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NASA NTRS1994

Evolutionary sequences of very hot, low-mass, accreting white dwarfs with application to symbiotic variables and ultrasoft/supersoft low-luminosity x-ray sources

We present the first detailed model results of quasi-static evolutionary sequences of very hot low-mass white dwarfs accreting hydrogen-rich material at rates between 1 x 10(exp -7) and 1 x 10(exp -9) solar mass/yr. Most of the sequences were generated from starting models whose core thermal structures were not thermally relaxed in the thermal pulse cycle-averaged sense of an asymptotic giant branch stellar core. Hence, the evolution at constant accretion rate was not invariably characterized by series of identical shell flashes. Sequences exhibiting stable steady state nuclear burning at the accretion supply rate as well as sequences exhibiting recurrent thermonuclear shell flashes are presented and discussed. In some cases, the white dwarf accretors remain small (less than 10(exp 11) cm) and very hot even during the shell flash episode. They then experience continued but reduced hydrogen shell burning during the longer quiescent intervals while their surface temperatures increase both because of compressional heating and envelope structure readjustment in response to accretion over thousands of years. Both accretion and continued hydrogen burning power these models with luminosities of a few times 10(exp 37) ergs/s. We suggest that the physical properties of these model sequences are of considerable relevance to the observed outburst and quiescent behavior of those symbiotic variables and symbiotic novae containing low-mass white dwarfs. We also suggest that our models are relevant to the observational characteristics of the growing class of low-luminosity, supersoft/ultrasoft X-ray sources in globular clusters, and the Magellanic Clouds.

Sion, Edward M.↗

NASA NTRS1997

The Carbon-Rich Dust Sequence: Infrared Spectral Classification of Carbon Stars

We have developed a classification system for the infrared spectral emission from carbon stars, using a sample of 96 bright carbon-rich variables associated with the asymptotic giant branch. In addition to the stellar contribution, most spectra include the 11.2 micron emission feature from SiC and either a smooth cool continuum from amorphous carbon or a secondary emission feature at 9.0 microns. We have identified a carbon-rich dust sequence along which the amorphous carbon component grows while the 9.0 micron feature declines in strength. Along this spectral sequence, the fraction of Miras increases, as does the period of variability, the mass-loss rate, and the thickness of the circumstellar shell. Thus the carbon-rich dust sequence appears to be an evolutionary sequence. One class of spectra shows a particularly strong 9.0 micron feature, Enhanced C/O ratio, and several other unusual properties that suggest a different sequence, perhaps related to J stars.

Solan, G. C.↗

NASA NTRS2004

Main-Sequence CMEs as Magnetic Explosions: Compatibility with Observed Kinematics

We examine the kinematics of 26 CMEs of the morphological main sequence of CMEs, those having the classic three-part bubble structure of (1) a bright front eveloping (2) a dark cavity within which rides (3) a bright blob/filamentary feature. Each CME is observed in Yohkoh/SXT images to originate from near the limb (> or equal to 0.7 R(sub Sun) from disk center). The basic data (from the SOHO LASCO CME Catalog) for the kinematics of each CME are the sequence of LASCO images of the CME, the time of each image, the measured radial distance of the front edge of the CME in each image, and the measured angular extent of the CME. About half of our CMEs (12) occur with a flare, and the rest (14) occur without a flare. While the average linear-fit speed of the flare CMEs (1000 km/s) is twice that of the non-flare CMEs (510 km/s), the flare CMEs and the non-flare CMEs are similar in that some have nearly flat velocity-height (radial extent) profiles (little acceleration), some have noticeably falling velocity profiles (noticeable deceleration), and the rest have velocity profiles that rise considerably through the outer corona (blatant acceleration). This suggests that in addition to sharing similar morphology, main-sequence CMEs all have basically the same driving mechanism. The observed radial progression of each of our 26 CMEs is fit by a simple model magnetic plasmoid that is in pressure balance with the radial magnetic field in the outer corona and that propels itself outward by magnetic expansion, doing no net work on its surroundings. On average over the 26 CMEs, this model fits the observations as well as the assumption of constant acceleration. This is compatible with main-sequence CMEs being magnetically driven, basically magnetic explosions, with the velocity profile in the outer corona being largely dictated by the initial Alfien speed in the CME (when the front is at approx. 3 (sub Sun), analogous to the mass of a main-sequence star dictating the luminosity.

