Sorghum bicolor cultivar:BTx623 Raw sequence reads
A time-course RNA-seq analysis of sorghum BTx623 seedlings under drought, heat, and salinity stress.
abiotic stress↗
SEARCH · Engineering Papers
Results for “sequence analysis”
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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Stability of sequences generated by nonlinear differential systems
A local stability analysis is presented for both the analytic and numerical solutions of the initial value problem for a system of ordinary differential equations. It is shown that, using a proper choice of Liapunov function, a connected region of stable initial values of both the analytic solution and the one-leg k-step numerical solution can be approximated. Attention is given to the example of the two-dimensional problem involving the stability of the longitudinal equations of motion of a gliding jet aircraft.
Brown, R. L.↗
Ayame/PAM-D apogee kick motor nozzle failure analysis
The failure of two communication satellites during firing sequence were examined. The correlation/comparison of the circumstances of the Ayame incidents and the failure of the STAR 48 (DM-2) motor are reviewed. The massive nozzle failure of the AKM to determine the impact on spacecraft performance is examined. It is recommended that a closer watch is kept on systems techniques,
Source record↗
The auxin efflux carrier PIN1a regulates vascular patterning in cereal roots
Barley (Hordeum vulgare) is an important global cereal crop and a model in genetic studies. Despite advances in characterising barley genomic resources, few mutant studies have identified genes controlling root architecture and anatomy, which plays a critical role in capturing soil resources. Our phenotypic screening of a TILLING mutant collection identified line TM5992 exhibiting a short-root phenotype compared with wild-type (WT) Morex background. Outcrossing TM5992 with barley variety Proctor and subsequent SNP array-based bulk segregant analysis, fine mapped the mutation to a cM scale. Exome sequencing pinpointed a mutation in the candidate gene HvPIN1a, further confirming this by analysing independent mutant alleles. Detailed analysis of root growth and anatomy in Hvpin1a mutant alleles exhibited a slower growth rate, shorter apical meristem and striking vascular patterning defects compared to WT. Expression and mutant analyses of PIN1 members in the closely related cereal brachypodium (Brachypodium distachyon) revealed that BdPIN1a and BdPIN1b were redundantly expressed in root vascular tissues but only Bdpin1a mutant allele displayed root vascular defects similar to Hvpin1a. We conclude that barley PIN1 genes have sub-functionalised in cereals, compared to Arabidopsis (Arabidopsis thaliana), where PIN1a sequences control root vascular patterning.
59 BASIC BIOLOGICAL SCIENCES↗
Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation, and gene location. Performance and scalability of protein similarity search have proven to be a bottleneck in many bioinformatics pipelines due to increase in cheap and abundant sequencing data. This work presents a new distributed-memory software PASTIS. PASTIS relies on sparse matrix computations for efficient identification of possibly similar proteins. We use distributed sparse matrices for scalability and show that the sparse matrix infrastructure is a great fit for protein similarity search when coupled with a fully-distributed dictionary of sequences that allow remote sequence requests to be fulfilled. Our algorithm incorporates the unique bias in amino acid sequence substitution in search without altering basic sparse matrix model, and in turn, achieves ideal scaling up to millions of protein sequences.
97 MATHEMATICS AND COMPUTING↗
Sequential High-Resolution Wind Profile Measurements
Tropospheric flow and lower stratospheric flow as measured by 94 sequences of high-resolution Jimsphere balloon data are presented and discussed. The 70 and 24 sequential series are presented for the Kennedy Space Center, Florida, and Point Mugu, California, areas, respectively. Supplemental data, consisting of the associative temperature profiles and surface and 200 mb synoptic maps, are also presented. The measurements are discussed relative to both the engineering and disciplinary areas. An initial subjective analysis of mesoscale features observed on some sequences is presented.
Johnson, D. L.↗
Multivariate analysis of peptide-driven nucleation and growth of Au nanoparticles
The design space of sequence defined molecules for inorganic nanoparticle synthesis is exceedingly large. We present an experimental and data analysis workflow for studying the effects of peptide modification on Au nanoparticle synthesis outcomes.
