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At least 1,603 records · Page 89
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Omics Metadata Management Software v. 1 (OMMS)

Our application, the Omics Metadata Management Software (OMMS), answers both needs, empowering experimentalists to generate intuitive, consistent metadata, and to perform bioinformatics analyses and information management tasks via a simple and intuitive web-based interface. Several use cases with short-read sequence datasets are provided to showcase the full functionality of the OMMS, from metadata curation tasks, to bioinformatics analyses and results management and downloading. The OMMS can be implemented as a stand alone-package for individual laboratories, or can be configured for web-based deployment supporting geographically dispersed research teams. Our software was developed with open-source bundles, is flexible, extensible and easily installed and run by operators with general system administration and scripting language literacy.

Source record↗
DOE OSTI2014

Replication Bypass of the trans-4-Hydroxynonenal-Derived (6S,8R,11S)-1,N[superscript 2]-Deoxyguanosine DNA Adduct by the Sulfolobus solfataricus DNA Polymerase IV

trans-4-Hydroxynonenal (HNE) is the major peroxidation product of {omega}-6 polyunsaturated fatty acids in vivo. Michael addition of the N{sub 2}-amino group of dGuo to HNE followed by ring closure of N1 onto the aldehyde results in four diastereomeric 1,N{sub 2}-dGuo (1,N{sub 2}-HNE-dGuo) adducts. The (6S,8R,11S)-HNE-1,N{sub 2}-dGuo adduct was incorporated into the 18-mer templates 5'-d(TCATXGAATCCTTCCCCC)-3' and d(TCACXGAATCCTTCCCCC)-3', where X = (6S,8R,11S)-HNE-1,N{sub 2}-dGuo adduct. These differed in the identity of the template 5'-neighbor base, which was either Thy or Cyt, respectively. Each of these templates was annealed with either a 13-mer primer 5'-d(GGGGGAAGGATTC)-3' or a 14-mer primer 5'-d(GGGGGAAGGATTCC)-3'. The addition of dNTPs to the 13-mer primer allowed analysis of dNTP insertion opposite to the (6S,8R,11S)-HNE-1,N{sub 2}-dGuo adduct, whereas the 14-mer primer allowed analysis of dNTP extension past a primed (6S,8R,11S)-HNE-1,N{sub 2}-dGuo:dCyd pair. The Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) belongs to the Y-family of error-prone polymerases. Replication bypass studies in vitro reveal that this polymerase inserted dNTPs opposite the (6S,8R,11S)-HNE-1,N{sub 2}-dGuo adduct in a sequence-specific manner. If the template 5'-neighbor base was dCyt, the polymerase inserted primarily dGTP, whereas if the template 5'-neighbor base was dThy, the polymerase inserted primarily dATP. The latter event would predict low levels of Gua {yields} Thy mutations during replication bypass when the template 5'-neighbor base is dThy. When presented with a primed (6S,8R,11S)-HNE-1,N{sub 2}-dGuo:dCyd pair, the polymerase conducted full-length primer extension. Structures for ternary (Dpo4-DNA-dNTP) complexes with all four template-primers were obtained. For the 18-mer:13-mer template-primers in which the polymerase was confronted with the (6S,8R,11S)-HNE-1,N{sub 2}-dGuo adduct, the (6S,8R,11S)-1,N{sub 2}-dGuo lesion remained in the ring-closed conformation at the active site. The incoming dNTP, either dGTP or dATP, was positioned with Watson-Crick pairing opposite the template 5'-neighbor base, dCyt or dThy, respectively. In contrast, for the 18-mer:14-mer template-primers with a primed (6S,8R,11S)-HNE-1,N{sub 2}-dGuo:dCyd pair, ring opening of the adduct to the corresponding N{sub 2}-dGuo aldehyde species occurred. This allowed Watson-Crick base pairing at the (6S,8R,11S)-HNE-1,N{sub 2}-dGuo:dCyd pair.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ultra-short-period Planets Are Stable against Tidal Inspiral

