Search NASA⌕ Search

SEARCH · Search NASA

Results for “sequence features”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

The smectic Z A phase: Antiferroelectric smectic order as a prelude to the ferroelectric nematic

We have structurally characterized the liquid crystal (LC) phase that can appear as an intermediate state when a dielectric nematic, having polar disorder of its molecular dipoles, transitions to the almost perfectly polar-ordered ferroelectric nematic. This intermediate phase, which fills a 100-y-old void in the taxonomy of smectic LCs and which we term the “smectic Z A ,” is antiferroelectric, with the nematic director and polarization oriented parallel to smectic layer planes, and the polarization alternating in sign from layer to layer with a 180 Å period. A Landau free energy, originally derived from the Ising model of ferromagnetic ordering of spins in the presence of dipole–dipole interactions, and applied to model incommensurate antiferroelectricity in crystals, describes the key features of the nematic–SmZ A –ferroelectric nematic phase sequence.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Application of State Quantization-Based Methods in HEP Particle Transport Simulation

Simulation of particle-matter interactions in complex geometries is one of the main tasks in high energy physics (HEP) research. An essential aspect of it is an accurate and efficient particle transportation in a non-uniform magnetic field, which includes the handling of volume crossings within a predefined 3D geometry. Quantized State Systems (QSS) is a family of numerical methods that provides attractive features for particle transportation processes, such as dense output (sequences of polynomial segments changing only according to accuracy-driven discrete events) and lightweight detection and handling of volume crossings (based on simple root-finding of polynomial functions). In this work we present a proof-of-concept performance comparison between a QSS-based standalone numerical solver and an application based on the Geant4 simulation toolkit, with its default Runge-Kutta based adaptive step method. In a case study with a charged particle circulating in a vacuum (with interactions with matter turned off), in a uniform magnetic field, and crossing up to 200 volume boundaries twice per turn, simulation results showed speedups of up to 6 times in favor of QSS while it being 10 times slower in the case with zero volume boundaries.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Infrared spectroscopy of nearby radio active early-type galaxies - II: spectral atlas

ABSTRACT We present a near-infrared spectroscopic atlas of nearby, bright early-type galaxies with radio emission, containing 163 galaxies observed by the Palomar 200″ TripleSpec instrument, measuring the emission line fluxes for H, He, [Fe ii], and H2 and determined the nuclear excitation mechanisms. By stacking spectra, we deduced the H2 excitation temperature (1957 ± 182 K) and dominant excitation mechanism (thermal and shock heating combined) from the K-band emission line sequence. Stacking also produces an ‘average’ spectrum of absorption features and spectral indices from the literature; the CO12 absorption line index versus J − K colour shows a trend of stronger nuclear activity producing a weaker CO12 index and a redder (flatter) continuum. The correlations between the radio and the emission-line luminosities finds a trend with radio power; however, the large scatter in the upper limits shows that the two are not directly coupled and the duty cycles of SF and AGN activity are not synchronized.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Learning Heterogeneous Features Jointly: A Deep End-to-End Framework for Multi-Step Short-Term Wind Power Prediction

Leveraging multiple heterogeneous measurements to predict wind power has long been a challenging task in the electrical community. In this paper, a deep architecture incorporated with multitask learning and multimodal learning for wind power prediction, termed predictive stacked autoencoder (PSAE), is presented. PSAE is a unified framework integrating multiple stacked autoencoders (SAEs), one feature fusion layer, and one prediction terminal layer, which expands the architecture from two spatial dimensions, including the depth and width, compared to conventional prediction models. Initially, the SAEs at the bottom of PSAE extracted features from multiple kinds of measurements respectively. Following, the feature fusion layer encodes the high-order features extracted by different SAEs into a unified feature that is more informative and representative for wind power prediction. Finally, the prediction terminal layer functions as a regression machine which generates the predicted targets based on the fusion features. Trained in an end-to-end (E2E) manner, PSAE is capable of learning heterogeneous features jointly and achieving the prediction task of sequence-to-sequence (S2S). Experiments for multi-step short-term predictions are conducted on real-world data, and the results demonstrate the superiority of PSAE to prior methods.

