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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
NASA NTRS1986

Archean foreland basin tectonics in the Witwatersrand, South Africa

The Witwatersrand Basin of South Africa is the best-known of Archean sedimentary basins and contains some of the largest gold reserves in the world. Sediments in the basin include a lower flysch-type sequence and an upper molassic facies, both of which contain abundant silicic volcanic detritus. The strata are thicker and more proximal on the northwestern side of the basin which is, at least locally, bound by thrust faults. These features indicate that the Witwatersrand strata may have been deposited in a foreland basin and a regional geologic synthesis suggests that this basin developed initially on the cratonward side of an Andean-type arc. Remarkably similar Phanerozoic basins may be found in the southern Andes above zones of shallow subduction. It is suggested that the continental collision between the Kaapvaal and Zimbabwe Cratons at about 2.7 Ga caused further subsidence and deposition in the Witwatersrand Basin. Regional uplift during this later phase of development placed the basin on the cratonward edge of a collision-related plateau, now represented by the Limpopo Province. Similarities are seen between this phase of Witwatersrand Basin evolution and that of active basins north of the Tibetan Plateau. The geologic evidence does not agree with earlier suggestions that the Witwatersrand strata were deposited in a rift or half-graben.

Burke, K.↗
NASA NTRS1986

Archean foreland basin tectonics in the Witwatersrand, South Africa

The Witwatersrand Basin of South Africa is the best-known of Archean sedimentary basins and contains some of the largest gold reserves in the world. Sediments in the basin include a lower flysch-type sequence and an upper molassic facies, both of which contain abundant silicic volcanic detritus. The strata are thicker and more proximal on the northwestern side of the basin which is, at least locally, bound by thrust faults. These features indicate that the Witwatersrand strata may have been deposited in a foreland basin and a regional geologic synthesis suggests that this basin developed initially on the cratonward side of an Andean-type arc. Remarkably similar Phanerozoic basins may be found in the southern Andes above zones of shallow subduction. It is suggested that the continental collision between the Kaapvaal and Zimbabwe Cratons at about 2.7 Ga caused further subsidence and deposition in the Witwatersrand Basin. Regional uplift during this later phase of development placed the basin on the cratonward edge of a collision-related plateau, now represented by the Limpopo Province. Similarities are seen between this Phase of Witywatersrand Basin evolution and that of active basins north of the Tibetan Plateau. The geologic evidence does not agree with earlier suggestions that the Witwatersrand strata were deposited in a rift or half-graben.

Burke, K.↗
NASA NTRS1993

An infrared study of the remarkable dusty M star HR 3126

HR 3126 is a unique M giant star embedded in the bipolar reflection nebula IC 2220. In this paper we present new photometric and spectroscopic observations of HR 3126 and combine them with existing data from the literature in an extensive reappraisal of the star's properties at infrared wavelengths. The spectral energy distribution is consistent with an optical classification of M0-3 II with infrared excess. The dust shell cannot be fitted by a single-temperature blackbody: at least three components are required, with temperatures in the range 35-1300 K. On the basis of spectroscopy at 1-4 and 7-25 microns, combined with an assessment of various color-color diagrams, we are able to reject the hypothesis that HR 3126 is carbon-rich. Weak silicate emission features are detected at 10 and 19 microns, and a previous report of silicon carbide emission at 11.2 microns is not substantiated. It seems likely that HR 2136 is in a phase of advanced and rapid postmain-sequence evolution, possibly beginning its ascent of the asymptotic giant branch.

Chiar, J. E.↗
DOE OSTI2021

Automatic method of material identification for computed tomography

A method is provided for isolating and labeling discrete features in a spectral radiographic image recorded as a set of images in different energy channels. The disclosed method involves creating a profile for each of at least some pixels in the spectral radiographic image. The profiles are sequences of pixel values, in which each pixel value is a photon count or a similar radiographic exposure value indicative of the attenuation of a portion of the scanning beam in a respective energy channel. Iterative hierarchical clustering is used to cluster the pixels on the basis of their respective profiles. Labels are assigned to one or more of the resulting clusters. In implementations, each label can be associated with an inferred material composition or with an inference that the material composition is unknown.

