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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Morphological and Genomic Features of the New Klosneuvirinae Isolate Fadolivirus IHUMI-VV54

Since the discovery of Mimivirus, viruses with large genomes encoding components of the translation machinery and other cellular processes have been described as belonging to the nucleocytoplasmic large DNA viruses. Recently, genome-resolved metagenomics led to the discovery of more than 40 viruses that have been grouped together in a proposed viral subfamily named Klosneuvirinae. Members of this group had genomes of up to 2.4Mb in size and featured an expanded array of translation system genes. Yet, despite the large diversity of the Klosneuvirinae in metagenomic data, there are currently only two isolates available. Here, we report the isolation of a novel giant virus known as Fadolivirus from an Algerian sewage site and provide morphological data throughout its replication cycle in amoeba and a detailed genomic characterization. The Fadolivirus genome, which is more than 1.5Mb in size, encodes 1,452 predicted proteins and phylogenetic analyses place this viral isolate as a near relative of the metagenome assembled Klosneuvirus and Indivirus. The genome encodes for 66 tRNAs, 23 aminoacyl-tRNA synthetases and a wide range of transcription factors, surpassing Klosneuvirus and other giant viruses. The Fadolivirus genome also encodes putative vacuolar-type proton pumps with the domains D and A, potentially constituting a virus-derived system for energy generation. The successful isolation of Fadolivirus will enable future hypothesis-driven experimental studies providing deeper insights into the biology of the Klosneuvirinae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Elemental Mixing State of Aerosol Particles Collected in Central Amazonia during GoAmazon2014/15

Two complementary techniques, Scanning Transmission X-ray Microscopy/Near Edge Fine Structure spectroscopy (STXM/NEXAFS) and Scanning Electron Microscopy/Energy Dispersive X-ray spectroscopy (SEM/EDX), have been quantitatively combined to characterize individual atmospheric particles. This pair of techniques was applied to particle samples at three sampling sites (ATTO, ZF2, and T3) in the Amazon basin as part of the Observations and Modeling of the Green Ocean Amazon (GoAmazon2014/5) field campaign during the dry season of 2014. The combined data was subjected to k-means clustering using mass fractions of the following elements: C, N, O, Na, Mg, P, S, Cl, K, Ca, Mn, Fe, Ni, and Zn. Cluster analysis identified 12 particle types, across different sampling sites and particle sizes. Samples from the remote Amazon Tall Tower Observatory (ATTO, also T0a) exhibited less cluster variety and fewer anthropogenic clusters than samples collected at the sites nearer to the Manaus metropolitan region, ZF2 (also T0t) or T3. Samples from the ZF2 site contained aged/anthropogenic clusters not readily explained by transport from ATTO or Manaus, possibly suggesting the effects of long range atmospheric transport or other local aerosol sources present during sampling. In addition, this data set allowed for recently established diversity parameters to be calculated. All sample periods had high mixing state indices (χ) that were >0.8. Two individual particle diversity (D i ) populations were observed, with particles <0.5 μm having a D i of ~2.4 and >0.5 μm particles having a D i of ~3.6, which likely correspond to fresh and aged aerosols respectively. The diversity parameters determined by the quantitative method presented here will serve to aid in the accurate representation of aerosol mixing state, source apportionment, and aging in both less polluted and more industrialized environments in the Amazon Basin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils

Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the “core” microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired “core” microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired “core” bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.

Jaswal, Rajneesh (ORCID:0000000217841805)↗
DOE OSTI2016

MODELS OF THE η CORVI DEBRIS DISK FROM THE KECK INTERFEROMETER, SPITZER, AND HERSCHEL

Debris disks are signposts of analogs to small-body populations of the solar system, often, however, with much higher masses and dust production rates. The disk associated with the nearby star η Crv is especially striking, as it shows strong mid- and far-infrared excesses despite an age of ∼1.4 Gyr. We undertake constructing a consistent model of the system that can explain a diverse collection of spatial and spectral data. We analyze Keck Interferometer Nuller measurements and revisit Spitzer and additional spectrophotometric data, as well as resolved Herschel images, to determine the dust spatial distribution in the inner exozodi and in the outer belt. We model in detail the two-component disk and the dust properties from the sub-AU scale to the outermost regions by fitting simultaneously all measurements against a large parameter space. The properties of the cold belt are consistent with a collisional cascade in a reservoir of ice-free planetesimals at 133 AU. It shows marginal evidence for asymmetries along the major axis. KIN enables us to establish that the warm dust consists of a ring that peaks between 0.2 and 0.8 AU. To reconcile this location with the ∼400 K dust temperature, very high albedo dust must be invoked, and a distribution of forsterite grains starting from micron sizes satisfies this criterion, while providing an excellent fit to the spectrum. We discuss additional constraints from the LBTI and near-infrared spectra, and we present predictions of what James Webb Space Telescope can unveil about this unusual object and whether it can detect unseen planets.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

