Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex.

PubMed

Jenkins, Adam M; Waterhouse, Robert M; Muskavitch, Marc A T

2015-04-23

Long non-coding RNAs (lncRNAs) have been defined as mRNA-like transcripts longer than 200 nucleotides that lack significant protein-coding potential, and many of them constitute scaffolds for ribonucleoprotein complexes with critical roles in epigenetic regulation. Various lncRNAs have been implicated in the modulation of chromatin structure, transcriptional and post-transcriptional gene regulation, and regulation of genomic stability in mammals, Caenorhabditis elegans, and Drosophila melanogaster. The purpose of this study is to identify the lncRNA landscape in the malaria vector An. gambiae and assess the evolutionary conservation of lncRNAs and their secondary structures across the Anopheles genus. Using deep RNA sequencing of multiple Anopheles gambiae life stages, we have identified 2,949 lncRNAs and more than 300 previously unannotated putative protein-coding genes. The lncRNAs exhibit differential expression profiles across life stages and adult genders. We find that across the genus Anopheles, lncRNAs display much lower sequence conservation than protein-coding genes. Additionally, we find that lncRNA secondary structure is highly conserved within the Gambiae complex, but diverges rapidly across the rest of the genus Anopheles. This study offers one of the first lncRNA secondary structure analyses in vector insects. Our description of lncRNAs in An. gambiae offers the most comprehensive genome-wide insights to date into lncRNAs in this vector mosquito, and defines a set of potential targets for the development of vector-based interventions that may further curb the human malaria burden in disease-endemic countries.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sesigur, Haluk; Cili, Feridun

Seismic isolation is an effective design strategy to mitigate the seismic hazard wherein the structure and its contents are protected from the damaging effects of an earthquake. This paper presents the Hangar Project in Sabiha Goekcen Airport which is located in Istanbul, Turkey. Seismic isolation system where the isolation layer arranged at the top of the columns is selected. The seismic hazard analysis, superstructure design, isolator design and testing were based on the Uniform Building Code (1997) and met all requirements of the Turkish Earthquake Code (2007). The substructure which has the steel vertical trusses on facades and RC Hmore » shaped columns in the middle axis of the building was designed with an R factor limited to 2.0 in accordance with Turkish Earthquake Code. In order to verify the effectiveness of the isolation system, nonlinear static and dynamic analyses are performed. The analysis revealed that isolated building has lower base shear (approximately 1/4) against the non-isolated structure.« less

SETI in vivo: testing the we-are-them hypothesis

NASA Astrophysics Data System (ADS)

Makukov, Maxim A.; Shcherbak, Vladimir I.

2018-04-01

After it was proposed that life on Earth might descend from seeding by an earlier extraterrestrial civilization motivated to secure and spread life, some authors noted that this alternative offers a testable implication: microbial seeds could be intentionally supplied with a durable signature that might be found in extant organisms. In particular, it was suggested that the optimal location for such an artefact is the genetic code, as the least evolving part of cells. However, as the mainstream view goes, this scenario is too speculative and cannot be meaningfully tested because encoding/decoding a signature within the genetic code is something ill-defined, so any retrieval attempt is doomed to guesswork. Here we refresh the seeded-Earth hypothesis in light of recent observations, and discuss the motivation for inserting a signature. We then show that `biological SETI' involves even weaker assumptions than traditional SETI and admits a well-defined methodological framework. After assessing the possibility in terms of molecular and evolutionary biology, we formalize the approach and, adopting the standard guideline of SETI that encoding/decoding should follow from first principles and be convention-free, develop a universal retrieval strategy. Applied to the canonical genetic code, it reveals a non-trivial precision structure of interlocked logical and numerical attributes of systematic character (previously we found these heuristically). To assess this result in view of the initial assumption, we perform statistical, comparison, interdependence and semiotic analyses. Statistical analysis reveals no causal connection of the result to evolutionary models of the genetic code, interdependence analysis precludes overinterpretation, and comparison analysis shows that known variations of the code lack any precision-logic structures, in agreement with these variations being post-LUCA (i.e. post-seeding) evolutionary deviations from the canonical code. Finally, semiotic analysis shows that not only the found attributes are consistent with the initial assumption, but that they make perfect sense from SETI perspective, as they ultimately maintain some of the most universal codes of culture.

On fuzzy semantic similarity measure for DNA coding.

PubMed

Ahmad, Muneer; Jung, Low Tang; Bhuiyan, Md Al-Amin

2016-02-01

A coding measure scheme numerically translates the DNA sequence to a time domain signal for protein coding regions identification. A number of coding measure schemes based on numerology, geometry, fixed mapping, statistical characteristics and chemical attributes of nucleotides have been proposed in recent decades. Such coding measure schemes lack the biologically meaningful aspects of nucleotide data and hence do not significantly discriminate coding regions from non-coding regions. This paper presents a novel fuzzy semantic similarity measure (FSSM) coding scheme centering on FSSM codons׳ clustering and genetic code context of nucleotides. Certain natural characteristics of nucleotides i.e. appearance as a unique combination of triplets, preserving special structure and occurrence, and ability to own and share density distributions in codons have been exploited in FSSM. The nucleotides׳ fuzzy behaviors, semantic similarities and defuzzification based on the center of gravity of nucleotides revealed a strong correlation between nucleotides in codons. The proposed FSSM coding scheme attains a significant enhancement in coding regions identification i.e. 36-133% as compared to other existing coding measure schemes tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms. Copyright © 2015 Elsevier Ltd. All rights reserved.

Incorporation of Dynamic SSI Effects in the Design Response Spectra

NASA Astrophysics Data System (ADS)

Manjula, N. K.; Pillai, T. M. Madhavan; Nagarajan, Praveen; Reshma, K. K.

2018-05-01

Many studies in the past on dynamic soil-structure interactions have revealed the detrimental and advantageous effects of soil flexibility. Based on such studies, the design response spectra of international seismic codes are being improved worldwide. The improvements required for the short period range of the design response spectra in the Indian seismic code (IS 1893:2002) are presented in this paper. As the recent code revisions has not incorporated the short period amplifications, proposals given in this paper are equally applicable for the latest code also (IS 1893:2016). Analyses of single degree of freedom systems are performed to predict the required improvements. The proposed modifications to the constant acceleration portion of the spectra are evaluated with respect to the current design spectra in Eurocode 8.

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.

PubMed

Seligmann, Hervé; Warthi, Ganesh

2017-01-01

A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5'-ZXX-3'/5'-XXZ-3').

Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).

PubMed

Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil

2015-02-01

The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Geometric phase coded metasurface: from polarization dependent directive electromagnetic wave scattering to diffusion-like scattering.

PubMed

Chen, Ke; Feng, Yijun; Yang, Zhongjie; Cui, Li; Zhao, Junming; Zhu, Bo; Jiang, Tian

2016-10-24

Ultrathin metasurface compromising various sub-wavelength meta-particles offers promising advantages in controlling electromagnetic wave by spatially manipulating the wavefront characteristics across the interface. The recently proposed digital coding metasurface could even simplify the design and optimization procedures due to the digitalization of the meta-particle geometry. However, current attempts to implement the digital metasurface still utilize several structural meta-particles to obtain certain electromagnetic responses, and requiring time-consuming optimization especially in multi-bits coding designs. In this regard, we present herein utilizing geometric phase based single structured meta-particle with various orientations to achieve either 1-bit or multi-bits digital metasurface. Particular electromagnetic wave scattering patterns dependent on the incident polarizations can be tailored by the encoded metasurfaces with regular sequences. On the contrast, polarization insensitive diffusion-like scattering can also been successfully achieved by digital metasurface encoded with randomly distributed coding sequences leading to substantial suppression of backward scattering in a broadband microwave frequency. The proposed digital metasurfaces provide simple designs and reveal new opportunities for controlling electromagnetic wave scattering with or without polarization dependence.

Geometric phase coded metasurface: from polarization dependent directive electromagnetic wave scattering to diffusion-like scattering

PubMed Central

Chen, Ke; Feng, Yijun; Yang, Zhongjie; Cui, Li; Zhao, Junming; Zhu, Bo; Jiang, Tian

2016-01-01

Ultrathin metasurface compromising various sub-wavelength meta-particles offers promising advantages in controlling electromagnetic wave by spatially manipulating the wavefront characteristics across the interface. The recently proposed digital coding metasurface could even simplify the design and optimization procedures due to the digitalization of the meta-particle geometry. However, current attempts to implement the digital metasurface still utilize several structural meta-particles to obtain certain electromagnetic responses, and requiring time-consuming optimization especially in multi-bits coding designs. In this regard, we present herein utilizing geometric phase based single structured meta-particle with various orientations to achieve either 1-bit or multi-bits digital metasurface. Particular electromagnetic wave scattering patterns dependent on the incident polarizations can be tailored by the encoded metasurfaces with regular sequences. On the contrast, polarization insensitive diffusion-like scattering can also been successfully achieved by digital metasurface encoded with randomly distributed coding sequences leading to substantial suppression of backward scattering in a broadband microwave frequency. The proposed digital metasurfaces provide simple designs and reveal new opportunities for controlling electromagnetic wave scattering with or without polarization dependence. PMID:27775064

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bae, Euiyoung; Bingman, Craig A.; Aceti, David J.

LOC79017 (MW 21.0 kDa, residues 1-188) was annotated as a hypothetical protein encoded by Homo sapiens chromosome 7 open reading frame 24. It was selected as a target by the Center for Eukaryotic Structural Genomics (CESG) because it did not share more than 30% sequence identity with any protein for which the three-dimensional structure is known. The biological function of the protein has not been established yet. Parts of LOC79017 were identified as members of uncharacterized Pfam families (residues 1-95 as PB006073 and residues 104-180 as PB031696). BLAST searches revealed homologues of LOC79017 in many eukaryotes, but none of themmore » have been functionally characterized. Here, we report the crystal structure of H. sapiens protein LOC79017 (UniGene code Hs.530024, UniProt code O75223, CESG target number go.35223).« less

Identification of genes involved in serum tolerance in the clinical strain Cronobacter sakazakii ES5.

PubMed

Schwizer, Sarah; Tasara, Taurai; Zurfluh, Katrin; Stephan, Roger; Lehner, Angelika

2013-02-15

Cronobacter spp. are opportunistic pathogens that can cause septicemia and infections of the central nervous system primarily in premature, low-birth weight and/or immune-compromised neonates. Serum resistance is a crucial virulence factor for the development of systemic infections, including bacteremia. It was the aim of the current study to identify genes involved in serum tolerance in a selected Cronobacter sakazakii strain of clinical origin. Screening of 2749 random transposon knock out mutants of a C. sakazakii ES 5 library for modified serum tolerance (compared to wild type) revealed 10 mutants showing significantly increased/reduced resistance to serum killing. Identification of the affected sites in mutants displaying reduced serum resistance revealed genes encoding for surface and membrane proteins as well as regulatory elements or chaperones. By this approach, the involvement of the yet undescribed Wzy_C superfamily domain containing coding region in serum tolerance was observed and experimentally confirmed. Additionally, knock out mutants with enhanced serum tolerance were observed. Examination of respective transposon insertion loci revealed regulatory (repressor) elements, coding regions for chaperones and efflux systems as well as the coding region for the protein YbaJ. Real time expression analysis experiments revealed, that knock out of the gene for this protein negatively affects the expression of the fimA gene, which is a key structural component of the formation of fimbriae. Fimbriae are structures of high immunogenic potential and it is likely that absence/truncation of the ybaJ gene resulted in a non-fimbriated phenotype accounting for the enhanced survival of this mutant in human serum. By using a transposon knock out approach we were able to identify genes involved in both increased and reduced serum tolerance in Cronobacter sakazakii ES5. This study reveals first insights in the complex nature of serum tolerance of Cronobacter spp.

Single stock dynamics on high-frequency data: from a compressed coding perspective.

PubMed

Fushing, Hsieh; Chen, Shu-Chun; Hwang, Chii-Ruey

2014-01-01

High-frequency return, trading volume and transaction number are digitally coded via a nonparametric computing algorithm, called hierarchical factor segmentation (HFS), and then are coupled together to reveal a single stock dynamics without global state-space structural assumptions. The base-8 digital coding sequence, which is capable of revealing contrasting aggregation against sparsity of extreme events, is further compressed into a shortened sequence of state transitions. This compressed digital code sequence vividly demonstrates that the aggregation of large absolute returns is the primary driving force for stimulating both the aggregations of large trading volumes and transaction numbers. The state of system-wise synchrony is manifested with very frequent recurrence in the stock dynamics. And this data-driven dynamic mechanism is seen to correspondingly vary as the global market transiting in and out of contraction-expansion cycles. These results not only elaborate the stock dynamics of interest to a fuller extent, but also contradict some classical theories in finance. Overall this version of stock dynamics is potentially more coherent and realistic, especially when the current financial market is increasingly powered by high-frequency trading via computer algorithms, rather than by individual investors.

Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae).

PubMed

Dubey, Bhawna; Meganathan, P R; Haque, Ikramul

2012-07-01

This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.

Single Stock Dynamics on High-Frequency Data: From a Compressed Coding Perspective

PubMed Central

Fushing, Hsieh; Chen, Shu-Chun; Hwang, Chii-Ruey

2014-01-01

High-frequency return, trading volume and transaction number are digitally coded via a nonparametric computing algorithm, called hierarchical factor segmentation (HFS), and then are coupled together to reveal a single stock dynamics without global state-space structural assumptions. The base-8 digital coding sequence, which is capable of revealing contrasting aggregation against sparsity of extreme events, is further compressed into a shortened sequence of state transitions. This compressed digital code sequence vividly demonstrates that the aggregation of large absolute returns is the primary driving force for stimulating both the aggregations of large trading volumes and transaction numbers. The state of system-wise synchrony is manifested with very frequent recurrence in the stock dynamics. And this data-driven dynamic mechanism is seen to correspondingly vary as the global market transiting in and out of contraction-expansion cycles. These results not only elaborate the stock dynamics of interest to a fuller extent, but also contradict some classical theories in finance. Overall this version of stock dynamics is potentially more coherent and realistic, especially when the current financial market is increasingly powered by high-frequency trading via computer algorithms, rather than by individual investors. PMID:24586235

[Convergent origin of repeats in genes coding for globular proteins. An analysis of the factors determining the presence of inverted and symmetrical repeats].

PubMed

Solov'ev, V V; Kel', A E; Kolchanov, N A

1989-01-01

The factors, determining the presence of inverted and symmetrical repeats in genes coding for globular proteins, have been analysed. An interesting property of genetical code has been revealed in the analysis of symmetrical repeats: the pairs of symmetrical codons corresponded to pairs of amino acids with mostly similar physical-chemical parameters. This property may explain the presence of symmetrical repeats and palindromes only in genes coding for beta-structural proteins-polypeptides, where amino acids with similar physical-chemical properties occupy symmetrical positions. A stochastic model of evolution of polynucleotide sequences has been used for analysis of inverted repeats. The modelling demonstrated that only limiting of sequences (uneven frequencies of used codons) is enough for arising of nonrandom inverted repeats in genes.

Penetration of filamentary structures in the x-point region of spherical tokamaks

NASA Astrophysics Data System (ADS)

Baver, D. A.; Myra, J. R.; Scotti, F.; Zweben, S. J.; Militello, F.; Walkden, N.

2017-10-01

ArbiTER is a flexible eigenvalue code designed for plasma physics applications. It is used here to gain insight into the spatial dependence of filamentary structures in the scrape-off layer of spherical tokamaks. In particular, observations on MAST reveal the presence of a quiescent x-point region. Observations in NSTX similarly reveal a reduction in divertor fluctuations near the separatrix and a loss of midplane correlation. We will report on the penetration of filamentary structures into the vicinity of the x-point, as well as growth rate trends, for a variety of profiles and toroidal mode numbers. This will determine whether linear properties of these structures can explain experimental observations. Work supported by the U.S. Department of Energy Office of Science, Office of Fusion Energy Sciences, under Award Number DE-FG02-02ER54678.

Genomewide analysis of Drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation

PubMed Central

Westholm, Jakub O.; Miura, Pedro; Olson, Sara; Shenker, Sol; Joseph, Brian; Sanfilippo, Piero; Celniker, Susan E.; Graveley, Brenton R.; Lai, Eric C.