It has been unambiguously shown both in individual systems and at the population level that hot Jupiters experience tidal inspiral before the end of their host stars’ main-sequence lifetimes. Ultra-short-period (USP) planets have orbital periods P < 1 day, rocky compositions, and are expected to experience tidal decay on similar timescales to hot Jupiters if the efficiency of tidal dissipation inside their host stars parameterized as Q{sub ∗}{sup ′} is independent of P and/or secondary mass M {sub p}. Any difference between the two classes of systems would reveal that a model with constant Q{sub ∗}{sup ′} is insufficient. If USP planets experience tidal inspiral, then USP planet systems will be relatively young compared to similar stars without USP planets. Because it is a proxy for relative age, we calculate the Galactic velocity dispersions of USP planet candidate host and non-host stars using data from Gaia Data Release 2 supplemented with ground-based radial velocities. We find that main-sequence USP planet candidate host stars have kinematics consistent with similar stars in the Kepler field without observed USP planets. This indicates that USP planet hosts have similar ages to field stars and that USP planets do not experience tidal inspiral during the main-sequence lifetimes of their host stars. The survival of USP planets requires that Q{sub ∗}{sup ′} ≳ 10{sup 7} at P ≈ 0.7 day and M{sub p}≈2.6 M{sub ⊕}. This result demands that Q{sub ∗}{sup ′} depend on the orbital period and/or mass of the secondary in the range 0.5 day≲P≲5 days and 1 M{sub ⊕}≲M{sub p}≲1000 M{sub ⊕}.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1987

Understanding natural language for spacecraft sequencing

The paper describes a natural language understanding system, START, that translates English text into a knowledge base. The understanding and the generating modules of START share a Grammar which is built upon reversible transformations. Users can retrieve information by querying the knowledge base in English; the system then produces an English response. START can be easily adapted to many different domains. One such domain is spacecraft sequencing. A high-level overview of sequencing as it is practiced at JPL is presented in the paper, and three areas within this activity are identified for potential application of the START system. Examples are given of an actual dialog with START based on simulated data for the Mars Observer mission.

Katz, Boris↗
DOE OSTI2024

$\mathrm{COBRA}$ improves the completeness and contiguity of viral genomes assembled from metagenomes

Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2005

Validation of NHB 8060.1C, Test 18 Arc Tracking, September 30, 1991

A test project was conducted to validate Test 18 of NASA Handbook (NHB) 8060.1C and, if necessary, identify and recommend improvements in the procedures or criteria of the test. The NHB 8060.1C, Test 18 test system was modified to produce better discrimination of test results. Changes, and their effects on test results, in the graphite immersion-depth, test timing sequence, and atmospheric conditions were investigated for the wire-insulation constructions tested. Based on the test results, the graphite immersion-depths (between 0.8 mm and 1.6 mm), the timing sequence, and the change in the test conditions from ambient to three environments common in manned spaceflight did not significantly affect test results. The criteria used in Test 18 of NHB 8060.1C was found to be appropriate for qualifying arc-tracking and arc-propagation characteristics of wire-insulation materials, Using the Test 18 criteria, Kapton and ETFE were considered inappropriate for use, while PTFE was considered appropriate. Recommendations from this test project for Test 18 of NHB 8060.1C include changing the experimental setup and configurational tests and performing qualification testing in air rather than in the three environments common in manned spaceflight.

Linley, Larry↗
DOE OSTI2020

Autonomous Selective Parts-Based Tracking

Object tracking from videos is still a challenging task due to various changes throughout a video sequence including occlusions, motion blur, scale and other deformation changes. In this paper, we propose a selective parts-based approach, using correlation filters, that makes choices based on a consensus of the parts and global tracking. Moreover, we further enhance our parts-based approach by introducing a segmentation-assisted parts initialization. In addition, we present a genetic algorithm-based method to autonomously select various parameters of the tracking algorithm, as opposed to the common practice of manually tuning those parameters. In contrast to existing part-based methods, the proposed method does not dilute accurate tracking by averaging results over multiple parts at every frame. Instead, we take a selective approach based on the relative weight of the responses across parts. Moreover, we only make location corrections when a part diverges, and rely on these location corrections to maintain an accurate appearance model. In the case of occlusions, which are among the main reasons for using a parts-based approach, our proposed approach consistently achieves the best performance. It is due to the ability to handle occlusion and not dilute decisions with incorrect parts, that our proposed approach enables state-of-the-art performance. The approach we propose was evaluated on videos from three different challenging benchmark datasets. Our approach has resulted in better overall precision and success rates for three different base tracking approaches.

42 ENGINEERING↗
DOE OSTI2021

Reconfigurable Two‐Dimensional DNA Lattices: Static and Dynamic Angle Control

Abstract Branched DNA motifs serve as the basic construction elements for all synthetic DNA nanostructures. However, precise control of branching orientation remains a key challenge to further heighten the overall structural order. In this study, we use two strategies to control the branching orientation. The first one is based on immobile Holliday junctions which employ specific nucleotide sequences at the branch points which dictate their orientation. The second strategy is to use angle‐enforcing struts to fix the branching orientation with flexible spacers at the branch points. We have also demonstrated that the branching orientation control can be achieved dynamically, either by canonical Watson–Crick base pairing or non‐canonical nucleobase interactions (e.g., i‐motif and G‐quadruplex). With precise angle control and feedback from the chemical environment, these results will enable novel DNA nanomechanical sensing devices, and precisely‐ordered three‐dimensional architectures.