A Catalog of Quasar Properties from Sloan Digital Sky Survey Data Release 16

We present a catalog of continuum and emission-line properties for 750,414 broad-line quasars included in the Sloan Digital Sky Survey Data Release 16 quasar catalog (DR16Q), measured from optical spectroscopy. These quasars cover broad ranges in redshift (0.1 ≲ z ≲ 6) and luminosity (44 ≲ log(L bol /erg s -1 ) ≲ 48), and probe lower luminosities than an earlier compilation of SDSS DR7 quasars. Derived physical quantities such as single-epoch virial black hole masses and bolometric luminosities are also included in this catalog. We present improved systemic redshifts and realistic redshift uncertainties for DR16Q quasars using the measured line peaks and correcting for velocity shifts of various lines with respect to the systemic velocity. About 1%, 1.4%, and 11% of the original DR16Q redshifts deviate from the systemic redshifts by |ΔV| > 1500 km s -1 , |ΔV| $\in$ [1000, 1500] km s -1 , and |ΔV| $\in$ [500, 1000] km s -1 , respectively; about 1900 DR16Q redshifts were catastrophically wrong (|ΔV| > 10,000 km s -1 ). We demonstrate the utility of this data product in quantifying the spectral diversity and correlations among physical properties of quasars with large statistical samples.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2,500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7,128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1984

Prospects for three-dimensional projective and tomographic imaging radar networks

Results of a study demonstrating the feasibility of broadband and speckle-free projective imaging of a complex shaped scattering object in the 6-17 GHz range with centimeter resolution are presented. It is shown how angular, spectral, and polarization diversities can be combined in the data acquisition process with a unique target-derived reference technique to access the three-dimensional Fourier space of the scatterer cost-effectively. Imagea retrieval algorithms, based on the projection slice theorem and knowledge of object symmetry, are utilized in obtaining images of a model aircraft with near optical resolution. The implications for high-resolution three-dimensional tomographic imaging radar networks are discussed.

Farhat, N. H.↗
NASA NTRS1988

Selected Tether Applications Cost Model

Diverse cost-estimating techniques and data combined into single program. Selected Tether Applications Cost Model (STACOM 1.0) is interactive accounting software tool providing means for combining several independent cost-estimating programs into fully-integrated mathematical model capable of assessing costs, analyzing benefits, providing file-handling utilities, and putting out information in text and graphical forms to screen, printer, or plotter. Program based on Lotus 1-2-3, version 2.0. Developed to provide clear, concise traceability and visibility into methodology and rationale for estimating costs and benefits of operations of Space Station tether deployer system.

Keeley, Michael G.↗
NASA NTRS1989

The AMSC mobile satellite system: Design summary and comparative analysis

Mobile satellite communications will be provided in the United States by the American Mobile Satellite Consortium (AMSC). Telesat Mobile, Inc. (TMI) and AMSC are jointly developing MSAT, the first regional Mobile Satellite Service (MSS) system. MSAT will provide diverse mobile communications services - including voice, data and position location - to mobiles on land, water, and in the air throughout North America. Described here are the institutional relationships between AMSC, TMI and other organizations participating in MSAT, including the Canadian Department of Communications and NASA. The regulatory status of MSAT in the United States and international allocations to MSS are reviewed. The baseline design is described.

Noreen, Gary K.↗
NASA NTRS1990

Process and information integration via hypermedia

Success stories for advanced automation prototypes abound in the literature but the deployments of practical large systems are few in number. There are several factors that militate against the maturation of such prototypes into products. Here, the integration of advanced automation software into large systems is discussed. Advanced automation systems tend to be specific applications that need to be integrated and aggregated into larger systems. Systems integration can be achieved by providing expert user-developers with verified tools to efficiently create small systems that interface to large systems through standard interfaces. The use of hypermedia as such a tool in the context of the ground control centers that support Shuttle and space station operations is explored. Hypermedia can be an integrating platform for data, conventional software, and advanced automation software, enabling data integration through the display of diverse types of information and through the creation of associative links between chunks of information. Further, hypermedia enables process integration through graphical invoking of system functions. Through analysis and examples, researchers illustrate how diverse information and processing paradigms can be integrated into a single software platform.

