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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Unified rational protein engineering with sequence-based deep representation learning

Rational protein engineering requires a holistic understanding of protein function. Here, we apply deep learning to unlabeled amino-acid sequences to distill the fundamental features of a protein into a statistical representation that is semantically rich and structurally, evolutionarily and biophysically grounded. We show that the simplest models built on top of this unified representation (UniRep) are broadly applicable and generalize to unseen regions of sequence space. Our data-driven approach predicts the stability of natural and de novo designed proteins, and the quantitative function of molecularly diverse mutants, competitively with the state-of-the-art methods. UniRep further enables two orders of magnitude efficiency improvement in a protein engineering task. Lastly, UniRep is a versatile summary of fundamental protein features that can be applied across protein engineering informatics.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1979

Multiclass Bayes error estimation by a feature space sampling technique

A general Gaussian M-class N-feature classification problem is defined. An algorithm is developed that requires the class statistics as its only input and computes the minimum probability of error through use of a combined analytical and numerical integration over a sequence simplifying transformations of the feature space. The results are compared with those obtained by conventional techniques applied to a 2-class 4-feature discrimination problem with results previously reported and 4-class 4-feature multispectral scanner Landsat data classified by training and testing of the available data.

Mobasseri, B. G.↗
NASA NTRS1973

Outflow of chromospheric emission features from the rim of a sunspot

In viewing a 16 mm movie made from a time sequence of spectroheliograms, some of these emission features are found to move outward from the rim of the sunspot until they are eventually lost in the small plage. There are two interpretations for the streaming of the magnetic features. It is possible that kinks in the line of force propagate along a horizontal extension of the penumbral magnetic field. Alternatively, fragments of the sunspot magnetic field are carried away by the photospheric velocity field.

Liu, S.-Y.↗
DOE OSTI2022

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies

Mapping positional features from one-dimensional (1D) sequences onto three-dimensional (3D) structures of biological macromolecules is a powerful tool to show geometric patterns of biochemical annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level. We present a new library designed to display fully customizable interactive views between 1D positional features of protein and/or nucleic acid sequences and their 3D structures as isolated chains or components of macromolecular assemblies.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1986

Detection of CN emission in Comet P/Halley

The first detection of the CN 3883 A band in emission in Comet P/Halley (1982) in February 1985 is reported. The detection technique, which is described, used blind offsets from secondary reference stars to the comet's predicted position, and involved plotting the comet's track on an enlargement of an appropriate section of the Palomar Sky Survey E plates. The strong solar continuum in the resulting cometary spectrum demonstrates the dominance of the dust reflection spectrum and the reflection from the nucleus. The 3883 A feature is identified with the v = 0 band sequence of the blue system of CN; no other significant features were identified in the spectrum.

Wyckoff, S.↗
NASA NTRS1989

The horse-collar aurora - A frequent pattern of the aurora in quiet times

The frequent appearance of the 'horse-collar aurora' pattern in quiet-time DE 1 images is reported, presenting a two-hour image sequence that displays the basic features and shows that it sometimes evolves toward the theta configuration. There is some evidence for interplanetary magnetic field B(y) influence on the temporal development of the pattern. A preliminary statistical analysis finds the pattern appearing in one-third or more of the image sequences recorded during quiet times.

Hones, E. W., Jr.↗
DOE OSTI2024

Whole-genome demography of COVID-19 virus during its pandemic period and on “panvalent” vaccine design

With over 16 million submitted genomic sequences, the SARS-CoV-2 (SC2) virus, the cause of the most recent worldwide COVID-19 pandemic, has become the most sequenced genome of all known viruses, revealing, for example, a vast number of expanding viral lineages. Since the pandemic phase appears to be over, we performed a retrospective re-examination of the demographic grouping pattern and their genomic characteristics during the entire pandemic period up to the peak of the last pandemic wave. For our study, we extracted from the NCBI only unique viral sequences and converted each sequence data to a relational vector, indicating the presence/absence of each variational event compared to a “reference” sequence. Our study revealed several genomic features that are unexpected or different from those of previous studies. For example, approximately 44,000 variants with unique sequences emerged during the pandemic period; they group into only four major viral-genomic groups and each has a set of mostly unique highly-conserved variant-genotypes (HCVGs); and a small set from the first (“ancestral”) group was inherited by the three (“descendant”) groups, suggesting that HCVGs in the next group may be predictable from the current group(s). Such a concept may be potentially important in designing “panvalent” vaccines against the current and future waves of viral infections.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2011