Wang, Wen↗
DOE OSTI2013

EFFICIENT SELECTION AND CLASSIFICATION OF INFRARED EXCESS EMISSION STARS BASED ON AKARI AND 2MASS DATA

The selection of young stellar objects (YSOs) based on excess emission in the infrared is easily contaminated by post-main-sequence stars and various types of emission line stars with similar properties. We define in this paper stringent criteria for an efficient selection and classification of stellar sources with infrared excess emission based on combined Two Micron All Sky Survey (2MASS) and AKARI colors. First of all, bright dwarfs and giants with known spectral types were selected from the Hipparcos Catalogue and cross-identified with the 2MASS and AKARI Point Source Catalogues to produce the main-sequence and the post-main-sequence tracks, which appear as expected as tight tracks with very small dispersion. However, several of the main-sequence stars indicate excess emission in the color space. Further investigations based on the SIMBAD data help to clarify their nature as classical Be stars, which are found to be located in a well isolated region on each of the color-color (C-C) diagrams. Several kinds of contaminants were then removed based on their distribution in the C-C diagrams. A test sample of Herbig Ae/Be stars and classical T Tauri stars were cross-identified with the 2MASS and AKARI catalogs to define the loci of YSOs with different masses on the C-C diagrams. Well classified Class I and Class II sources were taken as a second test sample to discriminate between various types of YSOs at possibly different evolutionary stages. This helped to define the loci of different types of YSOs and a set of criteria for selecting YSOs based on their colors in the near- and mid-infrared. Candidate YSOs toward IC 1396 indicating excess emission in the near-infrared were employed to verify the validity of the new source selection criteria defined based on C-C diagrams compiled with the 2MASS and AKARI data. Optical spectroscopy and spectral energy distributions of the IC 1396 sample yield a clear identification of the YSOs and further confirm the criteria defined for exploring the nature and properties of unknown excess emission sources in the infrared without optical identification.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Inferred Hα flux as a star formation rate indicator at z ∼ 4–5: implications for dust properties, burstiness, and the z = 4–8 star formation rate functions

We derive Hα fluxes for a large spectroscopic and photometric-redshift-selected sample of sources over GOODS-North and South in the redshift range z = 3.8–5.0 with deep Hubble Space Telescope (HST), Spitzer/IRAC, and ground-based observations. The Hα flux is inferred based on the offset between the IRAC 3.6 μm flux and that predicted from the best-fit spectral energy distribution (SED). We demonstrate that the Hα flux correlates well with dust-corrected UV star formation rate (SFR) and therefore can serve as an independent SFR indicator. However, we also find a systematic offset in the SFR{sub Hα}/SFR{sub UV+β} ratios for z ∼ 4–5 galaxies relative to local relations (assuming the same dust corrections for nebular regions and stellar light). We show that we can resolve the modest tension in the inferred SFRs by assuming bluer intrinsic UV slopes (increasing the dust correction), a rising star formation history, or assuming a low-metallicity stellar population with a hard ionizing spectrum (increasing the L{sub Hα}/SFR ratio). Using Hα as an SFR indicator, we find a normalization of the star formation main sequence in good agreement with recent SED-based determinations and also derive the SFR functions at z∼4--8. In addition, we assess for the first time the burstiness of star formation in z∼4 galaxies on <100 Myr timescales by comparing UV and Hα-based sSFRs; their one-to-one relationship argues against significantly bursty star formation histories.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

ORBIT AND STELLAR PROPERTIES OF THE YOUNG TRIPLE V807 Tau

We present new orbital measurements of the pre-main-sequence triple system, V807 Tau, using adaptive optics imaging at the Keck Observatory. We computed an orbit for the close pair, V807 Tau Ba-Bb, with a period of 12.312 {+-} 0.058 years and a semi-major axis of 38.59 {+-} 0.16 mas. By modeling the center of mass motion of the components in the close pair relative to the wide component, V807 Tau A, we measured a mass ratio of 0.843 {+-} 0.050 for Bb/Ba. Combined with the total mass from the relative orbit, we derived individual masses of M{sub Ba} = 0.564 {+-} 0.018 (d/140 pc){sup 3} M{sub Sun} and M{sub Bb} = 0.476 {+-} 0.017 (d/140 pc){sup 3} M{sub Sun} at an average distance of 140 pc to the Taurus star-forming region. We computed spectral energy distributions to determine the luminosities of the three components. We also measured their spectral types, effective temperatures, and rotational velocities based on spatially resolved spectra obtained at the Keck Observatory. If the rotational axes are aligned, then the projected rotational velocities imply that V807 Tau Ba and Bb are rotating much faster than V807 Tau A. The uncertainty in the stellar effective temperatures and distance to the system currently limit the comparison of our dynamical mass measurements with predictions based on evolutionary tracks for pre-main-sequence stars. We also report preliminary results from a program to map the 3.6 cm radio emission from V807 Tau using the Very Long Baseline Array. With continued monitoring, these observations will provide a precise parallax for placing the dynamical masses on an absolute scale.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Reconfigurable Two-Dimensional DNA Lattices: Static and Dynamic Angle Control