Jimenez, Jr., Edward Steven↗
DOE OSTI2023

Structural and Biophysical Properties of a [4Fe-4S] Ferredoxin-Like Protein from Synechocystis sp. PCC 6803 with a Unique Two Domain Structure

Electron carrier proteins (ECPs), binding iron-sulfur clusters, are vital components within the intricate network of metabolic and photosynthetic reactions. They play a crucial role in the distribution of reducing equivalents. In Synechocystis sp. PCC 6803, the ECP network includes at least nine ferredoxins. Previous research, including global expression analyses and protein binding studies, has offered initial insights into the functional roles of individual ferredoxins within this network. This study primarily focuses on Ferredoxin 9 (slr2059). Through sequence analysis and computational modeling, Ferredoxin 9 emerges as a unique ECP with a distinctive two-domain architecture. It consists of a C-terminal iron-sulfur binding domain and an N-terminal domain with homology to Nil-domain proteins, connected by a structurally rigid 4-amino acid linker. Notably, in contrast to canonical [2Fe-2S] ferredoxins exemplified by PetF (ssl0020), which feature highly acidic surfaces facilitating electron transfer with photosystem I reaction centers, models of Ferredoxin 9 reveal a more neutral to basic protein surface. Using a combination of electron paramagnetic resonance spectroscopy and square-wave voltammetry on heterologously produced Ferredoxin 9, this study demonstrates that the protein coordinates 2x[4Fe-4S]2+/1+ redox-active and magnetically interacting clusters, with measured redox potentials of -420 +/- 9 mV and -516 +/- 10 mV vs SHE. A more in-depth analysis of Fdx9's unique structure and protein sequence suggests that this type of Nil-2[4Fe-4S] multi-domain ferredoxin is well conserved in cyanobacteria, bearing structural similarities to proteins involved in homocysteine synthesis in methanogens.

cyanobacteria↗
DOE OSTI2021

PSpecteR: A User-Friendly and Interactive Application for Visualizing Top-Down and Bottom-Up Proteomics Data in R

Visual examination of mass spectrometry data is necessary to assess data quality and to facilitate data exploration. Graphics provide the means to evaluate spectral properties, test alternative peptide/protein sequence matches, prepare annotated spectra for publication, and fine-tune parameters during wet lab procedures. Visual inspection of MS data is hindered by proprietary proteomics visualization software designed for particular workflows and academic software that lack visualization tools. We built PSpecteR, an open-source and interactive R Shiny web application to address these issues, with support for several steps of proteomics data processing, including: reading various mass spectrometry files, running open-source database search tools, labelling spectra with fragmentation patterns, testing post-translational modifications, plotting where identified fragments map to reference sequences, and visualizing algorithmic output and metadata. All figures, tables, and spectra are exportable within one easy-to-use graphical user interface. Our current software provides a flexible and modern R framework to support fast implementation of additional features. The open source code is readily available (https://github.com/EMSL-Computing/PSpecteR), and a PSpecteR Docker container (https://hub.docker.com/r/emslcomputing) is available for easy local installation.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2017

Diatom centromeres suggest a mechanism for nuclear DNA acquisition

Significance Centromeres are genomic sites facilitating chromosome segregation during cell division. We report our discovery of diatom centromeres and the description of centromere identity in the stramenopile protists. We also show that simple requirements for diatom centromeres permit ecologically relevant foreign DNA molecules to function as diatom centromeres by “hijacking” chromosome maintenance features. Because little is known at the molecular level about chromosome maintenance in diatoms, this paper provides experimental data with broad implications for cellular biology studies and biotechnology applications. The ability to maintain circular artificial chromosomes using foreign DNA sequences is unique among organisms with studied centromeres and opens up fascinating evolutionary questions about the mechanisms of nuclear gene acquisition from the multiple endosymbiotic events characterizing the stramenopile lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dose-dependent consequences of sub-chronic fentanyl exposure on neuron and glial co-cultures

