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At least 1,477 records · Page 82
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Metagenome-assembled genomes from Wind River Basin floodplain sediments Riverton, Wyoming site (May to September 2017)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken roughly every month in the period May 18 to September 13 in 2017 at a location (Pit2) close to DOE Legacy Management well 855 at the Riverton, Wyoming floodplain site in the Wind River Basin (WRB). The groundwater at this site exhibits persistent U, Mo, and sulfate plumes and is one of the field sites in focus for the SLAC Groundwater Quality SFA program. Cores were taken with a hand-auger and separated into 5-20 cm segments based on soil horizonation down to 150 cm depth below surface. Each segment was subsampled for microbial analyses. Corresponding 16S rRNA gene amplicon data is available at the NCBI Single Read Archive (SRA) Database BioProject ID PRJNA626616, and soil geochemistry data at doi:10.15485/1631972. 40 metagenomes were sequenced through JGI and can be found under Gold sequencing project: Gs0142591. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 6993 MAG fasta files and a csv file with quality, taxonomic classification (GTDB RS220), and metagenome accessions for MAGs generated from the Wind River Basin (WRB). This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1976

Demonstration program for Omega receiver prototype microcomputer data processing

The JOLT (TM) commercial microcomputer, based on the MOS Technology 6502 processor chip, for use in Omega navigation system is evaluated. A computer program was prepared in hand-assembled code to demonstrate receiver operation. The processor provides binary processing with interrupts enabled, a carriage return is given to initialize the teleprinter, and a jump is performed to enter the program loop to wait for an interrupt. The program loop operates continuously testing the interrupt flag. The interrupt routine reads the receiver status word and determines whether the current time-slot is the A slot. If so, the interrupt flag, which is also the data index pointer, is reset to zero. The status word is stored in the status buffer. If the time-slot is not A, the interrupt flag/pointer is incremented by one to index the phase and status to the proper buffer words for later use by the print routine.

Lilley, R. W.↗
NASA NTRS1993

Optical system storage design with diffractive optical elements

Optical data storage systems are gaining widespread acceptance due to their high areal density and the ability to remove the high capacity hard disk from the system. In magneto-optical read-write systems, a small rotation of the polarization state in the return signal from the MO media is the signal which must be sensed. A typical arrangement used for detecting these signals and correcting for errors in tracking and focusing on the disk is illustrated. The components required to achieve these functions are listed. The assembly and alignment of this complex system has a direct impact on cost, and also affects the size, weight, and corresponding data access rates. As a result, integrating these optical components and improving packaging techniques is an active area of research and development. Most designs of binary optic elements have been concerned with optimizing grating efficiency. However, rigorous coupled wave models for vector field diffraction from grating surfaces can be extended to determine the phase and polarization state of the diffracted field, and the design of polarization components. A typical grating geometry and the phase and polarization angles associated with the incident and diffracted fields are shown. In our current stage of work, we are examining system configurations which cascade several polarization functions on a single substrate. In this design, the beam returning from the MO disk illuminates a cascaded grating element which first couples light into the substrate, then introduces a quarter wave retardation, then a polarization rotation, and finally separates s- and p-polarized fields through a polarization beam splitter. The input coupler and polarization beam splitter are formed in volume gratings, and the two intermediate elements are zero-order elements.

Kostuk, Raymond K.↗
NASA NTRS1988

Sensitivity of control-augmented structure obtained by a system decomposition method

The verification of a method for computing sensitivity derivatives of a coupled system is presented. The method deals with a system whose analysis can be partitioned into subsets that correspond to disciplines and/or physical subsystems that exchange input-output data with each other. The method uses the partial sensitivity derivatives of the output with respect to input obtained for each subset separately to assemble a set of linear, simultaneous, algebraic equations that are solved for the derivatives of the coupled system response. This sensitivity analysis is verified using an example of a cantilever beam augmented with an active control system to limit the beam's dynamic displacements under an excitation force. The verification shows good agreement of the method with reference data obtained by a finite difference technique involving entire system analysis. The usefulness of a system sensitivity method in optimization applications by employing a piecewise-linear approach to the same numerical example is demonstrated. The method's principal merits are its intrinsically superior accuracy in comparison with the finite difference technique, and its compatibility with the traditional division of work in complex engineering tasks among specialty groups.

Sobieszczanskisobieski, Jaroslaw↗
NASA NTRS1991

Sensitivity of control-augmented structure obtained by a system decomposition method

The verification of a method for computing sensitivity derivatives of a coupled system is presented. The method deals with a system whose analysis can be partitioned into subsets that correspond to disciplines and/or physical subsystems that exchange input-output data with each other. The method uses the partial sensitivity derivatives of the output with respect to input obtained for each subset separately to assemble a set of linear, simultaneous, algebraic equations that are solved for the derivatives of the coupled system response. This sensitivity analysis is verified using an example of a cantilever beam augmented with an active control system to limit the beam's dynamic displacements under an excitation force. The verification shows good agreement of the method with reference data obtained by a finite difference technique involving entire system analysis. The usefulness of a system sensitivity method in optimization applications by employing a piecewise-linear approach to the same numerical example is demonstrated. The method's principal merits are its intrinsically superior accuracy in comparison with the finite difference technique, and its compatibility with the traditional division of work in complex engineering tasks among specialty groups.