Branched DNA motifs serve as the basic construction elements for all synthetic DNA nanostructures. However, precise control of branching orientation remains a key challenge to further heighten the overall structural order. Here in this study, we use two strategies to control the branching orientation. The first one is based on immobile Holliday junctions which employ specific nucleotide sequences at the branch points which dictate their orientation. The second strategy is to use angle-enforcing struts to fix the branching orientation with flexible spacers at the branch points. We have also demonstrated that the branching orientation control can be achieved dynamically, either by canonical Watson–Crick base pairing or non-canonical nucleobase interactions (e.g., i-motif and G-quadruplex). With precise angle control and feedback from the chemical environment, these results will enable novel DNA nanomechanical sensing devices, and precisely-ordered three-dimensional architectures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2004

NASA Tech Briefs, May 2004

Topics include: Embedded Heaters for Joining or Separating Plastic Parts; Curing Composite Materials Using Lower-Energy Electron Beams; Aluminum-Alloy-Matrix/Alumina-Reinforcement Composites; Fibrous-Ceramic/Aerogel Composite Insulating Tiles; Urethane/Silicone Adhesives for Bonding Flexing Metal Parts; Scalable Architecture for Multihop Wireless ad Hoc Networks; Improved Thermoplastic/Iron-Particle Transformer Cores; Cooperative Lander-Surface/Aerial Microflyer Missions for Mars Exploration Dual-Frequency Airborne Scanning Rain Radar Antenna System Eight-Channel Continuous Timer Reduction of Phase Ambiguity in an Offset-QPSK Receiver Ambient-Light-Canceling Camera Using Subtraction of Frames Lightweight, Flexible, Thin, Integrated Solar-Power Packs Windows(Registered Trademark)-Based Software Models Cyclic Oxidation Behavior Software for Analyzing Sequences of Flow-Related Images Improved Ball-and-Socket Docking Mechanism Two-Stage Solenoid Ordered Nanostructures Made Using Chaperonin Polypeptides Low-Temperature Plasma Functionalization of Carbon Nanotubes Improved Cryostat for Cooling a Wide Panel Current Pulses Momentarily Enhance Thermoelectric Cooling Hand-Held Color Meters Based on Interference Filters Calculating Mass Diffusion in High-Pressure Binary Fluids Fresnel Lenses for Wide-Aperture Optical Receivers Increasing Accuracy in Computed Inviscid Boundary Conditions Higher-Order Finite Elements for Computing Thermal Radiation Radar for Monitoring Hurricanes from Geostationary Orbit Time-Transfer System for Two Orbiting Spacecraft

Source record↗
NASA NTRS1991

Validation of vision-based obstacle detection algorithms for low-altitude helicopter flight

A validation facility being used at the NASA Ames Research Center is described which is aimed at testing vision based obstacle detection and range estimation algorithms suitable for low level helicopter flight. The facility is capable of processing hundreds of frames of calibrated multicamera 6 degree-of-freedom motion image sequencies, generating calibrated multicamera laboratory images using convenient window-based software, and viewing range estimation results from different algorithms along with truth data using powerful window-based visualization software.