Fentanyl is one of the most common opioid analgesics administered to patients undergoing surgery or for chronic pain management. While the side effects of chronic fentanyl abuse are recognized (e.g., addiction, tolerance, impairment of cognitive functions, and inhibit nociception, arousal, and respiration), it remains poorly understood what and how changes in brain activity from chronic fentanyl use influences the respective behavioral outcome. Here, we examined the functional and molecular changes to cortical neural network activity following sub-chronic exposure to two fentanyl concentrations, a low (0.01 μM) and high (10 μM) dose. Primary rat co-cultures, containing cortical neurons, astrocytes, and oligodendrocyte precursor cells, were seeded in wells on either a 6-well multi-electrode array (MEA, for electrophysiology) or a 96-well tissue culture plate (for serial endpoint bulk RNA sequencing analysis). Once networks matured (at 28 days in vitro ), co-cultures were treated with 0.01 or 10 μM of fentanyl for 4 days and monitored daily. Only high dose exposure to fentanyl resulted in a decline in features of spiking and bursting activity as early as 30 min post-exposure and sustained for 4 days in cultures. Transcriptomic analysis of the complex cultures after 4 days of fentanyl exposure revealed that both the low and high dose induced gene expression changes involved in synaptic transmission, inflammation, and organization of the extracellular matrix. Collectively, the findings of this in vitro study suggest that while neuroadaptive changes to neural network activity at a systems level was detected only at the high dose of fentanyl, transcriptomic changes were also detected at the low dose conditions, suggesting that fentanyl rapidly elicits changes in plasticity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

On the eccentricity excitation in post-main-sequence binaries

Several classes of stellar binaries with post-main-sequence (post-MS) components—millisecond pulsars with the white dwarf companions (MSP+WD) and periods of P{sub b}∼30 days, binaries hosting post-asymptotic giant branch stars, or barium stars with P{sub b} ∼ several years—feature high eccentricities (up to 0.4) despite the expectation of their efficient tidal circularization during their post-MS evolution. It was suggested that the eccentricities of these binaries can be naturally excited by their tidal coupling to the circumbinary disk, formed by the material ejected from the binary. Here we critically reassess this idea using simple arguments rooted in the global angular momentum conservation of the disk+binary system. Compared to previous studies, we (1) fully account for the viscous spreading of the circumbinary disk, (2) consider the possibility of reaccretion from the disk onto the binary (in agreement with simulations and empirical evidence), and (3) allow for the reduced viscosity after the disk expands, cools, and forms dust. These ingredients conspire to significantly lower the efficiency of eccentricity excitation by the disk tides. We find that explaining eccentricities of the post-MS binaries is difficult and requires massive (≳10{sup −2} M{sub ⊙}), long-lived (≳10{sup 5} years) circumbinary disks that do not reaccrete. While disk tides may account for the eccentricities of the MSP+WD binaries, we show reaccretion to also be detrimental for these systems. Reduced efficiency of the disk-driven excitation motivates the study of alternative mechanisms for producing the peculiar eccentricities of the post-MS binaries.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1977

Nevada Test Site craters used for astronaut training

Craters produced by chemical and nuclear explosives at the Nevada Test Site were used to train astronauts before their lunar missions. The craters have characteristics suitable for reconnaissance-type field investigations. The Schooner test produced a crater about 300 m across and excavated more than 72 m of stratigraphic section deposited in a fairly regular fashion so that systematic observations yield systematic results. Other features common on the moon, such as secondary craters and glass-coated rocks, are present at Schooner crater. Smaller explosive tests on Buckboard Mesa excavated rocks from three horizontal alteration zones within basalt flows so that the original sequence of the zones could be determined. One crater illustrated the characteristics of craters formed across vertical boundaries between rock units. Although the exercises at the Nevada Test Site were only a small part of the training of the astronauts, voice transcripts of Apollo missions 14, 16, and 17 show that the exercises contributed to astronaut performance on the moon.

Moore, H. J.↗
NASA NTRS1978

Conclusions derived from the evidence on accretion in meteorites

A study of the evidence on accretion in meteorites shows that gross chemical features of chondritic meteorite type were established by accretion of materials with characteristic chemical and isotopic compositions. Some meteorites have been subjected to intensive mechanical and/or thermal processes. Mixing has occurred among meteorite types, presumably late in the accretion sequence. From the materials which appear to have escaped substantial modification it can be concluded that the relative velocities between accreting grains varied but in some cases were very low. Accretion took place after most, if not all, of the gaseous components had been separated from the condensed portion of solar matter.