Sobieszczanski-Sobieski, Jaroslaw↗
NASA NTRS1974

Program for the analysis of time series

A digital computer program for the Fourier analysis of discrete time data is described. The program was designed to handle multiple channels of digitized data on general purpose computer systems. It is written, primarily, in a version of FORTRAN 2 currently in use on CDC 6000 series computers. Some small portions are written in CDC COMPASS, an assembler level code. However, functional descriptions of these portions are provided so that the program may be adapted for use on any facility possessing a FORTRAN compiler and random-access capability. Properly formatted digital data are windowed and analyzed by means of a fast Fourier transform algorithm to generate the following functions: (1) auto and/or cross power spectra, (2) autocorrelations and/or cross correlations, (3) Fourier coefficients, (4) coherence functions, (5) transfer functions, and (6) histograms.

Brown, T. J.↗
DOE OSTI2020

Covalently Linked, Two-Dimensional Quantum Dot Assemblies

Using nanoscale building blocks to construct hierarchical materials is a radical new branch point in materials discovery that promises new structures and emergent functionality. Understanding the design principles that govern nanoparticle assembly is critical to moving this field forward. By exploiting mixed ligand environments to target patchy nanoparticle surfaces, we have demonstrated a novel method of colloidal quantum dot (QD) assembly that gives rise to 2D structures. The equilibration of solutions of spherical and quasispherical QDs, including CdS, CdSe, and InP, with 2,2'-bipyridine-5,5'-diacrylic acid resulted in the preferential formation of 2D assemblies over the course of days as determined by transmission electron microscopy analysis. Small-angle X-ray scattering confirms the existence of the QD assemblies in solution. The dependence of the assembly on linker properties (length and rigidity), linker concentration, and total concentration was investigated, together with the data point to a mechanism involving ligand redistribution to create a patchy surface that maximizes the steric repulsion of neighboring QDs. By operating in an underexchanged regime, the arising patchiness results in enthalpically preferred directions of cross-linking that can be accessed by thermal equilibration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

In situ spin coater for multimodal grazing incidence x-ray scattering studies

We present herein a custom-made, in situ, multimodal spin coater system with an integrated heating stage that can be programmed with spinning and heating recipes and that is coupled with synchrotron-based, grazing-incidence wide- and small-angle x-ray scattering. The spin coating system features an adaptable experimental chamber, with the ability to house multiple ancillary probes such as photoluminescence and visible optical cameras, to allow for true multimodal characterization and correlated data analysis. This system enables monitoring of structural evolutions such as perovskite crystallization and polymer self-assembly across a broad length scale (2 Å–150 nm) with millisecond temporal resolution throughout a complete thin film fabrication process. The use of this spin coating system allows scientists to gain a deeper understanding of temporal processes of a material system, to develop ideal conditions for thin film manufacturing.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

A methodology to compute the critical current limit in Nb3Sn magnets

Numerous experiments have shown that the loads applied to Nb3Sn strands and cables can reduce their critical current. Experiments, performed on uniaxially loaded strands, allowed to define clear laws to describe the evolution of the critical surface as a function of the applied current, field, temperature and strain. It is, however, still unclear how these laws can be applied to superconducting magnets. The present paper proposes a methodology to estimate the critical current and temperature margin reduction on superconducting magnets due to stress on the superconducting material. The methodology is tested on the MQXF magnets, a quadrupole developed for the High Luminosity LHC project, and successfully validated by comparing computed strain with data from strain gauge measurements. Overall, results suggested that, because of the stresses arising in winding during assembly, cool-down and powering, the current limit of the magnet is lower than the expected short sample limit, and that the most critical region does not coincide with the peak field location.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation

Microbes commonly organize into communities consisting of hundreds of species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance profiles of these microbial communities. These snapshots, when collected from multiple samples, can reveal the co-occurrence of microbes, providing a glimpse into the network of associations in these communities. However, the inference of networks from 16S data involves numerous steps, each requiring specific tools and parameter choices. Moreover, the extent to which these steps affect the final network is still unclear. In this study, we perform a meticulous analysis of each step of a pipeline that can convert 16S sequencing data into a network of microbial associations. Through this process, we map how different choices of algorithms and parameters affect the co-occurrence network and identify the steps that contribute substantially to the variance. We further determine the tools and parameters that generate robust co-occurrence networks and develop consensus network algorithms based on benchmarks with mock and synthetic data sets. The Microbial Co-occurrence Network Explorer, or MiCoNE (available at https://github.com/segrelab/MiCoNE) follows these default tools and parameters and can help explore the outcome of these combinations of choices on the inferred networks. We envisage that this pipeline could be used for integrating multiple data sets and generating comparative analyses and consensus networks that can guide our understanding of microbial community assembly in different biomes.

