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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 307 records · Page 17

Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences

Detection of chimeric artifacts formed when PCR is used to retrieve naturally occurring small-subunit (SSU) rRNA sequences may rely on demonstrating that different sequence domains have different phylogenetic affiliations. We evaluated the CHECK_CHIMERA method of the Ribosomal Database Project and another method which we developed, both based on determining nearest neighbors of different sequence domains, for their ability to discern artificially generated SSU rRNA chimeras from authentic Ribosomal Database Project sequences. The reliability of both methods decreases when the parental sequences which contribute to chimera formation are more than 82 to 84% similar. Detection is also complicated by the occurrence of authentic SSU rRNA sequences that behave like chimeras. We developed a naive statistical test based on CHECK_CHIMERA output and used it to evaluate previously reported SSU rRNA chimeras. Application of this test also suggests that chimeras might be formed by retrieving SSU rRNAs as cDNA. The amount of uncertainty associated with nearest-neighbor analyses indicates that such tests alone are insufficient and that better methods are needed.

NASA Discipline Exobiology↗

Combinatorial transcription factor binding encodes cis -regulatory wiring of mouse forebrain GABAergic neurogenesis

Transcription factors (TFs) bind combinatorially to cis-regulatory elements, orchestrating transcriptional programs. Although studies of chromatin state and chromosomal interactions have demonstrated dynamic neurodevelopmental cis-regulatory landscapes, parallel understanding of TF interactions lags. To elucidate combinatorial TF binding driving mouse basal ganglia development, we integrated chromatin immunoprecipitation sequencing (ChIP-seq) for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and gene expression data, and functional enhancer assays. We identified sets of putative regulatory elements with shared TF binding (TF-pRE modules) that orchestrate distinct processes of GABAergic neurogenesis and suppress other cell fates. The majority of pREs were bound by one or two TFs; however, a small proportion were extensively bound. These sequences had exceptional evolutionary conservation and motif density, complex chromosomal interactions, and activity as in vivo enhancers. Our results provide insights into the combinatorial TF-pRE interactions that activate and repress expression programs during telencephalon neurogenesis and demonstrate the value of TF binding toward modeling developmental transcriptional wiring.

59 BASIC BIOLOGICAL SCIENCES↗

Viromics approaches for the study of viral diversity and ecology in microbiomes

Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.

Ecology↗

A modular and extensible CHARMM-compatible model for all-atom simulation of polypeptoids

Peptoids (N-substituted glycines) are a class of sequence-defined synthetic peptidomimetic polymers with applications including drug delivery, catalysis, and biomimicry. Classical molecular simulations have been used to predict and understand the conformational dynamics of single chains and their self-assembly into morphologies including sheets, tubes, spheres, and fibrils. The CGenFF-NTOID model based on the CHARMM General Force Field has demonstrated success in accurate all-atom molecular modeling of peptoid structure and thermodynamics. Extension of this force field to new peptoid side chains has historically required reparameterization of side chain bonded interactions against ab initio data. This fitting protocol improves the accuracy of the force field but is also burdensome and precludes modular extensibility of the model to arbitrary peptoid sequences. In this work, we develop and demonstrate a Modular Side Chain CGenFF-NTOID (MoSiC-CGenFF-NTOID) as an extension of CGenFF-NTOID employing a modular decomposition of the peptoid backbone and side chain parameterizations, wherein arbitrary side chains within the large family of substituted methyl groups (i.e., –CH 3 , –CH 2 R, –CHRR', and –CRR'R") are directly ported from CGenFF. We validate this approach against ab initio calculations and experimental data to develop a MoSiC-CGenFF-NTOID model for all 20 natural amino acid side chains along with 13 commonly used synthetic side chains and present an extensible paradigm to efficiently determine whether a novel side chain can be directly incorporated into the model or whether refitting of the CGenFF parameters is warranted. We make the model freely available to the community along with a tool to perform automated initial structure generation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geology of the Sklodowska Region, Lunar Farside

Investigation of an area on the lunar farside has resulted in a geologic map, development of a regional stratigraphic sequence, and interpretation of surface materials. Apollo 15 metric photographs were used in conjunction with photogrammetric techniques to produce a base map to which geologic units were later added. Geologic units were first delineated on the metric photographs and then transferred to the base map. Materials were defined and described from selected Lunar Orbiter and Apollo 15 metric, panoramic, and Hasselblad photographs on the basis of distinctive morphologic characteristics.