17 WIND ENERGY↗
DOE OSTI2018

Functional Profiling and Crystal Structures of Isothiocyanate Hydrolases Found in Gut-Associated and Plant-Pathogenic Bacteria

Isothiocyanates (ITCs) are produced by cruciferous plants to protect them against herbivores and infection by microbes. These compounds are of particular interest due to their antimicrobial and anticarcinogenic properties. The breakdown of ITCs in nature is catalyzed by isothiocyanate hydrolases (ITCases), a novel family within the metallo-β-lactamase (MBL)-fold superfamily of proteins. saxA genes that code for ITCases are particularly widespread in insect- and plant-associated bacteria. Enzymatic characterization of seven phylogenetically related but distinct ITCases revealed similar activities on six selected ITCs, suggesting that phylogenetic diversity does not determine the substrate specificity of ITCases. X-ray crystallography studies of two ITCases sharing 42% amino acid sequence identity revealed a highly conserved tertiary structure. Notable features of ITCases include a hydrophobic active site with two Zn 2+ ions coordinating water/hydroxide and a flexible cap that is implicated in substrate recognition and covers the active site. Furthermore, this report reveals the function and structure of the previously uncharacterized family of isothiocyanate hydrolases within the otherwise relatively well-studied superfamily of metallo-β-lactamases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Full Karyotype Interphase Cell Analysis

Aneuploidy seems to play not only a decisive role in embryonal development but also in tumorigenesis where chromosomal and genomic instability reflect a universal feature of malignant tumors. The cost of whole genome sequencing has fallen significantly, but it is still prohibitive for many institutions and clinical settings. No applied, cost-effective, and efficient technique has been introduced yet aiming at research to assess the ploidy status of all 24 different human chromosomes in interphases simultaneously, especially in single cells. Here, we present the selection of human probe DNA and a technique using multistep fluorescence in situ hybridization (FISH) employing four sets of six labeled FISH probes able to delineate all 24 human chromosomes in interphase cells. This full karyotype analysis approach will provide additional diagnostic potential for single cell analysis. The use of spectral imaging (SIm) has enabled the use of up to eight different fluorochrome labels simultaneously. Thus, scoring can be easily assessed by visual inspection, because SIm permits computer-assigned and distinguishable pseudo-colors to each probe during image processing. This enables full karyotype analysis by FISH of single-cell interphase nuclei.

Baumgartner, Adi↗
DOE OSTI2016

Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples

The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis). In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging due to both biological (evolutionary diverse samples) and computational (petabytes of sequence data) issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances) or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST) scheme). Finally, when analyzing empirical data (wholegenome sequence data from 18,997 Salmonella isolates) there are features (e.g., genomic, assembly, and contamination) that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla

Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the “Candidate phylum Rokubacteria,” formerly known as SPAM, represents an interesting exception, by having large genomes (6–8 Mbps), high GC content (66–71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual Rokubacteria cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior cultivation and metagenomic studies. Our analyses suggest that Rokubacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers, and the deep subsurface, with no reports from marine environments to date.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1966

Spacecraft development

Flight sequence, capsule design, pyrotechnic applications, escape modes, and safety features for Gemini spacecraft

SAFETY DEVICE↗
NASA NTRS1980

Application of an automatic cloud tracking technique to Meteosat water vapor and infrared observations

The automatic cloud tracking system was applied to METEOSAT 6.7 micrometers water vapor measurements to learn whether the system can track the motions of water vapor patterns. Data for the midlatitudes, subtropics, and tropics were selected from a sequence of METEOSAT pictures for 25 April 1978. Trackable features in the water vapor patterns were identified using a clustering technique and the features were tracked by two different methods. In flat (low contrast) water vapor fields, the automatic motion computations were not reliable, but in areas where the water vapor fields contained small scale structure (such as in the vicinity of active weather phenomena) the computations were successful. Cloud motions were computed using METEOSAT infrared observations (including tropical convective systems and midlatitude jet stream cirrus).

