximum, minimum...average, median, and modal ice concentrations for each 5-km cell . The median value, which represents an estimate of the 50-percent point of the ice...incorporating the progression and decay of the time-dependent ice cover was complicated by the fact that different grid cell sizes were used for mapping the ice

Buried MoO x/Ag Electrode Enables High-Efficiency Organic/Silicon Heterojunction Solar Cells with a High Fill Factor.

PubMed

Xia, Zhouhui; Gao, Peng; Sun, Teng; Wu, Haihua; Tan, Yeshu; Song, Tao; Lee, Shuit-Tong; Sun, Baoquan

2018-04-25

Silicon (Si)/organic heterojunction solar cells based on poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) and n-type Si have attracted wide interests because they promise cost-effectiveness and high-efficiency. However, the limited conductivity of PEDOT:PSS leads to an inefficient hole transport efficiency for the heterojunction device. Therefore, a high dense top-contact metal grid electrode is required to assure the efficient charge collection efficiency. Unfortunately, the large metal grid coverage ratio electrode would lead to undesirable optical loss. Here, we develop a strategy to balance PEDOT:PSS conductivity and grid optical transmittance via a buried molybdenum oxide/silver grid electrode. In addition, the grid electrode coverage ratio is optimized to reduce its light shading effect. The buried electrode dramatically reduces the device series resistance, which leads to a higher fill factor (FF). With the optimized buried electrode, a record FF of 80% is achieved for flat Si/PEDOT:PSS heterojunction devices. With further enhancement adhesion between the PEDOT:PSS film and Si substrate by a chemical cross-linkable silance, a power conversion efficiency of 16.3% for organic/textured Si heterojunction devices is achieved. Our results provide a path to overcome the inferior organic semiconductor property to enhance the organic/Si heterojunction solar cell.

ORPC RivGen Hydrokinetic Turbine Wake Characterization

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

Thomson, Jim; Guerra, Maricarmen

Field measurements of mean flow and turbulence parameters at the Kvichak river prior to and after the deployment of ORPC's RivGen hydrokinetic turbine. Data description and turbine wake analysis are presented in the attached manuscript "Wake measurements from a hydrokinetic river turbine" by Guerra and Thomson (recently submitted to Renewable Energy). There are three data sets: NoTurbine (prior to deployment), Not_Operational_Turbine (turbine underwater, but not operational), and Operational_Turbine. The data has been quality controlled and organized into a three-dimensional grid using a local coordinate system described in the paper. All data sets are in Matlab format (.mat). Variables available inmore » the data sets are: qx: X coordinate matrix (m) qy: Y coordinate matrix (m) z : z coordinate vector (m) lat : grid cell latitude (degrees) lon: grid cell longitude (degrees) U : velocity magnitude (m/s) Ux: x velocity (m/s) Vy: y velocity (m/s) W: vertical velocity (m/s) Pseudo_beam.b_i: pseudo-along beam velocities (i = 1 to 4) (m/s) (structure with raw data within each grid cell) beam5.b5: 5th-beam velocity (m/s) (structure with raw data within each grid cell) tke: turbulent kinetic energy (m2/s2) epsilon: TKE dissipation rate (m2/s3) Reynolds stresses: uu, vv, ww, uw, vw (m2/s2) Variables from the Not Operational Turbine data set are identified with _T Variables from the Operational Turbine data set are identified with _TO« less

A general gridding, discretization, and coarsening methodology for modeling flow in porous formations with discrete geological features

NASA Astrophysics Data System (ADS)

Karimi-Fard, M.; Durlofsky, L. J.

2016-10-01

A comprehensive framework for modeling flow in porous media containing thin, discrete features, which could be high-permeability fractures or low-permeability deformation bands, is presented. The key steps of the methodology are mesh generation, fine-grid discretization, upscaling, and coarse-grid discretization. Our specialized gridding technique combines a set of intersecting triangulated surfaces by constructing approximate intersections using existing edges. This procedure creates a conforming mesh of all surfaces, which defines the internal boundaries for the volumetric mesh. The flow equations are discretized on this conforming fine mesh using an optimized two-point flux finite-volume approximation. The resulting discrete model is represented by a list of control-volumes with associated positions and pore-volumes, and a list of cell-to-cell connections with associated transmissibilities. Coarse models are then constructed by the aggregation of fine-grid cells, and the transmissibilities between adjacent coarse cells are obtained using flow-based upscaling procedures. Through appropriate computation of fracture-matrix transmissibilities, a dual-continuum representation is obtained on the coarse scale in regions with connected fracture networks. The fine and coarse discrete models generated within the framework are compatible with any connectivity-based simulator. The applicability of the methodology is illustrated for several two- and three-dimensional examples. In particular, we consider gas production from naturally fractured low-permeability formations, and transport through complex fracture networks. In all cases, highly accurate solutions are obtained with significant model reduction.