2014-01-01

Circularization was recently recognized to broadly expand transcriptome complexity. Here, we exploit massive Drosophila total RNA-sequencing data, >5 billion paired-end reads from >100 libraries covering diverse developmental stages, tissues and cultured cells, to rigorously annotate >2500 fruitfly circular RNAs. These mostly derive from back-splicing of protein-coding genes and lack poly(A) tails, and circularization of hundreds of genes is conserved across multiple Drosophila species. We elucidate structural and sequence properties of Drosophila circular RNAs, which exhibit commonalities and distinctions from mammalian circles. Notably, Drosophila circular RNAs harbor >1000 well-conserved canonical miRNA seed matches, especially within coding regions, and coding conserved miRNA sites reside preferentially within circularized exons. Finally, we analyze the developmental and tissue specificity of circular RNAs, and note their preferred derivation from neural genes and enhanced accumulation in neural tissues. Interestingly, circular isoforms increase dramatically relative to linear isoforms during CNS aging, and constitute a novel aging biomarker. PMID:25544350

SECIS elements in the coding regions of selenoprotein transcripts are functional in higher eukaryotes

PubMed Central

Mix, Heiko; Lobanov, Alexey V.; Gladyshev, Vadim N.

2007-01-01

Expression of selenocysteine (Sec)-containing proteins requires the presence of a cis-acting mRNA structure, called selenocysteine insertion sequence (SECIS) element. In bacteria, this structure is located in the coding region immediately downstream of the Sec-encoding UGA codon, whereas in eukaryotes a completely different SECIS element has evolved in the 3′-untranslated region. Here, we report that SECIS elements in the coding regions of selenoprotein mRNAs support Sec insertion in higher eukaryotes. Comprehensive computational analysis of all available viral genomes revealed a SECIS element within the ORF of a naturally occurring selenoprotein homolog of glutathione peroxidase 4 in fowlpox virus. The fowlpox SECIS element supported Sec insertion when expressed in mammalian cells as part of the coding region of viral or mammalian selenoproteins. In addition, readthrough at UGA was observed when the viral SECIS element was located upstream of the Sec codon. We also demonstrate successful de novo design of a functional SECIS element in the coding region of a mammalian selenoprotein. Our data provide evidence that the location of the SECIS element in the untranslated region is not a functional necessity but rather is an evolutionary adaptation to enable a more efficient synthesis of selenoproteins. PMID:17169995

The Appearance of Change in "Fried Green Tomatoes."

ERIC Educational Resources Information Center

Bisplinghoff, Gretchen

An examination of key symbols and structures of the recent film, "Fried Green Tomatoes," reveals the nature of the process of coding representations of the real world and its effects. The movie depicts two parallel stories of female friendship. Changes and development of the characters are primarily portrayed through changes in their…

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

PubMed Central

Carlile, Thomas M.; Rojas-Duran, Maria F.; Zinshteyn, Boris; Shin, Hakyung; Bartoli, Kristen M.; Gilbert, Wendy V.

2014-01-01

Post-transcriptional modification of RNA nucleosides occurs in all living organisms. Pseudouridine, the most abundant modified nucleoside in non-coding RNAs1, enhances the function of transfer RNA and ribosomal RNA by stabilizing RNA structure2–8. mRNAs were not known to contain pseudouridine, but artificial pseudouridylation dramatically affects mRNA function – it changes the genetic code by facilitating non-canonical base pairing in the ribosome decoding center9,10. However, without evidence of naturally occurring mRNA pseudouridylation, its physiological was unclear. Here we present a comprehensive analysis of pseudouridylation in yeast and human RNAs using Pseudo-seq, a genome-wide, single-nucleotide-resolution method for pseudouridine identification. Pseudo-seq accurately identifies known modification sites as well as 100 novel sites in non-coding RNAs, and reveals hundreds of pseudouridylated sites in mRNAs. Genetic analysis allowed us to assign most of the new modification sites to one of seven conserved pseudouridine synthases, Pus1–4, 6, 7 and 9. Notably, the majority of pseudouridines in mRNA are regulated in response to environmental signals, such as nutrient deprivation in yeast and serum starvation in human cells. These results suggest a mechanism for the rapid and regulated rewiring of the genetic code through inducible mRNA modifications. Our findings reveal unanticipated roles for pseudouridylation and provide a resource for identifying the targets of pseudouridine synthases implicated in human disease11–13. PMID:25192136

Probabilistic Assessment of National Wind Tunnel

NASA Technical Reports Server (NTRS)

Shah, A. R.; Shiao, M.; Chamis, C. C.

1996-01-01

A preliminary probabilistic structural assessment of the critical section of National Wind Tunnel (NWT) is performed using NESSUS (Numerical Evaluation of Stochastic Structures Under Stress) computer code. Thereby, the capabilities of NESSUS code have been demonstrated to address reliability issues of the NWT. Uncertainties in the geometry, material properties, loads and stiffener location on the NWT are considered to perform the reliability assessment. Probabilistic stress, frequency, buckling, fatigue and proof load analyses are performed. These analyses cover the major global and some local design requirements. Based on the assumed uncertainties, the results reveal the assurance of minimum 0.999 reliability for the NWT. Preliminary life prediction analysis results show that the life of the NWT is governed by the fatigue of welds. Also, reliability based proof test assessment is performed.

RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336”

PubMed Central

Kumar, Ranjit; Lawrence, Mark L.; Watt, James; Cooksey, Amanda M.; Burgess, Shane C.; Nanduri, Bindu

2012-01-01

Genome structural annotation, i.e., identification and demarcation of the boundaries for all the functional elements in a genome (e.g., genes, non-coding RNAs, proteins and regulatory elements), is a prerequisite for systems level analysis. Current genome annotation programs do not identify all of the functional elements of the genome, especially small non-coding RNAs (sRNAs). Whole genome transcriptome analysis is a complementary method to identify “novel” genes, small RNAs, regulatory regions, and operon structures, thus improving the structural annotation in bacteria. In particular, the identification of non-coding RNAs has revealed their widespread occurrence and functional importance in gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Histophilus somni, one of the causative agents of Bovine Respiratory Disease (BRD) as well as bovine infertility, abortion, septicemia, arthritis, myocarditis, and thrombotic meningoencephalitis. In this study, we report a single nucleotide resolution transcriptome map of H. somni strain 2336 using RNA-Seq method. The RNA-Seq based transcriptome map identified 94 sRNAs in the H. somni genome of which 82 sRNAs were never predicted or reported in earlier studies. We also identified 38 novel potential protein coding open reading frames that were absent in the current genome annotation. The transcriptome map allowed the identification of 278 operon (total 730 genes) structures in the genome. When compared with the genome sequence of a non-virulent strain 129Pt, a disproportionate number of sRNAs (∼30%) were located in genomic region unique to strain 2336 (∼18% of the total genome). This observation suggests that a number of the newly identified sRNAs in strain 2336 may be involved in strain-specific adaptations. PMID:22276113

RNA-seq based transcriptional map of bovine respiratory disease pathogen "Histophilus somni 2336".

PubMed

Kumar, Ranjit; Lawrence, Mark L; Watt, James; Cooksey, Amanda M; Burgess, Shane C; Nanduri, Bindu

2012-01-01

Genome structural annotation, i.e., identification and demarcation of the boundaries for all the functional elements in a genome (e.g., genes, non-coding RNAs, proteins and regulatory elements), is a prerequisite for systems level analysis. Current genome annotation programs do not identify all of the functional elements of the genome, especially small non-coding RNAs (sRNAs). Whole genome transcriptome analysis is a complementary method to identify "novel" genes, small RNAs, regulatory regions, and operon structures, thus improving the structural annotation in bacteria. In particular, the identification of non-coding RNAs has revealed their widespread occurrence and functional importance in gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Histophilus somni, one of the causative agents of Bovine Respiratory Disease (BRD) as well as bovine infertility, abortion, septicemia, arthritis, myocarditis, and thrombotic meningoencephalitis. In this study, we report a single nucleotide resolution transcriptome map of H. somni strain 2336 using RNA-Seq method.The RNA-Seq based transcriptome map identified 94 sRNAs in the H. somni genome of which 82 sRNAs were never predicted or reported in earlier studies. We also identified 38 novel potential protein coding open reading frames that were absent in the current genome annotation. The transcriptome map allowed the identification of 278 operon (total 730 genes) structures in the genome. When compared with the genome sequence of a non-virulent strain 129Pt, a disproportionate number of sRNAs (∼30%) were located in genomic region unique to strain 2336 (∼18% of the total genome). This observation suggests that a number of the newly identified sRNAs in strain 2336 may be involved in strain-specific adaptations.

Thermodynamic Effects of Noncoded and Coded Methionine Substitutions in Calmodulin

PubMed Central

Yamniuk, Aaron P.; Ishida, Hiroaki; Lippert, Dustin; Vogel, Hans J.

2009-01-01

The methionine residues in the calcium (Ca2+) regulatory protein calmodulin (CaM) are structurally and functionally important. They are buried within the N- and C-domains of apo-CaM but become solvent-exposed in Ca2+-CaM, where they interact with numerous target proteins. Previous structural studies have shown that methionine substitutions to the noncoded amino acids selenomethionine, ethionine, or norleucine, or mutation to leucine do not impact the main chain structure of CaM. Here we used differential scanning calorimetry to show that these substitutions enhance the stability of both domains, with the largest increase in melting temperature (19–26°C) achieved with leucine or norleucine in the apo-C-domain. Nuclear magnetic resonance spectroscopy experiments also revealed the loss of a slow conformational exchange process in the Leu-substituted apo-C-domain. In addition, isothermal titration calorimetry experiments revealed considerable changes in the enthalpy and entropy of target binding to apo-CaM and Ca2+-CaM, but the free energy of binding was largely unaffected due to enthalpy-entropy compensation. Collectively, these results demonstrate that noncoded and coded methionine substitutions can be accommodated in CaM because of the structural plasticity of the protein. However, adjustments in side-chain packing and dynamics lead to significant differences in protein stability and the thermodynamics of target binding. PMID:19217866

Novel cis-acting element within the capsid-coding region enhances flavivirus viral-RNA replication by regulating genome cyclization.

PubMed

Liu, Zhong-Yu; Li, Xiao-Feng; Jiang, Tao; Deng, Yong-Qiang; Zhao, Hui; Wang, Hong-Jiang; Ye, Qing; Zhu, Shun-Ya; Qiu, Yang; Zhou, Xi; Qin, E-De; Qin, Cheng-Feng

2013-06-01

cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5' cyclization sequence (5'CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5'CS, and the presence of DCS-PK facilitates the formation of 5'-3' RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution.

Novel cis-Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

PubMed Central

Liu, Zhong-Yu; Li, Xiao-Feng; Jiang, Tao; Deng, Yong-Qiang; Zhao, Hui; Wang, Hong-Jiang; Ye, Qing; Zhu, Shun-Ya; Qiu, Yang; Zhou, Xi; Qin, E-De

2013-01-01

cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5′ cyclization sequence (5′CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5′CS, and the presence of DCS-PK facilitates the formation of 5′-3′ RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution. PMID:23576500

A Comparative Study on Seismic Analysis of Bangladesh National Building Code (BNBC) with Other Building Codes

NASA Astrophysics Data System (ADS)

Bari, Md. S.; Das, T.

2013-09-01

Tectonic framework of Bangladesh and adjoining areas indicate that Bangladesh lies well within an active seismic zone. The after effect of earthquake is more severe in an underdeveloped and a densely populated country like ours than any other developed countries. Bangladesh National Building Code (BNBC) was first established in 1993 to provide guidelines for design and construction of new structure subject to earthquake ground motions in order to minimize the risk to life for all structures. A revision of BNBC 1993 is undergoing to make this up to date with other international building codes. This paper aims at the comparison of various provisions of seismic analysis as given in building codes of different countries. This comparison will give an idea regarding where our country stands when it comes to safety against earth quake. Primarily, various seismic parameters in BNBC 2010 (draft) have been studied and compared with that of BNBC 1993. Later, both 1993 and 2010 edition of BNBC codes have been compared graphically with building codes of other countries such as National Building Code of India 2005 (NBC-India 2005), American Society of Civil Engineering 7-05 (ASCE 7-05). The base shear/weight ratios have been plotted against the height of the building. The investigation in this paper reveals that BNBC 1993 has the least base shear among all the codes. Factored Base shear values of BNBC 2010 are found to have increased significantly than that of BNBC 1993 for low rise buildings (≤20 m) around the country than its predecessor. Despite revision of the code, BNBC 2010 (draft) still suggests less base shear values when compared to the Indian and American code. Therefore, this increase in factor of safety against the earthquake imposed by the proposed BNBC 2010 code by suggesting higher values of base shear is appreciable.

Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids.

PubMed

Niu, Zhitao; Pan, Jiajia; Zhu, Shuying; Li, Ludan; Xue, Qingyun; Liu, Wei; Ding, Xiaoyu

2017-01-01

Apostasioideae, consists of only two genera, Apostasia and Neuwiedia , which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla ), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase ( ndh ) genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci- ndhA intron, matK-5'trnK , clpP-psbB , rps8-rpl14 , trnT-trnL , 3'trnK-matK , clpP intron , psbK-trnK , trnS-psbC , and ndhF-rpl32 -that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed.

Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids

PubMed Central

Niu, Zhitao; Pan, Jiajia; Zhu, Shuying; Li, Ludan; Xue, Qingyun; Liu, Wei; Ding, Xiaoyu

2017-01-01

Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase (ndh) genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci—ndhA intron, matK-5′trnK, clpP-psbB, rps8-rpl14, trnT-trnL, 3′trnK-matK, clpP intron, psbK-trnK, trnS-psbC, and ndhF-rpl32—that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed. PMID:29046685

Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

USDA-ARS?s Scientific Manuscript database

Cycles of whole genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied...

3D topology of orientation columns in visual cortex revealed by functional optical coherence tomography.

PubMed

Nakamichi, Yu; Kalatsky, Valery A; Watanabe, Hideyuki; Sato, Takayuki; Rajagopalan, Uma Maheswari; Tanifuji, Manabu

2018-04-01

Orientation tuning is a canonical neuronal response property of six-layer visual cortex that is encoded in pinwheel structures with center orientation singularities. Optical imaging of intrinsic signals enables us to map these surface two-dimensional (2D) structures, whereas lack of appropriate techniques has not allowed us to visualize depth structures of orientation coding. In the present study, we performed functional optical coherence tomography (fOCT), a technique capable of acquiring a 3D map of the intrinsic signals, to study the topology of orientation coding inside the cat visual cortex. With this technique, for the first time, we visualized columnar assemblies in orientation coding that had been predicted from electrophysiological recordings. In addition, we found that the columnar structures were largely distorted around pinwheel centers: center singularities were not rigid straight lines running perpendicularly to the cortical surface but formed twisted string-like structures inside the cortex that turned and extended horizontally through the cortex. Looping singularities were observed with their respective termini accessing the same cortical surface via clockwise and counterclockwise orientation pinwheels. These results suggest that a 3D topology of orientation coding cannot be fully anticipated from 2D surface measurements. Moreover, the findings demonstrate the utility of fOCT as an in vivo mesoscale imaging method for mapping functional response properties of cortex in the depth axis. NEW & NOTEWORTHY We used functional optical coherence tomography (fOCT) to visualize three-dimensional structure of the orientation columns with millimeter range and micrometer spatial resolution. We validated vertically elongated columnar structure in iso-orientation domains. The columnar structure was distorted around pinwheel centers. An orientation singularity formed a string with tortuous trajectories inside the cortex and connected clockwise and counterclockwise pinwheel centers in the surface orientation map. The results were confirmed by comparisons with conventional optical imaging and electrophysiological recordings.

DRG coding practice: a nationwide hospital survey in Thailand.

PubMed

Pongpirul, Krit; Walker, Damian G; Rahman, Hafizur; Robinson, Courtland

2011-10-31

Diagnosis Related Group (DRG) payment is preferred by healthcare reform in various countries but its implementation in resource-limited countries has not been fully explored. This study was aimed (1) to compare the characteristics of hospitals in Thailand that were audited with those that were not and (2) to develop a simplified scale to measure hospital coding practice. A questionnaire survey was conducted of 920 hospitals in the Summary and Coding Audit Database (SCAD hospitals, all of which were audited in 2008 because of suspicious reports of possible DRG miscoding); the questionnaire also included 390 non-SCAD hospitals. The questionnaire asked about general demographics of the hospitals, hospital coding structure and process, and also included a set of 63 opinion-oriented items on the current hospital coding practice. Descriptive statistics and exploratory factor analysis (EFA) were used for data analysis. SCAD and Non-SCAD hospitals were different in many aspects, especially the number of medical statisticians, experience of medical statisticians and physicians, as well as number of certified coders. Factor analysis revealed a simplified 3-factor, 20-item model to assess hospital coding practice and classify hospital intention. Hospital providers should not be assumed capable of producing high quality DRG codes, especially in resource-limited settings.

Ancient DNA sequence revealed by error-correcting codes.

PubMed

Brandão, Marcelo M; Spoladore, Larissa; Faria, Luzinete C B; Rocha, Andréa S L; Silva-Filho, Marcio C; Palazzo, Reginaldo

2015-07-10

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.