Moore, Ron↗

NASA NTRS2006

Anomaly Detection in Large Sets of High-Dimensional Symbol Sequences

This paper addresses the problem of detecting and describing anomalies in large sets of high-dimensional symbol sequences. The approach taken uses unsupervised clustering of sequences using the normalized longest common subsequence (LCS) as a similarity measure, followed by detailed analysis of outliers to detect anomalies. As the LCS measure is expensive to compute, the first part of the paper discusses existing algorithms, such as the Hunt-Szymanski algorithm, that have low time-complexity. We then discuss why these algorithms often do not work well in practice and present a new hybrid algorithm for computing the LCS that, in our tests, outperforms the Hunt-Szymanski algorithm by a factor of five. The second part of the paper presents new algorithms for outlier analysis that provide comprehensible indicators as to why a particular sequence was deemed to be an outlier. The algorithms provide a coherent description to an analyst of the anomalies in the sequence, compared to more normal sequences. The algorithms we present are general and domain-independent, so we discuss applications in related areas such as anomaly detection.

Budalakoti, Suratna↗

NASA NTRS2008

Sequence History Update Tool

The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

Khanampompan, Teerapat↗

NASA NTRS2012

Interuser Interference Analysis for Direct-Sequence Spread-Spectrum Systems Part I: Partial-Period Cross-Correlation

This presentation discusses an analysis approach to evaluate the interuser interference for Direct-Sequence Spread-Spectrum (DSSS) Systems for Space Network (SN) Users. Part I of this analysis shows that the correlation property of pseudo noise (PN) sequences is the critical factor which determines the interuser interference performance of the DSSS system. For non-standard DSSS systems in which PN sequence s period is much larger than one data symbol duration, it is the partial-period cross-correlation that determines the system performance. This study reveals through an example that a well-designed PN sequence set (e.g. Gold Sequence, in which the cross-correlation for a whole-period is well controlled) may have non-controlled partial-period cross-correlation which could cause severe interuser interference for a DSSS system. Since the analytical derivation of performance metric (bit error rate or signal-to-noise ratio) based on partial-period cross-correlation is prohibitive, the performance degradation due to partial-period cross-correlation will be evaluated using simulation in Part II of this analysis in the future.

Ni, Jianjun (David)↗

NASA NTRS2014

The Cassini Solstice Mission: Streamlining Operations by Sequencing with PIEs

The Cassini Solstice Mission (CSM) is the second extended mission phase of the highly successful Cassini/Huygens mission to Saturn. Conducted at a much-reduced funding level, operations for the CSM have been streamlined and simplified significantly. Integration of the science timeline, which involves allocating observation time in a balanced manner to each of the five different science disciplines (with representatives from the twelve different science instruments), has long been a labor-intensive endeavor. Lessons learned from the prime mission (2004-2008) and first extended mission (Equinox mission, 2008-2010) were utilized to design a new process involving PIEs (Pre-Integrated Events) to ensure the highest priority observations for each discipline could be accomplished despite reduced work force and overall simplification of processes. Discipline-level PIE lists were managed by the Science Planning team and graphically mapped to aid timeline deconfliction meetings prior to assigning discrete segments of time to the various disciplines. Periapse segments are generally discipline-focused, with the exception of a handful of PIEs. In addition to all PIEs being documented in a spreadsheet, allocated out-of-discipline PIEs were entered into the Cassini Information Management System (CIMS) well in advance of timeline integration. The disciplines were then free to work the rest of the timeline internally, without the need for frequent interaction, debate, and negotiation with representatives from other disciplines. As a result, the number of integration meetings has been cut back extensively, freeing up workforce. The sequence implementation process was streamlined as well, combining two previous processes (and teams) into one. The new Sequence Implementation Process (SIP) schedules 22 weeks to build each 10-week-long sequence, and only 3 sequence processes overlap. This differs significantly from prime mission during which 5-week-long sequences were built in 24 weeks, with 6 overlapping processes.

