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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 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
NASA NTRS1990

The case for relationship of the flavobacteria and their relatives to the green sulfur bacteria

Analysis of 16S rRNA sequences suggests, but does not convincingly demonstrate a specific relationship between the eubacterial phylum defined by the flavobacteria and their relatives and that defined by the green sulfur bacteria. Consequently, we have sequenced the 23S rRNA from several representatives of the former group and one of the latter in order to bring more data to bear upon this point. The 23S rRNA data alone strongly suggest a specific relationship between the two phyla, and, together with the 16S rRNA results, provides what we consider now to be a convincing case for this specific relationship.

NASA Discipline Number 52-30↗
NASA NTRS1994

How long did it take for life to begin and evolve to cyanobacteria?

There is convincing paleontological evidence showing that stromatolite-building phototactic prokaryotes were already in existence 3.5 x 10(9) years ago. Late accretion impacts may have killed off life on our planet as late as 3.8 x 10(9) years ago. This leaves only 300 million years to go from the prebiotic soup to the RNA world and to cyanobacteria. However, 300 million years should be more than sufficient time. All known prebiotic reactions take place in geologically rapid time scales, and very slow prebiotic reactions are not feasible because the intermediate compounds would have been destroyed due to the passage of the entire ocean through deep-sea vents every 10(7) years or in even less time. Therefore, it is likely that self-replicating systems capable of undergoing Darwinian evolution emerged in a period shorter than the destruction rates of its components (<5 million years). The time for evolution from the first DNA/protein organisms to cyanobacteria is usually thought to be very long. However, the similarities of many enzymatic reactions, together with the analysis of the available sequence data, suggest that a significant number of the components involved in basic biological processes are the result of ancient gene duplication events. Assuming that the rate of gene duplication of ancient prokaryotes was comparable to today's present values, the development of a filamentous cyanobacterial-like genome would require approximately 7 x 10(6) years--or perhaps much less. Thus, in spite of the many uncertainties involved in the estimates of time for life to arise and evolve to cyanobacteria, we see no compelling reason to assume that this process, from the beginning of the primitive soup to cyanobacteria, took more than 10 million years.

Non-NASA Center↗
NASA NTRS1992

Spatial orientation of the vestibular system

1. A simplified three-dimensional state space model of visual vestibular interaction was formulated. Matrix and dynamical system operators representing coupling from the semicircular canals and the visual system to the velocity storage integrator were incorporated into the model. 2. It was postulated that the system matrix for a tilted position was a composition of two linear transformations of the system matrix for the upright position. One transformation modifies the eigenvalues of the system matrix while another rotates the pitch and roll eigenvectors with the head, while maintaining the yaw axis eigenvector approximately spatially invariant. Using this representation, the response characteristics of the pitch, roll, and yaw eye velocity were obtained in terms of the eigenvalues and associated eigenvectors. 3. Using OKAN data obtained from monkeys and comparing to the model predictions, the eigenvalues and eigenvectors of the system matrix were identified as a function of tilt to the side or of tilt to the prone positions, using a modification of the Marquardt algorithm. The yaw eigenvector for right-side-down tilt and for downward pitch cross-coupling was approximately 30 degrees from the spatial vertical. For the prone position, the eigenvector was computed to be approximately 20 degrees relative to the spatial vertical. For both side-down and prone positions, oblique OKN induced along eigenvector directions generated OKAN which decayed to zero along a straight line with approximately a single time constant. This was verified by a spectral analysis of the residual sequence about the straight line fit to the decaying data. The residual sequence was associated with a narrow autocorrelation function and a wide power spectrum. 4. Parameters found using the Marquardt algorithm were incorporated into the model. Diagonal matrices in a head coordinate frame were introduced to represent the direct pathway and the coupling of the visual system to the integrator. Model simulations predicted the behavior of yaw and pitch OKN and OKAN when the animal was upright, as well as the cross-coupling in the tilted position. The trajectories in velocity space were also accurately simulated. 5. There were similarities between the monkey eigenvectors and human perception of the spatial vertical. For side-down tilts and downward eye velocity cross-coupling, there was only an Aubert (A) effect. For upward eye velocity cross-coupling there were both Muller (E) and Aubert (A) effects. The mean of the eigenvectors for upward and downward eye velocities overlay human 1 x g perceptual data.(ABSTRACT TRUNCATED AT 400 WORDS).