Endlich, R. M.↗
NASA NTRS1991

Geologic mapping of MTM quads 40292 and 40297: In the Utopian lowlands north of the Nilosyrtis Mensae, Mars

Geologic mapping at 1:500,000 scale of the Mars transverse Mercator (MTM) quads 40292 and 40297 is being conducted under the auspices of the Mars Geologic Mapping Program. The study area is located in the southwestern portion of Utopia Planitia immediately north of the Nilosyrtis Mensae, between latitudes 37.5 and 42.5 degrees and longitudes 290 and 300 degrees. The goals of the mapping are to identify the major geologic features in the study area and to determine the sequence and scope of the geologic events that have modified the lowland side of the global dichotomy boundary in this region in order to at least partially constrain models of dichotomy boundary origin and evolution. The progress made towards achieving these goals is reported.

Williams, Steven H.↗
NASA NTRS2003

Towards Automating Spacecraft Attitude Sensor Calibration

With a view towards reducing cost and complexity for spacecraft early mission support at the NASA Goddard Space Flight Center (GSFC), efforts are being made to automate the attitude sensor calibration process. This paper addresses one of the major components needed by such a system. The beneficiaries of an improved calibration process are missions that demand moderate to high precision attitude knowledge or that need to perform accurate attitude slews. Improved slew accuracy reduces the time needed for re-acquisition of fine-pointing after each attitude maneuver, Rapid target acquisition can be very important for astronomical targeting or for off-nadir surface feature targeting by Earth-oriented spacecraft. The normal sequence of on-orbit calibration starts with alignment calibration of the star trackers and possibly the Sun sensor. Their relative alignment needs to be determined using a sufficiently large data set so their fields of view are adequately sampled. Next, the inertial reference unit (IRU) is calibrated for corrections to its alignment and scale factors. The IRU biases are estimated continuously by the onboard attitude control system, but the IRU alignment and scale factors are usually determined on the ground using a batch-processing method on a data set that includes several slews sufficient to give full observability of all the IRU calibration parameters. Finally, magnetometer biases, alignment, and its coupling to the magnetic torquers are determined in order io improve momentum management and occasionally for use in the attitude determination system. The detailed approach used for automating calibrations will depend on whether the automated system resides on the ground or on the spacecraft with an ultimate goal of autonomous calibration. Current efforts focus on a ground-based system driving subsystems that could run either on the ground or onboard. The distinction is that onboard calibration should process the data sequentially rather than in a single large batch since onboard computer data storage is limited. Very good batch- processing calibration utilities have been developed and used extensively at NASA/GSFC for mission support but no sequential calibration utilities are available. To meet this need, this paper presents the mathematical description of a sequential IRU calibration system. The system has been tested using flight data from the Rossi X-ray Timing Explorer (RXTE) during a series of attitude slews. The paper also discusses the current state of the overall automated system and describes plans for adding sequential alignment calibration and other additions that will reduce the amount of analyst time and input.

