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All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

Development and Application of Weld Track Thermal Analysis for the Exploration Extravehicular Mobility Unit

NASA is studying the next generation of space suit for safe operations in space, from the International Space Station to the lunar surface as part of the Exploration Extravehicular Mobility Unit project. The backplate structure of the portable life support system (PLSS) serves as the attachment point for assembly of the PLSS and contains embedded cooling channels. The thermal loop plumbing assembly and backplate are combined into a single component such that the fluid lines run through the midplane of the backplate. The manufacturing of the Ti-6Al-4V backplate consists of machining channels into a plate, welding cover plates on each channel using an electron beam, and additional machining for excess material removal and final detail. Careful control of the electron beam weld process is necessary to completely seal cover plates, produce consistent weld tracks, and produce channels with uniform cross sections free of debris and defects. The backplate contains multiple weld channels with unique geometries. The weld process parameters include choosing the beam current and focus, accelerating voltage, travel speed, pause times between weld tracks, and sequence of weld tracks. A transient finite element thermal analysis was developed to provide support for choosing and controlling the weld process parameters to maintain a consistent melt pool along each of the weld tracks. A moving distributed heat source is modeled to represent the heat input generated by the electron beam. The heat source model is a critical input to the analysis for accurate temperature predictions during the weld process. A modified conical heat source was developed to account for the change in working distance between the backplate and cover plates. The geometry of the material being welded must be accounted for by the heat source model to define the correct energy input. The weld process control is designed according to the predicted thermal history and melt pool dimensions for each of the weld channels. The analysis model, modified heat source, temperature and melt pool predictions, application of the thermal data to the weld parameters, and comparison with micrograph cross-sections from weld trials will be discussed in this presentation.

Electron Beam Welding↗
DOE OSTI2025

Assembly of small silica nanoparticles using lipid-tethered DNA ‘bonds’

Single-stranded DNA molecules modified with cholesterol functional groups are physically tethered to silica nanoparticles (diameter 25 nm) that are encapsulated in a lipid bilayer. Such tethering increases the azimuthal mobility of the DNA molecules across the nanoparticle surface and enables nonspecific bonding, eliminating the need for specialized surface chemistries (such as silane or thiol ligands). To induce assembly, double-stranded DNA ‘bridge’ molecules are then added with complementary nucleotides to the DNA ‘anchor’ molecules that are physically tethered to the lipids on the surface of the particles. Assembly is observed to occur at room temperature and without the need for temperature annealing. Using automated liquid handling tools, assemblies are created in high throughput and rapidly characterized using SAXS. It is determined that the relative concentration of DNA-to-silica and the ionic strength of the solution are important parameters that affect the resulting assembly. Analysis of SAXS data is performed using coarse-grained particle dynamics simulations. The results support the spontaneous formation of semi-crystalline particle assemblies by particle condensation, where the interparticle distance is tuned by the sequence of the DNA ‘bridge’ used to link the particles. Crystallinity analysis performed on the resulting simulations, optimized to match SAXS observations, suggest that particle clusters display increased crystallinity in the center of the clusters, but their maximum size remains relatively small (sub-micron) before settling occurs, which limits the extent of crystallization.

Chiang, Huat Thart [Univ. of Washington, Seattle, ↗
DOE OSTI2024

Impedance Scan of Inverter-Based Resources and Diesel Generator for Stability Analysis: Preprint

