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At least 253 records · Page 14

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

Abstract Background Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. Results Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. Conclusion We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.

Krinos, Arianna I. (ORCID:0000000197678392)↗

Neutral sheet crossings by ISEE-3 in the distant magnetotail

Magnetic field data from ISEE-3 in the distant magnetotail at crossings of the field reversal (or neutral sheet) region were analyzed to determine the instantaneous direction of the normal component Bz at the crossing. A crossing identified as being almost always tailward of the steady-state X-line was selected. Data for 1 hr are discussed to illustrate difficulties. One particular smooth crossing shows that complicated microstructure can occur in times less than 1 min. Averaging over long times may eliminate essential information. Inspection of the magnetic field data at the highest resolution, however, shows that the direction of the plasma sheet flows and the sense of Bz across the neutral sheet do not always agree with the reconnection models. Rather, they indicate that the low latitude boundary layer may play a significant role in the dynamics of the magnetotail.

Heikkila, W. J.↗

A graphically oriented specification language for automatic code generation. GRASP/Ada: A Graphical Representation of Algorithms, Structure, and Processes for Ada, phase 1

The first phase of a three-phase effort to develop a new graphically oriented specification language which will facilitate the reverse engineering of Ada source code into graphical representations (GRs) as well as the automatic generation of Ada source code is described. A simplified view of the three phases of Graphical Representations for Algorithms, Structure, and Processes for Ada (GRASP/Ada) with respect to three basic classes of GRs is presented. Phase 1 concentrated on the derivation of an algorithmic diagram, the control structure diagram (CSD) (CRO88a) from Ada source code or Ada PDL. Phase 2 includes the generation of architectural and system level diagrams such as structure charts and data flow diagrams and should result in a requirements specification for a graphically oriented language able to support automatic code generation. Phase 3 will concentrate on the development of a prototype to demonstrate the feasibility of this new specification language.

Cross, James H., II↗

Implicit time-marching solution of the Navier-Stokes equations for thrust reversing and thrust vectoring nozzle flows

An implicit finite volume method is investigated for the solution of the compressible Navier-Stokes equations for flows within thrust reversing and thrust vectoring nozzles. Thrust reversing nozzles typically have sharp corners, and the rapid expansion and large turning angles near these corners are shown to cause unacceptable time step restrictions when conventional approximate factorization methods are used. In this investigation these limitations are overcome by using second-order upwind differencing and line Gauss-Siedel relaxation. This method is implemented with a zonal mesh so that flows through complex nozzle geometries may be efficiently calculated. Results are presented for five nozzle configurations including two with time varying geometries. Three cases are compared with available experimental data and the results are generally acceptable.

Imlay, S. T.↗

An assessment of ground effects determined by static and dynamic testing techniques

A new testing technique was developed wherein the rate of descent can be included as a parameter in ground effects investigations. This technique simulates the rate of descent by horizontal motion of a model over an inclined ground board in the Langley Vortex Research Facility (VRF) During initial evaluations of the technique, dynamic ground effects data were obtained over the inclined ground board, steady state ground effects data were obtained over a flat portion of the ground board, and the results were compared to conventional static wind tunnel ground effect data both with and without a moving belt ground plane simulation. Initial testing and analysis led to the following conclusions: the moving belt ground plane had little effect on static ground effects for the configurations tested unless thrust reversers were employed; in general, rate-of-descent reduced ground effects to the point that for reversed thrust cases an expected loss of lift due to ground effects was eliminated at approach conditions; and, in general, the steady state results from the VRF matched static results obtained from the wind tunnel once the flow field stabilized over the flat portion of the ground board.

Paulson, John W., Jr.↗

An Active Broad Area Cooling Model of a Cryogenic Propellant Tank with a Single Stage Reverse Turbo-Brayton Cycle Cryocooler

