Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Base Sequence”

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 1,747 records · Page 97
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Genomes OnLine database (GOLD) v.7: updates and new features

The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project. Currently GOLD hosts information on 33 415 Studies, 49 826 Biosamples, 313 324 Organisms, 215 881 Sequencing Projects and 174 454 Analysis Projects with a total of 541 metadata fields, of which 80 are based on controlled vocabulary (CV) terms. GOLD provides a user-friendly web interface to browse sequencing projects and launch advanced search tools across four classification levels. Users submit metadata on a wide range of Sequencing and Analysis Projects in GOLD before depositing sequence data to the Integrated Microbial Genomes (IMG) system for analysis. GOLD conforms with and supports the rules set by the Genomic Standards Consortium (GSC) Minimum Information standards. The current version of GOLD (v.7) has seen the number of projects and associated metadata increase exponentially over the years. This paper provides an update on the current status of GOLD and highlights the new features added over the last two years.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1997

Soft-Decision Decoding of Binary Linear Block Codes Based on an Iterative Search Algorithm

This correspondence presents a suboptimum soft-decision decoding scheme for binary linear block codes based on an iterative search algorithm. The scheme uses an algebraic decoder to iteratively generate a sequence of candidate codewords one at a time using a set of test error patterns that are constructed based on the reliability information of the received symbols. When a candidate codeword is generated, it is tested based on an optimality condition. If it satisfies the optimality condition, then it is the most likely (ML) codeword and the decoding stops. If it fails the optimality test, a search for the ML codeword is conducted in a region which contains the ML codeword. The search region is determined by the current candidate codeword and the reliability of the received symbols. The search is conducted through a purged trellis diagram for the given code using the Viterbi algorithm. If the search fails to find the ML codeword, a new candidate is generated using a new test error pattern, and the optimality test and search are renewed. The process of testing and search continues until either the MEL codeword is found or all the test error patterns are exhausted and the decoding process is terminated. Numerical results show that the proposed decoding scheme achieves either practically optimal performance or a performance only a fraction of a decibel away from the optimal maximum-likelihood decoding with a significant reduction in decoding complexity compared with the Viterbi decoding based on the full trellis diagram of the codes.

Lin, Shu↗
NASA NTRS1994

The Final Approach Spacing Tool

A system for assisting terminal area air traffic controllers in the management and control of arrival traffic, referred to as the Final Approach Spacing Tool (FAST), is being developed at NASA Ames Research Center. In a cooperative program, NASA and FAA have efforts underway to install and evaluate the system at the Dallas/Fort Worth Terminal Radar Approach Control facility. This paper will review the software architecture, the algorithms components, and the human-machine interface. The system is based on continuous updates of a detailed trajectory analyses of all arrival aircraft. FAST interprets the results of these trajectory analyses to build an efficient and procedurally acceptable plan for the arrival traffic that consists of a sequence, schedule, and runway assignment. The system utilizes a heuristically-based conflict resolution algorithm to build a solution trajectory that satisfies the plan, It extracts a series of speed and heading advisories from the solution trajectory to assist the controller in efficiently managing and controlling the arrival traffic down to the runway. The advisories are displayed in a graphical format to the controller. In addition to the radar tracking data, the system also relies on a series of data bases. These data bases contain aircraft performance models, airline preferred operational procedures, airspace structure, air traffic procedural models, and a three dimensional wind model. Field evaluation of FAST is expected to begin in 1994.

Davis, Thomas J.↗
DOE OSTI2012

Convergence of the Transcriptional Responses to Heat Shock and Singlet Oxygen Stresses

Cells often mount transcriptional responses and activate specific sets of genes in response to stress-inducing signals such as heat or reactive oxygen species. Transcription factors in the RpoH family of bacterial alternative σ factors usually control gene expression during a heat shock response. Interestingly, several α-proteobacteria possess two or more paralogs of RpoH, suggesting some functional distinction. We investigated the target promoters of Rhodobacter sphaeroides RpoH I and RpoH II using genome-scale data derived from gene expression profiling and the direct interactions of each protein with DNA in vivo. We found that the RpoH I and RpoH II regulons have both distinct and overlapping gene sets. We predicted DNA sequence elements that dictate promoter recognition specificity by each RpoH paralog. We found that several bases in the highly conserved TTG in the -35 element are important for activity with both RpoH homologs; that the T-9 position, which is over-represented in the RpoH I promoter sequence logo, is critical for RpoH I –dependent transcription; and that several bases in the predicted -10 element were important for activity with either RpoH II or both RpoH homologs. Genes that are transcribed by both RpoH I and RpoH II are predicted to encode for functions involved in general cell maintenance. The functions specific to the RpoHI regulon are associated with a classic heat shock response, while those specific to RpoHII are associated with the response to the reactive oxygen species, singlet oxygen. We propose that a gene duplication event followed by changes in promoter recognition by RpoHI and RpoHII allowed convergence of the transcriptional responses to heat and singlet oxygen stress in R. sphaeroides and possibly other bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg

The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as Archaea from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the ‘Global Archaea Diversity’ (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the Archaea, offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

An HST survey for 100–1000 au companions around young stellar objects in the Orion molecular clouds: Evidence for environmentally dependent multiplicity

We present a near-infrared survey for the visual multiples in the Orion molecular clouds region at separations between 100 and 1000 au. These data were acquired at 1.6 μm with the NICMOS and WFC3 cameras on the Hubble Space Telescope. Additional photometry was obtained for some of the sources at 2.05 μm with NICMOS and in the L′ band with NSFCAM2 on NASA’s InfraRed Telescope Facility. Toward 129 protostars and 197 pre-main-sequence stars with disks observed with WFC3, we detect 21 and 28 candidate companions between the projected separations of 100–1000 au, of which less than 5 and 8, respectively, are chance line-of-sight coincidences. The resulting companion fraction (CF) after the correction for the line-of-sight contamination is 14.4{sub −1.3}{sup +1.1}% for protostars and 12.5{sub −0.8}{sup +1.2}% for the pre-main-sequence stars. These values are similar to those found for main-sequence stars, suggesting that there is little variation in the CF with evolution, although several observational biases may mask a decrease in the CF from protostars to the main-sequence stars. After segregating the sample into two populations based on the surrounding surface density of young stellar objects, we find that the CF in the high stellar density regions (Σ{sub YSO} > 45 pc{sup −2}) is approximately 50% higher than that found in the low stellar density regions (Σ{sub YSO} < 45 pc{sup −2}). We interpret this as evidence for the elevated formation of companions at 100–1000 au in the denser environments of Orion. We discuss possible reasons for this elevated formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Analysis of Line Distance Elements for Various Ibr Controllers and System Conditions

The large-scale penetration of inverter-based resources in power systems has challenged protection engineers because of the different fault behaviors these sources provide compared to conventional generation systems. The main challenges include a low level of fault current magnitude, unpredictable angles of sequence currents, and lack of inertia that can lead to maloperation of conventional phasor-based protection elements. This paper presents a sensitivity analysis of transmission line distance protection elements during phase-to-ground and phase-to-phase faults for different inverter controllers and power system conditions. It also summarizes which line protection elements remain secure near IBR terminations and identifies the ones affected by the inverter-based response. The paper concludes by highlighting that regulating negative-sequence current injection during the fault aids correct protection decisions, but does not address the entire challenge. Finally, alternative protection elements to those affected by the inverter fault response are discussed.

24 POWER TRANSMISSION AND DISTRIBUTION↗
NASA NTRS1994

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective

The 16S and 23S rRNA higher-order structures inferred from comparative analysis are now quite refined. The models presented here differ from their immediate predecessors only in minor detail. Thus, it is safe to assert that all of the standard secondary-structure elements in (prokaryotic) rRNAs have been identified, with approximately 90% of the individual base pairs in each molecule having independent comparative support, and that at least some of the tertiary interactions have been revealed. It is interesting to compare the rRNAs in this respect with tRNA, whose higher-order structure is known in detail from its crystal structure (36) (Table 2). It can be seen that rRNAs have as great a fraction of their sequence in established secondary-structure elements as does tRNA. However, the fact that the former show a much lower fraction of identified tertiary interactions and a greater fraction of unpaired nucleotides than the latter implies that many of the rRNA tertiary interactions remain to be located. (Alternatively, the ribosome might involve protein-rRNA rather than intramolecular rRNA interactions to stabilize three-dimensional structure.) Experimental studies on rRNA are consistent to a first approximation with the structures proposed here, confirming the basic assumption of comparative analysis, i.e., that bases whose compositions strictly covary are physically interacting. In the exhaustive study of Moazed et al. (45) on protection of the bases in the small-subunit rRNA against chemical modification, the vast majority of bases inferred to pair by covariation are found to be protected from chemical modification, both in isolated small-subunit rRNA and in the 30S subunit. The majority of the tertiary interactions are reflected in the chemical protection data as well (45). On the other hand, many of the bases not shown as paired in Fig. 1 are accessible to chemical attack (45). However, in this case a sizeable fraction of them are also protected against chemical modification (in the isolated rRNA), which suggests that considerable higher-order structure remains to be found (although all of it may not involve base-base interactions and so may not be detectable by comparative analysis). The agreement between the higher-order structure of the small-subunit rRNA and protection against chemical modification is not perfect, however; some bases shown to covary canonically are accessible to chemical modification (45).(ABSTRACT TRUNCATED AT 400 WORDS).