Vandermey, Nancy↗

NASA NTRS2020

GN&C Sequencing for Orion Rendezvous, Proximity Operations, and Docking

As part of the Artemis program to return humans to the lunar surface, the National Aeronautics and Space Administration is planning to use the Orion Multi- Purpose Crew Vehicle to transport crew to a small orbital platform called Gate- way in cislunar space. To facilitate this activity, Orion is required to perform Rendezvous, Proximity Operations, and Docking (RPOD) with both the Gate- way and the launch vehicle upper stage. The Orion spacecraft uses sequencing in the form of Phases, Segments, Activities, and Modes (PSAM) to configure Guidance, Navigation, & Control (GN&C) software during each portion of the mission. Significant updates to Orion PSAM definitions are required for RPOD. This paper describes the process of defining these new sequencing elements, implementing them in prototype flight software, and testing them in an integrated simulation environment. First, requirements are specified to determine the nominal and off-nominal sequencing behavior necessary to complete the mission. These requirements also specify which software functions should be fully autonomous and which functions require manual interactions from crew or ground operators. Next, the RPOD concept of operations is defined with detailed events listed in a mission timeline. Third, a state machine diagram is developed to show all PSAM states, including all possible transitions between them. After this, the PSAM states and transitions are entered into a sequencing software emulator and parameter values and modes are defined for GN&C software elements. Finally, the PSAM architecture is tested within an integrated simulation environment by connecting it with prototypes of relevant GN&C flight software elements and with detailed vehicle models. After the sequencing design has been finalized and tested, it is implemented in flight software.

Schulte, Peter Z.↗

NASA NTRSDate not supplied

Congruence of Clusters Defined By Whole Genome Sequencing and MALDI-TOF for Bacteria Isolated From Cleanrooms

Introduction: Oligotrophic conditions can render cleanrooms inhospitable to microbes. Despite these constraints, fungi and bacteria are frequently isolated from surfaces in astromaterials cleanrooms at the Johnson Space Center. Bacillus species are of particular concern because endospores belonging to this genus are resilient and can affect astromaterials. Current monitoring programs rely on 16S rRNA sequencing and the VITEK2 Compact system. These methods have limited power to resolve Bacillus species. Matrix-assisted laser desorption - time of flight mass spectrometry (MALDI-TOF MS), provides a rapid, low cost, method of identifying bacterial isolates and has a higher resolution than 16S rRNA sequencing, particularly for Bacillus species; however, few studies have compared this method to the industry gold standard, whole genome sequencing (WGS). Methods: Based on 16S rRNA classification, we selected 14 isolates for analysis with MALDI-TOF and WGS. Mass spectra were generated with MALDI-TOF MS and processed with custom scripts to identify clusters of closely related isolates and calculate a matrix of pairwise cosine similarity scores. Hybrid Illumina and Nanopore sequencing were used to generate draft genomes. Pairwise similarity scores were calculated from these genomes based on the average amino acid identity (AAI) predicted from single copy core genes. Congruence of clustering between these methods, was assessed by calculating adjusted Rand and Wallace coefficients. Results: Clusters of species generated from MALDI-TOF MS showed good agreement of phylotypes generated with WGS. Pairs of strains that were > 94% similar to each other in terms of predicted amino acid sequences consistently showed cosine similarities of mass spectra > 0.65 and, of the 9 clusters identified with WGS, 8 were identical with MALDI-TOF. This corresponds to an adjusted Rand index of 0.95 and a 95% confidence interval of 0.80 – 1.00 for adjusted Wallace coefficients. The only discordance was for a pair of isolates that were classified as Paenibacillus species. This pair showed relatively high similarity (0.84) in terms of MALDI-TOF MS but only 85% similarity in terms of AAI. Conclusion: This study shows that MALDI-TOF and WGS exhibit a similar ability to delineate Bacillus species isolated from cleanrooms and taxonomic units described by these two methods are consistent with one another. Since MALDI-TOF MS is low in cost and high in throughput, this approach appears to be an ideal option for routine microbial monitoring and identifying Bacillus species.

Farnaz Mazhari↗

NASA NTRSDate not supplied

Method Development for In-situ Detection of Latent Herpesvirus DNA from Saliva using Nanopore Sequencing