Impedance-based methods are widely used for power system stability analysis with inverter-based resources (IBRs), e.g., assessing dynamic interactions between the power grid and an IBR, control interactions between multiple IBRs, and the sub-synchronous oscillation and damping phenomenon. Since it is difficult to get a numerical model 100% matching with the hardware IBR, using the hardware inverter directly to obtain its output impedance has become a prominent approach nowadays. Therefore, this article presents the impedance scan using hardware IBRs, and also a hardware diesel generator as it still stays with the grid before the grid completely goes to renewable. The devices under test (DuTs) for the impedance scan includes two 3-..phi.., 480 V, 60 Hz commercial grid-forming IBRs (one of 250 kVA and another of 125 kVA rating) in series with ..delta..-Y transformers, one 3-..phi.., 480 V, 60 Hz commercial grid-following IBR (of 125 kVA rating), and a 3-..phi.., 480 V, 60 Hz commercial diesel generator (of 187.5 kVA rating). Using voltage signals perturbed with sub-, inter-, and higher harmonic components, and measuring the current response, the positive-sequence impedances are computed via an offline- based post-analysis. Moreover, best-fit transfer functions are estimated that closely resemble the measured data points of the positive-sequence impedances. Based on the observations from various outcomes of the hardware experiments, this article also provides some fundamental insights on the equivalent positive- sequence impedance of a combination of multiple hardware components by comparing the estimated and the empirically computed impedances. A comparative insight on the damping capability of the DuTs using the positive-sequence impedances of the hardware is also discussed.

grid following inverter↗
DOE OSTI2017

Community detection in sequence similarity networks based on attribute clustering

Networks are powerful tools for the presentation and analysis of interactions in multi-component systems. A commonly studied mesoscopic feature of networks is their community structure, which arises from grouping together similar nodes into one community and dissimilar nodes into separate communities. Here in this paper, the community structure of protein sequence similarity networks is determined with a new method: Attribute Clustering Dependent Communities (ACDC). Sequence similarity has hitherto typically been quantified by the alignment score or its expectation value. However, pair alignments with the same score or expectation value cannot thus be differentiated. To overcome this deficiency, the method constructs, for pair alignments, an extended alignment metric, the link attribute vector, which includes the score and other alignment characteristics. Rescaling components of the attribute vectors qualitatively identifies a systematic variation of sequence similarity within protein superfamilies. The problem of community detection is then mapped to clustering the link attribute vectors, selection of an optimal subset of links and community structure refinement based on the partition density of the network. ACDC-predicted communities are found to be in good agreement with gold standard sequence databases for which the "ground truth" community structures (or families) are known. ACDC is therefore a community detection method for sequence similarity networks based entirely on pair similarity information. A serial implementation of ACDC is available from https://cmb.ornl.gov/resources/developments

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1996

A mutation in protein phosphatase 2A regulatory subunit A affects auxin transport in Arabidopsis

The phytohormone auxin controls processes such as cell elongation, root hair development and root branching. Tropisms, growth curvatures triggered by gravity, light and touch, are also auxin-mediated responses. Auxin is synthesized in the shoot apex and transported through the stem, but the molecular mechanism of auxin transport is not well understood. Naphthylphthalamic acid (NPA) and other inhibitors of auxin transport block tropic curvature responses and inhibit root and shoot elongation. We have isolated a novel Arabidopsis thaliana mutant designated roots curl in NPA (rcn1). Mutant seedlings exhibit altered responses to NPA in root curling and hypocotyl elongation. Auxin efflux in mutant seedlings displays increased sensitivity to NPA. The rcn1 mutation was transferred-DNA (T-DNA) tagged and sequences flanking the T-DNA insert were cloned. Analysis of the RCN1 cDNA reveals that the T-DNA insertion disrupts a gene for the regulatory A subunit of protein phosphatase 2A (PP2A-A). The RCN1 gene rescues the rcn1 mutant phenotype and also complements the temperature-sensitive phenotype of the Saccharomyces cerevisiae PP2A-A mutation, tpd3-1. These data implicate protein phosphatase 2A in the regulation of auxin transport in Arabidopsis.

Non-NASA Center↗
DOE OSTI2018

Characterization of Novel and Efficient Poly-3-hydroxybutyrate (PHB) Producing Bacteria Isolated from Rhizospheric Soils