Review↗
DOE OSTI2021

Molecular phylogenetic analysis of the Paguristes tortugae Schmitt, 1933 complex and selected other Paguroidea (Crustacea: Decapoda: Anomura)

Morphological characters, as presently applied to describe members of the Paguristes tortugae Schmitt, 1933 species complex, appear to be of limited value in inferring phylogenetic relationships within the genus, and may have similarly misinformed understanding of relationships between members of this complex and those presently assigned to the related genera Areopaguristes Rahayu & McLaughlin, 2010 and Pseudopaguristes McLaughlin, 2002. Previously undocumented observations of similarities and differences in color patterns among populations additionally suggest genetic divergences within some species, or alternatively seem to support phylogenetic groupings of some species. In the present study, a Maximum Likelihood (ML) phylogenetic analysis was undertaken based on the H3, 12S mtDNA, and 16S mtDNA sequences of 148 individuals, primarily representatives of paguroid species from the western Atlantic. This molecular analysis supported a polyphyletic Diogenidae Ortmann, 1892, although incomplete taxonomic sampling among the genera of Diogenidae limits the utility of this finding for resolving family level relationships. Several hypotheses regarding the evolutionary relationships among hermit crab genera were refuted by the Kishino-Hasegawa (KH). ShimodairaHasegawa (SH) and Approximately Unbiased (AU) tree topology tests, among them the hypothesis that Areopaguristes is monophyletic. A lack of support for the monophyly of Areopaguristes calls into question the phylogenetic validity of gill number for the differentiation of Paguristes, Areopaguristes, and Pseudopaguristes. The study was inconclusive with regard to the relationships among these three genera, but previously unknown diversity within both Paguristes and Areopaguristes was demonstrated. Existence of an undescribed species confounded under the name Paguristes tortugae Schmitt, 1933 was supported by genetics, morphology, and coloration. A second undescribed species with remarkable similarity to Areopaguristes hummi Wass, 1955 was discovered based on genetics and coloration.

12S↗
NASA NTRS2002

Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset

MOTIVATION: The phylogenetic structure of the bacterial world has been intensively studied by comparing sequences of 16S ribosomal RNA (16S rRNA). This database of sequences is now widely used to design probes for the detection of specific bacteria or groups of bacteria one at a time. The success of such methods reflects the fact that there are local sequence segments that are highly characteristic of particular organisms or groups of organisms. It is not clear, however, the extent to which such signature sequences exist in the 16S rRNA dataset. A better understanding of the numbers and distribution of highly informative oligonucleotide sequences may facilitate the design of hybridization arrays that can characterize the phylogenetic position of an unknown organism or serve as the basis for the development of novel approaches for use in bacterial identification. RESULTS: A computer-based algorithm that characterizes the extent to which any individual oligonucleotide sequence in 16S rRNA is characteristic of any particular bacterial grouping was developed. A measure of signature quality, Q(s), was formulated and subsequently calculated for every individual oligonucleotide sequence in the size range of 5-11 nucleotides and for 15mers with reference to each cluster and subcluster in a 929 organism representative phylogenetic tree. Subsequently, the perfect signature sequences were compared to the full set of 7322 sequences to see how common false positives were. The work completed here establishes beyond any doubt that highly characteristic oligonucleotides exist in the bacterial 16S rRNA sequence dataset in large numbers. Over 16,000 15mers were identified that might be useful as signatures. Signature oligonucleotides are available for over 80% of the nodes in the representative tree.