Research toward latent herpesvirus reactivation has been intensively addressed through Space Shuttle and International Space Station (ISS) investigations. This work has provided the understanding that persistent reactivation of herpesviruses from asymptomatic crew can be detected through viral shedding in saliva, urine, and blood. Occasionally, viral reactivation from the latency stage can pose a threat to crew health (clinical manifestation) before, during, and after flight missions. Furthermore, previous work detailing correlations with immunity indicate that monitoring viral reactivation could be implemented to assess potential immune dysfunction. While in-flight monitoring is desirable, there is no well-established procedure or method for real-time evaluations, and research to date has relied on postflight, ground-based analysis. The development of portable molecular technologies like the miniPCR™ (miniPCR Bio) thermal cycler and the MinION™ sequencer (Oxford Nanopore Technologies) have confirmed that real-time monitoring is possible in extreme and low resource environments. These devices, combined with simple sample preparation methods, have been used to demonstrate bacterial identification onboard the ISS, as well as rapid viral detection in remote locations on Earth. The work here builds upon previous molecular advancements onboard the ISS toward the development and validation of a spaceflight-compatible method for viral detection from crew samples. Several herpesviruses can be detected in saliva, which provides a non-invasive means to collect samples for monitoring. While the basis for this method lies in previous spaceflight investigations, key points for method optimization include DNA extraction from saliva, viral primer selection, and bioinformatic processes for data analysis. To increase viral yield, numerous DNA extraction methods have been evaluated and will be discussed in detail. For initial development and testing, varicella-zoster virus (VZV) is being targeted though open reading frame 51 and 63 (ORF51, ORF63), as the replication origin-binding protein is highly expressed during latency. Optimization of the thermal cycling parameters has resulted in the ability to test the entire process. The full method has been tested with both viral VZV DNA standards and saliva spiked with varying concentrations of VZV. Viral sequence data were mapped to the reference sequence using minimap2. Prior to mapping, DNA sequencing reads were filtered for length and quality, barcodes were removed, and alignment identity calculated. Following further assessments, statistics were compared across multiple sequencing experiments and are being used to determine the success of the protocols. Forward work will include the incorporation of herpes simplex virus 1 (HSV-1) and Epstein-Barr virus (EBV) primers as well as the validation of results to the terrestrial qPCR standard assay. Upon full validation of the developed method, saliva will be collected from 20 healthy subjects and spiked with viral DNA. These samples will be split and assayed with the MinION and standard qPCR assay.

Hang N Nguyen↗

NASA NTRS1995

Statistical and linguistic features of DNA sequences

We present evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range--indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationary" feature of the sequence of base pairs by applying a new algorithm called Detrended Fluctuation Analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and noncoding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to all eukaryotic DNA sequences (33 301 coding and 29 453 noncoding) in the entire GenBank database. We describe a simple model to account for the presence of long-range power-law correlations which is based upon a generalization of the classic Levy walk. Finally, we describe briefly some recent work showing that the noncoding sequences have certain statistical features in common with natural languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function. We suggest that noncoding regions in plants and invertebrates may display a smaller entropy and larger redundancy than coding regions, further supporting the possibility that noncoding regions of DNA may carry biological information.

Non-NASA Center↗

NASA NTRS1993

Generalized Levy-walk model for DNA nucleotide sequences

We propose a generalized Levy walk to model fractal landscapes observed in noncoding DNA sequences. We find that this model provides a very close approximation to the empirical data and explains a number of statistical properties of genomic DNA sequences such as the distribution of strand-biased regions (those with an excess of one type of nucleotide) as well as local changes in the slope of the correlation exponent alpha. The generalized Levy-walk model simultaneously accounts for the long-range correlations in noncoding DNA sequences and for the apparently paradoxical finding of long subregions of biased random walks (length lj) within these correlated sequences. In the generalized Levy-walk model, the lj are chosen from a power-law distribution P(lj) varies as lj(-mu). The correlation exponent alpha is related to mu through alpha = 2-mu/2 if 2 < mu < 3. The model is consistent with the finding of "repetitive elements" of variable length interspersed within noncoding DNA.

NASA Discipline Number 14-10↗

NASA NTRS1992

Crosslinking transcription factors to their recognition sequences with PtII complexes

We have prepared phosphorothioate-containing cyclic oligodeoxynucleotides that fold into 'dumbbells' containing CRE and TRE sequences, the binding sequences for the CREB and JUN proteins, respectively. Six phosphorothioate residues were introduced into each of the recognition sequences. K2PtCl4 crosslinks CRE to CREB and TRE to JUN. The extent of crosslinking is about eight times greater than that observed with standard oligodeoxynucleotides and amounts to 30-50% of the efficiency of non-covalent association as estimated by gel-shift assays. Crosslinking is reversed by incubation with NaCN. The crosslinking reaction is specific--a dumbbell oligonucleotide with six phosphorothioate groups introduced into the Sp1 recognition sequence could not be crosslinked efficiently to CREB or JUN proteins with K2PtCl4. The binding of TRE to CREB is not strong enough for effective detection by gel-shift assays, but the TRE-CREB complex is crosslinked efficiently by K2PtCl4 and can then readily be detected.