Feature and Pose Constrained Visual Aided Inertial Navigation for Computationally Constrained Aerial Vehicles

A Feature and Pose Constrained Extended Kalman Filter (FPC-EKF) is developed for highly dynamic computationally constrained micro aerial vehicles. Vehicle localization is achieved using only a low performance inertial measurement unit and a single camera. The FPC-EKF framework augments the vehicle's state with both previous vehicle poses and critical environmental features, including vertical edges. This filter framework efficiently incorporates measurements from hundreds of opportunistic visual features to constrain the motion estimate, while allowing navigating and sustained tracking with respect to a few persistent features. In addition, vertical features in the environment are opportunistically used to provide global attitude references. Accurate pose estimation is demonstrated on a sequence including fast traversing, where visual features enter and exit the field-of-view quickly, as well as hover and ingress maneuvers where drift free navigation is achieved with respect to the environment.

autonomous operation↗
NASA NTRS1995

Evidence for chemical processing of precometary icy grains in circumstellar environments of pre-main-sequence stars

We report the detection of a broad absorption feature near 2166/cm in the spectrum of the Taurus cloud cource Elias 18. This pre-main-sequence source is the second in Taurus, the third in our survey, and the fifth known in the sky to show the broad 2166/cm absorption feature. Of equal importance, this feature is not seen toward several other embedded sources in our survey, nor is it seen toward the source Elias 16, located behind the Taurus cloud. Laboratory experiments with interstellar ice analogs show that such a feature is associated with a complex C triple bonded to N containing compound (called X(C triple bonded to N)) that results from high-energy processing (ultraviolet irradiation or ion bombardment) of simple ice components into more complex, organic components. We find a nonlinear anticorrelation between the abundance of X(C triple bonded to N) and frozen CO components in nonpolar lattices. We find no correlation between the abundance of X(C triple bonded to N) and frozen CO in polar lattices. Because the abundances of frozen CO and H2O are strongly correlated with each other and with visual extinction toward sources embedded in and located behind the Taurus molecular cloud, these ice components usually are associated with intracloud material. Our results indicate that X(C triple bonded to N) molecules result from chemical processing of dust grains dominated by nonpolar icy mantles in the local environments of pre-main-sequence stars. Such processing of icy grains in the early solar system may be an important source of organic compounds observed in minor solar system bodies. The delivery of these organic compounds to the surface of the primitive Earth through comet impacts may have provided the raw materials for prebiotic chemistry.

Tegler, Stephen C.↗
DOE OSTI2026

Sampling Microbial Dynamics in the Salish Sea Estuary: Evaluating Methods to Capture Cyanobacteria and Cyanophage

Introduction: Picocyanobacteria from the genera Prochlorococcus and Synechococcus thrive across the globe in aquatic environments, have relatively small genomes, and have growth dynamics regulated by both viral interactions and abiotic conditions, making them excellent model organisms for exploring host-pathogencoevolution. Methods: We developed and refined methods to sample and sequence cyanobacteria, cyanophages, and measured features of their abiotic environment. Results: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons. Our preferred final protocol from this exploratory effort included a combination of in-line and single vacuum flask filtrations, which reduced filtration processing time by over threefold in some cases compared to other tested methods, such as a fully in-line sequence or in-site filtrations. We successfully extracted an average of approximately 400–1200 ng for all filter fractions, with some variations between kits. Discussion: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons.

Salish Sea↗
DOE OSTI2022

Image feature extraction and galaxy classification: a novel and efficient approach with automated machine learning

ABSTRACT In this work, we explore the possibility of applying machine learning methods designed for 1D problems to the task of galaxy image classification. The algorithms used for image classification typically rely on multiple costly steps, such as the point spread function deconvolution and the training and application of complex Convolutional Neural Networks of thousands or even millions of parameters. In our approach, we extract features from the galaxy images by analysing the elliptical isophotes in their light distribution and collect the information in a sequence. The sequences obtained with this method present definite features allowing a direct distinction between galaxy types. Then, we train and classify the sequences with machine learning algorithms, designed through the platform Modulos AutoML. As a demonstration of this method, we use the second public release of the Dark Energy Survey (DES DR2). We show that we are able to successfully distinguish between early-type and late-type galaxies, for images with signal-to-noise ratio greater than 300. This yields an accuracy of $86{{\ \rm per\ cent}}$ for the early-type galaxies and $93{{\ \rm per\ cent}}$ for the late-type galaxies, which is on par with most contemporary automated image classification approaches. The data dimensionality reduction of our novel method implies a significant lowering in computational cost of classification. In the perspective of future data sets obtained with e.g. Euclid and the Vera Rubin Observatory, this work represents a path towards using a well-tested and widely used platform from industry in efficiently tackling galaxy classification problems at the peta-byte scale.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1995