Polyhydroxybutyrate (PHB) is an eco-friendly, biodegradable plastic which exhibits properties very similar to the conventional plastic, thus, having high potential for replacing non-degradable conventional polypropylene plastic that is responsible for several environmental problems at global level. The present study focuses on the isolation and characterization of potential novel PHB producers. A total of 194 PHB producing bacteria were isolated from rhizospheric soils of three different crops; and subjected to microscopic, biochemical and molecular characterization studies. Quantification of PHB production exhibited significant amount of PHB accumulation (120–132 mg/ml) by a few isolates (KW-4, MS-6, RoW-1, AW-1 and RoS-4). Fourier transform infrared spectroscopy (FTIR) analysis of PHB extracted from the isolates was found to be comparable to the spectra of standard PHB, thus, establishing the chemical nature of the extracted polymer. Detection of PHB granules by transmission electron microscopy (TEM) confirmed the isolates to be efficient PHB producers. For molecular characterization of the isolates, phbC gene amplification studies were undertaken, which resulted into an amplification product of 1089 bp, representing the complete PHB synthase gene. Using 16S rRNA gene amplification and sequencing, the selected isolates were identified as belonging to four major genera, viz., Bacillus, Lysinibacillus, Clostridium and Klebsiella; however, Bacillus being the predominant genera. Analysis of 16S rDNA sequences showed that a few isolates exhibited significant differences from their nearest neighbours (similarity level ranging between 93 and 99%), thus, strongly suggesting that they might represent novel strains. Some of these probable novel high PHB producers reported in the present study hold high potential to be exploited for further industrial-scale mass production of biodegradable polymer.

36 MATERIALS SCIENCE↗
NASA NTRS2004

A parametric study of single-wall carbon nanotube growth by laser ablation

Results of a parametric study of carbon nanotube production by the double-pulse laser oven process are presented. The effect of various operating parameters on the production of single-wall carbon nanotubes (SWCNTs) is estimated by characterizing the nanotube material using analytical techniques, including scanning electron microscopy, transmission electron microscopy, thermo gravimetric analysis and Raman spectroscopy. The study included changing the sequence of the laser pulses, laser energy, pulse separation, type of buffer gas used, operating pressure, flow rate, inner tube diameter, as well as its material, and oven temperature. It was found that the material quality and quantity improve with deviation from normal operation parameters such as laser energy density higher than 1.5 J/cm2, pressure lower than 67 kPa, and flow rates higher than 100 sccm. Use of helium produced mainly small diameter tubes and a lower yield. The diameter of SWCNTs decreases with decreasing oven temperature and lower flow rates.

Nanotubes, Carbon/chemistry↗
NASA NTRS2015

Simulation of Liquid Rocket Engine Failure Propagation Using Self-Evolving Scenarios

Traditional probabilistic risk assessment approaches often require failure scenarios to be explicitly defined through event sequences that are then quantified as part of the integrated analysis. This approach becomes difficult when failure propagation paths change as a function of the system operation. Additionally, if the propagation paths represent interactions among even a modest number of components, the scenario count becomes combinatorially intractable. This paper presents an alternate approach for quantifying the probability of failure propagation in such a case. Rather than explicitly defining scenario sequences, simple physical models are created for each of the components. In this way, only the physical states and rules of component interactions must be defined, rather than event sequences for each individual scenario. Initiating failures are introduced into the system, either randomly or as defined by relative likelihood, and the failures cascade through the system via the interaction rules. This process is repeated using Monte Carlo methods and, as a result, the most probable scenarios “self-evolve” in terms of both sequence path and frequency. This approach was applied to failures occurring in the engine compartment of a space launch vehicle with four liquid rocket engines and four high-pressure helium tanks. Each engine was modeled with key components, such as turbomachinery, combustion chamber, propellant lines, and additional support systems. Three test cases were conducted with different high-energy engine failures. End results of interest included an additional engine-out failure and tank burst, which represent the loss-of-mission (LOM) and loss-of-crew (LOC) failure environments, respectively. Observations show that almost every scenario outcome is unique and that many scenarios involve complex chain reactions that are difficult to predict. This validates the usefulness of the modeling approach in assessing the overall risks to the crew during a launch vehicle abort.