As focus shifts towards long-duration space exploration missions, an increased interest in active thermal control of cryogenic propellants to achieve zero boil-off of cryogens has emerged. An active thermal control concept of considerable merit is the integration of a broad area cooling system for a cryogenic propellant tank with a combined cryocooler and circulator system that can be used to reduce or even eliminate liquid cryogen boil-off. One prospective cryocooler and circulator combination is the reverse turbo-Brayton cycle cryocooler. This system is unique in that it has the ability to both cool and circulate the coolant gas efficiently in the same loop as the broad area cooling lines, allowing for a single cooling gas loop, with the primary heat rejection occurring by way of a radiator and/or aftercooler. Currently few modeling tools exist that can size and characterize an integrated reverse turbo-Brayton cycle cryocooler in combination with a broad area cooling design. This paper addresses efforts to create such a tool to assist in gaining a broader understanding of these systems, and investigate their performance in potential space missions. The model uses conventional engineering and thermodynamic relationships to predict the preliminary design parameters, including input power requirements, pressure drops, flow rate, cycle performance, cooling lift, broad area cooler line sizing, and component operating temperatures and pressures given the cooling load operating temperature, heat rejection temperature, compressor inlet pressure, compressor rotational speed, and cryogenic tank geometry. In addition, the model allows for the preliminary design analysis of the broad area cooling tubing, to determine the effect of tube sizing on the reverse turbo-Brayton cycle system performance. At the time this paper was written, the model was verified to match existing theoretical documentation within a reasonable margin. While further experimental data is needed for full validation, this tool has already made significant steps towards giving a clearer understanding of the performance of a reverse turbo-Brayton cycle cryocooler integrated with broad area cooling technology for zero boil-off active thermal control.

Guzik, Monica C.↗

Evaluating the impact of anatomical and physiological variability on human equivalent doses using PBPK models

Abstract Addressing human anatomical and physiological variability is a crucial component of human health risk assessment of chemicals. Experts have recommended probabilistic chemical risk assessment paradigms in which distributional adjustment factors are used to account for various sources of uncertainty and variability, including variability in the pharmacokinetic behavior of a given substance in different humans. In practice, convenient assumptions about the distribution forms of adjustment factors and human equivalent doses (HEDs) are often used. Parameters such as tissue volumes and blood flows are likewise often assumed to be lognormally or normally distributed without evaluating empirical data for consistency with these forms. In this work, we performed dosimetric extrapolations using physiologically based pharmacokinetic (PBPK) models for dichloromethane (DCM) and chloroform that incorporate uncertainty and variability to determine if the HEDs associated with such extrapolations are approximately lognormal and how they depend on the underlying distribution shapes chosen to represent model parameters. We accounted for uncertainty and variability in PBPK model parameters by randomly drawing their values from a variety of distribution types. We then performed reverse dosimetry to calculate HEDs based on animal points of departure for each set of sampled parameters. Corresponding samples of HEDs were tested to determine the impact of input parameter distributions on their central tendencies, extreme percentiles, and degree of conformance to lognormality. This work demonstrates that the measurable attributes of human variability should be considered more carefully and that generalized assumptions about parameter distribution shapes may lead to inaccurate estimates of extreme percentiles of HEDs.

Toxicology↗

Flow-Field Measurements in a Wing-Fuselage Junction Using an Embedded Particle Image Velocimetry System

A novel, embedded, 2D Particle Image Velocimetry system has been developed and implemented to obtain off-body velocity measurements in the junction of an 8% wing-body configuration in the NASA Langley Research Center 14- by 22-Foot Subsonic Tunnel. Although the initial purpose for implementing the system during this test was to evaluate system performance and identify potential risks, the system worked remarkably well and a considerable amount of data were obtained in the wing-fuselage junction near the trailing edge at a Reynolds Number of 2.4 Million and angle of attack of 5 degrees. In addition to providing notable efficiencies with regard to image acquisition and test operations, the PIV system proved to be quite capable of capturing unique details of the flow separation to complement the extensive suite of measurement techniques applied during the test. Instantaneous PIV vector fields reveal that the flow separation is not stationary but rather highly dynamic. Mean flow statistics calculated from the PIV measurements highlight where reverse flow and Reynolds stresses are concentrated in the separated region and agree well with results from the embedded Laser Doppler Velocimeter system and Computational Fluid Dynamics. The comparisons and additional insight gained during this effort will help guide system improvements for follow-on tests.