Suorsa, Raymond↗
DOE OSTI2016

acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

Abstract Background A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable quality control efforts are put into post-sequencing analysis. Contamination screening generally relies on reference-based methods such as database alignment or marker gene search, which limits the set of detectable contaminants to organisms with closely related reference species. As genomic coverage in the tree of life is highly fragmented, there is an urgent need for a reference-free methodology for contaminant identification in sequence data. Results We present acdc, a tool specifically developed to aid the quality control process of genomic sequence data. By combining supervised and unsupervised methods, it reliably detects both known and de novo contaminants. First, 16S rRNA gene prediction and the inclusion of ultrafast exact alignment techniques allow sequence classification using existing knowledge from databases. Second, reference-free inspection is enabled by the use of state-of-the-art machine learning techniques that include fast, non-linear dimensionality reduction of oligonucleotide signatures and subsequent clustering algorithms that automatically estimate the number of clusters. The latter also enables the removal of any contaminant, yielding a clean sample. Furthermore, given the data complexity and the ill-posedness of clustering, acdc employs bootstrapping techniques to provide statistically profound confidence values. Tested on a large number of samples from diverse sequencing projects, our software is able to quickly and accurately identify contamination. Results are displayed in an interactive user interface. Acdc can be run from the web as well as a dedicated command line application, which allows easy integration into large sequencing project analysis workflows. Conclusions Acdc can reliably detect contamination in single-cell genome data. In addition to database-driven detection, it complements existing tools by its unsupervised techniques, which allow for the detection of de novo contaminants. Our contribution has the potential to drastically reduce the amount of resources put into these processes, particularly in the context of limited availability of reference species. As single-cell genome data continues to grow rapidly, acdc adds to the toolkit of crucial quality assurance tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX

Many viruses express factors that reduce host gene expression through widespread degradation of cellular mRNA. An example of this class of proteins is the mRNA-targeting endoribonuclease SOX from the gamma-herpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV). Previous studies indicated that cleavage of messenger RNAs (mRNA) by SOX occurs at specific locations defined by the sequence of the target RNA, which is at odds with the down-regulation of a large portion of cellular transcripts. In this study, we address this paradox by using high-throughput sequencing of cleavage intermediates combined with a custom bioinformatics-based analysis pipeline to identify SOX cleavage sites across the mRNA transcriptome. These data, coupled with targeted mutagenesis, reveal that while cleavage sites are specific and reproducible, they are defined by a degenerate sequence motif containing a small number of conserved residues rather than a strong consensus sequence. This degenerate element is well represented in both human and KSHV mRNA, and its presence correlates with RNA destabilization by SOX. This represents a new endonuclease targeting strategy, in which use of a degenerate targeting element enables RNA cleavage at specific locations without restricting the range of targets. Furthermore, it shows that strong target selectivity can be achieved without a high degree of sequence specificity.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1989

Generation of precedence relations for mechanical assemblies

Planning of assembly sequences is essential to the manufacturing system design process. Several methodologies have been proposed to represent all the feasible assembly sequences. In this thesis, three algorithms are presented to generate three sets of precedence relations based on all the infeasible assembly tasks, all the infeasible assembly states, and all the feasible assembly sequences, respectively. The equivalence of the resulting sets of precedence relations to the AND/OR graph is established. A new property, the real time property, of a representation of assembly sequences is defined and discussed. A representation of assembly sequences is said to have the real time property, if it is possible to generate the next assembly task by testing locally in the representation, and it will guarantee that the generated assembly task will not lead the assembly sequence to a dead end situation, in which no feasible assembly task can be performed any more. It is shown that the correctness and completeness of one representation can not guarantee the real time property of the representation. It is proven that the directed graph representation and the set of precedence relations based on all the infeasible assembly states have the real time property, while the AND/OR graph representation and the set of precedence relations based on all the infeasible assembly tasks do not have the real time property. Finally in the thesis, the PLEIDEAS system, a PLanning Environment for Integrated DEsign of Assembly Systems, is described and illustrated by an example.

Zhang, Hui↗
NASA NTRS1996

Detectability of the Reflection Signal from Inner Planets

Mayor and Queloz (1996) and Marcy and Butler (1996) have found massive planets with orbital periods Tp=approx.4 days around two solar-like stars (51 Pegasi and v Andromeda). These planets are most likely similar in size and composition to the gas giants in our solar system (Burrows et al 1996). Based on this expectation and assuming the same albedo as Jupiter, we examined the feasibility of searching for similar planets with a dedicated space-based 1-m telescope. The Kepler mission will survey approximately 70,000 main-sequence dwarf stars from 9 to 14 mag continuously for four years to detect transiting Earthlike planets. Based on the detection statistics of Marcy and Butler, we expect to detect 1400 inner-orbit giant planets. Such planets in a much wider range of orbital inclinations (i) will produce nearly sinusoidal modulations of the star light flux due to the varying planetary phases. The relative signal amplitudes are of order 2x10(exp -5) and decrease as Tp(exp 4/3) for i >> 0deg. We estimated the expected signal to noise ratio (SNR) using the solar irradiance measurements from the ACRIM 1 experiment along with expected shot and detector noises. The figure shows SNR as a function of Tp for a 12 mag star, and indicates the planet radius required for detection. The survey will be sensitive to planets with periods from 12 hr to approx.8 days at the 6 sigma level.

Borucki, W. J.↗