Sedlak, Joseph↗
NASA NTRS1997

Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures

We have begun to examine the basis for incongruence between hot spring microbial mat populations detected by cultivation or by 16S rRNA methods. We used denaturing gradient gel electrophoresis (DGGE) to monitor enrichments and isolates plated therefrom. At near extincting inoculum dilutions we observed Chloroflexus-like and cyanobacterial populations whose 16S rRNA sequences have been detected in the 'New Pit' Spring Chloroflexus mat and the Octopus Spring cyanobacterial mat. Cyanobacterial populations enriched from 44 to 54 degrees C and 56 to 63 degrees C samples at near habitat temperatures were similar to those previously detected in mat samples of comparable temperatures. However, a lower temperature enrichment from the higher temperature sample selected for the populations found in the lower temperature sample. Three Thermus populations detected by both DGGE and isolation exemplify even more how enrichment may bias our view of community structure. The most abundant population was adapted to the habitat temperature (50 degrees C), while populations adapted to 65 degrees C and 70 degrees C were 10(2)- and 10(4)-fold less abundant, respectively. However, enrichment at 70 degrees C favored the least abundant strain. Inoculum dilution and incubation at the habitat temperature favored the more numerically relevant populations. We enriched many other aerobic chemoorganotrophic populations at various inoculum dilutions and substrate concentrations, most of whose 16S rRNA sequences have not been detected in mats. A common feature of numerically relevant cyanobacterial, Chloroflexus-like and aerobic chemorganotrophic populations, is that they grow poorly and resist cultivation on solidified medium, suggesting plating bias, and that the medium composition and incubation conditions may not reflect the natural microenvironments these populations inhabit.

Non-NASA Center↗
NASA NTRS2009

Preliminary Geological Map of the Fortuna Tessera (V-2) Quadrangle, Venus

The Fortuna Tessera quadrangle (50-75 N, 0-60 E) is a large region of tessera [1] that includes the major portion of Fortuna and Laima Tesserae [2]. Near the western edge of the map area, Fortuna Tessera is in contact with the highest moun-tain belt on Venus, Maxwell Montes. Deformational belts of Sigrun-Manto Fossae (extensional structures) and Au ra Dorsa (contractional structures) separate the tessera regions. Highly deformed terrains correspond to elevated regions and mildly deformed units are with low-lying areas. The sets of features within the V-2 quadrangle permit us to address the following important questions: (1) the timing and processes of crustal thickening/thinning, (2) the nature and origin of tesserae and deformation belts and their relation to crustal thickening processes, (3) the existence or absence of major evolutionary trends of volcanism and tectonics. The key feature in all of these problems is the regional sequence of events. Here we present description of units that occur in the V-2 quadrangle, their regional correlation chart (Fig. 1), and preliminary geological map of the region (Fig. 2).

Ivanov, M. A.↗
NASA NTRS2014

Characterization of the Inner Knot of the Crab: The Site of the Gamma-Ray Flares?

Subsequent to the detections AGILE and Fermi/LAT of the gamma-ray flares from the Crab Nebula in the fall of 2010, this team has been monitoring the X-Ray emission from the Crab on a regular basis. Initially X-Ray observations took place once per month when viewing constraints allowed. More recently observations with Chandra and HST have taken place four times per year. There have been notable exceptions, e.g. in April of 2011 and March 2013 when we initiated a set of Chandra Target of opportunity observations in conjunction with bright gamma-ray flares. Often Keck observations were obtained. The aim of this program to characterize, in depth, the X-ray, optical, and infrared variations that take place in the nebula, and, by so doing, determine the regions which contribute to the harder X-ray variations and, if possible, determine the precise location within the Nebula of the origin of the gamma-ray flares. As part of this project members of the team have applied Singular Value Decomposition techniques to sequences of images in order to more accurately characterize features and their behavior. The current status of the project will be discussed highlighting studies of the inner knot and possible correlations with the gamma-ray flares.

Chandra↗
NASA NTRS2014

Monitoring of the Crab Nebula with Chandra and Other Observatories Including HST

Subsequent to the detections AGILE and Fermi/LAT of the gamma‐ray flares from the Crab Nebula in the fall of 2010, this team has been monitoring the X‐Ray emission from the Crab on a regular basis. X‐Ray observations have taken place typically once per month when viewing constraints allow and more recently four times per year. There have been notable exceptions, e.g. in April of 2011 and March 2013 when we initiated a set of Chandra Target of opportunity observations in conjunction with bright gamma‐ray flares. For much of the time regular HST observations were made in conjunction with the Chandra observations. The aim of this program to further characterize, in depth, the X‐Ray and optical variations that take place in the nebula, and by so doing determine the regions which contribute to the harder X‐ray variations and, if possible, determine the precise location within the Nebula of the origin of the gamma‐ray flares. As part of this project members of the team have developed Singular Value Decomposition techniques to sequences of images in order to more accurately characterize features. The current status of the project will be presented highlighting studies of the inner knot and possible correlations with the flares.