Rocket Engine↗
NASA NTRS2021

Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station using Nanopore Sequencing

For the past two decades, microbial monitoring of the International Space Station (ISS) has relied on culture-dependent methods that require return to Earth for analysis. This has a number of limitations, with the most significant being bias towards the detection of culturable organisms and the inherent delay between sample collection and ground-based analysis. In recent years, portable and easy-to-use molecular-based tools, such as Oxford Nanopore Technologies’ MinION™ sequencer and miniPCR bio’s miniPCR™ thermal cycler, have been validated onboard the ISS. Here, we report on the development, validation, and implementation of a swab-to-sequencer method that provides a culture-independent solution to real-time microbial profiling onboard the ISS. Method development focused on analysis of swabs collected in a low-biomass environment with limited facility resources and stringent controls on allowed processes and reagents. ISS-optimized procedures included enzymatic DNA extraction from a swab tip, bead-based purifications, altered buffers, and the use of miniPCR and the MinION. Validation was conducted through extensive ground-based assessments comparing current standard culture-dependent and newly developed culture-independent methods. Similar microbial distributions were observed between the two methods; however, as expected, the culture-independent data revealed microbial profiles with greater diversity. Protocol optimization and verification was established during NASA Extreme Environment Mission Operations (NEEMO) analog missions 21 and 22, respectively. Unique microbial profiles obtained from analog testing validated the swab-to-sequencer method in an extreme environment. Finally, four independent swab-to-sequencer experiments were conducted onboard the ISS by two crewmembers. Microorganisms identified from ISS swabs were consistent with historical culture-based data, and primarily consisted of commonly observed human-associated microbes. This simplified method has been streamlined for high ease-of-use for a non-trained crew to complete in an extreme environment, thereby enabling environmental and human health diagnostics in real-time as future missions take us beyond low-Earth orbit.

microbiology↗
DOE OSTI2012

GALAXY-SCALE STAR FORMATION ON THE RED SEQUENCE: THE CONTINUED GROWTH OF S0s AND THE QUIESCENCE OF ELLIPTICALS

This paper examines star formation (SF) in relatively massive, primarily early-type galaxies (ETGs) at z {approx} 0.1. A sample is drawn from bulge-dominated Galaxy Evolution Explorer/Sloan Digital Sky Survey (GALEX/SDSS) galaxies on the optical red sequence with strong UV excess and yet quiescent SDSS spectra. High-resolution far-UV imaging of 27 such ETGs using Hubble Space Telescope Advanced Camera for Surveys/Solar Blind Channel (ACS/SBC) reveals structured UV morphology in 93% of the sample, consistent with low-level ongoing SF ({approx}0.5 M{sub Sun} yr{sup -1}). In 3/4 of the sample the SF is extended on galaxy scales (25-75 kpc), while the rest contains smaller (5-15 kpc) SF patches in the vicinity of an ETG-presumably gas-rich satellites being disrupted. Optical imaging reveals that all ETGs with galaxy-scale SF in our sample have old stellar disks (mostly S0 type). None is classified as a true elliptical. In our sample, galaxy-scale SF takes the form of UV rings of varying sizes and morphologies. For the majority of such objects we conclude that the gas needed to fuel current SF has been accreted from the intergalactic medium, probably in a prolonged, quasi-static manner, leading in some cases to additional disk buildup. The remaining ETGs with galaxy-scale SF have UV and optical morphologies consistent with minor merger-driven SF or with the final stages of SF in fading spirals. Our analysis excludes that all recent SF on the red sequence resulted from gas-rich mergers. We find further evidence that galaxy-scale SF is almost exclusively an S0 phenomenon ({approx}20% S0s have SF) by examining the overall optically red SDSS ETGs. Conclusion is that significant number of field S0s maintain or resume low-level SF because the preventive feedback is not in place or is intermittent. True ellipticals, on the other hand, stay entirely quiescent even in the field.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Proposed minimal standards for description of methanogenic archaea

Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA–DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.