Selective Heterogeneity in Exoprotease Production by Bacillus subtilis

PubMed Central

Davidson, Fordyce A.; Seon-Yi, Chung; Stanley-Wall, Nicola R.

2012-01-01

Bacteria have elaborate signalling mechanisms to ensure a behavioural response that is most likely to enhance survival in a changing environment. It is becoming increasingly apparent that as part of this response, bacteria are capable of cell differentiation and can generate multiple, mutually exclusive co-existing cell states. These cell states are often associated with multicellular processes that bring benefit to the community as a whole but which may be, paradoxically, disadvantageous to an individual subpopulation. How this process of cell differentiation is controlled is intriguing and remains a largely open question. In this paper, we consider an important aspect of cell differentiation that is known to occur in the Gram-positive bacterium Bacillus subtilis: we investigate the role of two master regulators DegU and Spo0A in the control of extra-cellular protease production. Recent work in this area focussed the on role of DegU in this process and suggested that transient effects in protein production were the drivers of cell-response heterogeneity. Here, using a combination of mathematical modelling, analysis and stochastic simulations, we provide a complementary analysis of this regulatory system that investigates the roles of both DegU and Spo0A in extra-cellular protease production. In doing so, we present a mechanism for bimodality, or system heterogeneity, without the need for a bistable switch in the underlying regulatory network. Moreover, our analysis leads us to conclude that this heterogeneity is in fact a persistent, stable feature. Our results suggest that system response is divided into three zones: low and high signal levels induce a unimodal or undifferentiated response from the cell population with all cells OFF and ON, respectively for exoprotease production. However, for intermediate levels of signal, a heterogeneous response is predicted with a spread of activity levels, representing typical “bet-hedging” behaviour. PMID:22745669

Geometrically Flexible and Efficient Flow Analysis of High Speed Vehicles Via Domain Decomposition, Part 1: Unstructured-Grid Solver for High Speed Flows

NASA Technical Reports Server (NTRS)

White, Jeffery A.; Baurle, Robert A.; Passe, Bradley J.; Spiegel, Seth C.; Nishikawa, Hiroaki

2017-01-01

The ability to solve the equations governing the hypersonic turbulent flow of a real gas on unstructured grids using a spatially-elliptic, 2nd-order accurate, cell-centered, finite-volume method has been recently implemented in the VULCAN-CFD code. This paper describes the key numerical methods and techniques that were found to be required to robustly obtain accurate solutions to hypersonic flows on non-hex-dominant unstructured grids. The methods and techniques described include: an augmented stencil, weighted linear least squares, cell-average gradient method, a robust multidimensional cell-average gradient-limiter process that is consistent with the augmented stencil of the cell-average gradient method and a cell-face gradient method that contains a cell skewness sensitive damping term derived using hyperbolic diffusion based concepts. A data-parallel matrix-based symmetric Gauss-Seidel point-implicit scheme, used to solve the governing equations, is described and shown to be more robust and efficient than a matrix-free alternative. In addition, a y+ adaptive turbulent wall boundary condition methodology is presented. This boundary condition methodology is deigned to automatically switch between a solve-to-the-wall and a wall-matching-function boundary condition based on the local y+ of the 1st cell center off the wall. The aforementioned methods and techniques are then applied to a series of hypersonic and supersonic turbulent flat plate unit tests to examine the efficiency, robustness and convergence behavior of the implicit scheme and to determine the ability of the solve-to-the-wall and y+ adaptive turbulent wall boundary conditions to reproduce the turbulent law-of-the-wall. Finally, the thermally perfect, chemically frozen, Mach 7.8 turbulent flow of air through a scramjet flow-path is computed and compared with experimental data to demonstrate the robustness, accuracy and convergence behavior of the unstructured-grid solver for a realistic 3-D geometry on a non-hex-dominant grid.

Three-dimensional zonal grids about arbitrary shapes by Poisson's equation

NASA Technical Reports Server (NTRS)

Sorenson, Reese L.

1988-01-01

A method for generating 3-D finite difference grids about or within arbitrary shapes is presented. The 3-D Poisson equations are solved numerically, with values for the inhomogeneous terms found automatically by the algorithm. Those inhomogeneous terms have the effect near boundaries of reducing cell skewness and imposing arbitrary cell height. The method allows the region of interest to be divided into zones (blocks), allowing the method to be applicable to almost any physical domain. A FORTRAN program called 3DGRAPE has been written to implement the algorithm. Lastly, a method for redistributing grid points along lines normal to boundaries will be described.