Kauffman, J. D.↗

Video detection and analysis techniques of transient astronomical phenomena

Low-light-level television systems have been utilized to gain information on meteors, aurorae, and other faint, transient astronomical phenomena. Such phenomena change not only their position as a function of time, but also their photometric and spectral characteristics in as little as 1/60 second, thus requiring unique methods of analysis. Data observed with television systems and recorded on video tape have been analyzed with a system utilizing both analog and digital techniques. Both off-the-shelf equipment and inhouse developments are used to isolate sequences of moving images and to store them in a form suitable for photometric and spectral reduction. Current emphasis of the analysis effort is directed at the measurement of the first-order emission lines of meteor spectra, the results of which will yield important compositional information concerning the nature of the impinging meteoroid.

Clifton, K. S.↗

Boundary conditions for the numerical solution of elliptic equations in exterior regions

Elliptic equations in exterior regions frequently require a boundary condition at infinity to ensure the well-posedness of the problem. Examples of practical applications include the Helmholtz equation and Laplace's equation. Computational procedures based on a direct discretization of the elliptic problem require the replacement of the condition on a finite artificial surface. Direct imposition of the condition at infinity along the finite boundary results in large errors. A sequence of boundary conditions is developed which provides increasingly accurate approximations to the problem in the infinite domain. Estimates of the error due to the finite boundary are obtained for several cases. Computations are presented which demonstrate the increased accuracy that can be obtained by the use of the higher order boundary conditions. The examples are based on a finite element formulation but finite difference methods can also be used.

Bayliss, A.↗

Global picture of a Be star

An attempt is made to synthesize the observational material on Be stars into a empirical pattern of atmospheric structure. The sequence of atmospheric regions is developed and empirical-numerical estimates of location and structure of the regions are described. Inferences are drawn concerning the general stellar structure required to generate the nonthermal fluxes which produce the observed atmospheric pattern. In particular the atmospheric and subatmospheric origins of mass flux are addressed.

Thomas, R. N.↗

Preliminary structural model for the southwestern part of the Michipicoten greenstone belt, Ontario

The southwestern part of the Michipicoten Greenstone Belt includes a 100 sq km fume kill extending northeastwards from the twon of Wawa, Ontario. Except for a strip along the Magpie River that is covered by Pleistocene gravels, outcrop in the fume kill averages about 30-50%. Within this area are all the major lithologic belts characteristic of the southwestern fourth of the Michipicoten Greenstone Belt. All of the area mapped to date lies within Chabenel Township, recently mapped at 4" = 1 mile. Following a brief reconnaissance in 1983, mapping at a scale of 1" = 400' was begun within and adjacent to the fume kill in 1984. Two objectives are sought (1) determinaion of the geometry and sequence of folding, faulting, cleavage development, and intrusion; and (2) defining and tracing lithologic packages, and evaluating the nature of the contacts between these packages. Results for objective (1) are discussed in a companion abstract; this abstract will present tentative results for objective.

Mcgill, G. E.↗

Wind shear and turbulence simulation

The aviation community is increasing its reliance on flight simulators. This is true both in pilot training and in research and development. In moving research concepts through the development pipeline, there is a sequence of events which take place: analysis, ground based simulation, inflight simulation, and flight testing. Increasing fidelity as progress toward the flight testing arena is accompanied by increasing cost. The question that seems to be posed in relation to the meteorological aspects of flight simulation is, How much fidelity is enough and can it be quantified. As a part of the Langley Simulation Technology Program, there are three principal areas of focus, one being improved simulation of weather hazards. A close liaison with the JAWS project was established because of the Langley Simulation Technology interests regarding reliable simulation of severe convective weather phenomena and their impact on aviation systems. Simulation offers the only feasible approach for examining the utility of new technology and new procedures for coping with severe convective weather phenomena such as wind shear. These simulation concepts are discussed in detail.