Herndon, J. M.↗
NASA NTRS1989

A parallel row-based algorithm for standard cell placement with integrated error control

A new row-based parallel algorithm for standard-cell placement targeted for execution on a hypercube multiprocessor is presented. Key features of this implementation include a dynamic simulated-annealing schedule, row-partitioning of the VLSI chip image, and two novel approaches to control error in parallel cell-placement algorithms: (1) Heuristic Cell-Coloring; (2) Adaptive Sequence Length Control.

Sargent, Jeff S.↗
NASA NTRS1991

Dynamics of vegetation and soils of oak/saw palmetto scrub after fire: Observations from permanent transects

Ten permanent 15 m transects previously established in two oak/saw palmetto scrub stands burned in December 1986, while two transects remained unburned. Vegetation in the greater than 0.5 m and the less than 0.5 m layers on these transects was sampled at 6, 12, 18, 24, and 36 months postburn and determined structural features of the vegetation (height, percent bare ground, total cover). The vegetation data were analyzed from each sampling by height layer using detrended correspondence analysis ordination. Vegetation data for the greater than 0.5 m layer for the entire time sequence were combined and analyzed using detrended correspondence analysis ordination. Soils were sampled at 6, 12, 18, and 24 months postburn and analyzed for pH, conductivity, organic matter, exchangeable cations (Ca, Mg, K, Na), NO3-N, NH4-N, Al, available metals (Cu, Fe, Mn, Zn), and PO4-P. Shrub species recovered at different rates postfire with saw palmetto reestablishing cover greater than 0.5 m within one year, but the scrub oaks had not returned to preburn cover greater than 0.5 m in 3 years after the fire. These differences in growth rates resulted in dominance shifts after the fire with saw palmetto increasing relative to the scrub oaks. Overall changes in species richness were minor, although changes occurred in species richness by height layers due to different growth rates. Soils of well drained and poorly drained sites differed markedly. Soil responses to the fire appeared minor. Soil pH increased at 6 and 12 months postfire; calcium increased at 6 months postburn. Nitrate-nitrogen increased at 12 months postburn. Low values of conductivity, PO4-P, Mg, K, Na, and Fe at 12 months postburn may be related to heavy rainfall the preceding month. Seasonal variability in some soil parameters appeared to occur.

Schmalzer, Paul A.↗
NASA NTRS2001

Development of Low-Noise High Value Chromium Silicide Resistors for Cryogenic Detector Applications

Extremely high sensitivity detectors, such as silicon bolometers are required in many NASA missions for detection of photons from the x-ray to the far infrared regions. Typically, these detectors are cooled to well below the liquid helium (LHe) temperature (4.2 K) to achieve the maximum detection performance. As photoconductors, they are generally operated with a load resistor and a pre-set bias voltage, which is then coupled to the input gate of a source-follower Field Effect Transistor (FET) circuit. It is imperative that the detector system signal to noise performance be limited by the noise of the detector and not by the noise of the external components. The load resistor value is selected to optimize the detector performance. These two criteria tend to be contradictory in that these detectors require load resistors in the hundreds of megaohms, which leads to a higher Johnson noise. Additionally, the physical size of the resistor must be small for device integration as required by such missions as the NASA High Resolution Airborne Wide-Band Camera (HAWC) instrument and the Submillimeter High Angular Resolution Camera (SHARC) for the Caltech Submillimeter Observatory (CSO). We have designed, fabricated and characterized thin film resistors using a CrSi/TiW/Al metal system on optical quality quartz substrates. The resistor values range from 100 megaohms to over 650 megaohms and are Johnson noise limited at LHe temperatures. The resistor film is sputtered with a sheet resistance ranging from 300 ohms to 1600 ohms and the processing sequence developed for these devices allows for chemically fine tuning the sheet resistance in-situ. The wafer fabrication process was of sufficiently high yield (>80%) providing clusters of good resistors for integrated multiple detector channels, a very important feature in the assembly of these two instruments.