Soil Sampling Techniques For Alabama Grain Fields

NASA Technical Reports Server (NTRS)

Thompson, A. N.; Shaw, J. N.; Mask, P. L.; Touchton, J. T.; Rickman, D.

2003-01-01

Characterizing the spatial variability of nutrients facilitates precision soil sampling. Questions exist regarding the best technique for directed soil sampling based on a priori knowledge of soil and crop patterns. The objective of this study was to evaluate zone delineation techniques for Alabama grain fields to determine which method best minimized the soil test variability. Site one (25.8 ha) and site three (20.0 ha) were located in the Tennessee Valley region, and site two (24.2 ha) was located in the Coastal Plain region of Alabama. Tennessee Valley soils ranged from well drained Rhodic and Typic Paleudults to somewhat poorly drained Aquic Paleudults and Fluventic Dystrudepts. Coastal Plain s o i l s ranged from coarse-loamy Rhodic Kandiudults to loamy Arenic Kandiudults. Soils were sampled by grid soil sampling methods (grid sizes of 0.40 ha and 1 ha) consisting of: 1) twenty composited cores collected randomly throughout each grid (grid-cell sampling) and, 2) six composited cores collected randomly from a -3x3 m area at the center of each grid (grid-point sampling). Zones were established from 1) an Order 1 Soil Survey, 2) corn (Zea mays L.) yield maps, and 3) airborne remote sensing images. All soil properties were moderately to strongly spatially dependent as per semivariogram analyses. Differences in grid-point and grid-cell soil test values suggested grid-point sampling does not accurately represent grid values. Zones created by soil survey, yield data, and remote sensing images displayed lower coefficient of variations (8CV) for soil test values than overall field values, suggesting these techniques group soil test variability. However, few differences were observed between the three zone delineation techniques. Results suggest directed sampling using zone delineation techniques outlined in this paper would result in more efficient soil sampling for these Alabama grain fields.

Reactive Power Compensation Using an Energy Management System

DTIC Science & Technology

2014-09-01

bulk power grid or independent of the grid in islanded mode using various DG sources ( photovoltaic panels, fuel cells, gas generators, batteries...developed in order to forecast the system’s response to both capacitive and inductive power demands on the grid. The process was then confirmed in a...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release; distribution is unlimited REACTIVE POWER

The GBT Diffuse Ionized Gas Survey (GDIGS)

NASA Astrophysics Data System (ADS)

Luisi, Matteo; Anderson, Loren Dean; Liu, Bin; Bania, Thomas; Balser, Dana; Wenger, Trey; Haffner, Lawrence Matthew

2018-01-01

Diffuse ionized gas in the Galactic mid-plane known as the "Warm Ionized Medium" (WIM) makes up ~20% of the gas mass of the Milky Way and >90% of its ionized gas. It is the last major component of the interstellar medium (ISM) that has not yet been studied at high spatial and spectral resolution, and therefore many of its fundamental properties remain unclear. The Green Bank Telescope (GBT) Diffuse Ionized Gas Survey (GDIGS) is a new large survey of the Milky Way disk at C-band (4-8 GHz). The main goals of GDIGS are to investigate the properties of the WIM and to determine the connection between the WIM and high-mass star formation over the Galactic longitude and latitude range of 32 deg > l > -5 deg, |b| < 0.5 deg. We use the new VEGAS spectrometer to simultaneously observe 22 Hn-alpha radio recombination lines, 25 Hn-beta lines, 8 Hn-gamma lines, and 9 molecular lines (namely CH3OH and H2CO), and also continuum at ~60 frequencies. We average the Hn-alpha lines to produce Nyquist-sampled maps on a spatial grid of 1 arcmin, a velocity resolution of 0.5 km/s and rms sensitivities of ~3 mJy per beam. GDIGS observations are currently underway and are expected to be completed by late 2018. These data will allow us to: 1) Study for the first time the inner-Galaxy WIM unaffected by confusion from discrete HII regions, 2) determine the distribution of the inner Galaxy WIM, 3) investigate the ionization state of the WIM, 4) explore the connection between the WIM and HII regions, and 5) analyze the effect of leaked photons from HII regions on ISM dust temperatures.

Analysis of atmospheric ozone measurements made from a B-747 airliner during March 1975

NASA Technical Reports Server (NTRS)

Holdeman, J. D.; Falconer, P. D.