Bowles, Roland L.↗

The evolution of a coronal streamer prior to mass ejection

A model describing the quasi-static evolution of a coronal helmet streamer as it is inflated with excess mass was developed. The model produces a sequence of magnetostatic equilibria for a magnetic field configuration that includes a current sheet in the equatorial plane as well as distributed volume currents. The equilibrium solutions are given as Legendre series, and the height at which the current sheet starts is adjusted iteratively to maintain constant flux in the closed-field region. The model was fit to SMM coronagraph/polarimeter observations showing the slow growth of a coronal streamer prior to its disruption in association with an eruptive prominence and mass ejection on August 18, 1980. The results suggest that the early phase of this event is consistent with the quasi-static evolution of the corona in response to the slow addition of mass to the closed-field region of the streamer.

Wolfson, Richard↗

Backward Assembly Planning With DFA Analysis

System of algorithms developed to automate planning of sequences of manufacturing or field operations in which components are put together into assemblies. Results of DFA analysis also used to modify designs to optimize them with respect to assembly considerations.

Lee, Sukhan↗

The analysis of star catalogs. 1: An intercomparison among the FK3, the FK4, and the FK5

Progress in the construction of the fundamental catalogs allows one to ask the following questions: 'Now that we have the FK5 with which to measure by, how good was the FK4? The FK3? How realistic were the error estimates they gave for their equatorial coordinates and their proper motions? Have their residual systematic differences continued to decrease in amplitude?' and so forth. Similar questions could be asked of the GC and the N30, and a companion paper will similarly analyze them. Finally, the identical series of questions could be asked of the AGK2, AGK3, AGK3U sequence. In this paper we develop a general method to objectively investigate, post facto, the true quality of star catalog error estimates. We present a complete mathematical formulation of the questions above and delineate the calculations needed to address them. Our initial numerical applications are restricted to a straightforward examination of the mean errors of the coordinates and proper motions in the FK3 (using the FK4 and the FK5 for comparison) and in the FK4 (using the FK5 for comparison). However, we can simply and consistently interpret the results of these computations -- for the FK catalogs fail to follow the predictions of mathematical statistics -- only if the FK3 and the FK4 contain higher angular frequency systematic errors. These errors, at the mean epochs of place of the older catalogs, are larger than the random errors in the FK5 system. We expect that our new ability to discern these features means that we can also prevent them during compilation. Finally, note that the concepts behind our procedures are completely general and can be applied to any set of compiled data -- astrometric, photometric, geodetic, and so forth.

Bucciarelli, B.↗

Mars 2001 Lander Mission: Measurement Synergy Through Coordinated Operations Planning And Implementation