Jenkins, Luther N.↗

Partition Thickness Considerations for Additively Manufactured Acoustic Liners

Three types of uniform-depth liners are evaluated to explore the effects of partition thickness on the surface impedance achieved with additively manufactured liners. A transmission line code is used to predict the effects of sound transmission through empty chambers and wire mesh facesheets, and is combined with the Motsinger and Kraft model to account for sound transmission through perforated facesheets. The inclusion of partitions causes a blockage effect, i.e., a portion of the surface is ‘blocked’ (nonactive surface). For liners with no facesheet, these blockage effects are incorporated simply by accounting for the change in cross sectional area between the individual chamber and the unit cell that includes half of a partition thickness around the perimeter of this chamber. Comparison of impedances predicted in this manner with data acquired in the NASA Langley Normal Incidence Tube (NIT) confirms the efficacy of this modeling approach. Two approaches are considered to account for the inclusion of a wiremesh or perforated plate facesheet on these same cores. The first accounts for the effects of partition thickness before including the transfer impedance across the facesheet, while the second reverses these steps. A comparison of data acquired in the NASA NIT with modeled impedances suggests the first approach is best when the facesheet is a wire mesh, but the second approach is preferred when a perforated plate facesheet is used. It is hypothesized that this is due to the fact that a lumped element model is used to compute the transfer impedance across a wire mesh, while the corresponding transfer impedance across a perforated sheet explicitly incorporates the efffects of the liner core. However, comparisons of data acquired in the NASA Langley Grazing Flow Impedance Tube with modeled impedances seem slightly better when the first approach is employed with a perforated plate facesheet. Thus, the effects of partition thickness on liners with perforated sheets subjected to grazing incidence sound require further review

acoustic↗

Evaluation of scramjet nozzle configurations and film cooling for reduction of wall heating

Experiments on relaminarization, or reverse transition of turbulent flow, have been conducted with a scramjet combustor and nozzle model. The Mach-2.7 direct-connect scramjet combustor employed swept-ramp fuel injectors, and the entering flow simulated Mach-6 to Mach-7 flight conditions. Tests were also conducted without combustor fuel to produce a higher nozzle entrance Mach number and lower pressures. Additional tests were conducted to evaluate the effectiveness of film cooling on the cowl region. At each test condition studied, the entrance radius had no significant effect on the measured downstream wall heating rates. Analysis of the data when fuel was injected into the combustor shows good agreement with turbulent theory; for the tests without fuel injection and combustion, the data downstream of the nozzle entrance radius are intermediate to the calculated turbulent and laminar solutions. Results of film-cooling tests, conducted with both hydrogen and nitrogen injectants, showed that, per unit mass, the hydrogen was approximately three to four times more effective than nitrogen in reducing the downstream wall heating rates.

Baker, N. R.↗

Magnetic Damping of g-Jitter Induced Double-Diffusive Convection

This paper describes a numerical study of the g-jitter driven double diffusive convective flows, thermal and concentration distributions in binary alloy melt systems subject to an external magnetic field. The study is based on the finite element solution of transient magnetohydrodynamic equations governing the momentum, thermal and solutal transport in the melt pool. Numerical simulations are conducted using the synthesized single- and multi- frequency g-jitter as well as the real g-jitter data taken during space flights with or without an applied magnetic field. It is found that for the conditions studied, the main melt flow follows approximately a lineal- superposition of velocity components induced by individual g-jitter components, regardless of whether a magnetic field exists or not. The flow field is characterized by a recirculating double diffusive convection loop oscillating in time with a defined frequency equal to that of the driving g-jitter force. An applied magnetic field has little effect on the oscillating recirculating pattern, except around the moment in time when the flow reverses its direction. The field has no effect on the oscillation period, but it changes the phase angle. It is very effective in suppressing the flow intensity and produces a notable reduction of the solutal striation and time fluctuations in the melt. For a given magnetic field strength, the magnetic damping effect is more pronounced on the velocity associated with the largest g-jitter component present and/or the g-jitter spiking peaks. A stronger magnetic field is more effective in suppressing the melt convection and also is more helpful in bringing the convection in phase with the g-jitter driving force. The applied field is particularly useful in suppressing the effect of real g-jitter spikes on both flow and solutal distributions. With appropriately selected magnetic fields, the convective flows caused by g-jitter can be reduced sufficiently and diffusion dominant. solutal transport in the melt is possible.

Shu, Y.↗

Paleomagnetism and Tectonic Interpretations of the Taos Plateau Volcanic Field, Rio Grande Rift, New Mexico

