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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.

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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A 20 Gbps PAM4 data transmitter ASIC for particle physics experiments

We present the design and test results of a novel data transmitter ASIC operating up to 20.48 Gbps with 4-level Pulse-Amplitude-Modulation (PAM4) for particle physics experiments. This ASIC, named GBS20, is fabricated in a 65 nm CMOS technology. Two serializers share a 5.12 GHz Phase Locked Loop (PLL) clock. The outputs from the serializers are combined into a PAM4 signal that directly drives a Vertical-Cavity-Surface-Emitting-Laser (VCSEL). The input data channels, each at 1.28 Gbps, are scrambled with an internal 2$^{7}$-1 Pseudo-Random Binary Sequence (PRBS), which also serves as a frame aligner. GBS20 is tested to work at 10.24 and 20.48 Gbps with a VCSEL-based Transmitter-Optical-Subassembly (TOSA). The power consumption of GBS20 is below 238 mW and reduced to 164 mW in the low-power mode.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2011

DETECTION OF SUPERGRANULATION ALIGNMENT IN POLAR REGIONS OF THE SUN BY HELIOSEISMOLOGY

We report on a new phenomenon of 'alignment' of supergranulation cells in the polar regions of the Sun. Recent high-resolution data sets obtained by the Solar Optical Telescope on board the Hinode satellite enabled us to investigate supergranular structures in high-latitude regions of the Sun. We have carried out a local helioseismology time-distance analysis of the data and detected acoustic travel-time variations due to the supergranular flows. The supergranulation cells in both the north and south polar regions show systematic alignment patterns in the north-south direction. The south-pole data sets obtained in a month-long Hinode campaign indicate that the supergranulation alignment property may be quite common in the polar regions. We also discuss the latitudinal dependence of the supergranulation cell sizes; the data show that the east-west cell size decreases toward higher latitudes.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1994

Impact basins in Southern Daedalia, Mars: Evidence for clustered impactors?

The distribution of ancient massifs and old cratered terrain in the southern Daedalia region indicate the presence of at least two and probably three impact basins of large size. One of these is located near where Craddock et al. placed their center for the Daedalia Basin, but it has very different ring diameters. These basins have rings exceeding 1000 km diameter and overlap significantly with centers separated by 500 to 600 km at nearly identical latitudes of -26 to -29 deg. The smaller westernmost basin appears slightly better preserved, but there is little evidence for obvious superposition that might imply a temporal sequence. Recognizing the improbability of random impacts producing aligned, nearly contemporaneous features, we suggest these basins may have resulted from clustered impactors.

Frey, Herbert↗
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 NTRS2003

Using Fractional Clock-Period Delays in Telemetry Arraying

A set of special digital all-pass finite-impulse- response (FIR) filters produces phase shifts equivalent to delays that equal fractions of the sampling or clock period of a telemetry-data-processing system. These filters have been used to enhance the arraying of telemetry signals that have been received at multiple ground stations from spacecraft (see figure). Somewhat more specifically, these filters have been used to align, in the time domain, the telemetry-data sequences received by the various antennas, in order to maximize the signal-to-noise ratio of the composite telemetric signal obtained by summing the signals received by the antennas. The term arraying in this context denotes a method of enhanced reception of telemetry signals in which several antennas are used to track a single spacecraft. Each antenna receives a signal that comprises a sum of telemetry data plus noise, and these sum data are sent to an arraying combiner for processing. Correlation is the means used to align the set of data from one antenna with that from another antenna. After the data from all the antennas have been aligned in the time domain, they are all added together, sample by sample.

Fort, David↗
NASA NTRS1984

Rapid Test Bed Concentrator (TBC) Alignment Techniques

A new, labor and cost saving method was developed to eliminate the procedure of covering all (220) mirrors and uncovering then one-by-one in sequence to adjust each to the focal plane. This latest method being used to align mirrors of a parabolic solar concentrator utilizes a computer-derived target of discreet images made up of individual mirror reflections on a plane in front of the intended, nominal, focal point. Incorporating this computer technique increases accuracy and gives potential to develop flux distributions required by different receiver designs.

Argoud, M. J.↗
DOE OSTI2013

Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based on a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium , E. coli K12 and C. crescenttus , we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Simrank: Rapid and sensitive general-purpose k-mer search tool

Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project (http://nihroadmap.nih.gov/hmp). Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variablelength protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw amino acids k-mer features.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

ABSTRACT In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variable-length protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw k-mer features. Availability Implementations of our method will be available under the Apache 2 licence at http://llp.berkeley.edu/dimotif and http://llp.berkeley.edu/protvecx .

Asgari, Ehsaneddin↗
DOE OSTI2011

Rotational structures and the wobbling mode in {sup 167}Ta

Excited states in the neutron-deficient nucleus {sup 167}Ta were studied through the {sup 120}Sn({sup 51}V,4n) reaction. Twelve rotational bands have been observed and the relative excitation energy of each sequence is now known owing to the multiple interband connections. Several quasineutron alignments were observed that aided in the quasiparticle assignments of these bands. The resulting interpretation is in line with observations in neighboring nuclei. Trends in the wobbling phonon energy seen in {sup 161,163,165,167}Lu and {sup 167}Ta are also discussed and particle-rotor model calculations (assuming constant moments of inertia) are found to be inconsistent with the experimental data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2011

VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Physically motivated global alignment method for electron tomography