Ancient DNA sequence revealed by error-correcting codes

PubMed Central

Brandão, Marcelo M.; Spoladore, Larissa; Faria, Luzinete C. B.; Rocha, Andréa S. L.; Silva-Filho, Marcio C.; Palazzo, Reginaldo

2015-01-01

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. PMID:26159228

[Structured quality report of urologic clinics according to section 137 SGB V. Useful information for the patient, marketing tool of the hospitals, leverage wielded by the health insurance companies, or junk data?].

PubMed

Volkmer, B; Petschl, S; Härtel, M; Bopp, G; Herkommer, K; Gschwend, J

2006-04-01

In 2005, German hospitals were legally obliged to publish a structured quality report on their data of 2004 including the top 10 diagnosis-related groups, top 10 diagnoses, and top 10 procedures for every specialty. The aim was to increase the transparency for patients, doctors, and health insurance companies. Comparing the quality reports of 248 departments of urology revealed very uniform distributions of diagnoses and diagnosis-related groups. There was a large variety of top 10 procedures, resulting from different interpretations of the coding system, leading to diminished accuracy. The quality reports provide coding specialists with important data, but for patients and nonspecialized doctors, this system is not helpful in improving transparency.

Structural diversity of supercoiled DNA

PubMed Central

Irobalieva, Rossitza N.; Fogg, Jonathan M.; Catanese, Daniel J.; Sutthibutpong, Thana; Chen, Muyuan; Barker, Anna K.; Ludtke, Steven J.; Harris, Sarah A.; Schmid, Michael F.; Chiu, Wah; Zechiedrich, Lynn

2015-01-01

By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function. PMID:26455586

Structural diversity of supercoiled DNA

NASA Astrophysics Data System (ADS)

Irobalieva, Rossitza N.; Fogg, Jonathan M.; Catanese, Daniel J.; Sutthibutpong, Thana; Chen, Muyuan; Barker, Anna K.; Ludtke, Steven J.; Harris, Sarah A.; Schmid, Michael F.; Chiu, Wah; Zechiedrich, Lynn

2015-10-01

By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols

USDA-ARS?s Scientific Manuscript database

The Persian walnut (Juglans regia L.), a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich...

Start-Up Scenario in Gyrotrons with a Nonstationary Microwave-Field Structure

NASA Astrophysics Data System (ADS)

Nusinovich, G. S.; Yeddulla, M.; Antonsen, T. M., Jr.; Vlasov, A. N.

2006-03-01

Megawatt class gyrotrons operate in very high-order modes. Therefore, control of a gyrotron oscillator’s start-up is important for excitation of the desired mode in the presence of the many undesired modes. Analysis of such scenario using the self-consistent code MAGY [M. Botton , IEEE Trans. Plasma Sci. 26,ITPSBD0093-3813 882 (1998)10.1109/27.700860] reveals that during start-up not only mode amplitudes vary in time, but also their axial structure can be time dependent. Simulations done for a 1.5 MW gyrotron show that the excitation of a single operating TE22,6 mode can exhibit a sort of intermittency when, first, it is excited as a mode whose axial structure extends outside the interaction cavity, then it ceases and then reappears as a mode mostly localized in the cavity. This phenomenon makes it necessary to analyze start-up scenarios in such gyrotrons with the use of codes that account for the possible evolution of field profiles.

Investigation of the mechanism of meiotic DNA cleavage by VMA1-derived endonuclease uncovers a meiotic alteration in chromatin structure around the target site.

PubMed

Fukuda, Tomoyuki; Ohta, Kunihiro; Ohya, Yoshikazu

2006-06-01

VMA1-derived endonuclease (VDE), a homing endonuclease in Saccharomyces cerevisiae, is encoded by the mobile intein-coding sequence within the nuclear VMA1 gene. VDE recognizes and cleaves DNA at the 31-bp VDE recognition sequence (VRS) in the VMA1 gene lacking the intein-coding sequence during meiosis to insert a copy of the intein-coding sequence at the cleaved site. The mechanism underlying the meiosis specificity of VMA1 intein-coding sequence homing remains unclear. We studied various factors that might influence the cleavage activity in vivo and found that VDE binding to the VRS can be detected only when DNA cleavage by VDE takes place, implying that meiosis-specific DNA cleavage is regulated by the accessibility of VDE to its target site. As a possible candidate for the determinant of this accessibility, we analyzed chromatin structure around the VRS and revealed that local chromatin structure near the VRS is altered during meiosis. Although the meiotic chromatin alteration exhibits correlations with DNA binding and cleavage by VDE at the VMA1 locus, such a chromatin alteration is not necessarily observed when the VRS is embedded in ectopic gene loci. This suggests that nucleosome positioning or occupancy around the VRS by itself is not the sole mechanism for the regulation of meiosis-specific DNA cleavage by VDE and that other mechanisms are involved in the regulation.

Investigation of the Mechanism of Meiotic DNA Cleavage by VMA1-Derived Endonuclease Uncovers a Meiotic Alteration in Chromatin Structure around the Target Site

PubMed Central

Fukuda, Tomoyuki; Ohta, Kunihiro; Ohya, Yoshikazu

2006-01-01

VMA1-derived endonuclease (VDE), a homing endonuclease in Saccharomyces cerevisiae, is encoded by the mobile intein-coding sequence within the nuclear VMA1 gene. VDE recognizes and cleaves DNA at the 31-bp VDE recognition sequence (VRS) in the VMA1 gene lacking the intein-coding sequence during meiosis to insert a copy of the intein-coding sequence at the cleaved site. The mechanism underlying the meiosis specificity of VMA1 intein-coding sequence homing remains unclear. We studied various factors that might influence the cleavage activity in vivo and found that VDE binding to the VRS can be detected only when DNA cleavage by VDE takes place, implying that meiosis-specific DNA cleavage is regulated by the accessibility of VDE to its target site. As a possible candidate for the determinant of this accessibility, we analyzed chromatin structure around the VRS and revealed that local chromatin structure near the VRS is altered during meiosis. Although the meiotic chromatin alteration exhibits correlations with DNA binding and cleavage by VDE at the VMA1 locus, such a chromatin alteration is not necessarily observed when the VRS is embedded in ectopic gene loci. This suggests that nucleosome positioning or occupancy around the VRS by itself is not the sole mechanism for the regulation of meiosis-specific DNA cleavage by VDE and that other mechanisms are involved in the regulation. PMID:16757746

Standing your Ground to Exoribonucleases: Function of Flavivirus Long Non-coding RNAs

PubMed Central

Charley, Phillida A.; Wilusz, Jeffrey

2015-01-01

Members of the Flaviviridae (e.g. Dengue virus, West Nile virus, and Hepatitis C virus) contain a positive-sense RNA genome that encodes a large polyprotein. It is now also clear most if not all of these viruses also produce an abundant subgenomic long non-coding RNA. These non-coding RNAs, which are called subgenomicflavivirus RNAs (sfRNAs) or Xrn1-resistant RNAs (xrRNAs), are stable decay intermediates generated from the viral genomic RNA through the stalling of the cellular exoribonuclease Xrn1 at highly structured regions. Several functions of these flavivirus long non-coding RNAs have been revealed in recent years. The generation of these sfRNAs/xrRNAs from viral transcripts results in the repression of Xrn1 and the dysregulation of cellular mRNA stability. The abundant sfRNAs also serve directly as a decoy for important cellular protein regulators of the interferon and RNA interference antiviral pathways. Thus the generation of long non-coding RNAs from flaviviruses, hepaciviruses and pestiviruses likely disrupts aspects of innate immunity and may directly contribute to viral replication, cytopathology and pathogenesis. PMID:26368052

Specific and Modular Binding Code for Cytosine Recognition in Pumilio/FBF (PUF) RNA-binding Domains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Shuyun; Wang, Yang; Cassidy-Amstutz, Caleb

2011-10-28

Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and themore » cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence.« less

The Redox Code.

PubMed

Jones, Dean P; Sies, Helmut

2015-09-20

The redox code is a set of principles that defines the positioning of the nicotinamide adenine dinucleotide (NAD, NADP) and thiol/disulfide and other redox systems as well as the thiol redox proteome in space and time in biological systems. The code is richly elaborated in an oxygen-dependent life, where activation/deactivation cycles involving O₂ and H₂O₂ contribute to spatiotemporal organization for differentiation, development, and adaptation to the environment. Disruption of this organizational structure during oxidative stress represents a fundamental mechanism in system failure and disease. Methodology in assessing components of the redox code under physiological conditions has progressed, permitting insight into spatiotemporal organization and allowing for identification of redox partners in redox proteomics and redox metabolomics. Complexity of redox networks and redox regulation is being revealed step by step, yet much still needs to be learned. Detailed knowledge of the molecular patterns generated from the principles of the redox code under defined physiological or pathological conditions in cells and organs will contribute to understanding the redox component in health and disease. Ultimately, there will be a scientific basis to a modern redox medicine.

The statistics of the vestibular input experienced during natural self-motion differ between rodents and primates.

PubMed

Carriot, Jérome; Jamali, Mohsen; Chacron, Maurice J; Cullen, Kathleen E

2017-04-15

In order to understand how the brain's coding strategies are adapted to the statistics of the sensory stimuli experienced during everyday life, the use of animal models is essential. Mice and non-human primates have become common models for furthering our knowledge of the neuronal coding of natural stimuli, but differences in their natural environments and behavioural repertoire may impact optimal coding strategies. Here we investigated the structure and statistics of the vestibular input experienced by mice versus non-human primates during natural behaviours, and found important differences. Our data establish that the structure and statistics of natural signals in non-human primates more closely resemble those observed previously in humans, suggesting similar coding strategies for incoming vestibular input. These results help us understand how the effects of active sensing and biomechanics will differentially shape the statistics of vestibular stimuli across species, and have important implications for sensory coding in other systems. It is widely believed that sensory systems are adapted to the statistical structure of natural stimuli, thereby optimizing coding. Recent evidence suggests that this is also the case for the vestibular system, which senses self-motion and in turn contributes to essential brain functions ranging from the most automatic reflexes to spatial perception and motor coordination. However, little is known about the statistics of self-motion stimuli actually experienced by freely moving animals in their natural environments. Accordingly, here we examined the natural self-motion signals experienced by mice and monkeys: two species commonly used to study vestibular neural coding. First, we found that probability distributions for all six dimensions of motion (three rotations, three translations) in both species deviated from normality due to long tails. Interestingly, the power spectra of natural rotational stimuli displayed similar structure for both species and were not well fitted by power laws. This result contrasts with reports that the natural spectra of other sensory modalities (i.e. vision, auditory and tactile) instead show a power-law relationship with frequency, which indicates scale invariance. Analysis of natural translational stimuli revealed important species differences as power spectra deviated from scale invariance for monkeys but not for mice. By comparing our results to previously published data for humans, we found the statistical structure of natural self-motion stimuli in monkeys and humans more closely resemble one another. Our results thus predict that, overall, neural coding strategies used by vestibular pathways to encode natural self-motion stimuli are fundamentally different in rodents and primates. © 2017 The Authors. The Journal of Physiology © 2017 The Physiological Society.

The statistics of the vestibular input experienced during natural self‐motion differ between rodents and primates

PubMed Central

Carriot, Jérome; Jamali, Mohsen; Chacron, Maurice J.

2017-01-01

Key points In order to understand how the brain's coding strategies are adapted to the statistics of the sensory stimuli experienced during everyday life, the use of animal models is essential.Mice and non‐human primates have become common models for furthering our knowledge of the neuronal coding of natural stimuli, but differences in their natural environments and behavioural repertoire may impact optimal coding strategies.Here we investigated the structure and statistics of the vestibular input experienced by mice versus non‐human primates during natural behaviours, and found important differences.Our data establish that the structure and statistics of natural signals in non‐human primates more closely resemble those observed previously in humans, suggesting similar coding strategies for incoming vestibular input.These results help us understand how the effects of active sensing and biomechanics will differentially shape the statistics of vestibular stimuli across species, and have important implications for sensory coding in other systems. Abstract It is widely believed that sensory systems are adapted to the statistical structure of natural stimuli, thereby optimizing coding. Recent evidence suggests that this is also the case for the vestibular system, which senses self‐motion and in turn contributes to essential brain functions ranging from the most automatic reflexes to spatial perception and motor coordination. However, little is known about the statistics of self‐motion stimuli actually experienced by freely moving animals in their natural environments. Accordingly, here we examined the natural self‐motion signals experienced by mice and monkeys: two species commonly used to study vestibular neural coding. First, we found that probability distributions for all six dimensions of motion (three rotations, three translations) in both species deviated from normality due to long tails. Interestingly, the power spectra of natural rotational stimuli displayed similar structure for both species and were not well fitted by power laws. This result contrasts with reports that the natural spectra of other sensory modalities (i.e. vision, auditory and tactile) instead show a power‐law relationship with frequency, which indicates scale invariance. Analysis of natural translational stimuli revealed important species differences as power spectra deviated from scale invariance for monkeys but not for mice. By comparing our results to previously published data for humans, we found the statistical structure of natural self‐motion stimuli in monkeys and humans more closely resemble one another. Our results thus predict that, overall, neural coding strategies used by vestibular pathways to encode natural self‐motion stimuli are fundamentally different in rodents and primates. PMID:28083981

Rooted tRNAomes and evolution of the genetic code

PubMed Central

Pak, Daewoo; Du, Nan; Kim, Yunsoo; Sun, Yanni

2018-01-01

ABSTRACT We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree. We propose the polyglycine hypothesis that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells. In order to describe how anticodons were allotted in evolution, the sectoring-degeneracy hypothesis is proposed. Based on sectoring, a simple stepwise model is developed, in which the code sectors from a 1→4→8→∼16 letter code. At initial stages of code evolution, we posit strong positive selection for wobble base ambiguity, supporting convergence to 4-codon sectors and ∼16 letters. In a later stage, ∼5–6 letters, including stops, were added through innovating at the anticodon wobble position. In archaea and bacteria, tRNA wobble adenine is negatively selected, shrinking the maximum size of the primordial genetic code to 48 anticodons. Because 64 codons are recognized in mRNA, tRNA-mRNA coevolution requires tRNA wobble position ambiguity leading to degeneracy of the code. PMID:29372672

De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences

PubMed Central

Reinhardt, Josephine A.; Wanjiru, Betty M.; Brant, Alicia T.; Saelao, Perot; Begun, David J.; Jones, Corbin D.

2013-01-01

How non-coding DNA gives rise to new protein-coding genes (de novo genes) is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs), while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important. PMID:24146629

Effects of various electrode configurations on music perception, intonation and speaker gender identification.

PubMed

Landwehr, Markus; Fürstenberg, Dirk; Walger, Martin; von Wedel, Hasso; Meister, Hartmut

2014-01-01

Advances in speech coding strategies and electrode array designs for cochlear implants (CIs) predominantly aim at improving speech perception. Current efforts are also directed at transmitting appropriate cues of the fundamental frequency (F0) to the auditory nerve with respect to speech quality, prosody, and music perception. The aim of this study was to examine the effects of various electrode configurations and coding strategies on speech intonation identification, speaker gender identification, and music quality rating. In six MED-EL CI users electrodes were selectively deactivated in order to simulate different insertion depths and inter-electrode distances when using the high definition continuous interleaved sampling (HDCIS) and fine structure processing (FSP) speech coding strategies. Identification of intonation and speaker gender was determined and music quality rating was assessed. For intonation identification HDCIS was robust against the different electrode configurations, whereas fine structure processing showed significantly worse results when a short electrode depth was simulated. In contrast, speaker gender recognition was not affected by electrode configuration or speech coding strategy. Music quality rating was sensitive to electrode configuration. In conclusion, the three experiments revealed different outcomes, even though they all addressed the reception of F0 cues. Rapid changes in F0, as seen with intonation, were the most sensitive to electrode configurations and coding strategies. In contrast, electrode configurations and coding strategies did not show large effects when F0 information was available over a longer time period, as seen with speaker gender. Music quality relies on additional spectral cues other than F0, and was poorest when a shallow insertion was simulated.

The effect of structural design parameters on FPGA-based feed-forward space-time trellis coding-orthogonal frequency division multiplexing channel encoders

NASA Astrophysics Data System (ADS)

Passas, Georgios; Freear, Steven; Fawcett, Darren

2010-08-01

Orthogonal frequency division multiplexing (OFDM)-based feed-forward space-time trellis code (FFSTTC) encoders can be synthesised as very high speed integrated circuit hardware description language (VHDL) designs. Evaluation of their FPGA implementation can lead to conclusions that help a designer to decide the optimum implementation, given the encoder structural parameters. VLSI architectures based on 1-bit multipliers and look-up tables (LUTs) are compared in terms of FPGA slices and block RAMs (area), as well as in terms of minimum clock period (speed). Area and speed graphs versus encoder memory order are provided for quadrature phase shift keying (QPSK) and 8 phase shift keying (8-PSK) modulation and two transmit antennas, revealing best implementation under these conditions. The effect of number of modulation bits and transmit antennas on the encoder implementation complexity is also investigated.