The tectonic response of the Taos Plateau volcanic field in the southern San Luis basin to the late stage extensional environment of the Rio Grande rift was investigated using paleomagnetic techniques. Sixty-two sites (533 samples) of Pliocene volcanic units were collected covering four major rock types with ages of 4.7 to 1.8 Ma. Twenty-two of these sites were from stratigraphic sections of the lower, middle and upper Servilleta Basalt collected in the Rio Grande gorge at two locations 19 km apart. Flows from the lower and middle members in the southern gorge record reversed polarities, while those in Garapata Canyon are normal with an excursion event in the middle of the sequence. The uppermost flows of the upper member at both sites display normal directions. Although these sections correlate chemically, they seem to represent different magnetic time periods during the Gilbert Reversed-Polarity Chiron. Alternating field demagnetization, aided by principal component analysis, yields 55 sites with stable directions representing both normal and reversed polarities, and five sites indicating transitional fields. Mean direction of the normal and inverted reversed sites is I=49.3 deg. and D=356.7 deg. (alpha(sub 95)=3.6 deg). Angular dispersion of the virtual geomagnetic poles is 16.3 deg, which is consistent with paleosecular variation model G, fit to data from the past 5 m.y. Comparison with the expected direction indicates no azimuthal rotation of the Taos Plateau volcanic field; inclination flattening for the southern part of the plateau is 8.3 deg +/- 5.3 deg. Previous paleomagnelic data indicate 10 deg- 15 deg counterclockwise rotation of die Espanola block to the south over the past 5 m.y. The data suggest the Taos Plateau volcanic field, showing no rotation and some flattening in the south and east, has acted as a stable buttress and has been downwarped by overriding of the southeastern end of the plateau by the Picuris Mountains, which make up the northern corner of the counterclockwise rotating Espanola block.

Brown, Laurie L.↗

The aerodynamics of circulation control

Two dimensional subsonic wind tunnel tests were conducted on a 20% thickness: chord ratio circulation controlled elliptic aerofoil section equipped with forward and reverse blowing slots. Overall performance measurements were made over a range of trailing edge blowing momentum coefficients from 0 to 0.04; some included the effect of leading edge blowing. A detailed investigation of the trailing edge wall jet, using split film probes, hot wire probes and total head tubes, provided measurements of mean velocity components, Reynolds normal and shear stresses, and radial static pressure. The closure of the two dimensional angular momentum and continuity equations was examined using the measured data, with and without correction, and the difficulty of obtaining a satisfactory solution illustrated. Suggestions regarding the nature of the flow field which should aid the understanding of Coanda effect and the theoretical solution of highly curved wall jet flows are presented.

Wood, N. J.↗

Pioneer 9 and OGO 5 observations of an interplanetary multiple shock ensemble on February 2, 1969

A multiple shock system was observed upstream (0.13 AU) of the earth by Pioneer 9 on February 2, 1969. The same system was observed at earth by Ogo 5 and was reported separately in the literature. This paper compares the two sets of observations in still further detail. Both magnetic-field and plasma data are used in a least-squares best-fit method to compute the characteristics of the fast forward shock wave (Pioneer 9 only) and two fast reverse shock waves. Nearly all major features (shock, piston, and tangential discontinuity) retained their characteristics during the transit of the shock ensemble from Pioneer 9 to Ogo 5. The genesis of the ensemble is believed to be due to a complex stream-stream interaction. A substantial density increase (including a large rise of alpha/proton abundance) at Ogo 5, but unobserved at Pioneer 9, is explained by a sudden meridional shift to a flow from below the ecliptic plane while the streams were en route to earth. This study demonstrates a spatial and temporal plasma inhomogeneity which is superimposed on the persistent major features.

Dryer, M.↗

An Examination of Parameters Affecting Large Eddy Simulations of Flow Past a Square Cylinder

Separated flow over a bluff body is analyzed via large eddy simulations. The turbulent flow around a square cylinder features a variety of complex flow phenomena such as highly unsteady vortical structures, reverse flow in the near wall region, and wake turbulence. The formation of spanwise vortices is often times artificially suppressed in computations by either insufficient depth or a coarse spanwise resolution. As the resolution is refined and the domain extended, the artificial turbulent energy exchange between spanwise and streamwise turbulence is eliminated within the wake region. A parametric study is performed highlighting the effects of spanwise vortices where the spanwise computational domain's resolution and depth are varied. For Re=22,000, the mean and turbulent statistics computed from the numerical large eddy simulations (NLES) are in good agreement with experimental data. Von-Karman shedding is observed in the wake of the cylinder. Mesh independence is illustrated by comparing a mesh resolution of 2 million to 16 million. Sensitivities to time stepping were minimized and sampling frequency sensitivities were nonpresent. While increasing the spanwise depth and resolution can be costly, this practice was found to be necessary to eliminating the artificial turbulent energy exchange.