NASA Discipline Life Sciences Technologies↗
DOE OSTI2017

Steam Reforming of Acetic Acid over Co-Supported Catalysts: Coupling Ketonization for Greater Stability

We report on the markedly improved stability of a novel 2-bed catalytic system, as compared to a conventional 1-bed steam reforming catalyst, for the production of H2 from acetic acid. The 2-bed catalytic system comprises of i) a basic oxide ketonization catalyst for the conversion of acetic acid to acetone, and a ii) Co-based steam reforming catalyst, both catalytic beds placed in sequence within the same unit operation. Steam reforming catalysts are particularly prone to catalytic deactivation when steam reforming acetic acid, used here as a model compound for the aqueous fraction of bio-oil. Catalysts comprising MgAl2O4, ZnO, CeO2, and activated carbon (AC) both with and without Co-addition were evaluated for conversion of acetic acid and acetone, its ketonization product, in the presence of steam. It was found that over the bare oxide support only ketonization activity was observed and coke deposition was minimal. With addition of Co to the oxide support steam reforming activity was facilitated and coke deposition was significantly increased. Acetone steam reforming over the same Co-supported catalysts demonstrated more stable performance and with less coke deposition than with acetic acid feedstock. DFT analysis suggests that over Co surface CHxCOO species are more favorably formed from acetic acid versus acetone. These CHxCOO species are strongly bound to the Co catalyst surface and could explain the higher propensity for coke formation from acetic acid. Based on these findings, in order to enhance stability of the steam reforming catalyst a dual-bed (2-bed) catalyst system was implemented. Comparing the 2-bed and 1-bed (Co-supported catalyst only) systems under otherwise identical reaction conditions the 2-bed demonstrated significantly improved stability and coke deposition was decreased by a factor of 4.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2025

Influence of Control and Limiter Schemes on Sequence-Domain Fault Models of Grid-Forming Inverter-Interfaced Distributed Generators

Unlike synchronous generators, the fault response of grid-forming (GFM) inverter-interfaced distributed generators (IIDGs) is notably governed by the selection of control and current limiting strategies rather than inherent physical traits. While recent research has focused on the sequence domain fault model of GFM IIDGs, a research gap exists in elucidating the influence of control and current limiting schemes on this model's characteristics. This article aims to fill this void by examining how different control and current limiting schemes influence the positive and negative sequence impedances in the phasor-domain fault model of GFM IIDGs. This investigation encompasses droop-based, virtual synchronous machine-based, and virtual oscillator-based reference generation controls alongside rotating and stationary reference-frame-based voltage controls. Furthermore, saturation-based, latching-based, circular and virtual impedance-based current limiting schemes are analyzed. To achieve this goal, a thorough numerical simulation study is conducted. Findings indicate that outer reference generation controls exhibit minimal impact. Conversely, the choice of voltage control and various current limiting schemes emerge as the predominant factors shaping the sequence models of GFM IIDGs. These analyses and results are instrumental in devising reliable protection strategies within inverter-based grids, as a comprehensive understanding of electrical elements in the sequence domain is imperative for effective protective measures.

current limiters↗
NASA NTRS1974

Transitions 2s/2/ 2p/k/ - 2s 2p/k+1/ of the F I, O I, and N I isoelectronic sequences

Transitions of the type 2s/2/ 2p/k/ - 2s 2p/k+1/ have been identified for the elements from titanium through nickel for ions of the fluorine, oxygen, and nitrogen isoelectronic sequences. Wavelengths, visual intensity estimates, and energies are given. The energy differences of levels of the ground configuration are compared with predictions based on semiempirical equations derived by Edlen. Some of the lines of these isoelectronic sequences should be strong lines in solar-flare spectra.