Analysis of the temperature sensitivity of Japanese rubella vaccine strain TO-336.vac and its effect on immunogenicity in the guinea pig.

PubMed

Okamoto, Kiyoko; Ami, Yasushi; Suzaki, Yuriko; Otsuki, Noriyuki; Sakata, Masafumi; Takeda, Makoto; Mori, Yoshio

2016-04-01

The marker of Japanese domestic rubella vaccines is their lack of immunogenicity in guinea pigs. This has long been thought to be related to the temperature sensitivity of the viruses, but supporting evidence has not been described. In this study, we generated infectious clones of TO-336.vac, a Japanese domestic vaccine, TO-336.GMK5, the parental virus of TO-336.vac, and their mutants, and determined the molecular bases of their temperature sensitivity and immunogenicity in guinea pigs. The results revealed that Ser(1159) in the non-structural protein-coding region was responsible for the temperature sensitivity of TO-336.vac dominantly, while the structural protein-coding region affected the temperature sensitivity subordinately. The findings further suggested that the temperature sensitivity of TO-336.vac affected the antibody induction in guinea pigs after subcutaneous inoculation. Copyright © 2016 Elsevier Inc. All rights reserved.

Distributed polar-coded OFDM based on Plotkin's construction for half duplex wireless communication

NASA Astrophysics Data System (ADS)

Umar, Rahim; Yang, Fengfan; Mughal, Shoaib; Xu, HongJun

2018-07-01

A Plotkin-based polar-coded orthogonal frequency division multiplexing (P-PC-OFDM) scheme is proposed and its bit error rate (BER) performance over additive white gaussian noise (AWGN), frequency selective Rayleigh, Rician and Nakagami-m fading channels has been evaluated. The considered Plotkin's construction possesses a parallel split in its structure, which motivated us to extend the proposed P-PC-OFDM scheme in a coded cooperative scenario. As the relay's effective collaboration has always been pivotal in the design of cooperative communication therefore, an efficient selection criterion for choosing the information bits has been inculcated at the relay node. To assess the BER performance of the proposed cooperative scheme, we have also upgraded conventional polar-coded cooperative scheme in the context of OFDM as an appropriate bench marker. The Monte Carlo simulated results revealed that the proposed Plotkin-based polar-coded cooperative OFDM scheme convincingly outperforms the conventional polar-coded cooperative OFDM scheme by 0.5 0.6 dBs over AWGN channel. This prominent gain in BER performance is made possible due to the bit-selection criteria and the joint successive cancellation decoding adopted at the relay and the destination nodes, respectively. Furthermore, the proposed coded cooperative schemes outperform their corresponding non-cooperative schemes by a gain of 1 dB under an identical condition.

DRG coding practice: a nationwide hospital survey in Thailand

PubMed Central

2011-01-01

Background Diagnosis Related Group (DRG) payment is preferred by healthcare reform in various countries but its implementation in resource-limited countries has not been fully explored. Objectives This study was aimed (1) to compare the characteristics of hospitals in Thailand that were audited with those that were not and (2) to develop a simplified scale to measure hospital coding practice. Methods A questionnaire survey was conducted of 920 hospitals in the Summary and Coding Audit Database (SCAD hospitals, all of which were audited in 2008 because of suspicious reports of possible DRG miscoding); the questionnaire also included 390 non-SCAD hospitals. The questionnaire asked about general demographics of the hospitals, hospital coding structure and process, and also included a set of 63 opinion-oriented items on the current hospital coding practice. Descriptive statistics and exploratory factor analysis (EFA) were used for data analysis. Results SCAD and Non-SCAD hospitals were different in many aspects, especially the number of medical statisticians, experience of medical statisticians and physicians, as well as number of certified coders. Factor analysis revealed a simplified 3-factor, 20-item model to assess hospital coding practice and classify hospital intention. Conclusion Hospital providers should not be assumed capable of producing high quality DRG codes, especially in resource-limited settings. PMID:22040256

Efficient coding of spectrotemporal binaural sounds leads to emergence of the auditory space representation

PubMed Central

Młynarski, Wiktor

2014-01-01

To date a number of studies have shown that receptive field shapes of early sensory neurons can be reproduced by optimizing coding efficiency of natural stimulus ensembles. A still unresolved question is whether the efficient coding hypothesis explains formation of neurons which explicitly represent environmental features of different functional importance. This paper proposes that the spatial selectivity of higher auditory neurons emerges as a direct consequence of learning efficient codes for natural binaural sounds. Firstly, it is demonstrated that a linear efficient coding transform—Independent Component Analysis (ICA) trained on spectrograms of naturalistic simulated binaural sounds extracts spatial information present in the signal. A simple hierarchical ICA extension allowing for decoding of sound position is proposed. Furthermore, it is shown that units revealing spatial selectivity can be learned from a binaural recording of a natural auditory scene. In both cases a relatively small subpopulation of learned spectrogram features suffices to perform accurate sound localization. Representation of the auditory space is therefore learned in a purely unsupervised way by maximizing the coding efficiency and without any task-specific constraints. This results imply that efficient coding is a useful strategy for learning structures which allow for making behaviorally vital inferences about the environment. PMID:24639644

The Relationship of Physical Property Indicators and Clay Soil Structural Strength of Tomsk Oblast Territory

NASA Astrophysics Data System (ADS)

Kramarenko, V. V.; Nikitenkov, A. N.; Molokov, V. Y.; Matveenko, I. A.; Shramok, A. V.

2015-11-01

The article deals with the characteristic of initial condition in fine-grained soils - its structural strength - pstr. Estimation and measurement of this factor at soil testing are of primary importance for defining its physical and mechanical properties as well as for subsequent calculation of foundation settlements that is insufficiently covered in Code of practice, national standard and inefficiently applicable in practice of engineering geological investigations. The article reveals the relationship between soil physical property, its occurrence depth, which will make possible to forecast pstr over the given territory.

A retroviral oncogene, akt, encoding a serine-threonine kinase containing an SH2-like region.

PubMed

Bellacosa, A; Testa, J R; Staal, S P; Tsichlis, P N

1991-10-11

The v-akt oncogene codes for a 105-kilodalton fusion phosphoprotein containing Gag sequences at its amino terminus. Sequence analysis of v-akt and biochemical characterization of its product revealed that it codes for a protein kinase C-related serine-threonine kinase whose cellular homolog is expressed in most tissues, with the highest amount found in thymus. Although Akt is a serine-threonine kinase, part of its regulatory region is similar to the Src homology-2 domain, a structural motif characteristic of cytoplasmic tyrosine kinases that functions in protein-protein interactions. This suggests that Akt may form a functional link between tyrosine and serine-threonine phosphorylation pathways.

Consumer acceptance of a quick response (QR) code for the food traceability system: Application of an extended technology acceptance model (TAM).

PubMed

Kim, Yeong Gug; Woo, Eunju

2016-07-01

The objectives of this study are to apply the TAM using the addition of perceived information to individuals' behavioral intention to use the QR code for the food traceability system; and to determine the moderating effects of food involvement on the relationship between perceived information and perceived usefulness. Results from a survey of 420 respondents are analyzed using structural equation modeling. The study findings reveal that the extended TAM has a satisfactory fit to the data and that the underlying dimensions have a significant effect on consumers' intention to use the QR code for the food traceability system. In addition, food involvement plays a significant moderating function in the relationship between perceived information and perceived usefulness. The implications of this study for future research are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase.

PubMed

Li de La Sierra-Gallay, Ines; Collinet, Bruno; Graille, Marc; Quevillon-Cheruel, Sophie; Liger, Dominique; Minard, Philippe; Blondeau, Karine; Henckes, Gilles; Aufrère, Robert; Leulliot, Nicolas; Zhou, Cong-Zhao; Sorel, Isabelle; Ferrer, Jean-Luc; Poupon, Anne; Janin, Joël; van Tilbeurgh, Herman

2004-03-01

The protein product of the YGR205w gene of Saccharomyces cerevisiae was targeted as part of our yeast structural genomics project. YGR205w codes for a small (290 amino acids) protein with unknown structure and function. The only recognizable sequence feature is the presence of a Walker A motif (P loop) indicating a possible nucleotide binding/converting function. We determined the three-dimensional crystal structure of Se-methionine substituted protein using multiple anomalous diffraction. The structure revealed a well known mononucleotide fold and strong resemblance to the structure of small metabolite phosphorylating enzymes such as pantothenate and phosphoribulo kinase. Biochemical experiments show that YGR205w binds specifically ATP and, less tightly, ADP. The structure also revealed the presence of two bound sulphate ions, occupying opposite niches in a canyon that corresponds to the active site of the protein. One sulphate is bound to the P-loop in a position that corresponds to the position of beta-phosphate in mononucleotide protein ATP complex, suggesting the protein is indeed a kinase. The nature of the phosphate accepting substrate remains to be determined. Copyright 2004 Wiley-Liss, Inc.

Analysis of correlation structures in the Synechocystis PCC6803 genome.

PubMed

Wu, Zuo-Bing

2014-12-01

Transfer of nucleotide strings in the Synechocystis sp. PCC6803 genome is investigated to exhibit periodic and non-periodic correlation structures by using the recurrence plot method and the phase space reconstruction technique. The periodic correlation structures are generated by periodic transfer of several substrings in long periodic or non-periodic nucleotide strings embedded in the coding regions of genes. The non-periodic correlation structures are generated by non-periodic transfer of several substrings covering or overlapping with the coding regions of genes. In the periodic and non-periodic transfer, some gaps divide the long nucleotide strings into the substrings and prevent their global transfer. Most of the gaps are either the replacement of one base or the insertion/reduction of one base. In the reconstructed phase space, the points generated from two or three steps for the continuous iterative transfer via the second maximal distance can be fitted by two lines. It partly reveals an intrinsic dynamics in the transfer of nucleotide strings. Due to the comparison of the relative positions and lengths, the substrings concerned with the non-periodic correlation structures are almost identical to the mobile elements annotated in the genome. The mobile elements are thus endowed with the basic results on the correlation structures. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Correlation of codon biases and potential secondary structures with mRNA translation efficiency in unicellular organisms].

PubMed

Vladimirov, N V; Likhoshvaĭ, V A; Matushkin, Iu G

2007-01-01

Gene expression is known to correlate with degree of codon bias in many unicellular organisms. However, such correlation is absent in some organisms. Recently we demonstrated that inverted complementary repeats within coding DNA sequence must be considered for proper estimation of translation efficiency, since they may form secondary structures that obstruct ribosome movement. We have developed a program for estimation of potential coding DNA sequence expression in defined unicellular organism using its genome sequence. The program computes elongation efficiency index. Computation is based on estimation of coding DNA sequence elongation efficiency, taking into account three key factors: codon bias, average number of inverted complementary repeats, and free energy of potential stem-loop structures formed by the repeats. The influence of these factors on translation is numerically estimated. An optimal proportion of these factors is computed for each organism individually. Quantitative translational characteristics of 384 unicellular organisms (351 bacteria, 28 archaea, 5 eukaryota) have been computed using their annotated genomes from NCBI GenBank. Five potential evolutionary strategies of translational optimization have been determined among studied organisms. A considerable difference of preferred translational strategies between Bacteria and Archaea has been revealed. Significant correlations between elongation efficiency index and gene expression levels have been shown for two organisms (S. cerevisiae and H. pylori) using available microarray data. The proposed method allows to estimate numerically the coding DNA sequence translation efficiency and to optimize nucleotide composition of heterologous genes in unicellular organisms. http://www.mgs.bionet.nsc.ru/mgs/programs/eei-calculator/.

The Disk of 48 Lib Revealed by NPOI

NASA Astrophysics Data System (ADS)

Lembryk, Ludwik; Tycner, C.; Sigut, A.; Zavala, R. T.

2013-01-01

We present a study of the disk around the Be star 48 Lib, where NLTE numerical disk models are being compared to the spectral and interferometric data to constrain the physical properties of the inner disk structure. The computational models are generated using the BEDISK code, which accounts for heating and cooling of various atoms in the disk and assumes solar chemical composition. A large set of self-consistent disk models produced with the BEDISK code is in turn used to generate synthetic spectra and images assuming a wide range of inclination angles using the BERAY code. The aim of this project is to constrain the physical properties as well as the inclination angles using both spectroscopic and interferometric data. The interferometric data were obtained using the Naval Precision Optical Interferometer (NPOI), with the focus on Hydrogen Balmer-alpha emission, which is the strongest emission line present due to the circumstellar structure. Because 48 Lib shows clear asymmetric spectral lines, we discuss how we model the asymmetric peaks of the Halpha line by combining two models computed with different density structures. The corresponding synthetic images of these combined density structures are then Fourier transformed and compared to the interferometric data. This numerical strategy has the potential to easily model the commonly observed variation of the ratio of the violet-to-red (V/R ratio) emission peaks and constrain the long-term variability associated with the disk of 48 Lib as well as other emission-line stars that show similar variability.

The influence of viral coding sequences on pestivirus IRES activity reveals further parallels with translation initiation in prokaryotes.

PubMed Central

Fletcher, Simon P; Ali, Iraj K; Kaminski, Ann; Digard, Paul; Jackson, Richard J

2002-01-01

Classical swine fever virus (CSFV) is a member of the pestivirus family, which shares many features in common with hepatitis C virus (HCV). It is shown here that CSFV has an exceptionally efficient cis-acting internal ribosome entry segment (IRES), which, like that of HCV, is strongly influenced by the sequences immediately downstream of the initiation codon, and is optimal with viral coding sequences in this position. Constructs that retained 17 or more codons of viral coding sequence exhibited full IRES activity, but with only 12 codons, activity was approximately 66% of maximum in vitro (though close to maximum in transfected BHK cells), whereas with just 3 codons or fewer, the activity was only approximately 15% of maximum. The minimal coding region elements required for high activity were exchanged between HCV and CSFV. Although maximum activity was observed in each case with the homologous combination of coding region and 5' UTR, the heterologous combinations were sufficiently active to rule out a highly specific functional interplay between the 5' UTR and coding sequences. On the other hand, inversion of the coding sequences resulted in low IRES activity, particularly with the HCV coding sequences. RNA structure probing showed that the efficiency of internal initiation of these chimeric constructs correlated most closely with the degree of single-strandedness of the region around and immediately downstream of the initiation codon. The low activity IRESs could not be rescued by addition of supplementary eIF4A (the initiation factor with ATP-dependent RNA helicase activity). The extreme sensitivity to secondary structure around the initiation codon is likely to be due to the fact that the eIF4F complex (which has eIF4A as one of its subunits) is not required for and does not participate in initiation on these IRESs. PMID:12515388

Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks

PubMed Central

Caetano-Anollés, Derek; Caetano-Anollés, Gustavo

2016-01-01

The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains. Here we review phylogenomic analyses that reconstruct the early history of the synthetase enzymes and the ribosome, their interactions with RNA, and the inception of amino acid charging and codon specificities in tRNA that are responsible for the genetic code. We also trace the age of domains and tRNA onto ancient tRNA homologies that were recently identified in rRNA. Our findings reveal a timeline of recruitment of tRNA building blocks for the formation of a functional ribosome, which holds both the biocatalytic functions of protein biosynthesis and the ability to store genetic memory in primordial RNA genomic templates. PMID:27918435

Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks.

PubMed

Caetano-Anollés, Derek; Caetano-Anollés, Gustavo

2016-12-02

The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains. Here we review phylogenomic analyses that reconstruct the early history of the synthetase enzymes and the ribosome, their interactions with RNA, and the inception of amino acid charging and codon specificities in tRNA that are responsible for the genetic code. We also trace the age of domains and tRNA onto ancient tRNA homologies that were recently identified in rRNA. Our findings reveal a timeline of recruitment of tRNA building blocks for the formation of a functional ribosome, which holds both the biocatalytic functions of protein biosynthesis and the ability to store genetic memory in primordial RNA genomic templates.

The complete mitochondrial genome of Arctic Calanus hyperboreus (Copepoda, Calanoida) reveals characteristic patterns in calanoid mitochondrial genome.

PubMed

Kim, Sanghee; Lim, Byung-Jin; Min, Gi-Sik; Choi, Han-Gu

2013-05-10

Copepoda is the most diverse and abundant group of crustaceans, but its phylogenetic relationships are ambiguous. Mitochondrial (mt) genomes are useful for studying evolutionary history, but only six complete Copepoda mt genomes have been made available and these have extremely rearranged genome structures. This study determined the mt genome of Calanus hyperboreus, making it the first reported Arctic copepod mt genome and the first complete mt genome of a calanoid copepod. The mt genome of C. hyperboreus is 17,910 bp in length and it contains the entire set of 37 mt genes, including 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. It has a very unusual gene structure, including the longest control region reported for a crustacean, a large tRNA gene cluster, and reversed GC skews in 11 out of 13 protein-coding genes (84.6%). Despite the unusual features, comparing this genome to published copepod genomes revealed retained pan-crustacean features, as well as a conserved calanoid-specific pattern. Our data provide a foundation for exploring the calanoid pattern and the mechanisms of mt gene rearrangement in the evolutionary history of the copepod mt genome. Copyright © 2012 Elsevier B.V. All rights reserved.