The 2001 Mars Surveyor Program Mission includes an orbiter with a gamma ray spectrometer and a multispectral thermal imager, and a lander with an extensive set of instrumentation, a robotic arm, and the Marie Curie Rover. The Mars 2001 Science Operations Working Group (SOWG) is a subgroup of the Project Science Group that has been formed to provide coordinated planning and implementation of scientific observations, particularly for the landed portion of the mission. The SOWG will be responsible for delivery of a science plan and, during operations, generation and delivery of conflict-free sequences. This group will also develop an archive plan that is compliant with Planetary Data System (PDS) standards, and will oversee generation, validation, and delivery of integrated archives to the PDS. In this report we cover one element of the SOWG planning activities, the development of a plan that maximizes the scientific return from lander-based observations by treating the instrument packages as an integrated payload. Scientific objectives for the lander mission have been defined. They include observations focused on determining the bedrock geology of the site through analyses of rocks and also local materials found in the soils, and the surficial geology of the site, including windblown deposits and the nature and history of formation of indurated sediments such as duricrust. Of particular interest is the identification and quantification of processes related to early warm, wet conditions and the presence of hydrologic or hydrothermal cycles. Determining the nature and origin of duricrust and associated salts is -very important in this regard. Specifically, did these deposits form in the vadose zone as pore water evaporated from soils or did they form by other processes, such as deposition of volcanic aerosols? Basic information needed to address these questions includes the morphology, topography, and geologic context of landforms and materials exposed at the site, together with quantitative information on material mineralogy, chemistry, and physical properties (rock textures; soil grain size and shape distributions; degree and nature of soil induration; soil magnetic properties). The calibration targets provide radiometric and mineralogical control surfaces. The magnets allow observations of magnetic phases. Patch plates are imaged to determine adhesive and abrasive properties of soils. Coordinated mission planning is crucial for optimizing the measurement synergy among the packages included on the lander. This planning has already begun through generation of multi-sol detailed operations activities. One focus has been to develop a scenario to use the arm to dig a soil trench to a depth of tens of centimeters. The activity will be monitored through use of Pancam and RAC to ensure nominal operations and to acquire data to determine subsurface physical properties (e.g., angle of repose of trench walls). Pancam and Mini-TES observations would also provide constraints on mineralogy and texture for the walls and bottom of the trench during excavation. If desired, soils excavated at depth could be deposited on the surface and Mossbauer and APXS measurements could be acquired for these materials. Soil samples from various depths would be delivered to MECA for characterization of aqueous geochemistry and physical properties of soil grains, particularly size, shape, and hardness. These physical properties would be determined by optical and atomic force microscopy. When completed, detailed information of soil properties as a function of depth would be obtained. These various data sets would constrain our understanding of whether or not there are systematic variations in soil characteristics as a function of depth. These variations might be related, for example, to evaporative moisture losses and formation of salt deposits, thereby indicating water transport processes occurred fairly recently. Many other value-added measurement scenarios are being developed. For example, characterizing the nature and dynamics of dust deposition will be done using MIP/DART to provide deposition rates, Pancam and RAC imaging of lander and rover surfaces to extrapolate these measurements to other areas, and a variety of measurements to determine if the bulk loose soil has the same characteristics as dust that accumulates during the mission. Bedrock geology of the site is primarily an APEX-focus setting, mineralogy, and texture, and APXS data to be we interest will be to determine the extent to which rock hydrothermal processes, given that APEX is the precursor 4 and 2005 rover missions. Additional information is contained in the original.

Arvidson, R.↗

Aerodynamic Decelerators for Planetary Exploration: Past, Present, and Future

In this paper, aerodynamic decelerators are defined as textile devices intended to be deployed at Mach numbers below five. Such aerodynamic decelerators include parachutes and inflatable aerodynamic decelerators (often known as ballutes). Aerodynamic decelerators play a key role in the Entry, Descent, and Landing (EDL) of planetary exploration vehicles. Among the functions performed by aerodynamic decelerators for such vehicles are deceleration (often from supersonic to subsonic speeds), minimization of descent rate, providing specific descent rates (so that scientific measurements can be obtained), providing stability (drogue function - either to prevent aeroshell tumbling or to meet instrumentation requirements), effecting further aerodynamic decelerator system deployment (pilot function), providing differences in ballistic coefficients of components to enable separation events, and providing height and timeline to allow for completion of the EDL sequence. Challenging aspects in the development of aerodynamic decelerators for planetary exploration missions include: deployment in the unusual combination of high Mach numbers and low dynamic pressures, deployment in the wake behind a blunt-body entry vehicle, stringent mass and volume constraints, and the requirement for high drag and stability. Furthermore, these aerodynamic decelerators must be qualified for flight without access to the exotic operating environment where they are expected to operate. This paper is an introduction to the development and application of aerodynamic decelerators for robotic planetary exploration missions (including Earth sample return missions) from the earliest work in the 1960s to new ideas and technologies with possible application to future missions. An extensive list of references is provided for additional study.

Juan R Cruz↗

The Cassini/Huygens mission to Saturn

This paper provides an overview of the mission but focuses primarily on the activities over the past year in preparation for Saturn arrival and beginning the scientific observations to be made in orbit. Details are provided on the completion, validation, and uplink of new on-board flight software, development and testing of the sequences to be used for orbit insertion and relay of the data stream from the Huygens probe as it descends through the atmosphere of Titan, and design and preparation of the science sequences to be performed by the orbiter.