Evidence for Chemical Processing of Precometary Icy Grains In Circumstellar Environments of Pre-Main-Sequence Stars

We report the detection of a broad absorption feature near 2166 cm-1 in the spectrum of the Taurus cloud source Elias 18. This pre-main-sequence source is the second in Taurus, the third in our survey, and the fifth known in the sky to show the broad 2166 cm-1 absorption feature. Of equal importance, this feature is not seen toward several other embedded sources in our survey, nor is it seen toward the source Elias 16, located behind the Taurus cloud. Laboratory experiments with interstellar ice analogs show that such a feature is associated with a complex C=-N containing compound [called X(C=-N)] that results from high-energy processing (ultraviolet irradiation or ion bombardment) of simple ice components into more complex, organic components, We find a nonlinear anticorrelation between the abundance of X(C=-N) and frozen CO in non- polar lattices. We find no correlation between the abundance of X(C=-N) and frozen CO in polar lattices. Because the abundances of frozen CO and H20 are strongly correlated with each other and with visual extinction toward sources embedded in and located behind the Taurus molecular cloud, these ice components usually are associated with intracloud material. Our results indicate that X(C=-N) molecules result from chemical processing of dust grains dominated by nonpolar icy mantles in the local environments of pre-main- sequence stars. Such processing of icy grains in the early solar system may be an important source of organic compounds observed in minor solar system bodies. The delivery of these organic compounds to the surface of the primitive Earth through comet impacts may have provided the raw materials for prebiotic chemistry.

Teglier, Stephen C.↗
DOE OSTI2018

Chimeric Fatty Acyl-Acyl Carrier Protein Thioesterases Provide Mechanistic Insight into Enzyme Specificity and Expression

Medium-chain fatty acids are commodity chemicals. Increasing and modifying the activity of thioesterases (TEs) on medium-chain fatty acyl-acyl carrier protein (acyl-ACP) esters may enable a high-yield microbial production of these molecules. The plant Cuphea palustris harbors two distinct TEs: C. palustris FatB1 ( Cp FatB1) (C 8 specificity, lower activity) and Cp FatB2 (C 14 specificity, higher activity) with 78% sequence identity. We combined structural features from these two enzymes to create several chimeric TEs, some of which showed nonnatural fatty acid production as measured by an enzymatic assay and gas chromatography-mass spectrometry (GC-MS). Substantially, chimera 4 exhibited an increased C 8 fatty acid production in correlation with improved microbial expression. This chimera led us to identify Cp FatB2-specific amino acids between positions 219 and 272 that lead to higher protein levels. Chimera 7 produced a broad range of fatty acids and appeared to combine a fatty acid binding pocket with long-chain specificity and an ACP interaction site that may activate fatty acid extrusion. Using homology modeling and in silico docking with ACP, we identified a “positive patch” within amino acids 162 to 218, which may direct the ACP interaction and regulate access to short-chain fatty acids. On the basis of this modeling, we transplanted putative ACP interaction sequences from Cp FatB1 into Cp FatB2 and created a chimeric thioesterase that produced medium-chain as well as long-chain fatty acids. Hence, the engineering of chimeric enzymes and characterizing their microbial activity and chain-length specificity suggested mechanistic insights into TE functions and also generated thioesterases with potentially useful properties. These observations may inform a rational engineering of TEs to allow alkyl chain length control. IMPORTANCE: Medium-chain fatty acids are important commodity chemicals. These molecules are used as plastic precursors and in shampoos and other detergents and could be used as biofuel precursors if production economics were favorable. Hydrocarbon-based liquid fuels must be optimized to have a desired boiling point, low freezing point, low viscosity, and other physical characteristics. Furthermore, the solubility and harshness of detergents and the flexibility of plastic polymers can be modulated. The length and distribution of the carbon chains in the hydrophobic tails determine these properties. The biological synthesis of cell membranes and fatty acids produces chains of primarily 16 to 18 carbons, which give rise to current biofuels. The ultimate goal of the work presented here is to engineer metabolic pathways to produce designer molecules with the correct number of carbons in a chain, so that such molecules could be used directly as specialty commodity chemicals or as fuels after minimal processing.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Buried and Visible Impact Basin Distribution on Mars: Comparison with Magnetization, Gravity and Crustal Thickness Models