42 ENGINEERING↗
The subsequence weight distribution of summed maximum length digital sequences
An attempt is made to develop mathematical formulas to provide the basis for the design of pseudorandom signals intended for applications requiring accurate knowledge of the statistics of the signals. The analysis approach involves calculating the first five central moments of the weight distribution of subsequences of hybrid-sum sequences. The hybrid-sum sequence is formed from the modulo-two sum of k maximum length sequences and is an extension of the sum sequences formed from two maximum length sequences that Gilson (1966) evaluated. The weight distribution of the subsequences serves as an approximation to the filtering process. The basic reason for the analysis of hybrid-sum sequences is to establish a large group of sequences with good statistical properties. It is shown that this can be accomplished much more efficiently using the hybrid-sum approach rather than forming the group strictly from maximum length sequences.
Weathers, G. D.↗
Unveiling a pervasive DNA adenine methylation regulatory network in the early-diverging fungus Rhizopus microsporus
Development of the DNA affinity purification and sequencing (DAP-seq) technique has allowed genome-scale studies of transcription factor (TF)-binding sites with high reproducibility. Here, we apply this technique to the human opportunistic pathogen Rhizopus microsporus, a mucoralean fungus belonging to the understudied group of early-diverging fungi. We characterize genome-wide binding sites of 58 TFs encoded by genes regulated through adenine methylation and representing major TF families. This analysis reveals their binding profiles and recognized sequences, expanding and diversifying the catalog of known fungal motifs. By integrating this data with DNA 6-methyladenine profiling, we uncover the extensive direct and indirect impact of this epigenetic modification on the regulation of gene expression. Furthermore, we use the generated data to identify TFs involved in biologically relevant processes such as zinc metabolism and light response. Our work enhances our understanding of regulatory mechanisms in R. microsporus and provides broader insights into gene regulation across the fungal kingdom.
Lax, Carlos [Universidad de Murcia (Spain)] (ORCID↗
Variational quantum state diagonalization
Abstract Variational hybrid quantum-classical algorithms are promising candidates for near-term implementation on quantum computers. In these algorithms, a quantum computer evaluates the cost of a gate sequence (with speedup over classical cost evaluation), and a classical computer uses this information to adjust the parameters of the gate sequence. Here we present such an algorithm for quantum state diagonalization. State diagonalization has applications in condensed matter physics (e.g., entanglement spectroscopy) as well as in machine learning (e.g., principal component analysis). For a quantum state ρ and gate sequence U , our cost function quantifies how far $$U\rho U^\dagger$$ U ρ U † is from being diagonal. We introduce short-depth quantum circuits to quantify our cost. Minimizing this cost returns a gate sequence that approximately diagonalizes ρ . One can then read out approximations of the largest eigenvalues, and the associated eigenvectors, of ρ . As a proof-of-principle, we implement our algorithm on Rigetti’s quantum computer to diagonalize one-qubit states and on a simulator to find the entanglement spectrum of the Heisenberg model ground state.
97 MATHEMATICS AND COMPUTING↗
A Bayesian nonparametric analysis for zero-inflated multivariate count data with application to microbiome study
High-throughput sequencing technology has enabled researchers to profile microbial communities from a variety of environments, but analysis of multivariate taxon count data remains challenging. Here, we develop a Bayesian nonparametric (BNP) regression model with zero inflation to analyse multivariate count data from microbiome studies. A BNP approach flexibly models microbial associations with covariates, such as environmental factors and clinical characteristics. The model produces estimates for probability distributions which relate microbial diversity and differential abundance to covariates, and facilitates community comparisons beyond those provided by simple statistical tests. We compare the model to simpler models and popular alternatives in simulation studies, showing, in addition to these additional community-level insights, it yields superior parameter estimates and model fit in various settings. The model's utility is demonstrated by applying it to a chronic wound microbiome data set and a Human Microbiome Project data set, where it is used to compare microbial communities present in different environments.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Analysis of SCALE Criticality and Sensitivity Calculations for Reflected HEU Cylinders [Slides]