Doschek, G. A.↗
DOE OSTI2018

Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae

Here, antimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to rapidly identify pathogens and predict antibiotic resistance phenotypes are becoming more feasible and may offer a way to reduce clinical test turnaround times compared to conventional culture-based methods, and in turn, improve patient outcomes. In this study, we use whole genome sequence data from 1668 clinical isolates of Klebsiella pneumoniae to develop a XGBoost-based machine learning model that accurately predicts minimum inhibitory concentrations (MICs) for 20 antibiotics. The overall accuracy of the model, within ± 1 two-fold dilution factor, is 92%. Individual accuracies are >= 90% for 15/20 antibiotics. We show that the MICs predicted by the model correlate with known antimicrobial resistance genes. Importantly, the genome-wide approach described in this study offers a way to predict MICs for isolates without knowledge of the underlying gene content. This study shows that machine learning can be used to build a complete in silico MIC prediction panel for K. pneumoniae and provides a framework for building MIC prediction models for other pathogenic bacteria.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Testing model atmospheres for young very-low-mass stars and brown dwarfs in the infrared: Evidence for significantly underestimated dust opacities

We test state-of-the-art model atmospheres for young very-low-mass stars and brown dwarfs in the infrared, by comparing the predicted synthetic photometry over 1.2–24 μm to the observed photometry of M-type spectral templates in star-forming regions. We find that (1) in both early and late young M types, the model atmospheres imply effective temperatures (T{sub eff}) several hundred Kelvin lower than predicted by the standard pre-main sequence (PMS) spectral type–T{sub eff} conversion scale (based on theoretical evolutionary models). It is only in the mid-M types that the two temperature estimates agree. (2) The T{sub eff} discrepancy in the early M types (corresponding to stellar masses ≳0.4 M{sub ⊙} at ages of a few Myr) probably arises from remaining uncertainties in the treatment of atmospheric convection within the atmospheric models, whereas in the late M types it is likely due to an underestimation of dust opacity. (3) The empirical and model-atmosphere J-band bolometric corrections are both roughly flat, and similar to each other, over the M-type T{sub eff} range. Thus the model atmospheres yield reasonably accurate bolometric luminosities (L{sub bol}), but lead to underestimations of mass and age relative to evolutionary expectations (especially in the late M types) due to lower T{sub eff}. We demonstrate this for a large sample of young Cha I and Taurus sources. (4) The trends in the atmospheric model J−K{sub s} colors, and their deviations from the data, are similar at PMS and main sequence ages, suggesting that the model dust opacity errors we postulate here for young ages also apply at field ages.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x.

EDGE bioinformatics was developed to help biologists process Next Generation Sequencing data (in the form of raw FASTQ files), even if they have little to no bioinformatics expertise. EDGE is a highly integrated and interactive web-based platform that is capable of running many of the standard analyses that biologists require for viral, bacterial/archaeal, and metagenomic samples. EDGE provides the following analytical workflows: quality trimming and host removal, assembly and annotation, comparisons against known references, taxonomy classification of reads and contigs, whole genome SNP-based phylogenetic analysis, and PCR analysis. EDGE provides an intuitive web-based interface for user input, allows users to visualize and interact with selected results (e.g. JBrowse genome browser), and generates a final detailed PDF report. Results in the form of tables, text files, graphic files, and PDFs can be downloaded. A user management system allows tracking of an individual’s EDGE runs, along with the ability to share, post publicly, delete, or archive their results.

Chain, Patrick↗
NASA NTRS1973

A sequence solution to the Fokker-Planck equation.

In this paper a new approach to nonlinear system analysis based on the Fokker-Planck equation is developed. The development begins as a modification of the parametrix method of partial differential equation theory and provides a sequence solution to the multidimensional time-varying Fokker-Planck equation. This sequence is simplified for the case where only a steady-state solution or a solution for the variance of a particular combination of states is desired. Equations are presented in a form suitable for obtaining numerical results using a digital computer.

Mayfield, W. W.↗
DOE OSTI2017

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x.

EDGE bioinformatics was developed to help biologists process Next Generation Sequencing data (in the form of raw FASTQ files), even if they have little to no bioinformatics expertise. EDGE is a highly integrated and interactive web-based platform that is capable of running many of the standard analyses that biologists require for viral, bacterial/archaeal, and metagenomic samples. EDGE provides the following analytical workflows: quality trimming and host removal, assembly and annotation, comparisons against known references, taxonomy classification of reads and contigs, whole genome SNP-based phylogenetic analysis, and PCR analysis. EDGE provides an intuitive web-based interface for user input, allows users to visualize and interact with selected results (e.g. JBrowse genome browser), and generates a final detailed PDF report. Results in the form of tables, text files, graphic files, and PDFs can be downloaded. A user management system allows tracking of an individual’s EDGE runs, along with the ability to share, post publicly, delete, or archive their results.

Chain, Patrick↗