Serum amyloid A1: Structure, function and gene polymorphism

PubMed Central

Sun, Lei; Ye, Richard D.

2017-01-01

Inducible expression of serum amyloid A (SAA) is a hallmark of the acute-phase response, which is a conserved reaction of vertebrates to environmental challenges such as tissue injury, infection and surgery. Human SAA1 is encoded by one of the four SAA genes and is the best-characterized SAA protein. Initially known as a major precursor of amyloid A (AA), SAA1 has been found to play an important role in lipid metabolism and contributes to bacterial clearance, the regulation of inflammation and tumor pathogenesis. SAA1 has five polymorphic coding alleles (SAA1.1 – SAA1.5) that encode distinct proteins with minor amino acid substitutions. Single nucleotide polymorphism (SNP) has been identified in both the coding and non-coding regions of human SAA1. Despite high levels of sequence homology among these variants, SAA1 polymorphisms have been reported as risk factors of cardiovascular diseases and several types of cancer. A recently solved crystal structure of SAA1.1 reveals a hexameric bundle with each of the SAA1 subunits assuming a 4-helix structure stabilized by the C-terminal tail. Analysis of the native SAA1.1 structure has led to the identification of a competing site for high-density lipoprotein (HDL) and heparin, thus providing the structural basis for a role of heparin and heparan sulfate in the conversion of SAA1 to AA. In this brief review, we compares human SAA1 with other forms of human and mouse SAAs, and discuss how structural and genetic studies of SAA1 have advanced our understanding of the physiological functions of the SAA proteins. PMID:26945629

Analysis of Radiation Effects in Silicon using Kinetic Monte Carlo Methods

DOE PAGES

Hehr, Brian Douglas

2014-11-25

The transient degradation of semiconductor device performance under irradiation has long been an issue of concern. Neutron irradiation can instigate the formation of quasi-stable defect structures, thereby introducing new energy levels into the bandgap that alter carrier lifetimes and give rise to such phenomena as gain degradation in bipolar junction transistors. Normally, the initial defect formation phase is followed by a recovery phase in which defect-defect or defect-dopant interactions modify the characteristics of the damaged structure. A kinetic Monte Carlo (KMC) code has been developed to model both thermal and carrier injection annealing of initial defect structures in semiconductor materials.more » The code is employed to investigate annealing in electron-irradiated, p-type silicon as well as the recovery of base current in silicon transistors bombarded with neutrons at the Los Alamos Neutron Science Center (LANSCE) “Blue Room” facility. Our results reveal that KMC calculations agree well with these experiments once adjustments are made, within the appropriate uncertainty bounds, to some of the sensitive defect parameters.« less

The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition

PubMed Central

Franco-Echevarría, Elsa; González-Polo, Noelia; Zorrilla, Silvia; Martínez-Lumbreras, Santiago; Santiveri, Clara M.; Campos-Olivas, Ramón; Sánchez, Mar; Calvo, Olga

2017-01-01

Abstract Transcription termination of non-coding RNAs is regulated in yeast by a complex of three RNA binding proteins: Nrd1, Nab3 and Sen1. Nrd1 is central in this process by interacting with Rbp1 of RNA polymerase II, Trf4 of TRAMP and GUAA/G terminator sequences. We lack structural data for the last of these binding events. We determined the structures of Nrd1 RNA binding domain and its complexes with three GUAA-containing RNAs, characterized RNA binding energetics and tested rationally designed mutants in vivo. The Nrd1 structure shows an RRM domain fused with a second α/β domain that we name split domain (SD), because it is formed by two non-consecutive segments at each side of the RRM. The GUAA interacts with both domains and with a pocket of water molecules, trapped between the two stacking adenines and the SD. Comprehensive binding studies demonstrate for the first time that Nrd1 has a slight preference for GUAA over GUAG and genetic and functional studies suggest that Nrd1 RNA binding domain might play further roles in non-coding RNAs transcription termination. PMID:28973465

The Redox Code

PubMed Central

Jones, Dean P.

2015-01-01

Abstract Significance: The redox code is a set of principles that defines the positioning of the nicotinamide adenine dinucleotide (NAD, NADP) and thiol/disulfide and other redox systems as well as the thiol redox proteome in space and time in biological systems. The code is richly elaborated in an oxygen-dependent life, where activation/deactivation cycles involving O2 and H2O2 contribute to spatiotemporal organization for differentiation, development, and adaptation to the environment. Disruption of this organizational structure during oxidative stress represents a fundamental mechanism in system failure and disease. Recent Advances: Methodology in assessing components of the redox code under physiological conditions has progressed, permitting insight into spatiotemporal organization and allowing for identification of redox partners in redox proteomics and redox metabolomics. Critical Issues: Complexity of redox networks and redox regulation is being revealed step by step, yet much still needs to be learned. Future Directions: Detailed knowledge of the molecular patterns generated from the principles of the redox code under defined physiological or pathological conditions in cells and organs will contribute to understanding the redox component in health and disease. Ultimately, there will be a scientific basis to a modern redox medicine. Antioxid. Redox Signal. 23, 734–746. PMID:25891126

Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster

PubMed Central

Wang, Wen; Brunet, Frédéric G.; Nevo, Eviatar; Long, Manyuan

2002-01-01

Non-protein-coding RNA genes play an important role in various biological processes. How new RNA genes originated and whether this process is controlled by similar evolutionary mechanisms for the origin of protein-coding genes remains unclear. A young chimeric RNA gene that we term sphinx (spx) provides the first insight into the early stage of evolution of RNA genes. spx originated as an insertion of a retroposed sequence of the ATP synthase chain F gene at the cytological region 60DB since the divergence of Drosophila melanogaster from its sibling species 2–3 million years ago. This retrosequence, which is located at 102F on the fourth chromosome, recruited a nearby exon and intron, thereby evolving a chimeric gene structure. This molecular process suggests that the mechanism of exon shuffling, which can generate protein-coding genes, also plays a role in the origin of RNA genes. The subsequent evolutionary process of spx has been associated with a high nucleotide substitution rate, possibly driven by a continuous positive Darwinian selection for a novel function, as is shown in its sex- and development-specific alternative splicing. To test whether spx has adapted to different environments, we investigated its population genetic structure in the unique “Evolution Canyon” in Israel, revealing a similar haplotype structure in spx, and thus similar evolutionary forces operating on spx between environments. PMID:11904380

Molecular cloning, expression and characterization of 100K gene of fowl adenovirus-4 for prevention and control of hydropericardium syndrome.

PubMed

Shah, M S; Ashraf, A; Khan, M I; Rahman, M; Habib, M; Qureshi, J A

2016-01-01

Fowl adenovirus-4 is an infectious agent causing Hydropericardium syndrome in chickens. Adenovirus are non-enveloped virions having linear, double stranded DNA. Viral genome codes for few structural and non structural proteins. 100K is an important non-structural viral protein. Open reading frame for coding sequence of 100K protein was cloned with oligo histidine tag and expressed in Escherichia coli as a fusion protein. Nucleotide sequence of the gene revealed that 100K gene of FAdV-4 has high homology (98%) with the respective gene of FAdV-10. Recombinant 100K protein was expressed in E. coli and purified by nickel affinity chromatography. Immunization of chickens with recombinant 100K protein elicited significant serum antibody titers. However challenge protection test revealed that 100K protein conferred little protection (40%) to the immunized chicken against pathogenic viral challenge. So it was concluded that 100K gene has 2397 bp length and recombinant 100K protein has molecular weight of 95 kDa. It was also found that the recombinant protein has little capacity to affect the immune response because in-spite of having an important role in intracellular transport & folding of viral capsid proteins during viral replication, it is not exposed on the surface of the virus at any stage. Copyright © 2015 The International Alliance for Biological Standardization. All rights reserved.

Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites.

PubMed

Rossmassler, Karen; Dietrich, Carsten; Thompson, Claire; Mikaelyan, Aram; Nonoh, James O; Scheffrahn, Rudolf H; Sillam-Dussès, David; Brune, Andreas

2015-11-26

Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Here, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential between the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among wood- and litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. Community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.

Synthesis, antimicrobial activity and gene structure of a novel member of the dermaseptin B family.

PubMed

Fleury, Y; Vouille, V; Beven, L; Amiche, M; Wróblewski, H; Delfour, A; Nicolas, P

1998-03-09

Dermaseptins are a family of cationic (Lys-rich) antimicrobial peptides that are abundant in the skin secretions of the arboreal frogs Phyllomedusa bicolor and P. sauvagii. In vitro, these peptides are microbicidal against a wide variety of microorganisms including Gram-positive and Gram-negative bacteria, yeasts, protozoa and fungi. To date, 6 dermaseptin B mature peptides, 24-34 residues long, 2 dermaseptin B cDNAs and 2 gene sequences have been identified in P. bicolor. To assess dermaseptin related genes further, we screened a P. bicolor genomic library with 32P-labeled cDNAs coding either for prepro-dermaseptins B1 or B2 (adenoregulin). A gene sequence was identified that coded a novel dermaseptin B, termed Drg3, which exhibits 23-42% amino acids identities with other members of the family. Analysis of the cDNAs coding precursors for several opioid and antimicrobial peptides originating from the skin of various amphibian species revealed that the 25-residue preproregion of these preproforms are all encoded by conserved nucleotides encompassed by the first coding exon of the Drg3 gene. Synthetic dermaseptin Drg3 exhibited a bactericidal activity towards several species of mollicutes (wall-less eubacteria), firmicutes (Gram-positive eubacteria), and gracilicutes (Gram-negative eubacteria), with minimal inhibitory concentrations (MICs) ranging from 6.25 to 100 microM. Experiments performed on Acholeplasma laidlawii cells revealed that this peptide is membranotropic and that if efficiently depolarizes the plasma membrane.

Hidden Genetic Variation in LCA9-Associated Congenital Blindness Explained by 5'UTR Mutations and Copy-Number Variations of NMNAT1.

PubMed

Coppieters, Frauke; Todeschini, Anne Laure; Fujimaki, Takuro; Baert, Annelot; De Bruyne, Marieke; Van Cauwenbergh, Caroline; Verdin, Hannah; Bauwens, Miriam; Ongenaert, Maté; Kondo, Mineo; Meire, Françoise; Murakami, Akira; Veitia, Reiner A; Leroy, Bart P; De Baere, Elfride

2015-12-01

Leber congenital amaurosis (LCA) is a severe autosomal-recessive retinal dystrophy leading to congenital blindness. A recently identified LCA gene is NMNAT1, located in the LCA9 locus. Although most mutations in blindness genes are coding variations, there is accumulating evidence for hidden noncoding defects or structural variations (SVs). The starting point of this study was an LCA9-associated consanguineous family in which no coding mutations were found in the LCA9 region. Exploring the untranslated regions of NMNAT1 revealed a novel homozygous 5'UTR variant, c.-70A>T. Moreover, an adjacent 5'UTR variant, c.-69C>T, was identified in a second consanguineous family displaying a similar phenotype. Both 5'UTR variants resulted in decreased NMNAT1 mRNA abundance in patients' lymphocytes, and caused decreased luciferase activity in human retinal pigment epithelial RPE-1 cells. Second, we unraveled pseudohomozygosity of a coding NMNAT1 mutation in two unrelated LCA patients by the identification of two distinct heterozygous partial NMNAT1 deletions. Molecular characterization of the breakpoint junctions revealed a complex Alu-rich genomic architecture. Our study uncovered hidden genetic variation in NMNAT1-associated LCA and emphasized a shift from coding to noncoding regulatory mutations and repeat-mediated SVs in the molecular pathogenesis of heterogeneous recessive disorders such as hereditary blindness. © 2015 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

Mapping temporal dynamics in social interactions with unified structural equation modeling: A description and demonstration revealing time-dependent sex differences in play behavior

PubMed Central

Beltz, Adriene M.; Beekman, Charles; Molenaar, Peter C. M.; Buss, Kristin A.

2013-01-01

Developmental science is rich with observations of social interactions, but few available methodological and statistical approaches take full advantage of the information provided by these data. The authors propose implementation of the unified structural equation model (uSEM), a network analysis technique, for observational data coded repeatedly across time; uSEM captures the temporal dynamics underlying changes in behavior at the individual level by revealing the ways in which a single person influences – concurrently and in the future – other people. To demonstrate the utility of uSEM, the authors applied it to ratings of positive affect and vigor of activity during children’s unstructured laboratory play with unfamiliar, same-sex peers. Results revealed the time-dependent nature of sex differences in play behavior. For girls more than boys, positive affect was dependent upon peers’ prior positive affect. For boys more than girls, vigor of activity was dependent upon peers’ current vigor of activity. PMID:24039386

A Flexible and Non-instrusive Approach for Computing Complex Structural Coverage Metrics

NASA Technical Reports Server (NTRS)

Whalen, Michael W.; Person, Suzette J.; Rungta, Neha; Staats, Matt; Grijincu, Daniela

2015-01-01

Software analysis tools and techniques often leverage structural code coverage information to reason about the dynamic behavior of software. Existing techniques instrument the code with the required structural obligations and then monitor the execution of the compiled code to report coverage. Instrumentation based approaches often incur considerable runtime overhead for complex structural coverage metrics such as Modified Condition/Decision (MC/DC). Code instrumentation, in general, has to be approached with great care to ensure it does not modify the behavior of the original code. Furthermore, instrumented code cannot be used in conjunction with other analyses that reason about the structure and semantics of the code under test. In this work, we introduce a non-intrusive preprocessing approach for computing structural coverage information. It uses a static partial evaluation of the decisions in the source code and a source-to-bytecode mapping to generate the information necessary to efficiently track structural coverage metrics during execution. Our technique is flexible; the results of the preprocessing can be used by a variety of coverage-driven software analysis tasks, including automated analyses that are not possible for instrumented code. Experimental results in the context of symbolic execution show the efficiency and flexibility of our nonintrusive approach for computing code coverage information

Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays

PubMed Central

2010-01-01

Background The identification of non-coding transcripts in human, mouse, and Escherichia coli has revealed their widespread occurrence and functional importance in both eukaryotic and prokaryotic life. In prokaryotes, studies have shown that non-coding transcripts participate in a broad range of cellular functions like gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Streptococcus pneumoniae (pneumococcus), an obligate human respiratory pathogen responsible for significant worldwide morbidity and mortality. Tiling microarrays enable genome wide mRNA profiling as well as identification of novel transcripts at a high-resolution. Results Here, we describe a high-resolution transcription map of the S. pneumoniae clinical isolate TIGR4 using genomic tiling arrays. Our results indicate that approximately 66% of the genome is expressed under our experimental conditions. We identified a total of 50 non-coding small RNAs (sRNAs) from the intergenic regions, of which 36 had no predicted function. Half of the identified sRNA sequences were found to be unique to S. pneumoniae genome. We identified eight overrepresented sequence motifs among sRNA sequences that correspond to sRNAs in different functional categories. Tiling arrays also identified approximately 202 operon structures in the genome. Conclusions In summary, the pneumococcal operon structures and novel sRNAs identified in this study enhance our understanding of the complexity and extent of the pneumococcal 'expressed' genome. Furthermore, the results of this study open up new avenues of research for understanding the complex RNA regulatory network governing S. pneumoniae physiology and virulence. PMID:20525227

The Sensitivity of Coded Mask Telescopes

NASA Technical Reports Server (NTRS)

Skinner, Gerald K.

2008-01-01

Simple formulae are often used to estimate the sensitivity of coded mask X-ray or gamma-ray telescopes, but t,hese are strictly only applicable if a number of basic assumptions are met. Complications arise, for example, if a grid structure is used to support the mask elements, if the detector spatial resolution is not good enough to completely resolve all the detail in the shadow of the mask or if any of a number of other simplifying conditions are not fulfilled. We derive more general expressions for the Poisson-noise-limited sensitivity of astronomical telescopes using the coded mask technique, noting explicitly in what circumstances they are applicable. The emphasis is on using nomenclature and techniques that result in simple and revealing results. Where no convenient expression is available a procedure is given which allows the calculation of the sensitivity. We consider certain aspects of the optimisation of the design of a coded mask telescope and show that when the detector spatial resolution and the mask to detector separation are fixed, the best source location accuracy is obtained when the mask elements are equal in size to the detector pixels.