The SCALE code package offers multiple nuclear data libraries supporting Monte Carlo transport, with sensitivity and uncertainty methods derived from MC transport solutions. Several libraries are multigroup, which introduce bias differing by system. Previous work has shown poor S/U results in several reflector materials: ICSBEP benchmark HMF-084 was selected to analyze biases and S/U method applicability to a variety of reflectors. Prior and ongoing work found inaccuracies in CSAS and TSUNAMI results, which were further investigated utilizing the HEU-MET-FAST-084 ICSBEP critical benchmark, chosen for its geometrical simplicity and variety of reflector materials. Perturbation of reflector thickness across various reflector materials allowed for an assortment of materials is to be tested swiftly for each sequence and method. Observation was an increasing bias of MG $k_{eff}$ relative to CE, in both direction and magnitude. IFP produced extremely reliable results. >85% of CLUTCH cases were found satisfactory.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
The emergence and transmission dynamics of HIV-1 CRF07_BC in Mainland China
A total of 1155 partial pol gene sequences of human immunodeficiency virus (HIV)-1 CRF07_BC were sampled between 1997 and 2015, spanning 13 provinces in Mainland China and risk groups [heterosexual, injecting drug users (IDU), and men who have sex with men (MSM)] to investigate the evolution, adaptation, spatiotemporal and risk group dynamics, migration patterns, and protein structure of HIV-1 CRF07_BC. Due to the unequal distribution of sequences across time, location, and risk group in the complete dataset (‘full1155’), subsampling methods were used. Maximum-likelihood and Bayesian phylogenetic analysis as well as discrete trait analysis of geographical location and risk group were carried out. To study mutations of a cluster of HIV-1 CRF07_BC (CRF07-1), we performed a comparative analysis of this cluster to the other CRF07_BC sequences (‘backbone_295’) and mapped the mutations observed in the respective protein structure. Our findings showed that HIV-1 CRF07_BC most likely originated among IDU in Yunnan Province between October 1992 to July 1993 [95 per cent hightest posterior density (HPD): May 1989–August 1995] and that IDU in Yunnan Province and MSM in Guangdong Province likely served as the viral sources during the early and more recent spread in Mainland China. We also revealed that HIV-1 CRF07-1 has been spreading for roughly 20 years and continues to cause local transmission in Mainland China and worldwide. Overall, our study sheds light on the dynamics of HIV-1 CRF07_BC distribution patterns in Mainland China. Our research may also be useful in formulating public health policies aimed at controlling acquired immune deficiency syndrome in Mainland China and globally.
60 APPLIED LIFE SCIENCES↗
Evolution of massive stars in very young clusters and associations
Statistics concerning the stellar content of young galactic clusters and associations which show well defined main sequence turnups have been analyzed in order to derive information about stellar evolution in high-mass galaxies. The analytical approach is semiempirical and uses natural spectroscopic groups of stars on the H-R diagram together with the stars' apparent magnitudes. The new approach does not depend on absolute luminosities and requires only the most basic elements of stellar evolution theory. The following conclusions are offered on the basis of the statistical analysis: (1) O-tupe main-sequence stars evolve to a spectral type of B1 during core hydrogen burning; (2) most O-type blue stragglers are newly formed massive stars burning core hydrogen; (3) supergiants lying redward of the main-sequence turnup are burning core helium; and most Wolf-Rayet stars are burning core helium and originally had masses greater than 30-40 solar mass. The statistics of the natural spectroscopic stars in young galactic clusters and associations are given in a table.
Stothers, R. B.↗
Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data
The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones. c2002 The Willi Hennig Society.
NASA Discipline Evolutionary Biology↗
Harnessing methods, data analysis, and near-real-time wastewater monitoring for enhanced public health response using high throughput sequencing
Not Available
Ramachandran, Padmini (ORCID:0000000239583843)↗
An analysis of the pulsational stability of very low mass stars on the hydrogen and deuterium main sequence
Explore the source record for details and available documents.
Opoien, J. W.↗
Silicon solar cells, a manufacturing cost analysis
A detailed cost analysis of solar cell module manufacturing, utilizing process sequences incorporating near-term technology, has been performed. The entire structuring of a factory to manufacture solar cell modules, starting from supplied polycrystalline silicon and other raw materials, was specified. This analysis then formed the basis for a sensitivity analysis of the major cost factors. The results of the cost and sensitivity analyses are presented here.
Grenon, L. A.↗