NASA Discipline Neuroscience↗
NASA NTRS2011

X-Ray Reflected Spectra from Accretion Disk Models. II. Diagnostic Tools for X-Ray Observations

We present a comprehensive study of the emission spectra from accreting sources. We use our new reflection code to compute the reflected spectra from an accretion disk illuminated by X-rays. This set of models covers different values of ionization parameter, solar iron abundance and photon index for the illuminating spectrum. These models also include the most complete and recent atomic data for the inner-shell of the iron and oxygen isonuclear sequences. We concentrate our analysis to the 2 - 10 keV energy region, and in particular to the iron K-shell emission lines. We show the dependency of the equivalent width (EW) of the Fe Ka with the ionization parameter. The maximum value of the EW is approx. 800 eV for models with log Epsilon approx. 1.5, and decreases monotonically as Epsilon increases. For lower values of Epsilon the Fe K(alpha) EW decreases to a minimum near log Epsilon approx. 0.8. We produce simulated CCD observations based on our reflection models. For low ionized, reflection dominated cases, the 2 -10 keV energy region shows a very broad, curving continuum that cannot be represented by a simple power-law. We show that in addition to the Fe K-shell emission, there are other prominent features such as the Si and S L(alpha) lines, a blend of Ar VIII-XI lines, and the Ca x K(alpha) line. In some cases the S xv blends with the He-like Si RRC producing a broad feature that cannot be reproduced by a simple Gaussian profile. This could be used as a signature of reflection.

Garcia, J.↗
NASA NTRS2016

Low Cost Entry, Descent, and Landing (EDL) Instrumentation for Planetary Missions

Missions that involve traversing through a planetary atmosphere are unique opportunities that require elements of entry, descent, and landing (EDL). Many aspects of the EDL sequence are qualified using analysis and simulation due to the inability to conduct appropriate ground tests, however validating flight data are often lacking, especially for missions not involving Earth re-entry. NASA has made strategic decisions to collect EDL flight data in order to improve future mission designs. For example, MEDLI1 and EFT-1 gathered hypersonic pressure and in-depth temperature data in the thermal protection system (TPS). However, the ability to collect EDL flight data from the smaller competed missions, such as Discovery and New Frontiers, has been limited in part due to the Principal Investigator-managed cost-caps (PIMCC). The recent NASA decision to consider EDL instrumentation earlier in the mission design cycle led to the inclusion of a requirement in the Discovery 2014 Announcement of Opportunity which requires all missions that involve EDL to include an Engineering Science Investigation (ESI).2 The ESI would involve sensors for aerothermal environment and TPS; atmosphere, aerodynamics, and flight dynamics; atmospheric decelerator; and/or vehicle structure.3 The ESI activity would be funded outside of the PIMCC.

and Landing↗
NASA NTRS2018

Validation of a Mesoscale Fiber Kinking Model Through Test and Analysis of Double Edge Notch Compression Specimens

Tests and analyses were conducted on a series of geometrically-scaled double edge notch compression specimens to validate the capability of the fiber-kinking model in the NASA continuum damage mechanics code for progressive damage analysis, CompDam. The tests and analyses focused on the fiber-kinking damage mechanism, which is of critical importance for predicting accurately longitudinal compression failure in carbon fiber reinforced polymer laminates. The fiber-kinking model in CompDam was augmented with a new capability to represent a hardening response once a kink band has fully formed, enabling prediction of band broadening. Correlation of the test and analysis results showed agreement in stiffness and strength with less than 10% error. The analysis predicts the same sequence of events leading to ultimate failure that was found in the test. The overall excellent correlation in terms of stiffness, strength, and failure process validates the capability of the model for predicting longitudinal compression failure in notched laminates with cross-ply layups.