Microbiology↗
DOE OSTI2015

Multi-analytical approach reveals potential microbial indicators in soil for sugarcane model systems

This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO 2 -C and N 2 O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria , Actinobacteria , Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria . Actinobacteria were more responsive to straw retention with Rubrobacterales , Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae , a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO 2 -C and N 2 O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria , Actinobacteria and Verrucomicrobia , and their subgroups acted as early-warning indicators of N+V amendments and straw retention in sugarcane-cultivated soils, which can alter the soil chemical factors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Locally advanced rectal cancer: qualitative and quantitative evaluation of diffusion-weighted magnetic resonance imaging in restaging after neoadjuvant chemo-radiotherapy

Purpose: To determine the added value of qualitative and quantitative evaluation of diffusion-weighted magnetic resonance imaging (DWI) in locally advanced rectal cancer (LARC) restaging after neoadjuvant chemo-radiotherapy (CRT). Materials and Methods: A retrospective study was performed of 21 patients with LARC treated with CRT. All patients were evaluated with 1.5 T conventional magnetic resonance imaging (MRI) and DWI (0–1000 s/mm²) before starting therapy and after neoadjuvant CRT. All included patients underwent surgery after CRT: the histopathological evaluation of surgical specimens represented the reference standard for local staging after neoadjuvant therapy. The qualitative analysis was carried out by two operators in consensus, who reviewed the conventional MR image set [T1-weighted and T2-weighted morphological sequences + dynamic contrast-enhanced sequences (DCE)] and the combined set of conventional and DW images. For the quantitative analysis, the apparent diffusion coefficient (ADC) values were measured at each examination. For each lesion, the mean ADC value (ADCpre and ADCpost) and the ΔADC (ADCpost – ADCpre) were calculated, and values of the three groups of response [complete response (pCR), partial response (pPR), stable disease (pSD)] were compared. Results: In LARC restaging, conventional MRI showed a sensitivity of 80% and a specificity of 50%, with a total diagnostic capacity of 71.40%, while by adding DWI sensitivity increased to 100%, specificity to 67%, and total diagnostic capacity to 90.40%. ΔADC correlates with treatment response and a cutoff of 1.35 × 10{sup −3} mm²/s predicts the pCR with a sensitivity of 93.3% and a specificity of 83.3%. Conclusions: Adding DWI to conventional sequences may improve MRI capability to evaluate tumor response to CRT. The quantitative DWI assessment is promising, but larger studies are required.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer

Tumour heterogeneity in primary prostate cancer is a well-established phenomenon. However, how the subclonal diversity of tumours changes during metastasis and progression to lethality is poorly understood. Here we reveal the precise direction of metastatic spread across four lethal prostate cancer patients using whole-genome and ultra-deep targeted sequencing of longitudinally collected primary and metastatic tumours. We find one case of metastatic spread to the surgical bed causing local recurrence, and another case of cross-metastatic site seeding combining with dynamic remoulding of subclonal mixtures in response to therapy. By ultra-deep sequencing end-stage blood, we detect both metastatic and primary tumour clones, even years after removal of the prostate. As a result, analysis of mutations associated with metastasis reveals an enrichment of TP53 mutations, and additional sequencing of metastases from 19 patients demonstrates that acquisition of TP53 mutations is linked with the expansion of subclones with metastatic potential which we can detect in the blood.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Impact of short-read sequencing on the misassembly of a plant genome

Abstract Background Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with highly uneven read coverages indicative of sequencing and assembly issues that could significantly impact any downstream analysis of plant genomes. In tomato for example, 0.6% (5.1 Mb) and 9.7% (79.6 Mb) of short-read based assembly had significantly higher and lower coverage compared to background, respectively. Results To understand what the causes may be for such uneven coverage, we first established machine learning models capable of predicting genomic regions with variable coverages and found that high coverage regions tend to have higher simple sequence repeat and tandem gene densities compared to background regions. To determine if the high coverage regions were misassembled, we examined a recently available tomato long-read based assembly and found that 27.8% (1.41 Mb) of high coverage regions were potentially misassembled of duplicate sequences, compared to 1.4% in background regions. In addition, using a predictive model that can distinguish correctly and incorrectly assembled high coverage regions, we found that misassembled, high coverage regions tend to be flanked by simple sequence repeats, pseudogenes, and transposon elements. Conclusions Our study provides insights on the causes of variable coverage regions and a quantitative assessment of factors contributing to plant genome misassembly when using short reads and the generality of these causes and factors should be tested further in other species.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Developing a Genetic Variant Calling Pipeline for Quantifying the Complex Mutagenic Load Accumulated in BioNutrients-1 Production Pack Samples