1976-01-01

Measurements of atmospheric ozone in the upper troposphere and lower stratosphere made during March 1975 as part of the NASA Global Atmospheric Sampling Program are reported and analyzed. The interrelationships between the ozone mixing ratio and geographical and meteorological parameters are examined in several case studies. The ozone data correlate well with the difference between the flight altitude and the height of the tropopause, as obtained from National Meteorological Center gridded data. The distribution of ozone mixing ratios with latitude at an altitude of 11 + or - 0.5 km shows a poleward increase and large variability at latitudes greater than 30 deg N in agreement with published mean ozone levels from the North American ozone sonde network.

Gene expression patterns combined with network analysis identify hub genes associated with bladder cancer.

PubMed

Bi, Dongbin; Ning, Hao; Liu, Shuai; Que, Xinxiang; Ding, Kejia

2015-06-01

To explore molecular mechanisms of bladder cancer (BC), network strategy was used to find biomarkers for early detection and diagnosis. The differentially expressed genes (DEGs) between bladder carcinoma patients and normal subjects were screened using empirical Bayes method of the linear models for microarray data package. Co-expression networks were constructed by differentially co-expressed genes and links. Regulatory impact factors (RIF) metric was used to identify critical transcription factors (TFs). The protein-protein interaction (PPI) networks were constructed by the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and clusters were obtained through molecular complex detection (MCODE) algorithm. Centralities analyses for complex networks were performed based on degree, stress and betweenness. Enrichment analyses were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Co-expression networks and TFs (based on expression data of global DEGs and DEGs in different stages and grades) were identified. Hub genes of complex networks, such as UBE2C, ACTA2, FABP4, CKS2, FN1 and TOP2A, were also obtained according to analysis of degree. In gene enrichment analyses of global DEGs, cell adhesion, proteinaceous extracellular matrix and extracellular matrix structural constituent were top three GO terms. ECM-receptor interaction, focal adhesion, and cell cycle were significant pathways. Our results provide some potential underlying biomarkers of BC. However, further validation is required and deep studies are needed to elucidate the pathogenesis of BC. Copyright © 2015 Elsevier Ltd. All rights reserved.

Assessment of rockfall susceptibility by integrating statistical and physically-based approaches

NASA Astrophysics Data System (ADS)

Frattini, Paolo; Crosta, Giovanni; Carrara, Alberto; Agliardi, Federico

In Val di Fassa (Dolomites, Eastern Italian Alps) rockfalls constitute the most significant gravity-induced natural disaster that threatens both the inhabitants of the valley, who are few, and the thousands of tourists who populate the area in summer and winter. To assess rockfall susceptibility, we developed an integrated statistical and physically-based approach that aimed to predict both the susceptibility to onset and the probability that rockfalls will attain specific reaches. Through field checks and multi-temporal aerial photo-interpretation, we prepared a detailed inventory of both rockfall source areas and associated scree-slope deposits. Using an innovative technique based on GIS tools and a 3D rockfall simulation code, grid cells pertaining to the rockfall source-area polygons were classified as active or inactive, based on the state of activity of the associated scree-slope deposits. The simulation code allows one to link each source grid cell with scree deposit polygons by calculating the trajectory of each simulated launch of blocks. By means of discriminant analysis, we then identified the mix of environmental variables that best identifies grid cells with low or high susceptibility to rockfalls. Among these variables, structural setting, land use, and morphology were the most important factors that led to the initiation of rockfalls. We developed 3D simulation models of the runout distance, intensity and frequency of rockfalls, whose source grid cells corresponded either to the geomorphologically-defined source polygons ( geomorphological scenario) or to study area grid cells with slope angle greater than an empirically-defined value of 37° ( empirical scenario). For each scenario, we assigned to the source grid cells an either fixed or variable onset susceptibility; the latter was derived from the discriminant model group (active/inactive) membership probabilities. Comparison of these four models indicates that the geomorphological scenario with variable onset susceptibility appears to be the most realistic model. Nevertheless, political and legal issues seem to guide local administrators, who tend to select the more conservative empirically-based scenario as a land-planning tool.

Filling in the GAPS: evaluating completeness and coverage of open-access biodiversity databases in the United States

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

Troia, Matthew J.; McManamay, Ryan A.

Primary biodiversity data constitute observations of particular species at given points in time and space. Open-access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open-access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records frommore » the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). In this study, we aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well-surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov–Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well-surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well-surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional sampling biases. Lastly, this comprehensive assessment of biodiversity data across the contiguous United States provides a prioritization scheme to fill in the gaps by contributing existing occurrence records to the public domain and planning future surveys.« less