Weisskopf, Martin C.↗
DOE OSTI2024

Targeted Biomining and Machine Learning Approaches in Critical Minerals Revealed by a Biogeochemical Survey of a Coal Mine Drainage Remediation System

Abandoned coal mine drainage (AMD) remediation systems in Pennsylvania can concentrate critical minerals and materials (CMM) at levels comparable to mining-grade ores. Remediation systems have varying engineering features and are open to the environment, resulting in diverse microbial colonization and seasonal climate influences that may impact CMM speciation. The location of CMMs, the types of bacterial communities tolerant of these pollutant conditions, and the influence of localized climate on CMM rich remediation systems are not well characterized. Through a one-year spatiotemporal survey of biogeochemistry at a remediation system, we have initiated the process to address these questions. Rare Earth Elements (REE) ranged 180-1,200 ppm and greater than 1,500 bacterial ASVs were classified via 16S sequencing. Analyses indicate biogeochemical differences are heavily influenced by engineering features. Additionally, REE precipitants correlate strongly with the elements Al, Cu, Zn, Be, and U. Unearthing these trends has refined our line of inquiry to explore biological mining opportunities more closely with these metals. Furthermore, we created a Machine Learning Model for predicting AMD REE content, with 89% accuracy, using the data from this study and several others. Further training data is required to create a more reputable model. Recently, global research efforts have prioritized modeling work or the use of the few historical surveys to design experiments. Through our data, we challenge this approach, emphasizing the importance of expanding fundamental survey efforts prior to advanced product design and experimentation.

critical minerals↗
DOE OSTI2023

The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11

SARS-CoV-2, the virus behind the COVID-19 pandemic, has changed over time to the extent that the current virus is substantially different from what originally led to the pandemic in 2019–2020. Viral variants have modified the severity and transmissibility of the disease and continue do so. How much of this change is due to viral fitness versus a response to immune pressure is hard to define. One class of antibodies that continues to afford some level of protection from emerging variants are those that closely overlap the binding site for angiotensin-converting enzyme 2 (ACE2) on the receptor binding domain (RBD). Some members of this class that were identified early in the course of the pandemic arose from the VH 3-53 germline gene (IGHV3-53*01) and had short heavy chain complementarity-determining region 3s (CDR H3s). Here, we describe the molecular basis of the SARS-CoV-2 RBD recognition by the anti-RBD monoclonal antibody CoV11 isolated early in the COVID-19 pandemic and show how its unique mode of binding the RBD determines its neutralization breadth. CoV11 utilizes a heavy chain VH 3-53 and a light chain VK 3-20 germline sequence to bind to the RBD. Two of CoV11’s four heavy chain changes from the VH 3-53 germline sequence, $Thr^{28}_{FWRH1}$ to Ile and $Ser^{31}_{CDRH1}$ to Arg, and some unique features in its CDR H3 increase its affinity to the RBD, while the four light chain changes from the VK 3-20 germline sequence sit outside of the RBD binding site. Antibodies of this type can retain significant affinity and neutralization potency against variants of concern (VOCs) that have diverged significantly from original virus lineage such as the prevalent omicron variant. We also discuss the mechanism by which VH 3-53 encoded antibodies recognize spike antigen and show how minimal changes to their sequence, their choice of light chain, and their mode of binding influence their affinity and impact their neutralization breadth.

60 APPLIED LIFE SCIENCES↗