Jhabvala, Murzy↗
NASA NTRS2004

Impactites of the Yaxcopoil-1 drilling site, Chicxulub impact structure: Petrography, geochemistry, and depositional environment

The impact breccias encountered in drill hole Yaxcopoil-1 (Yax-1) in the Chicxulub impact structure have been subdivided into six units. The two uppermost units are redeposited suevite and suevite, and together are only 28 m thick. The two units below are interpreted as a ground surge deposit similar to a pyroclastic flow in a volcanic regime with a fine-grained top (unit 3; 23 m thick; nuee ardente) and a coarse breccia (unit 4; approx.15 m thick) below. As such, they consist of a melange of clastic matrix breccia and melt breccia. The pyroclastic ground surge deposit and the two units 5 and 6 below are related to the ejecta curtain. Unit 5 (approx.24 m thick) is a silicate impact melt breccia, whereas unit 6 (10 m thick) is largely a carbonate melt breccia with some clastic-matrix components. Unit 5 and 6 reflect an overturning of the target stratigraphy. The suevites of units 1 and 2 were deposited after emplacement of the ejecta curtain debris. Reaction of the super-heated breccias with seawater led to explosive activity similar to phreomagmatic steam explosion in volcanic regimes. This activity caused further brecciation of melt and melt fragments. The fallback suevite deposit of units 1 and 2 is much thinner than suevite deposits at larger distances from the center of the impact structure than the 60 km of the Yax-1 drill site. This is evidence that the fallback suevite deposit (units 1 and 2) originally was much thicker. Unit 1 exhibits sedimentological features suggestive of suevite redeposition. Erosion possibly has occurred right after the IUT impact due to seawater backsurge, but erosion processes spanning thousands of years may also have been active. Therefore, the top of the 100 m thick impactite sequence at Yaxcopoil, in our opinion, is not the K/T boundary.

Dressler, Burkhard O.↗
NASA NTRS1999

Keck II Mid-Infrared Imaging of the Young Stellar Object WL16

WL16 is unique among the members of the young, forming star cluster embedded in the nearby p Oph cloud core in exhibiting an extended, high surface brightness disk in the emission features originating from solid-state aromatic hydrocarbons.

Circumstellar matter dust disk mid-infrared very s↗
NASA NTRS2013

Building a 2.5D Digital Elevation Model from 2D Imagery

When projecting imagery into a georeferenced coordinate frame, one needs to have some model of the geographical region that is being projected to. This model can sometimes be a simple geometrical curve, such as an ellipse or even a plane. However, to obtain accurate projections, one needs to have a more sophisticated model that encodes the undulations in the terrain including things like mountains, valleys, and even manmade structures. The product that is often used for this purpose is a Digital Elevation Model (DEM). The technology presented here generates a high-quality DEM from a collection of 2D images taken from multiple viewpoints, plus pose data for each of the images and a camera model for the sensor. The technology assumes that the images are all of the same region of the environment. The pose data for each image is used as an initial estimate of the geometric relationship between the images, but the pose data is often noisy and not of sufficient quality to build a high-quality DEM. Therefore, the source imagery is passed through a feature-tracking algorithm and multi-plane-homography algorithm, which refine the geometric transforms between images. The images and their refined poses are then passed to a stereo algorithm, which generates dense 3D data for each image in the sequence. The 3D data from each image is then placed into a consistent coordinate frame and passed to a routine that divides the coordinate frame into a number of cells. The 3D points that fall into each cell are collected, and basic statistics are applied to determine the elevation of that cell. The result of this step is a DEM that is in an arbitrary coordinate frame. This DEM is then filtered and smoothed in order to remove small artifacts. The final step in the algorithm is to take the initial DEM and rotate and translate it to be in the world coordinate frame [such as UTM (Universal Transverse Mercator), MGRS (Military Grid Reference System), or geodetic] such that it can be saved in a standard DEM format and used for projection.

Padgett, Curtis W.↗
DOE OSTI2022

Decoding the protein–ligand interactions using parallel graph neural networks

Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.

59 BASIC BIOLOGICAL SCIENCES↗