Hammen, David G.↗
NASA NTRS1994

Scientific analysis of satellite ranging data

A network of satellite laser ranging (SLR) tracking systems with continuously improving accuracies is challenging the modelling capabilities of analysts worldwide. Various data analysis techniques have yielded many advances in the development of orbit, instrument and Earth models. The direct measurement of the distance to the satellite provided by the laser ranges has given us a simple metric which links the results obtained by diverse approaches. Different groups have used SLR data, often in combination with observations from other space geodetic techniques, to improve models of the static geopotential, the solid Earth, ocean tides, and atmospheric drag models for low Earth satellites. Radiation pressure models and other non-conservative forces for satellite orbits above the atmosphere have been developed to exploit the full accuracy of the latest SLR instruments. SLR is the baseline tracking system for the altimeter missions TOPEX/Poseidon, and ERS-1 and will play an important role in providing the reference frame for locating the geocentric position of the ocean surface, in providing an unchanging range standard for altimeter calibration, and for improving the geoid models to separate gravitational from ocean circulation signals seen in the sea surface. However, even with the many improvements in the models used to support the orbital analysis of laser observations, there remain systematic effects which limit the full exploitation of SLR accuracy today.

Smith, David E.↗
NASA NTRS1995

Measuring Interfacial Tension Between Immiscible Liquids

Glass capillary tube technique measures interfacial tension between two immiscible liquids. Yields useful data over fairly wide range of interfacial tensions, both for pairs of liquids having equal densities and pairs of liquids having unequal densities. Data on interfacial tensions important in diverse industrial chemical applications, including enhanced extraction of oil; printing; processing foods; and manufacture of paper, emulsions, foams, aerosols, detergents, gel encapsulants, coating materials, fertilizers, pesticides, and cosmetics.

Rashidnia, Nasser↗
NASA NTRS2000

Acousto-Optic Imaging Spectrometers for Mars Surface Science

NASA's long term plan for Mars sample collection and return requires a highly streamlined approach for spectrally characterizing a landing site, documenting the mineralogical make-up of the site and guiding the collections of samples which represent the diversity of the site. Ideally, image data should be acquired at hundreds of VIS and IR wavelengths, in order to separately distinguish numerous anticipated species, using principal component analysis and linear unmixing. Cameras with bore-sighted point spectrometers can acquire spectra of isolated scene elements, but it requires 10(exp 2) to 10(exp 2) successive motions and precise relative pointing knowledge in order to create a single data cube which qualifies as a spectral map. These and other competing science objectives have to be accomplished within very short lander/rover operational lifetime (a few sols). True, 2-D imaging spectroscopy greatly speeds up the data acquisition process, since the spectra of all pixels in the scene are collected at once. This task can be accomplished with cameras that use electronically tunable acousto-optic tunable filters (AOTFs) as the optical tuning element. AOTFs made from TeO2 are now a mature technology, and operate at wavelengths from near-UV to about 5 microns. Because of incremental improvements in the last few years, present generation devices are rugged, radiation-hard and operate at temperatures down to at least 150K so they can be safely integrated into the ambient temperature optics of in-situ instruments such as planetary or small-body landers. They have been used for ground-based astronomy, and were also baselined for the ST-4 Champollion IR comet lander experiment (CIRCLE), prior to cancellation of the ST-4 mission last year. AIMS (for Acousto-optic Imaging spectrometer), is a prototype lander instrument which is being built at GSFC with support by the NASA OSS Advanced Technologies and Mission Studies, Mars Instrument Definition and Development Program (MIDP). AIMS is capable of tunable spectroscopic imaging of surface mineralogy, ices and dust between 0.5 and 2.4 microns, at a resolving power (lambda/delta lambda) which is typically several hundred. The design spatial resolution, similar to IMP and SSI, will allow mapping at scales down to about 1 cm.

Glenar, D. A.↗
NASA NTRS2009

Synthesis and Assimilation Systems - Essential Adjuncts to the Observing System

Assimilation systems synthesize diverse in-situ and satellite data streams into full four-dimensional state estimates by combining the strengths of each data set and also of the model. The resulting analysis provides an integrated view of the information in the various observations as well as derived estimates of unobserved quantities. Assimilation systems are particularly important for the ocean where subsurface observations, even today, are sparse and intermittent compared with the scales needed to represent ocean variability and where satellites only sense the surface. Increasingly, models and assimilation systems are being used to provide information about the current observing system and to help in the design plans for new observations. Whether it is as a user of observations or a contributor to evaluation of the observing system, ocean synthesis and assimilation systems are now an integral part of the global ocean observing and information system. Major advances have been made over the last decade under the auspices of WCRP's Climate Variability and Predictability Project (CLIVAR) and the Global Ocean Data Assimilation Experiment (GODAE). In addition to advances in the assimilation systems, there have been major developments in the observing system, with satellite altimetry, the tropical moored buoy arrays in the Pacific and Atlantic, and more recently Argo. These developments have led to significant advances in our understanding and prediction of ocean variations at both mesoscale and climate scales. Many challenges remain. Some of these challenges lie in the observations themselves, some in the assimilation systems that, even in the more recent era of unprecedented observations from satellite altimetry and Argo, provide different views of climate variations. Yet there are many examples of successful applications from ocean assimilation products. Use of these systems for assessing the observing system helps identify the strengths of each observation type, and indicates that none of the current observations is redundant. Indeed, the indication is that the ocean remains under-sampled and that further improvements in the observing system are needed for both climate monitoring and prediction. Future developments will be increasingly towards consistent analyses across components of the Earth system using, e.g., coupled atmosphere-ocean models.