16S rRNA↗
DOE OSTI2021

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC

Large amounts of metagenomically-derived data are submitted to PATRIC for analysis. In the future, we expect even more jobs submitted to PATRIC will use metagenomic data. One in-demand use case is the extraction of near-complete draft genomes from assembled contigs of metagenomic origin. The PATRIC metagenome binning service utilizes the PATRIC database to furnish a large, diverse set of reference genomes. We provide a new service for supervised extraction and annotation of high-quality, near-complete genomes from metagenomically-derived contigs. Reference genomes are assigned to putative draft genome bins based on the presence of single-copy universal marker roles in the sample, and contigs are sorted into these bins by their similarity to reference genomes in PATRIC. Each set of binned contigs represents a draft genome that will be annotated by RASTtk in PATRIC. A structured-language binning report is provided containing quality measurements and taxonomic information about the contig bins. The PATRIC metagenome binning service emphasizes extraction of high-quality genomes for downstream analysis using other PATRIC tools and services. Due to its supervised nature, the binning service is not appropriate for mining novel or extremely low-coverage genomes from metagenomic samples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cryo-EM structure of the diapause chaperone artemin

The protein artemin acts as both an RNA and protein chaperone and constitutes over 10% of all protein in Artemia cysts during diapause. However, its mechanistic details remain elusive since no high-resolution structure of artemin exists. Here we report the full-length structure of artemin at 2.04 Å resolution. The cryo-EM map contains density for an intramolecular disulfide bond between Cys22-Cys61 and resolves the entire C-terminus extending into the core of the assembled protein cage but in a different configuration than previously hypothesized with molecular modeling. We also provide data supporting the role of C-terminal helix F towards stabilizing the dimer form that is believed to be important for its chaperoning activity. We were able to destabilize this effect by placing a tag at the C-terminus to fully pack the internal cavity and cause limited steric hindrance.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1973

Characteristics of advanced hydrogen maser frequency standards

In house research and development at Goddard Space Flight Center to provide advanced frequency and time standards for the most demanding applications is concentrated primarily in field operable atomic hydrogen masers. Some of the most important goals for the new maser designs have been improved long and short term stability, elimination of the need for auto tuning, increased maser oscillation level, improved hydrogen economy, increased operational life, minimization of operator control or monitoring, improvement in magnetic isolation or sensitivity, and reduction in size and weight. New design concepts which have been incorporated in these masers to achieve these goals are described. The basic maser assemblies and control systems have recently been completed; the masers are oscillating; and operational testing has begun. Data illustrating the improvements in maser performance was available and presented.

Peters, H. E.↗
NASA NTRS1975

Permanent and separable aerospace tubing/ fitting evaluation program, volume 1

The tube fitting evaluation program was conducted to develop a standard overall test program including methods, procedures, and equipment as well as recommended test sequences for qualifying fitting/tubing assemblies. The program consisted of testing the MS flareless (separable) fitting and utilizing the results as baseline data from which all other fittings will be evaluated. Five separable designs and five permanent designs were tested in three sizes with two types of tubing materials. The basic design requirements were 4,000 psi operating pressure within the temperature range of minus 65 F to plus 450 F while also being compatible with 21-6-9 and titanium 3Al-2.5V tubing alloys.

Ursell, C. R.↗
NASA NTRS1978

Performance of a thermionic converter module utilizing emitter and collector heat pipes

A thermionic converter module simulating a configuration for an out-of-core thermionic nuclear reactor was designed, fabricated, and tested. The module consists of three cylindrical thermionic converters. The tungsten emitter of the converter is heated by a tungsten, lithium heat pipe. The emitter heat pipes are immersed in a furnace, insulated by MULTI-FOIL thermal insulation, and heated by tungsten radiation filaments. The performance of each thermionic converter was characterized before assembly into the module. Dynamic voltage, current curves were taken using a 60 Hz sweep and computerized data acquisition over a range of emitter, collector, and cesium-reservoir temperatures. An output power of 215 W was observed at an emitter temperature of 1750 K and a collector temperature of 855 K for a two diode module. With a three diode module, an output power of 270 W was observed at an average emitter temperature of 1800 K and a Collector temperature of 875 K.

Kroeger, E. W.↗
NASA NTRS1980

Image-based information, communication, and retrieval

IBIS/VICAR system combines video image processing and information management. Flexible programs require user to supply only parameters specific to particular application. Special-purpose input/output routines transfer image data with reduced memory requirements. New application programs are easily incorporated. Program is written in FORTRAN IV, Assembler, and OS JCL for batch execution and has been implemented on IBM 360.

Bryant, N. A.↗