Mankbadi, M. R.↗

Central Plasma Sheet Ion Properties as Inferred from Ionospheric Observations

A method of inferring central plasma sheet (CPS) temperature, density, and pressure from ionospheric observations is developed. The advantage of this method over in situ measurements is that the CPS can be studied in its entirely, rather than only in fragments. As a result, for the first time, comprehensive two-dimensional equatorial maps of CPS pressure, density, and temperature within the isotropic plasma sheet are produced. These particle properties are calculated from data taken by the Special Sensor for Precipitating Particles, version 4 (SSJ4) particle instruments onboard DMSP F8, F9, F10, and F11 satellites during the entire year of 1992. Ion spectra occurring in conjunction with electron acceleration events are specifically excluded. Because of the variability of magnetotail stretching, the mapping to the plasma sheet is done using a modified Tsyganenko [1989] magnetic field model (T89) adjusted to agree with the actual magnetotail stretch at observation time. The latter is inferred with a high degree of accuracy (correlation coefficient -0.9) from the latitude of the DMSP b2i boundary (equivalent to the ion isotropy boundary). The results show that temperature, pressure, and density all exhibit dawn-dusk asymmetries unresolved with previous measurements. The ion temperature peaks near the midnight meridian. This peak, which has been associated with bursty bulk flow events, widens in the Y direction with increased activity. The temperature is higher at dusk than at dawn, and this asymmetry increases with decreasing distance from the Earth. In contrast, the density is higher at dawn than at dusk, and there appears to be a density enhancement in the low-latitude boundary layer regions which increases with decreasing magnetic activity. In the near-Earth regions, the pressure is higher at dusk than at dawn, but this asymmetry weakens with increasing distance from the Earth and may even reverse so that at distances X less than approx. 10 to -12 R(sub E), depending on magnetic activity, the dawn sector has slightly higher pressure. The temperature and density asymmetries in the near-Earth region are consistent with the ion westward gradient/curvature drift as the ions ExB convect earthward. When the solar wind dynamic pressure increases, CPS density and pressure appear to increase, but the temperature remains relatively constant. Comparison with previously published work indicates good agreement between the inferred pressure, temperature, and density and those obtained from in situ data. This new method should provide a continuous mechanism to monitor the pressure, temperature, and density in the magnetotail with unprecedented comprehensiveness.

Wing, Simon↗

Bounds on the Rate-Dependent Plastic Flow of Tantalum up to 75 GPa

In this study we report on the continued development of thermodynamics-based analysis of shock waves propagation with the objective of extracting information related to materials strength at high strain rates and pressures. Building on previous results reported for peak stresses of 10 GPa and 25 GPa, we present a series of three-step gas-gun shock experiments designed to explore the pressure and strain rate dependence of plastic flow in polycrystalline tantalum. These experiments at nominal peak stresses of 50 GPa and 75 GPa show the irreversible deformation before pullback to be almost entirely confined to the shock loading, with negligible plastic relaxation on the post-shock plateau. We also add a reverse-ballistics shot at 25 GPa, which was designed to reveal the pullback response with negligible interference from free-surface effects. General thermodynamic considerations allow us to place bounds on the plastic behavior even for parts of the curve that change far too rapidly for the velocimetric time resolution of (conservatively) ~ 5 ns. To analyze the data, we found it necessary to substantially improve the interpolation/extrapolation scheme in order to improve its robustness, flexibility and range of applicability. We describe the new scheme based on splines, as well as an extension of free-surface corrections to the post-shock rarefaction waves. Reanalysis with the new scheme produces results essentially within the error bars previously reported, showing that the known systematic errors associated with free-surface effects are relatively inconsequential for determining thermodynamic paths.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Satellite observations of zonal electric fields near sunrise in the equatorial ionosphere

We report here on a number of examples of anomalous enhancements of eastward electric fields near sunrise in the equatorial ionospheric F-region. These examples were selected from the data base of the equatorial satellite, San Marco D (1988), which measured ionospheric electric fields during a period of solar minimum. The eastward electric fields reported correspond to vertical plasma drifts. The examples studied here are similar in signature and polarity to the pre-reversal electric field enhancements seen near sunset from ground-based radar systems. The morphology of these sunrise events, which are observed on about 14% of the morning-side satellite passes, are studied as a function of local zonal velocity, magnetic activity, geographic longitude and altitude. The nine events studied occur at locations where the zonal plasma flow is generally measured to be eastward, but reducing as a function of local time and at satellite longitudes where the magnetic declination has the opposite polarity as the declination of the sunrise terminator.

Aggson, T. L.↗