The RNA Exosome Adaptor ZFC3H1 Functionally Competes with Nuclear Export Activity to Retain Target Transcripts.

PubMed

Silla, Toomas; Karadoulama, Evdoxia; Mąkosa, Dawid; Lubas, Michal; Jensen, Torben Heick

2018-05-15

Mammalian genomes are promiscuously transcribed, yielding protein-coding and non-coding products. Many transcripts are short lived due to their nuclear degradation by the ribonucleolytic RNA exosome. Here, we show that abolished nuclear exosome function causes the formation of distinct nuclear foci, containing polyadenylated (pA + ) RNA secluded from nucleocytoplasmic export. We asked whether exosome co-factors could serve such nuclear retention. Co-localization studies revealed the enrichment of pA + RNA foci with "pA-tail exosome targeting (PAXT) connection" components MTR4, ZFC3H1, and PABPN1 but no overlap with known nuclear structures such as Cajal bodies, speckles, paraspeckles, or nucleoli. Interestingly, ZFC3H1 is required for foci formation, and in its absence, selected pA + RNAs, including coding and non-coding transcripts, are exported to the cytoplasm in a process dependent on the mRNA export factor AlyREF. Our results establish ZFC3H1 as a central nuclear pA + RNA retention factor, counteracting nuclear export activity. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Modeling of Nonlinear Beat Signals of TAE's

NASA Astrophysics Data System (ADS)

Zhang, Bo; Berk, Herbert; Breizman, Boris; Zheng, Linjin

2012-03-01

Experiments on Alcator C-Mod reveal Toroidal Alfven Eigenmodes (TAE) together with signals at various beat frequencies, including those at twice the mode frequency. The beat frequencies are sidebands driven by quadratic nonlinear terms in the MHD equations. These nonlinear sidebands have not yet been quantified by any existing codes. We extend the AEGIS code to capture nonlinear effects by treating the nonlinear terms as a driving source in the linear MHD solver. Our goal is to compute the spatial structure of the sidebands for realistic geometry and q-profile, which can be directly compared with experiment in order to interpret the phase contrast imaging diagnostic measurements and to enable the quantitative determination of the Alfven wave amplitude in the plasma core

Thermal hydraulic-severe accident code interfaces for SCDAP/RELAP5/MOD3.2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coryell, E.W.; Siefken, L.J.; Harvego, E.A.

1997-07-01

The SCDAP/RELAP5 computer code is designed to describe the overall reactor coolant system thermal-hydraulic response, core damage progression, and fission product release during severe accidents. The code is being developed at the Idaho National Engineering Laboratory under the primary sponsorship of the Office of Nuclear Regulatory Research of the U.S. Nuclear Regulatory Commission. The code is the result of merging the RELAP5, SCDAP, and COUPLE codes. The RELAP5 portion of the code calculates the overall reactor coolant system, thermal-hydraulics, and associated reactor system responses. The SCDAP portion of the code describes the response of the core and associated vessel structures.more » The COUPLE portion of the code describes response of lower plenum structures and debris and the failure of the lower head. The code uses a modular approach with the overall structure, input/output processing, and data structures following the pattern established for RELAP5. The code uses a building block approach to allow the code user to easily represent a wide variety of systems and conditions through a powerful input processor. The user can represent a wide variety of experiments or reactor designs by selecting fuel rods and other assembly structures from a range of representative core component models, and arrange them in a variety of patterns within the thermalhydraulic network. The COUPLE portion of the code uses two-dimensional representations of the lower plenum structures and debris beds. The flow of information between the different portions of the code occurs at each system level time step advancement. The RELAP5 portion of the code describes the fluid transport around the system. These fluid conditions are used as thermal and mass transport boundary conditions for the SCDAP and COUPLE structures and debris beds.« less

The Views of the Teachers about the Mind Mapping Technique in the Elementary Life Science and Social Studies Lessons Based on the Constructivist Method

ERIC Educational Resources Information Center

Seyihoglu, Aysegul; Kartal, Ayca

2010-01-01

The purpose of this study is to reveal the opinions of teachers on using the mind mapping technique in Life Science and Social Studies lessons. The participants of the study are 20 primary education teachers. In this study, a semi-structured interview technique was used. For content analysis, the themes and codes were defined, based on the views…

RNA structures as mediators of neurological diseases and as drug targets

PubMed Central

Bernat, Viachaslau; Disney, Matthew D.

2015-01-01

RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics. PMID:26139368

TCOF1 gene encodes a putative nucleolar phosphoprotein that exhibits mutations in Treacher Collins Syndrome throughout its coding region.

PubMed

Wise, C A; Chiang, L C; Paznekas, W A; Sharma, M; Musy, M M; Ashley, J A; Lovett, M; Jabs, E W

1997-04-01

Treacher Collins Syndrome (TCS) is the most common of the human mandibulofacial dysostosis disorders. Recently, a partial TCOF1 cDNA was identified and shown to contain mutations in TCS families. Here we present the entire exon/intron genomic structure and the complete coding sequence of TCOF1. TCOF1 encodes a low complexity protein of 1,411 amino acids, whose predicted protein structure reveals repeated motifs that mirror the organization of its exons. These motifs are shared with nucleolar trafficking proteins in other species and are predicted to be highly phosphorylated by casein kinase. Consistent with this, the full-length TCOF1 protein sequence also contains putative nuclear and nucleolar localization signals. Throughout the open reading frame, we detected an additional eight mutations in TCS families and several polymorphisms. We postulate that TCS results from defects in a nucleolar trafficking protein that is critically required during human craniofacial development.

Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation

DOE PAGES

Westholm, Jakub  O.; Miura, Pedro; Olson, Sara; ...

2014-11-26

Circularization was recently recognized to broadly expand transcriptome complexity. Here, we exploit massive Drosophila total RNA-sequencing data, >5 billion paired-end reads from >100 libraries covering diverse developmental stages, tissues, and cultured cells, to rigorously annotate >2,500 fruit fly circular RNAs. These mostly derive from back-splicing of protein-coding genes and lack poly(A) tails, and the circularization of hundreds of genes is conserved across multiple Drosophila species. We elucidate structural and sequence properties of Drosophila circular RNAs, which exhibit commonalities and distinctions from mammalian circles. Notably, Drosophila circular RNAs harbor >1,000 well-conserved canonical miRNA seed matches, especially within coding regions, and codingmore » conserved miRNA sites reside preferentially within circularized exons. Finally, we analyze the developmental and tissue specificity of circular RNAs and note their preferred derivation from neural genes and enhanced accumulation in neural tissues. Interestingly, circular isoforms increase substantially relative to linear isoforms during CNS aging and constitute an aging biomarker.« less

Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Westholm, Jakub  O.; Miura, Pedro; Olson, Sara

Circularization was recently recognized to broadly expand transcriptome complexity. Here, we exploit massive Drosophila total RNA-sequencing data, >5 billion paired-end reads from >100 libraries covering diverse developmental stages, tissues, and cultured cells, to rigorously annotate >2,500 fruit fly circular RNAs. These mostly derive from back-splicing of protein-coding genes and lack poly(A) tails, and the circularization of hundreds of genes is conserved across multiple Drosophila species. We elucidate structural and sequence properties of Drosophila circular RNAs, which exhibit commonalities and distinctions from mammalian circles. Notably, Drosophila circular RNAs harbor >1,000 well-conserved canonical miRNA seed matches, especially within coding regions, and codingmore » conserved miRNA sites reside preferentially within circularized exons. Finally, we analyze the developmental and tissue specificity of circular RNAs and note their preferred derivation from neural genes and enhanced accumulation in neural tissues. Interestingly, circular isoforms increase substantially relative to linear isoforms during CNS aging and constitute an aging biomarker.« less

Molecular basis for TANK recognition by TRAF1 revealed by the crystal structure of TRAF1/TANK complex.

PubMed

Kim, Chang Min; Jeong, Jae-Hee; Son, Young-Jin; Choi, Jun-Hyuk; Kim, Sunghwan; Park, Hyun Ho

2017-03-01

Tumor necrosis factor receptor-associated factor 1 (TRAF1) is a multifunctional adaptor protein involved in important processes of cellular signaling, including innate immunity and apoptosis. TRAF family member-associated NF-kappaB activator (TANK) has been identified as a competitive intracellular inhibitor of TRAF2 function. Although TRAF recognition by various receptors has been studied extensively in the field of TRAF-mediated biology, molecular and functional details of TANK recognition and interaction with TRAF1 have not been studied. In this study, we report the crystal structure of the TRAF1/TANK peptide complex. Quantitative interaction experiments showed that TANK peptide interacts with both TRAF1 and TRAF2 with similar affinity in a micromolar range. Our structural study also reveals that TANK binds TRAF1 using a minor minimal consensus motif for TRAF binding, Px(Q/E)xT. Coordinate and structural factor were deposited in the Protein Data Bank under PDB ID code 5H10. © 2017 Federation of European Biochemical Societies.

The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation

PubMed Central

Lee, Mihwa; Sadowska, Agata; Bekere, Indra; Ho, Diwei; Gully, Benjamin S.; Lu, Yanling; Iyer, K. Swaminathan; Trewhella, Jill; Fox, Archa H.; Bond, Charles S.

2015-01-01

SFPQ, (a.k.a. PSF), is a human tumor suppressor protein that regulates many important functions in the cell nucleus including coordination of long non-coding RNA molecules into nuclear bodies. Here we describe the first crystal structures of Splicing Factor Proline and Glutamine Rich (SFPQ), revealing structural similarity to the related PSPC1/NONO heterodimer and a strikingly extended structure (over 265 Å long) formed by an unusual anti-parallel coiled-coil that results in an infinite linear polymer of SFPQ dimers within the crystals. Small-angle X-ray scattering and transmission electron microscopy experiments show that polymerization is reversible in solution and can be templated by DNA. We demonstrate that the ability to polymerize is essential for the cellular functions of SFPQ: disruptive mutation of the coiled-coil interaction motif results in SFPQ mislocalization, reduced formation of nuclear bodies, abrogated molecular interactions and deficient transcriptional regulation. The coiled-coil interaction motif thus provides a molecular explanation for the functional aggregation of SFPQ that directs its role in regulating many aspects of cellular nucleic acid metabolism. PMID:25765647

Building a model for disease classification integration in oncology, an approach based on the national cancer institute thesaurus.

PubMed

Jouhet, Vianney; Mougin, Fleur; Bréchat, Bérénice; Thiessard, Frantz

2017-02-07

Identifying incident cancer cases within a population remains essential for scientific research in oncology. Data produced within electronic health records can be useful for this purpose. Due to the multiplicity of providers, heterogeneous terminologies such as ICD-10 and ICD-O-3 are used for oncology diagnosis recording purpose. To enable disease identification based on these diagnoses, there is a need for integrating disease classifications in oncology. Our aim was to build a model integrating concepts involved in two disease classifications, namely ICD-10 (diagnosis) and ICD-O-3 (topography and morphology), despite their structural heterogeneity. Based on the NCIt, a "derivative" model for linking diagnosis and topography-morphology combinations was defined and built. ICD-O-3 and ICD-10 codes were then used to instantiate classes of the "derivative" model. Links between terminologies obtained through the model were then compared to mappings provided by the Surveillance, Epidemiology, and End Results (SEER) program. The model integrated 42% of neoplasm ICD-10 codes (excluding metastasis), 98% of ICD-O-3 morphology codes (excluding metastasis) and 68% of ICD-O-3 topography codes. For every codes instantiating at least a class in the "derivative" model, comparison with SEER mappings reveals that all mappings were actually available in the model as a link between the corresponding codes. We have proposed a method to automatically build a model for integrating ICD-10 and ICD-O-3 based on the NCIt. The resulting "derivative" model is a machine understandable resource that enables an integrated view of these heterogeneous terminologies. The NCIt structure and the available relationships can help to bridge disease classifications taking into account their structural and granular heterogeneities. However, (i) inconsistencies exist within the NCIt leading to misclassifications in the "derivative" model, (ii) the "derivative" model only integrates a part of ICD-10 and ICD-O-3. The NCIt is not sufficient for integration purpose and further work based on other termino-ontological resources is needed in order to enrich the model and avoid identified inconsistencies.

Standardized verification of fuel cycle modeling

DOE PAGES

Feng, B.; Dixon, B.; Sunny, E.; ...

2016-04-05

A nuclear fuel cycle systems modeling and code-to-code comparison effort was coordinated across multiple national laboratories to verify the tools needed to perform fuel cycle analyses of the transition from a once-through nuclear fuel cycle to a sustainable potential future fuel cycle. For this verification study, a simplified example transition scenario was developed to serve as a test case for the four systems codes involved (DYMOND, VISION, ORION, and MARKAL), each used by a different laboratory participant. In addition, all participants produced spreadsheet solutions for the test case to check all the mass flows and reactor/facility profiles on a year-by-yearmore » basis throughout the simulation period. The test case specifications describe a transition from the current US fleet of light water reactors to a future fleet of sodium-cooled fast reactors that continuously recycle transuranic elements as fuel. After several initial coordinated modeling and calculation attempts, it was revealed that most of the differences in code results were not due to different code algorithms or calculation approaches, but due to different interpretations of the input specifications among the analysts. Therefore, the specifications for the test case itself were iteratively updated to remove ambiguity and to help calibrate interpretations. In addition, a few corrections and modifications were made to the codes as well, which led to excellent agreement between all codes and spreadsheets for this test case. Although no fuel cycle transition analysis codes matched the spreadsheet results exactly, all remaining differences in the results were due to fundamental differences in code structure and/or were thoroughly explained. As a result, the specifications and example results are provided so that they can be used to verify additional codes in the future for such fuel cycle transition scenarios.« less

Wing design for a civil tiltrotor transport aircraft

NASA Technical Reports Server (NTRS)

Rais-Rohani, Masoud

1994-01-01

The goal of this research is the proper tailoring of the civil tiltrotor's composite wing-box structure leading to a minimum-weight wing design. With focus on the structural design, the wing's aerodynamic shape and the rotor-pylon system are held fixed. The initial design requirement on drag reduction set the airfoil maximum thickness-to-chord ratio to 18 percent. The airfoil section is the scaled down version of the 23 percent-thick airfoil used in V-22's wing. With the project goal in mind, the research activities began with an investigation of the structural dynamic and aeroelastic characteristics of the tiltrotor configuration, and the identification of proper procedures to analyze and account for these characteristics in the wing design. This investigation led to a collection of more than thirty technical papers on the subject, some of which have been referenced here. The review of literature on the tiltrotor revealed the complexity of the system in terms of wing-rotor-pylon interactions. The aeroelastic instability or whirl flutter stemming from wing-rotor-pylon interactions is found to be the most critical mode of instability demanding careful consideration in the preliminary wing design. The placement of wing fundamental natural frequencies in bending and torsion relative to each other and relative to the rotor 1/rev frequencies is found to have a strong influence on the whirl flutter. The frequency placement guide based on a Bell Helicopter Textron study is used in the formulation of frequency constraints. The analysis and design studies are based on two different finite-element computer codes: (1) MSC/NASATRAN and (2) WIDOWAC. These programs are used in parallel with the motivation to eventually, upon necessary modifications and validation, use the simpler WIDOWAC code in the structural tailoring of the tiltrotor wing. Several test cases were studied for the preliminary comparison of the two codes. The results obtained so far indicate a good overall agreement between the two codes.

Crystal Structure of Cocosin, A Potential Food Allergen from Coconut (Cocos nucifera).

PubMed

Jin, Tengchuan; Wang, Cheng; Zhang, Caiying; Wang, Yang; Chen, Yu-Wei; Guo, Feng; Howard, Andrew; Cao, Min-Jie; Fu, Tong-Jen; McHugh, Tara H; Zhang, Yuzhu

2017-08-30

Coconut (Cocos nucifera) is an important palm tree. Coconut fruit is widely consumed. The most abundant storage protein in coconut fruit is cocosin (a likely food allergen), which belongs to the 11S globulin family. Cocosin was crystallized near a century ago, but its structure remains unknown. By optimizing crystallization conditions and cryoprotectant solutions, we were able to obtain cocosin crystals that diffracted to 1.85 Å. The cocosin gene was cloned from genomic DNA isolated from dry coconut tissue. The protein sequence deduced from the predicted cocosin coding sequence was used to guide model building and structure refinement. The structure of cocosin was determined for the first time, and it revealed a typical 11S globulin feature of a double layer doughnut-shaped hexamer.

Resident challenges with daily life in Chinese long-term care facilities: A qualitative pilot study.