Electron tomography is widely used for nanoscale determination of 3-D structures in many areas of science. Determining the 3-D structure of a sample from electron tomography involves three major steps: acquisition of sequence of 2-D projection images of the sample with the electron microscope, alignment of the images to a common coordinate system, and 3-D reconstruction and segmentation of the sample from the aligned image data. The resolution of the 3-D reconstruction is directly influenced by the accuracy of the alignment, and therefore, it is crucial to have a robust and dependable alignment method. In this paper, we develop a new alignment method which avoids the use of markers and instead traces the computed paths of many identifiable ‘local’ center-of-mass points as the sample is rotated. Compared with traditional correlation schemes, the alignment method presented here is resistant to cumulative error observed from correlation techniques, has very rigorous mathematical justification, and is very robust since many points and paths are used, all of which inevitably improves the quality of the reconstruction and confidence in the scientific results.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2015

De novo transcriptome assembly databases for the central nervous system of the medicinal leech

The study of non-model organisms stands to benefit greatly from genetic and genomic data. For a better understanding of the molecular mechanisms driving neuronal development, and to characterize the entire leech Hirudo medicinalis central nervous system (CNS) transcriptome we combined Trinity for de-novo assembly and Illumina HiSeq2000 for RNA-Seq. We present a set of 73,493 de-novo assembled transcripts for the leech, reconstructed from RNA collected, at a single ganglion resolution, from the CNS. This set of transcripts greatly enriches the available data for the leech. Here, we share two databases, such that each dataset allows a different type of search for candidate homologues. The first is the raw set of assembled transcripts. This set allows a sequence-based search. A comprehensive analysis of which revealed 22,604 contigs with high e-values, aligned versus the Swiss-Prot database. This analysis enabled the production of the second database, which includes correlated sequences to annotated transcript names, with the confidence of BLAST best hit.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Alignment of the ATLAS Inner Detector in Run 2

The performance of the ATLAS Inner Detector alignment has been studied using pp collision data at s√=13TeV collected by the ATLAS experiment during Run 2 (2015–2018) of the Large Hadron Collider (LHC). The goal of the detector alignment is to determine the detector geometry as accurately as possible and correct for time-dependent movements. The Inner Detector alignment is based on the minimization of track-hit residuals in a sequence of hierarchical levels, from global mechanical assembly structures to local sensors. Subsequent levels have increasing numbers of degrees of freedom; in total there are almost 750,000. The alignment determines detector geometry on both short and long timescales, where short timescales describe movements within an LHC fill. The performance and possible track parameter biases originating from systematic detector deformations are evaluated. Momentum biases are studied using resonances decaying to muons or to electrons. The residual sagitta bias and momentum scale bias after alignment are reduced to less than ~0.1 TeV -1 and 0.9×10 -3 , respectively. Impact parameter biases are also evaluated using tracks within jets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection

Generating top-down tandem mass spectra (MS/MS) for complex mixtures of proteoforms has become possible through improvements in fractionation, on-line separation, dissociation, and mass analysis. The algorithms to match tandem mass spectra to sequences have undergone a parallel evolution, with both spectral alignment and peak matching being paired with diverse methods for scoring proteoform-spectral matches (PrSMs). This study assesses state-of-the-art algorithms for top-down identification through three distinct challenges. The first is identifying a large yield of PrSMs while controlling false discovery rate (FDR) in identifying thousands of proteoforms from complex cell lysates via four software workflows: ProSight Proteome Discoverer, TopPIC, Informed Proteomics, and pTop. The second is the deconvolution of data from both Thermo Orbitrap-class and Bruker maXis Q-TOF instruments to produce consistent precursor charge and mass determinations while generating fragment mass lists to optimize identification. The third attempts to detect diverse post-translational modifications (PTMs) in proteoforms from cow milk and human ovarian tissue. The data demonstrate that existing software suites produce admirable sensitivity, in some cases identifying a third of collected tandem mass spectra with FDR controlled below 2%; the overlap in these PrSMs, however, illustrates real value in searching data with multiple search engines. Differences among identification workflows seem to result from each search algorithm incorporating its own deconvolution algorithm. By transmitting deconvolution data from multiple deconvolution routes (Thermo Xtract, Bruker Auto MSn, Mascot Distiller, TopFD, and FLASHDeconv) to the downstream TopPIC search algorithm, we were able to detect common causes of deconvolution disagreement. The detection of PTMs was very inconsistent among search algorithms, with some workflows suggesting as little as 1% of PrSMs from cow’s milk were singly-phosphorylated while other workflows found that 18% of PrSMs were singly-phosphorylated. Taken together, these results make a strong argument for top-down researchers to adopt a standard practice of analyzing each MS/MS experiment with at least two different search engines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Sensitive and error-tolerant annotation of protein-coding DNA with BATH

We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Crystallization and preliminary crystallographic analysis of the type IIL restriction enzyme MmeI in complex with DNA

Type IIL restriction enzymes have rejuvenated the search for user-specified DNA binding and cutting. By aligning and contrasting the highly comparable amino-acid sequences yet diverse recognition specificities across the family of enzymes, amino acids involved in DNA binding have been identified and mutated to produce alternative binding specificities. To date, the specificity of MmeI (a type IIL restriction enzyme) has successfully been altered at positions 3, 4 and 6 of the asymmetric TCCRAC (where R is a purine) DNA-recognition sequence. To further understand the structural basis of MmeI DNA-binding specificity, the enzyme has been crystallized in complex with its DNA substrate. The crystal belonged to space group P1, with unit-cell parameters a = 61.73, b = 94.96, c = 161.24 {angstrom}, {alpha} = 72.79, {beta} = 89.12, {gamma} = 71.68{sup o}, and diffracted to 2.6 {angstrom} resolution when exposed to synchrotron radiation. The structure promises to reveal the basis of MmeI DNA-binding specificity and will complement efforts to create enzymes with novel specificities.

59 BASIC BIOLOGICAL SCIENCES↗