Rienecker, Michele M.↗
NASA NTRS2003

Organizing Diverse, Distributed Project Information

SemanticOrganizer is a software application designed to organize and integrate information generated within a distributed organization or as part of a project that involves multiple, geographically dispersed collaborators. SemanticOrganizer incorporates the capabilities of database storage, document sharing, hypermedia navigation, and semantic-interlinking into a system that can be customized to satisfy the specific information-management needs of different user communities. The program provides a centralized repository of information that is both secure and accessible to project collaborators via the World Wide Web. SemanticOrganizer's repository can be used to collect diverse information (including forms, documents, notes, data, spreadsheets, images, and sounds) from computers at collaborators work sites. The program organizes the information using a unique network-structured conceptual framework, wherein each node represents a data record that contains not only the original information but also metadata (in effect, standardized data that characterize the information). Links among nodes express semantic relationships among the data records. The program features a Web interface through which users enter, interlink, and/or search for information in the repository. By use of this repository, the collaborators have immediate access to the most recent project information, as well as to archived information. A key advantage to SemanticOrganizer is its ability to interlink information together in a natural fashion using customized terminology and concepts that are familiar to a user community.

Keller, Richard M.↗
NASA NTRS2017

Machine Learning Approaches to Increasing Value of Spaceflight Omics Databases

The number of spaceflight bioscience mission opportunities is too small to allow all relevant biological and environmental parameters to be experimentally identified. Simulated spaceflight experiments in ground-based facilities (GBFs), such as clinostats, are each suitable only for particular investigations -- a rotating-wall vessel may be 'simulated microgravity' for cell differentiation (hours), but not DNA repair (seconds) -- and introduce confounding stimuli, such as motor vibration and fluid shear effects. This uncertainty over which biological mechanisms respond to a given form of simulated space radiation or gravity, as well as its side effects, limits our ability to baseline spaceflight data and validate mission science. Machine learning techniques autonomously identify relevant and interdependent factors in a data set given the set of desired metrics to be evaluated: to automatically identify related studies, compare data from related studies, or determine linkages between types of data in the same study. System-of-systems (SoS) machine learning models have the ability to deal with both sparse and heterogeneous data, such as that provided by the small and diverse number of space biosciences flight missions; however, they require appropriate user-defined metrics for any given data set. Although machine learning in bioinformatics is rapidly expanding, the need to combine spaceflight/GBF mission parameters with omics data is unique. This work characterizes the basic requirements for implementing the SoS approach through the System Map (SM) technique, a composite of a dynamic Bayesian network and Gaussian mixture model, in real-world repositories such as the GeneLab Data System and Life Sciences Data Archive. The three primary steps are metadata management for experimental description using open-source ontologies, defining similarity and consistency metrics, and generating testing and validation data sets. Such approaches to spaceflight and GBF omics data may soon enable unique insight into which measured phenomena correlate to biological mechanisms that are truly affected by spaceflight conditions; which are most likely to be confounded by other variables; and which are insufficiently characterized, significantly increasing existing and future science return from ISS and spaceflight missions.

Gentry, Diana↗
DOE OSTI2011

HIGH-RESOLUTION ATMOSPHERIC ENSEMBLE MODELING AT SRNL

The High-Resolution Mid-Atlantic Forecasting Ensemble (HME) is a federated effort to improve operational forecasts related to precipitation, convection and boundary layer evolution, and fire weather utilizing data and computing resources from a diverse group of cooperating institutions in order to create a mesoscale ensemble from independent members. Collaborating organizations involved in the project include universities, National Weather Service offices, and national laboratories, including the Savannah River National Laboratory (SRNL). The ensemble system is produced from an overlapping numerical weather prediction model domain and parameter subsets provided by each contributing member. The coordination, synthesis, and dissemination of the ensemble information are performed by the Renaissance Computing Institute (RENCI) at the University of North Carolina-Chapel Hill. This paper discusses background related to the HME effort, SRNL participation, and example results available from the RENCI website.

54 ENVIRONMENTAL SCIENCES↗