PubMed

Song, Yuting; Scales, Kezia; Anderson, Ruth A; Wu, Bei; Corazzini, Kirsten N

As traditional family-based care in China declines, the demand for residential care increases. Knowledge of residents' experiences with long-term care (LTC) facilities is essential to improving quality of care. This pilot study aimed to describe residents' experiences in LTC facilities, particularly as it related to physical function. Semi-structured open-ended interviews were conducted in two facilities with residents stratified by three functional levels (n = 5). Directed content analysis was guided by the Adaptive Leadership Framework. A two-cycle coding approach was used with a first-cycle descriptive coding and second-cycle dramaturgical coding. Interviews provided examples of challenges faced by residents in meeting their daily care needs. Five themes emerged: staff care, care from family members, physical environment, other residents in the facility, and personal strategies. Findings demonstrate the significance of organizational context for care quality and reveal foci for future research. Copyright © 2017 Elsevier Inc. All rights reserved.

Computer codes developed and under development at Lewis

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1992-01-01

The objective of this summary is to provide a brief description of: (1) codes developed or under development at LeRC; and (2) the development status of IPACS with some typical early results. The computer codes that have been developed and/or are under development at LeRC are listed in the accompanying charts. This list includes: (1) the code acronym; (2) select physics descriptors; (3) current enhancements; and (4) present (9/91) code status with respect to its availability and documentation. The computer codes list is grouped by related functions such as: (1) composite mechanics; (2) composite structures; (3) integrated and 3-D analysis; (4) structural tailoring; and (5) probabilistic structural analysis. These codes provide a broad computational simulation infrastructure (technology base-readiness) for assessing the structural integrity/durability/reliability of propulsion systems. These codes serve two other very important functions: they provide an effective means of technology transfer; and they constitute a depository of corporate memory.

Origin and evolution of the long non-coding genes in the X-inactivation center.

PubMed

Romito, Antonio; Rougeulle, Claire

2011-11-01

Random X chromosome inactivation (XCI), the eutherian mechanism of X-linked gene dosage compensation, is controlled by a cis-acting locus termed the X-inactivation center (Xic). One of the striking features that characterize the Xic landscape is the abundance of loci transcribing non-coding RNAs (ncRNAs), including Xist, the master regulator of the inactivation process. Recent comparative genomic analyses have depicted the evolutionary scenario behind the origin of the X-inactivation center, revealing that this locus evolved from a region harboring protein-coding genes. During mammalian radiation, this ancestral protein-coding region was disrupted in the marsupial group, whilst it provided in eutherian lineage the starting material for the non-translated RNAs of the X-inactivation center. The emergence of non-coding genes occurred by a dual mechanism involving loss of protein-coding function of the pre-existing genes and integration of different classes of mobile elements, some of which modeled the structure and sequence of the non-coding genes in a species-specific manner. The rising genes started to produce transcripts that acquired function in regulating the epigenetic status of the X chromosome, as shown for Xist, its antisense Tsix, Jpx, and recently suggested for Ftx. Thus, the appearance of the Xic, which occurred after the divergence between eutherians and marsupials, was the basis for the evolution of random X inactivation as a strategy to achieve dosage compensation. Copyright © 2011. Published by Elsevier Masson SAS.

Zipf's Law in Short-Time Timbral Codings of Speech, Music, and Environmental Sound Signals

PubMed Central

Haro, Martín; Serrà, Joan; Herrera, Perfecto; Corral, Álvaro

2012-01-01

Timbre is a key perceptual feature that allows discrimination between different sounds. Timbral sensations are highly dependent on the temporal evolution of the power spectrum of an audio signal. In order to quantitatively characterize such sensations, the shape of the power spectrum has to be encoded in a way that preserves certain physical and perceptual properties. Therefore, it is common practice to encode short-time power spectra using psychoacoustical frequency scales. In this paper, we study and characterize the statistical properties of such encodings, here called timbral code-words. In particular, we report on rank-frequency distributions of timbral code-words extracted from 740 hours of audio coming from disparate sources such as speech, music, and environmental sounds. Analogously to text corpora, we find a heavy-tailed Zipfian distribution with exponent close to one. Importantly, this distribution is found independently of different encoding decisions and regardless of the audio source. Further analysis on the intrinsic characteristics of most and least frequent code-words reveals that the most frequent code-words tend to have a more homogeneous structure. We also find that speech and music databases have specific, distinctive code-words while, in the case of the environmental sounds, this database-specific code-words are not present. Finally, we find that a Yule-Simon process with memory provides a reasonable quantitative approximation for our data, suggesting the existence of a common simple generative mechanism for all considered sound sources. PMID:22479497

I-Ching, dyadic groups of binary numbers and the geno-logic coding in living bodies.

PubMed

Hu, Zhengbing; Petoukhov, Sergey V; Petukhova, Elena S

2017-12-01

The ancient Chinese book I-Ching was written a few thousand years ago. It introduces the system of symbols Yin and Yang (equivalents of 0 and 1). It had a powerful impact on culture, medicine and science of ancient China and several other countries. From the modern standpoint, I-Ching declares the importance of dyadic groups of binary numbers for the Nature. The system of I-Ching is represented by the tables with dyadic groups of 4 bigrams, 8 trigrams and 64 hexagrams, which were declared as fundamental archetypes of the Nature. The ancient Chinese did not know about the genetic code of protein sequences of amino acids but this code is organized in accordance with the I-Ching: in particularly, the genetic code is constructed on DNA molecules using 4 nitrogenous bases, 16 doublets, and 64 triplets. The article also describes the usage of dyadic groups as a foundation of the bio-mathematical doctrine of the geno-logic code, which exists in parallel with the known genetic code of amino acids but serves for a different goal: to code the inherited algorithmic processes using the logical holography and the spectral logic of systems of genetic Boolean functions. Some relations of this doctrine with the I-Ching are discussed. In addition, the ratios of musical harmony that can be revealed in the parameters of DNA structure are also represented in the I-Ching book. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ion channeling study of defects in compound crystals using Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Turos, A.; Jozwik, P.; Nowicki, L.; Sathish, N.

2014-08-01

Ion channeling is a well-established technique for determination of structural properties of crystalline materials. Defect depth profiles have been usually determined basing on the two-beam model developed by Bøgh (1968) [1]. As long as the main research interest was focused on single element crystals it was considered as sufficiently accurate. New challenge emerged with growing technological importance of compound single crystals and epitaxial heterostructures. Overlap of partial spectra due to different sublattices and formation of complicated defect structures makes the two beam method hardly applicable. The solution is provided by Monte Carlo computer simulations. Our paper reviews principal aspects of this approach and the recent developments in the McChasy simulation code. The latter made it possible to distinguish between randomly displaced atoms (RDA) and extended defects (dislocations, loops, etc.). Hence, complex defect structures can be characterized by the relative content of these two components. The next refinement of the code consists of detailed parameterization of dislocations and dislocation loops. Defect profiles for variety of compound crystals (GaN, ZnO, SrTiO3) have been measured and evaluated using the McChasy code. Damage accumulation curves for RDA and extended defects revealed non monotonous defect buildup with some characteristic steps. Transition to each stage is governed by the different driving force. As shown by the complementary high resolution XRD measurements lattice strain plays here the crucial role and can be correlated with the concentration of extended defects.

Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites

DOE PAGES

Rossmassler, Karen; Dietrich, Carsten; Thompson, Claire; ...

2015-11-26

Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Furthermore, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential betweenmore » the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among woodand litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. In conclusion, the community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.« less

Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rossmassler, Karen; Dietrich, Carsten; Thompson, Claire

Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Furthermore, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential betweenmore » the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among woodand litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. In conclusion, the community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.« less

Genome Sequence of the Bacterium Streptomyces davawensis JCM 4913 and Heterologous Production of the Unique Antibiotic Roseoflavin

PubMed Central

Jankowitsch, Frank; Schwarz, Julia; Rückert, Christian; Gust, Bertolt; Szczepanowski, Rafael; Blom, Jochen; Pelzer, Stefan; Kalinowski, Jörn

2012-01-01

Streptomyces davawensis JCM 4913 synthesizes the antibiotic roseoflavin, a structural riboflavin (vitamin B2) analog. Here, we report the 9,466,619-bp linear chromosome of S. davawensis JCM 4913 and a 89,331-bp linear plasmid. The sequence has an average G+C content of 70.58% and contains six rRNA operons (16S-23S-5S) and 69 tRNA genes. The 8,616 predicted protein-coding sequences include 32 clusters coding for secondary metabolites, several of which are unique to S. davawensis. The chromosome contains long terminal inverted repeats of 33,255 bp each and atypical telomeres. Sequence analysis with regard to riboflavin biosynthesis revealed three different patterns of gene organization in Streptomyces species. Heterologous expression of a set of genes present on a subgenomic fragment of S. davawensis resulted in the production of roseoflavin by the host Streptomyces coelicolor M1152. Phylogenetic analysis revealed that S. davawensis is a close relative of Streptomyces cinnabarinus, and much to our surprise, we found that the latter bacterium is a roseoflavin producer as well. PMID:23043000

Structural organization and classification of cytochrome P450 genes in flax (Linum usitatissimum L.).

PubMed

Babu, Peram Ravindra; Rao, Khareedu Venkateswara; Reddy, Vudem Dashavantha

2013-01-15

Flax CYPome analysis resulted in the identification of 334 putative cytochrome P450 (CYP450) genes in the cultivated flax genome. Classification of flax CYP450 genes based on the sequence similarity with Arabidopsis orthologs and CYP450 nomenclature, revealed 10 clans representing 44 families and 98 subfamilies. CYP80, CYP83, CYP92, CYP702, CYP705, CYP708, CYP728, CYP729, CYP733 and CYP736 families are absent in the flax genome. The subfamily members exhibited conserved sequences, length of exons and phasing of introns. Similarity search of the genomic resources of wild flax species Linum bienne with CYP450 coding sequences of the cultivated flax, revealed the presence of 127 CYP450 gene orthologs, indicating amplification of novel CYP450 genes in the cultivated flax. Seven families CYP73, 74, 75, 76, 77, 84 and 709, coding for enzymes associated with phenylpropanoid/fatty acid metabolism, showed extensive gene amplification in the flax. About 59% of the flax CYP450 genes were present in the EST libraries. Copyright © 2012 Elsevier B.V. All rights reserved.

Wind turbine design codes: A comparison of the structural response

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buhl, M.L. Jr.; Wright, A.D.; Pierce, K.G.

2000-03-01

The National Wind Technology Center (NWTC) of the National Renewable Energy Laboratory is continuing a comparison of several computer codes used in the design and analysis of wind turbines. The second part of this comparison determined how well the programs predict the structural response of wind turbines. In this paper, the authors compare the structural response for four programs: ADAMS, BLADED, FAST{_}AD, and YawDyn. ADAMS is a commercial, multibody-dynamics code from Mechanical Dynamics, Inc. BLADED is a commercial, performance and structural-response code from Garrad Hassan and Partners Limited. FAST{_}AD is a structural-response code developed by Oregon State University and themore » University of Utah for the NWTC. YawDyn is a structural-response code developed by the University of Utah for the NWTC. ADAMS, FAST{_}AD, and YawDyn use the University of Utah's AeroDyn subroutine package for calculating aerodynamic forces. Although errors were found in all the codes during this study, once they were fixed, the codes agreed surprisingly well for most of the cases and configurations that were evaluated. One unresolved discrepancy between BLADED and the AeroDyn-based codes was when there was blade and/or teeter motion in addition to a large yaw error.« less

On complexity of trellis structure of linear block codes

NASA Technical Reports Server (NTRS)

Lin, Shu

1990-01-01

The trellis structure of linear block codes (LBCs) is discussed. The state and branch complexities of a trellis diagram (TD) for a LBC is investigated. The TD with the minimum number of states is said to be minimal. The branch complexity of a minimal TD for a LBC is expressed in terms of the dimensions of specific subcodes of the given code. Then upper and lower bounds are derived on the number of states of a minimal TD for a LBC, and it is shown that a cyclic (or shortened cyclic) code is the worst in terms of the state complexity among the LBCs of the same length and dimension. Furthermore, it is shown that the structural complexity of a minimal TD for a LBC depends on the order of its bit positions. This fact suggests that an appropriate permutation of the bit positions of a code may result in an equivalent code with a much simpler minimal TD. Boolean polynomial representation of codewords of a LBC is also considered. This representation helps in study of the trellis structure of the code. Boolean polynomial representation of a code is applied to construct its minimal TD. Particularly, the construction of minimal trellises for Reed-Muller codes and the extended and permuted binary primitive BCH codes which contain Reed-Muller as subcodes is emphasized. Finally, the structural complexity of minimal trellises for the extended and permuted, and double-error-correcting BCH codes is analyzed and presented. It is shown that these codes have relatively simple trellis structure and hence can be decoded with the Viterbi decoding algorithm.

Identification of Bombyx mori bidensovirus VD1-ORF4 reveals a novel protein associated with viral structural component.

PubMed

Li, Guohui; Hu, Zhaoyang; Guo, Xuli; Li, Guangtian; Tang, Qi; Wang, Peng; Chen, Keping; Yao, Qin

2013-06-01

Bombyx mori bidensovirus (BmBDV) VD1-ORF4 (open reading frame 4, ORF4) consists of 3,318 nucleotides, which codes for a predicted 1,105-amino acid protein containing a conserved DNA polymerase motif. However, its functions in viral propagation remain unknown. In the current study, the transcription of VD1-ORF4 was examined from 6 to 96 h postinfection (p.i.) by RT-PCR, 5'-RACE revealed the transcription initiation site of BmBDV ORF4 to be -16 nucleotides upstream from the start codon, and 3'-RACE revealed the transcription termination site of VD1-ORF4 to be +7 nucleotides downstream from termination codon. Three different proteins were examined in the extracts of BmBDV-infected silkworms midguts by Western blot using raised antibodies against VD1-ORF4 deduced amino acid, and a specific protein band about 53 kDa was further detected in purified virions using the same antibodies. Taken together, BmBDV VD1-ORF4 codes for three or more proteins during the viral life cycle, one of which is a 53 kDa protein and confirmed to be a component of BmBDV virion.

Investigation of structural, electronic, elastic and optical properties of Cd1-x-yZnxHgyTe alloys

NASA Astrophysics Data System (ADS)

Tamer, M.

2016-06-01

Structural, optical and electronic properties and elastic constants of Cd1-x-yZnx HgyTe alloys have been studied by employing the commercial code Castep based on density functional theory. The generalized gradient approximation and local density approximation were utilized as exchange correlation. Using elastic constants for compounds, bulk modulus, band gap, Fermi energy and Kramers-Kronig relations, dielectric constants and the refractive index have been found through calculations. Apart from these, X-ray measurements revealed elastic constants and Vegard's law. It is seen that results obtained from theory and experiments are all in agreement.

Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata.

PubMed

Krishna, Srikar; Nair, Aparna; Cheedipudi, Sirisha; Poduval, Deepak; Dhawan, Jyotsna; Palakodeti, Dasaradhi; Ghanekar, Yashoda

2013-01-07

Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem-loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping-pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration.

Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata

PubMed Central

Krishna, Srikar; Nair, Aparna; Cheedipudi, Sirisha; Poduval, Deepak; Dhawan, Jyotsna; Palakodeti, Dasaradhi; Ghanekar, Yashoda

2013-01-01

Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem–loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping–pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration. PMID:23166307

Extensive structural variations between mitochondrial genomes of CMS and normal peppers (Capsicum annuum L.) revealed by complete nucleotide sequencing.

PubMed

Jo, Yeong Deuk; Choi, Yoomi; Kim, Dong-Hwan; Kim, Byung-Dong; Kang, Byoung-Cheorl

2014-07-04

Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearrangements caused by recombination. However, the mitochondrial genome structure and the DNA rearrangements that may be related to CMS have not been characterized in Capsicum spp. We obtained the complete mitochondrial genome sequences of the pepper CMS line FS4401 (507,452 bp) and the fertile line Jeju (511,530 bp). Comparative analysis between mitochondrial genomes of peppers and tobacco that are included in Solanaceae revealed extensive DNA rearrangements and poor conservation in non-coding DNA. In comparison between pepper lines, FS4401 and Jeju mitochondrial DNAs contained the same complement of protein coding genes except for one additional copy of an atp6 gene (ψatp6-2) in FS4401. In terms of genome structure, we found eighteen syntenic blocks in the two mitochondrial genomes, which have been rearranged in each genome. By contrast, sequences between syntenic blocks, which were specific to each line, accounted for 30,380 and 17,847 bp in FS4401 and Jeju, respectively. The previously-reported CMS candidate genes, orf507 and ψatp6-2, were located on the edges of the largest sequence segments that were specific to FS4401. In this region, large number of small sequence segments which were absent or found on different locations in Jeju mitochondrial genome were combined together. The incorporation of repeats and overlapping of connected sequence segments by a few nucleotides implied that extensive rearrangements by homologous recombination might be involved in evolution of this region. Further analysis using mtDNA pairs from other plant species revealed common features of DNA regions around CMS-associated genes. Although large portion of sequence context was shared by mitochondrial genomes of CMS and male-fertile pepper lines, extensive genome rearrangements were detected. CMS candidate genes located on the edges of highly-rearranged CMS-specific DNA regions and near to repeat sequences. These characteristics were detected among CMS-associated genes in other species, implying a common mechanism might be involved in the evolution of CMS-associated genes.