NASA Discipline Exobiology↗

NASA NTRS1992

How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity

16S rRNA (genes coding for rRNA) sequence comparisons were conducted with the following three psychrophilic strains: Bacillus globisporus W25T (T = type strain) and Bacillus psychrophilus W16AT, and W5. These strains exhibited more than 99.5% sequence identity and within experimental uncertainty could be regarded as identical. Their close taxonomic relationship was further documented by phenotypic similarities. In contrast, previously published DNA-DNA hybridization results have convincingly established that these strains do not belong to the same species if current standards are used. These results emphasize the important point that effective identity of 16S rRNA sequences is not necessarily a sufficient criterion to guarantee species identity. Thus, although 16S rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable.

Non-NASA Center↗

NASA NTRS1993

Assignment of fatty acid-beta-oxidizing syntrophic bacteria to Syntrophomonadaceae fam. nov. on the basis of 16S rRNA sequence analyses

After enrichment from Chinese rural anaerobic digestor sludge, anaerobic, sporing and nonsporing, saturated fatty acid-beta-oxidizing syntrophic bacteria were isolated as cocultures with H2- and formate-utilizing Methanospirillum hungatei or Desulfovibrio sp. strain G-11. The syntrophs degraded C4 to C8 saturated fatty acids, including isobutyrate and 2-methylbutyrate. They were adapted to grow on crotonate and were isolated as pure cultures. The crotonate-grown pure cultures alone did not grow on butyrate in either the presence or the absence of some common electron acceptors. However, when they were reconstituted with M. hungatei, growth on butyrate again occurred. In contrast, crotonate-grown Clostridium kluyveri and Clostridium sticklandii, as well as Clostridium sporogenes, failed to grow on butyrate when these organisms were cocultured with M. hungatei. The crotonate-grown pure subcultures of the syntrophs described above were subjected to 16S rRNA sequence analysis. Several previously documented fatty acid-beta-oxidizing syntrophs grown in pure cultures with crotonate were also subjected to comparative sequence analyses. The sequence analyses revealed that the new sporing and nonsporing isolates and other syntrophs that we sequenced, which had either gram-negative or gram-positive cell wall ultrastructure, all belonged to the phylogenetically gram-positive phylum. They were not closely related to any of the previously known subdivisions in the gram-positive phylum with which they were compared, but were closely related to each other, forming a new subdivision in the phylum. We recommend that this group be designated Syntrophomonadaceae fam. nov.; a description is given.

NASA Discipline Number 52-30↗

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 NTRS1994

Correlation approach to identify coding regions in DNA sequences

Recently, it was observed that noncoding regions of DNA sequences possess long-range power-law correlations, whereas coding regions typically display only short-range correlations. We develop an algorithm based on this finding that enables investigators to perform a statistical analysis on long DNA sequences to locate possible coding regions. The algorithm is particularly successful in predicting the location of lengthy coding regions. For example, for the complete genome of yeast chromosome III (315,344 nucleotides), at least 82% of the predictions correspond to putative coding regions; the algorithm correctly identified all coding regions larger than 3000 nucleotides, 92% of coding regions between 2000 and 3000 nucleotides long, and 79% of coding regions between 1000 and 2000 nucleotides. The predictive ability of this new algorithm supports the claim that there is a fundamental difference in the correlation property between coding and noncoding sequences. This algorithm, which is not species-dependent, can be implemented with other techniques for rapidly and accurately locating relatively long coding regions in genomic sequences.

Non-NASA Center↗

NASA NTRS2012

Irreducible Tests for Space Mission Sequencing Software

As missions extend further into space, the modeling and simulation of their every action and instruction becomes critical. The greater the distance between Earth and the spacecraft, the smaller the window for communication becomes. Therefore, through modeling and simulating the planned operations, the most efficient sequence of commands can be sent to the spacecraft. The Space Mission Sequencing Software is being developed as the next generation of sequencing software to ensure the most efficient communication to interplanetary and deep space mission spacecraft. Aside from efficiency, the software also checks to make sure that communication during a specified time is even possible, meaning that there is not a planet or moon preventing reception of a signal from Earth or that two opposing commands are being given simultaneously. In this way, the software not only models the proposed instructions to the spacecraft, but also validates the commands as well.To ensure that all spacecraft communications are sequenced properly, a timeline is used to structure the data. The created timelines are immutable and once data is as-signed to a timeline, it shall never be deleted nor renamed. This is to prevent the need for storing and filing the timelines for use by other programs. Several types of timelines can be created to accommodate different types of communications (activities, measurements, commands, states, events). Each of these timeline types requires specific parameters and all have options for additional parameters if needed. With so many combinations of parameters available, the robustness and stability of the software is a necessity. Therefore a baseline must be established to ensure the full functionality of the software and it is here where the irreducible tests come into use.

sequencing test↗