Bergan, Andrew C.↗
NASA NTRSDate not supplied

GL4U: Using Space Biology Omics Data to Provide Bioinformatics Training for Students and Educators

NASA’s GeneLab project provides researchers open access to space-relevant multi-omics data via the Open Science Data Repository (OSDR) that can be mined to understand the effects of spaceflight on biological systems. To maximize the number of scientists who understand and utilize GeneLab data and data processing pipelines, GeneLab created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct (training students) and indirect (training educators) approaches. The GL4U pilot programs were conducted in June 2021 (direct training) and 2022 (indirect training). During the pilots, students and educators at Historically Black Colleges and Universities (HBCUs) and Minority Serving Institutions (MSIs) participated in a week-long (direct training) or two-week-long (indirect training) bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze space biology RNA sequencing data from OSDR. During the educator pilot, participants received materials, training, and the necessary compute resources to enable them to run the bootcamp at their home institutions, thereby extending the reach of this initiative. In July 2023, GeneLab is partnering with JPL to expand GL4U to include amplicon sequencing (Amp-Seq) analysis training. During the GL4U Amp-Seq bootcamp, student and educator participants will receive training on how to analyze and interpret Amp-Seq data using the NASA GeneLab data processing pipeline. All bootcamp material, including instructions for requesting compute resources, will be made publicly available on GitHub for educators to teach the GL4U content in subsequent semesters. GL4U provides undergraduate students from underrepresented groups the opportunity to learn about NASA and Space Biology, and to enhance their career prospects by gaining hands-on experience analyzing omics data, a skillset that is highly applicable and marketable in the life sciences. We present results from pre- and post-training surveys completed by all participants of the Amp-Seq bootcamp.

Amanda M Saravia-Butler↗
NASA NTRS1993

Finite-size effects on long-range correlations: implications for analyzing DNA sequences

We analyze the fluctuations in the correlation exponents obtained for noncoding DNA sequences. We find prominent sample-to-sample variations as well as variations within a single sample in the scaling exponent. To determine if these fluctuations may result from finite system size, we generate correlated random sequences of comparable length and study the fluctuations in this control system. We find that the DNA exponent fluctuations are consistent with those obtained from the control sequences having long-range power-law correlations. Finally, we compare our exponents for the DNA sequences with the exponents obtained from power-spectrum analysis and correlation-function techniques, and demonstrate that the original "DNA-walk" method is intrinsically more accurate due to reduced noise.

NASA Discipline Cardiopulmonary↗
NASA NTRS2001

Accuracy for detection of simulated lesions: comparison of fluid-attenuated inversion-recovery, proton density--weighted, and T2-weighted synthetic brain MR imaging

OBJECTIVE: The objective of our study was to determine the effects of MR sequence (fluid-attenuated inversion-recovery [FLAIR], proton density--weighted, and T2-weighted) and of lesion location on sensitivity and specificity of lesion detection. MATERIALS AND METHODS: We generated FLAIR, proton density-weighted, and T2-weighted brain images with 3-mm lesions using published parameters for acute multiple sclerosis plaques. Each image contained from zero to five lesions that were distributed among cortical-subcortical, periventricular, and deep white matter regions; on either side; and anterior or posterior in position. We presented images of 540 lesions, distributed among 2592 image regions, to six neuroradiologists. We constructed a contingency table for image regions with lesions and another for image regions without lesions (normal). Each table included the following: the reviewer's number (1--6); the MR sequence; the side, position, and region of the lesion; and the reviewer's response (lesion present or absent [normal]). We performed chi-square and log-linear analyses. RESULTS: The FLAIR sequence yielded the highest true-positive rates (p < 0.001) and the highest true-negative rates (p < 0.001). Regions also differed in reviewers' true-positive rates (p < 0.001) and true-negative rates (p = 0.002). The true-positive rate model generated by log-linear analysis contained an additional sequence-location interaction. The true-negative rate model generated by log-linear analysis confirmed these associations, but no higher order interactions were added. CONCLUSION: We developed software with which we can generate brain images of a wide range of pulse sequences and that allows us to specify the location, size, shape, and intrinsic characteristics of simulated lesions. We found that the use of FLAIR sequences increases detection accuracy for cortical-subcortical and periventricular lesions over that associated with proton density- and T2-weighted sequences.

NASA Discipline Neuroscience↗
NASA NTRS1995

Fractals in biology and medicine

Our purpose is to describe some recent progress in applying fractal concepts to systems of relevance to biology and medicine. We review several biological systems characterized by fractal geometry, with a particular focus on the long-range power-law correlations found recently in DNA sequences containing noncoding material. Furthermore, we discuss the finding that the exponent alpha quantifying these long-range correlations ("fractal complexity") is smaller for coding than for noncoding sequences. We also discuss the application of fractal scaling analysis to the dynamics of heartbeat regulation, and report the recent finding that the normal heart is characterized by long-range "anticorrelations" which are absent in the diseased heart.