Huygens↗

Stereoscopic Planar Laser-Induced Fluorescence Imaging at 500 kHz

A new measurement technique for obtaining time- and spatially-resolved image sequences in hypersonic flows is developed. Nitric-oxide planar laser-induced fluorescence (NO PLIF) has previously been used to investigate transition from laminar to turbulent flow in hypersonic boundary layers using both planar and volumetric imaging capabilities. Low flow rates of NO were typically seeded into the flow, minimally perturbing the flow. The volumetric imaging was performed at a measurement rate of 10 Hz using a thick planar laser sheet that excited NO fluorescence. The fluorescence was captured by a pair of cameras having slightly different views of the flow. Subsequent stereoscopic reconstruction of these images allowed the three-dimensional flow structures to be viewed. In the current paper, this approach has been extended to 50,000 times higher repetition rates. A laser operating at 500 kHz excites the seeded NO molecules, and a camera, synchronized with the laser and fitted with a beam-splitting assembly, acquires two separate images of the flow. The resulting stereoscopic images provide three-dimensional flow visualizations at 500 kHz for the first time. The 200 ns exposure time in each frame is fast enough to freeze the flow while the 500 kHz repetition rate is fast enough to time-resolve changes in the flow being studied. This method is applied to visualize the evolving hypersonic flow structures that propagate downstream of a discrete protuberance attached to a flat plate. The technique was demonstrated in the NASA Langley Research Center s 31-Inch Mach 10 Air Tunnel facility. Different tunnel Reynolds number conditions, NO flow rates and two different cylindrical protuberance heights were investigated. The location of the onset of flow unsteadiness, an indicator of transition, was observed to move downstream during the tunnel runs, coinciding with an increase in the model temperature.

Medford, Taylor L.↗

Variability in Surface BRDF at Different Spatial Scales (30 m-500 m) Over a Mixed Agricultural Landscape as Retrieved from Airborne and Satellite Spectral Measurements

Over the past decade, the role of multiangle remote sensing has been central to the development of algorithms for the retrieval of global land surface properties including models of the bidirectional reflectance distribution function (BRDF), albedo, land cover/dynamics, burned area extent, as well as other key surface biophysical quantities represented by the anisotropic reflectance characteristics of vegetation. In this study, a new retrieval strategy for fine-to-moderate resolution multiangle observations was developed, based on the operational sequence used to retrieve the Moderate Resolution Imaging Spectroradiometer (MODIS) Collection 5 reflectance and BRDF/albedo products. The algorithm makes use of a semiempirical kernel-driven bidirectional reflectance model to provide estimates of intrinsic albedo (i.e., directional-hemispherical reflectance and bihemispherical reflectance), model parameters describing the BRDF, and extensive quality assurance information. The new retrieval strategy was applied to NASA's Cloud Absorption Radiometer (CAR) data acquired during the 2007 Cloud and Land Surface Interaction Campaign (CLASIC) over the well-instrumented Atmospheric Radiation Measurement Program (ARM) Southern Great Plains (SGP) Cloud and Radiation Testbed (CART) site in Oklahoma, USA. For the case analyzed, we obtained approx.1.6 million individual surface bidirectional reflectance factor (BRF) retrievals, from nadir to 75 off-nadir, and at spatial resolutions ranging from 3 m - 500 m. This unique dataset was used to examine the interaction of the spatial and angular characteristics of a mixed agricultural landscape; and provided the basis for detailed assessments of: (1) the use of a priori knowledge in kernel-driven BRDF model inversions; (2) the interaction between surface reflectance anisotropy and instrument spatial resolution; and (3) the uncertain ties that arise when sub-pixel differences in the BRDF are aggregated to a moderate resolution satellite pixel. Results offer empirical evidence concerning the influence of scale and spatial heterogeneity in kernel-driven BRDF models; providing potential new insights into the behavior and characteristics of different surface radiative properties related to land/use cover change and vegetation structure.

Roman, Miguel O.↗