The large population of buried impact basins found in MOLA elevation data on Mars provides compelling evidence for a pre-Noachian crust below the oldest visible Early Noachian surface units, and lowland crust below the younger plains that is Early Noachian in age, older than much of the visible highlands, but not as old as the buried pre-Noachian highlands. The large (D greater than 200 km) buried basins are suggested by Quasi-Circular Depressions (QCDs) that are not apparent in image data, and include features up to 3000 lun diameter in both the lowlands (Utopia) and highlands (a newly found "Ares Basin"). There are about a dozen QCDs larger than 1000 km diameter. We have placed these large features in a relative age sequence based on superimposed smaller QCD. Only the youngest and most obvious of these (Hellas, Argyre, Isidis) lack magnetic anomalies within their main rings. These all have an N(200) cumulative crater density of less than 2.5. Somewhat older lowland-making basins (Utopia, Chryse, Acidalia) with an N(200) age of approximately 3.0, have weak magnetic anomalies, and the oldest, most subdued basins (including Ares) with N(200) greater than 3.5 have many strong magnetic anomalies within their main ring. These older basins likely formed before the main magnetic field died. We have compared our inventory of large QCDs with the distribution of gravity anomalies and with a crustal thickness model which shows many roughly circular areas of thinner crust completely or partly surrounded by narrow regions of thicker crust. These have the structure expected for impact basins, and many of them do correspond to the visible or buried QCDs we previously identified. But there are cases where the crustal thickness feature is offset from the QCD found in topography alone, and there are also several, sometimes large examples of such features which do not coincide with QCDs previously identified. For example, we find several likely buried basins revealed in the crustal thickness data in the Arcadia and Amazonis regions which we did not previously identify, including several features in the 600-1200 km diameter range.

Frey, Herbert↗
DOE OSTI2019

Unsupervised discovery of temporal sequences in high-dimensional datasets, with applications to neuroscience

Identifying low-dimensional features that describe large-scale neural recordings is a major challenge in neuroscience. Repeated temporal patterns (sequences) are thought to be a salient feature of neural dynamics, but are not succinctly captured by traditional dimensionality reduction techniques. Here, we describe a software toolbox—called seqNMF—with new methods for extracting informative, non-redundant, sequences from high-dimensional neural data, testing the significance of these extracted patterns, and assessing the prevalence of sequential structure in data. We test these methods on simulated data under multiple noise conditions, and on several real neural and behavioral data sets. In hippocampal data, seqNMF identifies neural sequences that match those calculated manually by reference to behavioral events. In songbird data, seqNMF discovers neural sequences in untutored birds that lack stereotyped songs. Thus, by identifying temporal structure directly from neural data, seqNMF enables dissection of complex neural circuits without relying on temporal references from stimuli or behavioral outputs.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1977

Image data-processing system for solar astronomy

The paper describes an image data processing system (IDAPS), its hardware/software configuration, and interactive and batch modes of operation for the analysis of the Skylab/Apollo Telescope Mount S056 X-Ray Telescope experiment data. Interactive IDAPS is primarily designed to provide on-line interactive user control of image processing operations for image familiarization, sequence and parameter optimization, and selective feature extraction and analysis. Batch IDAPS follows the normal conventions of card control and data input and output, and is best suited where the desired parameters and sequence of operations are known and when long image-processing times are required. Particular attention is given to the way in which this system has been used in solar astronomy and other investigations. Some recent results obtained by means of IDAPS are presented.

Wilson, R. M.↗
NASA NTRS1970

Apollo 12 photography 70 mm, 16 mm, and 35 mm frame index

For each 70-mm frame, the index presents information on: (1) the focal length of the camera, (2) the photo scale at the principal point of the frame, (3) the selenographic coordinates at the principal point of the frame, (4) the percentage of forward overlap of the frame, (5) the sun angle (medium, low, high), (6) the quality of the photography, (7) the approximate tilt (minimum and maximum) of the camera, and (8) the direction of tilt. A brief description of each frame is also included. The index to the 16-mm sequence photography includes information concerning the approximate surface coverage of the photographic sequence and a brief description of the principal features shown. A column of remarks is included to indicate: (1) if the sequence is plotted on the photographic index map and (2) the quality of the photography. The pictures taken using the lunar surface closeup stereoscopic camera (35 mm) are also described in this same index format.

Source record↗
DOE OSTI2022

Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica

Abstract Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli , use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica . A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide’s ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.

59 BASIC BIOLOGICAL SCIENCES↗