Microorganisms hold great promise for on demand production of labile nutrients and pharmaceuticals as well recycling and in situ resource utilization. The utilization of microorganisms for such tasks on space missions is hindered by the limited data on how microbes respond to spaceflight. For example, the genetic stability of microorganisms, and the genomic engineered traits added to deliver desired functions, over long-term storage in the spacecraft environment is poorly understood. The BioNutrients-1 (BN-1) mission conducted a 5-year study of desiccated storage in Low Earth Orbit (LEO) to evaluate the suitability of eight synthetic biology chassis organisms for long-duration space missions. We are employing high-depth, whole genome sequencing (WGS) to determine the mutagenic load that accumulated during long-term storage. Mutation analysis pipelines are well established for homogenous culture grown from a single colony, but the mutational landscape of the BN-1 samples present a unique analysis challenge, as every cell in the BN-1 samples had a unique genetic journey of DNA damage and repair. Consequently, sequence variants are expected at low allele frequency within samples. To address this genetic complexity, we apply two distinct computational approaches to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO. For reference genome free mutation detection, we utilized DiscoSNP++, which is a de Bruijn graph approach. For reference genome-based mutation detection we utilize GATK for Microbes, which is a Bayesian probabilistic approach. We will benchmark these approaches against the mutations originally identified using CRISP, a method optimized for pooled samples. Ultimately, quantifying the mutation load imposed by storage or growth on the ISS will help identify chassis organisms with both high levels of genome stability and viability, which are desirable traits for implementation of bioproduction in long-duration missions.

SNP↗
DOE OSTI2022

Traveler: Navigating Task Parallel Traces for Performance Analysis

Understanding the behavior of software in execution is a key step in identifying and fixing performance issues. This is especially important in high performance computing contexts where even minor performance tweaks can translate into large savings in terms of computational resource use. To aid performance analysis, developers may collect an execution trace —a chronological log of program activity during execution. As traces represent the full history, developers can discover a wide array of possibly previously unknown performance issues, making them an important artifact for exploratory performance analysis. However, interactive trace visualization is difficult due to issues of data size and complexity of meaning. Traces represent nanosecond-level events across many parallel processes, meaning the collected data is often large and difficult to explore. The rise of asynchronous task parallel programming paradigms complicates the relation between events and their probable cause. Here, to address these challenges, we conduct a continuing design study in collaboration with high performance computing researchers. We develop diverse and hierarchical ways to navigate and represent execution trace data in support of their trace analysis tasks. Through an iterative design process, we developed Traveler , an integrated visualization platform for task parallel traces. Traveler provides multiple linked interfaces to help navigate trace data from multiple contexts. We evaluate the utility of Traveler through feedback from users and a case study, finding that integrating multiple modes of navigation in our design supported performance analysis tasks and led to the discovery of previously unknown behavior in a distributed array library.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2004

Feature-Identification and Data-Compression Software

A report discusses the continuing development of Windows Interface for Nominal Displacement Selection (WINDS), a computer program for automated analysis of images of the Sun and planets acquired by scientific instruments aboard spacecraft. WINDS is intended to afford capabilities for identification of features, measurement of displacements and velocities, analysis of terrain and of atmospheres, and synthesis of animation sequences of images of terrains and atmospheres from small sets of samples by use of velocity-based interpolation. A major element of WINDS will be a nonlinear correlator capable of tracking small features in complex image sequences. For dynamic image sequences, the correlator will enable compression of data by factors >100. In processing image data, WINDS will take account of such factors as texture in image data, rotation of features during measurement intervals, effects of viewing and solar illumination angles, and vertical structures of atmospheres. WINDS will also take account of positions, aiming directions, and fields of view of cameras to determine three-dimensional feature structures by use of triangulation and stereoscopic analysis techniques.

Jong, Eric De↗