Review↗
DOE OSTI2024

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Abstract Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

Scaling in nature: from DNA through heartbeats to weather

The purpose of this report is to describe some recent progress in applying scaling concepts to various systems in nature. We review several systems characterized by scaling laws such as DNA sequences, heartbeat rates and weather variations. We discuss the finding that the exponent alpha quantifying the scaling in DNA in smaller for coding than for noncoding sequences. We also discuss the application of fractal scaling analysis to the dynamics of heartbeat regulation, and report the recent finding that the scaling exponent alpha is smaller during sleep periods compared to wake periods. We also discuss the recent findings that suggest a universal scaling exponent characterizing the weather fluctuations.

Review↗
NASA NTRS1980

An enhancement of NASTRAN for the seismic analysis of structures

New modules, bulk data cards and DMAP sequence were added to NASTRAN to aid in the seismic analysis of nuclear power plant structures. These allow input consisting of acceleration time histories and result in the generation of acceleration floor response spectra. The resulting system contains numerous user convenience features, as well as being reasonably efficient.

Burroughs, J. W.↗
DOE OSTI2020

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genomes OnLine Database (GOLD) v.8: overview and updates

The Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) is a manually curated, daily updated collection of genome projects and their metadata accumulated from around the world. The current version of the database includes over 1.17 million entries organized broadly into Studies (45 770), Organisms (387 382) or Biosamples (101 207), Sequencing Projects (355 364) and Analysis Projects (283 481). These four levels contain over 600 metadata fields, which includes 76 controlled vocabulary (CV) tables containing 3873 terms. GOLD provides an interactive web user interface for browsing and searching by a wide range of project and metadata fields. Users can enter details about their own projects in GOLD, which acts as a gatekeeper to ensure that metadata is accurately documented before submitting sequence information to the Integrated Microbial Genomes (IMG) system for analysis. In order to maintain a reference dataset for use by members of the scientific community, GOLD also imports projects from public repositories such as GenBank and SRA. Here, the current status of the database, along with recent updates and improvements are described in this manuscript.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Response surface modeling of CO 2 dynamic storage efficiency factor in high permeability thick sandstones

In order to utilize as much of the pore space for CO 2 storage in high permeability thick saline aquifers, it is vital to investigate the interactions of injected CO 2 with formation brine and rock. In order to quantify the displacement process, we investigate the dynamic storage efficiency factor (DSEF) for saline aquifers where pressure increase is minimal during the injection phase. Dimensionless numbers are derived from basic governing equations, constitutive equations, initial and boundary conditions using the inspection analysis. Then using the Hammersley sequence sampling, 178 numerical experiments are designed, and a compositional reservoir simulator is used to perform these simulations. In the next step, response surface regression analysis is used to establish a relationship between DSEF obtained from the numerical simulations and the corresponding dimensionless numbers. The simulation results show that for the studied conditions the underground dynamics is mostly influenced by the gravity number, followed by effective aspect ratio and dip numbers. The results from the response surface regression analysis are used to develop a correlation, which can be used to estimate the dynamic CO 2 storage capacity of relevant zones. This study provides quantitative measures for the different competing mechanisms involved in underground displacement of fluids in CO 2 geological storage, which can serve as a useful tool during planning phase of storage projects.

02 PETROLEUM↗
DOE OSTI2021

Characterization of axolotl lampbrush chromosomes by fluorescence in situ hybridization and immunostaining

The lampbrush chromosomes (LBCs) in oocytes of the Mexican axolotl (Ambystoma mexicanum) were identified some time ago by their relative lengths and predicted centromeres, but they have never been associated completely with the mitotic karyotype, linkage maps or genome assembly. We identified 9 of the axolotl LBCs using RNAseq to identify actively transcribed genes and 13 BAC (bacterial artificial clone) probes containing pieces of active genes. Using read coverage analysis to find candidate centromere sequences, we developed a centromere probe that localizes to all 14 centromeres. Measurements of relative LBC arm lengths and polymerase III localization patterns enabled us to identify all LBCs. This study presents a relatively simple and reliable way to identify each axolotl LBC cytologically and to anchor chromosome-length sequences (from the axolotl genome assembly) to the physical LBCs by immunostaining and fluorescence in situ hybridization. Our data will facilitate a more detailed transcription analysis of individual LBC loops.

60 APPLIED LIFE SCIENCES↗