Face Coding Is Bilateral in the Female Brain

PubMed Central

Proverbio, Alice Mado; Riva, Federica; Martin, Eleonora; Zani, Alberto

2010-01-01

Background It is currently believed that face processing predominantly activates the right hemisphere in humans, but available literature is very inconsistent. Methodology/Principal Findings In this study, ERPs were recorded in 50 right-handed women and men in response to 390 faces (of different age and sex), and 130 technological objects. Results showed no sex difference in the amplitude of N170 to objects; a much larger face-specific response over the right hemisphere in men, and a bilateral response in women; a lack of face-age coding effect over the left hemisphere in men, with no differences in N170 to faces as a function of age; a significant bilateral face-age coding effect in women. Conclusions/Significance LORETA reconstruction showed a significant left and right asymmetry in the activation of the fusiform gyrus (BA19), in women and men, respectively. The present data reveal a lesser degree of lateralization of brain functions related to face coding in women than men. In this light, they may provide an explanation of the inconsistencies in the available literature concerning the asymmetric activity of left and right occipito-temporal cortices devoted to face perception during processing of face identity, structure, familiarity or affective content. PMID:20574528

Identification of a Conserved Non-Protein-Coding Genomic Element that Plays an Essential Role in Alphabaculovirus Pathogenesis

PubMed Central

Kikhno, Irina

2014-01-01

Highly homologous sequences 154–157 bp in length grouped under the name of “conserved non-protein-coding element” (CNE) were revealed in all of the sequenced genomes of baculoviruses belonging to the genus Alphabaculovirus. A CNE alignment led to the detection of a set of highly conserved nucleotide clusters that occupy strictly conserved positions in the CNE sequence. The significant length of the CNE and conservation of both its length and cluster architecture were identified as a combination of characteristics that make this CNE different from known viral non-coding functional sequences. The essential role of the CNE in the Alphabaculovirus life cycle was demonstrated through the use of a CNE-knockout Autographa californica multiple nucleopolyhedrovirus (AcMNPV) bacmid. It was shown that the essential function of the CNE was not mediated by the presumed expression activities of the protein- and non-protein-coding genes that overlap the AcMNPV CNE. On the basis of the presented data, the AcMNPV CNE was categorized as a complex-structured, polyfunctional genomic element involved in an essential DNA transaction that is associated with an undefined function of the baculovirus genome. PMID:24740153

Face coding is bilateral in the female brain.

PubMed

Proverbio, Alice Mado; Riva, Federica; Martin, Eleonora; Zani, Alberto

2010-06-21

It is currently believed that face processing predominantly activates the right hemisphere in humans, but available literature is very inconsistent. In this study, ERPs were recorded in 50 right-handed women and men in response to 390 faces (of different age and sex), and 130 technological objects. Results showed no sex difference in the amplitude of N170 to objects; a much larger face-specific response over the right hemisphere in men, and a bilateral response in women; a lack of face-age coding effect over the left hemisphere in men, with no differences in N170 to faces as a function of age; a significant bilateral face-age coding effect in women. LORETA reconstruction showed a significant left and right asymmetry in the activation of the fusiform gyrus (BA19), in women and men, respectively. The present data reveal a lesser degree of lateralization of brain functions related to face coding in women than men. In this light, they may provide an explanation of the inconsistencies in the available literature concerning the asymmetric activity of left and right occipito-temporal cortices devoted to face perception during processing of face identity, structure, familiarity or affective content.

Burner liner thermal/structural load modeling: TRANCITS program user's manual

NASA Technical Reports Server (NTRS)

Maffeo, R.

1985-01-01

Transfer Analysis Code to Interface Thermal/Structural Problems (TRANCITS) is discussed. The TRANCITS code satisfies all the objectives for transferring thermal data between heat transfer and structural models of combustor liners and it can be used as a generic thermal translator between heat transfer and stress models of any component, regardless of the geometry. The TRANCITS can accurately and efficiently convert the temperature distributions predicted by the heat transfer programs to those required by the stress codes. It can be used for both linear and nonlinear structural codes and can produce nodal temperatures, elemental centroid temperatures, or elemental Gauss point temperatures. The thermal output of both the MARC and SINDA heat transfer codes can be interfaced directly with TRANCITS, and it will automatically produce stress model codes formatted for NASTRAN and MARC. Any thermal program and structural program can be interfaced by using the neutral input and output forms supported by TRANCITS.

44 CFR 71.4 - Documentation.

Code of Federal Regulations, 2012 CFR

2012-10-01

... evidence that the structure was not in compliance with the building code at the time it was built; and (2... evidence that the structure was not in compliance with the building code at the time it was built; and (2... structure and found no evidence that the structure was not in compliance with the building code at the time...

44 CFR 71.4 - Documentation.

Code of Federal Regulations, 2014 CFR

2014-10-01

... evidence that the structure was not in compliance with the building code at the time it was built; and (2... evidence that the structure was not in compliance with the building code at the time it was built; and (2... structure and found no evidence that the structure was not in compliance with the building code at the time...

44 CFR 71.4 - Documentation.

Code of Federal Regulations, 2011 CFR

2011-10-01

... evidence that the structure was not in compliance with the building code at the time it was built; and (2... evidence that the structure was not in compliance with the building code at the time it was built; and (2... structure and found no evidence that the structure was not in compliance with the building code at the time...

44 CFR 71.4 - Documentation.

Code of Federal Regulations, 2013 CFR

2013-10-01

... evidence that the structure was not in compliance with the building code at the time it was built; and (2... evidence that the structure was not in compliance with the building code at the time it was built; and (2... structure and found no evidence that the structure was not in compliance with the building code at the time...

44 CFR 71.4 - Documentation.

Code of Federal Regulations, 2010 CFR

2010-10-01

... evidence that the structure was not in compliance with the building code at the time it was built; and (2... evidence that the structure was not in compliance with the building code at the time it was built; and (2... structure and found no evidence that the structure was not in compliance with the building code at the time...

Sensory and Working Memory Representations of Small and Large Numerosities in the Crow Endbrain.

PubMed

Ditz, Helen M; Nieder, Andreas

2016-11-23

Neurons in the avian nidopallium caudolaterale (NCL), an endbrain structure that originated independently from the mammalian neocortex, process visual numerosities. To clarify the code for number in this anatomically distinct endbrain area in birds, neuronal responses to a broad range of numerosities were analyzed. We recorded single-neuron activity from the NCL of crows performing a delayed match-to-sample task with visual numerosities as discriminanda. The responses of >20% of randomly selected neurons were modulated significantly by numerosities ranging from one to 30 items. Numerosity-selective neurons showed bell-shaped tuning curves with one of the presented numerosities as preferred numerosity regardless of the physical appearance of the items. The resulting labeled-line code exhibited logarithmic compression obeying the Weber-Fechner law for magnitudes. Comparable proportions of selective neurons were found, not only during stimulus presentation, but also in the delay phase, indicating a dominant role of the NCL in numerical working memory. Both during sensory encoding and memorization of numerosities in working memory, NCL activity predicted the crows' number discrimination performance. These neuronal data reveal striking similarities across vertebrate taxa in their code for number despite convergently evolved and anatomically distinct endbrain structures. Birds are known for their capabilities to process numerical quantity. However, birds lack a six-layered neocortex that enables primates with numerical competence. We aimed to decipher the neuronal code for numerical quantity in the independently and distinctly evolved endbrain of birds. We recorded the activity of neurons in an endbrain association area termed nidopallium caudolaterale (NCL) from crows that assessed and briefly memorized numerosities from one to 30 dots. We report a neuronal code for sensory representation and working memory of numerosities in the crow NCL exhibiting several characteristics that are surprisingly similar to the ones found in primates. Our data suggest a common code for number in two different vertebrate taxa that has evolved based on convergent evolution. Copyright © 2016 the authors 0270-6474/16/3612044-09$15.00/0.

Complete genome sequencing and evolutionary analysis of Indian isolates of Dengue virus type 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dash, Paban Kumar, E-mail: pabandash@rediffmail.com; Sharma, Shashi; Soni, Manisha

Highlights: •Complete genome of Indian DENV-2 was deciphered for the first time in this study. •The recent Indian DENV-2 revealed presence of many unique amino acid residues. •Genotype shift (American to Cosmopolitan) characterizes evolution of DENV-2 in India. •Circulation of a unique clade of DENV-2 in South Asia was identified. -- Abstract: Dengue is the most important arboviral infection of global public health significance. It is now endemic in most parts of the South East Asia including India. Though Dengue virus type 2 (DENV-2) is predominantly associated with major outbreaks in India, complete genome information of Indian DENV-2 is notmore » available. In this study, the full-length genome of five DENV-2 isolates (four from 2001 to 2011 and one from 1960), from different parts of India was determined. The complete genome of the Indian DENV-2 was found to be 10,670 bases long with an open reading frame coding for 3391 amino acids. The recent Indian DENV-2 (2001–2011) revealed a nucleotide sequence identity of around 90% and 97% with an older Indian DENV-2 (1960) and closely related Sri Lankan and Chinese DENV-2 respectively. Presence of unique amino acid residues and non-conservative substitutions in critical amino acid residues of major structural and non-structural proteins was observed in recent Indian DENV-2. Selection pressure analysis revealed positive selection in few amino acid sites of the genes encoding for structural and non-structural proteins. The molecular phylogenetic analysis based on comparison of both complete coding region and envelope protein gene with globally diverse DENV-2 viruses classified the recent Indian isolates into a unique South Asian clade within Cosmopolitan genotype. A shift of genotype from American to Cosmopolitan in 1970s characterized the evolution of DENV-2 in India. Present study is the first report on complete genome characterization of emerging DENV-2 isolates from India and highlights the circulation of a unique clade in South Asia.« less

A first principles study of the electronic structure, elastic and thermal properties of UB2

NASA Astrophysics Data System (ADS)

Jossou, Ericmoore; Malakkal, Linu; Szpunar, Barbara; Oladimeji, Dotun; Szpunar, Jerzy A.

2017-07-01

Uranium diboride (UB2) has been widely deployed for refractory use and is a proposed material for Accident Tolerant Fuel (ATF) due to its high thermal conductivity. However, the applicability of UB2 towards high temperature usage in a nuclear reactor requires the need to investigate the thermomechanical properties, and recent studies have failed in highlighting applicable properties. In this work, we present an in-depth theoretical outlook of the structural and thermophysical properties of UB2, including but not limited to elastic, electronic and thermal transport properties. These calculations were performed within the framework of Density Functional Theory (DFT) + U approach, using Quantum ESPRESSO (QE) code considering the addition of Coulomb correlations on the uranium atom. The phonon spectra and elastic constant analysis show the dynamic and mechanical stability of UB2 structure respectively. The electronic structure of UB2 was investigated using full potential linear augmented plane waves plus local orbitals method (FP-LAPW+lo) as implemented in WIEN2k code. The absence of a band gap in the total and partial density of states confirms the metallic nature while the valence electron density plot reveals the presence of covalent bond between adjacent B-B atoms. We predicted the lattice thermal conductivity (kL) by solving Boltzmann Transport Equation (BTE) using ShengBTE. The second order harmonic and third-order anharmonic interatomic force constants required as input to ShengBTE was calculated using the Density-functional perturbation theory (DFPT). However, we predicted the electronic thermal conductivity (kel) using Wiedemann-Franz law as implemented in Boltztrap code. We also show that the sound velocity along 'a' and 'c' axes exhibit high anisotropy, which accounts for the anisotropic thermal conductivity of UB2.

Aminotryptophan-containing barstar: structure--function tradeoff in protein design and engineering with an expanded genetic code.

PubMed

Rubini, Marina; Lepthien, Sandra; Golbik, Ralph; Budisa, Nediljko

2006-07-01

The indole ring of the canonical amino acid tryptophan (Trp) possesses distinguished features, such as sterical bulk, hydrophobicity and the nitrogen atom which is capable of acting as a hydrogen bond donor. The introduction of an amino group into the indole moiety of Trp yields the structural analogs 4-aminotryptophan ((4-NH(2))Trp) and 5-aminotryptophan ((5-NH(2))Trp). Their hydrophobicity and spectral properties are substantially different when compared to those of Trp. They resemble the purine bases of DNA and share their capacity for pH-sensitive intramolecular charge transfer. The Trp --> aminotryptophan substitution in proteins during ribosomal translation is expected to result in related protein variants that acquire these features. These expectations have been fulfilled by incorporating (4-NH(2))Trp and (5-NH(2))Trp into barstar, an intracellular inhibitor of the ribonuclease barnase from Bacillus amyloliquefaciens. The crystal structure of (4-NH(2))Trp-barstar is similar to that of the parent protein, whereas its spectral and thermodynamic behavior is found to be remarkably different. The T(m) value of (4-NH(2))Trp- and (5-NH(2))Trp-barstar is lowered by about 20 degrees Celsius, and they exhibit a strongly reduced unfolding cooperativity and substantial loss of free energy in folding. Furthermore, folding kinetic study of (4-NH(2))Trp-barstar revealed that the denatured state is even preferred over native one. The combination of structural and thermodynamic analyses clearly shows how structures of substituted barstar display a typical structure-function tradeoff: the acquirement of unique pH-sensitive charge transfer as a novel function is achieved at the expense of protein stability. These findings provide a new insight into the evolution of the amino acid repertoire of the universal genetic code and highlight possible problems regarding protein engineering and design by using an expanded genetic code.

Revisiting the TALE repeat.

PubMed

Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

2014-04-01

Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

Vibrational Fingerprints of Low-Lying Pt(n)P(2n) (n = 1-5) Cluster Structures from Global Optimization Based on Density Functional Theory Potential Energy Surfaces.

PubMed

Jedidi, Abdesslem; Li, Rui; Fornasiero, Paolo; Cavallo, Luigi; Carbonniere, Philippe

2015-12-03

Vibrational fingerprints of small Pt(n)P(2n) (n = 1-5) clusters were computed from their low-lying structures located from a global exploration of their DFT potential energy surfaces with the GSAM code. Five DFT methods were assessed from the CCSD(T) wavenumbers of PtP2 species and CCSD relative energies of Pt2P4 structures. The eight first Pt(n)P(2n) isomers found are reported. The vibrational computations reveal (i) the absence of clear signatures made by overtone or combination bands due to very weak mechanical and electrical anharmonicities and (ii) some significant and recurrent vibrational fingerprints in correlation with the different PP bonding situations in the Pt(n)P(2n) structures.

Crystal structure and confirmation of the alanine:glyoxylate aminotransferase activity of the YFL030w yeast protein.

PubMed

Meyer, Philippe; Liger, Dominique; Leulliot, Nicolas; Quevillon-Cheruel, Sophie; Zhou, Cong-Zhao; Borel, Franck; Ferrer, Jean-Luc; Poupon, Anne; Janin, Joël; van Tilbeurgh, Herman

2005-12-01

We have determined the three-dimensional crystal structure of the protein encoded by the open reading frame YFL030w from Saccharomyces cerevisiae to a resolution of 2.6 A using single wavelength anomalous diffraction. YFL030w is a 385 amino-acid protein with sequence similarity to the aminotransferase family. The structure of the protein reveals a homodimer adopting the fold-type I of pyridoxal 5'-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure. The protein shows close structural resemblance with the human alanine:glyoxylate aminotransferase (EC 2.6.1.44), an enzyme involved in the hereditary kidney stone disease primary hyperoxaluria type 1. In this paper we show that YFL030w codes for an alanine:glyoxylate aminotransferase, highly specific for its amino donor and acceptor substrates.

Atomic structure of the Y complex of the nuclear pore

DOE PAGES

Kelley, Kotaro; Knockenhauer, Kevin E.; Kabachinski, Greg; ...

2015-03-30

The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. In this paper, we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved coremore » of the Y complex has six rather than seven members. Finally, evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.« less

Algorithm 782 : codes for rank-revealing QR factorizations of dense matrices.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bischof, C. H.; Quintana-Orti, G.; Mathematics and Computer Science

1998-06-01

This article describes a suite of codes as well as associated testing and timing drivers for computing rank-revealing QR (RRQR) factorizations of dense matrices. The main contribution is an efficient block algorithm for approximating an RRQR factorization, employing a windowed version of the commonly used Golub pivoting strategy and improved versions of the RRQR algorithms for triangular matrices originally suggested by Chandrasekaran and Ipsen and by Pan and Tang, respectively, We highlight usage and features of these codes.

RNA Structures as Mediators of Neurological Diseases and as Drug Targets.

PubMed

Bernat, Viachaslau; Disney, Matthew D

2015-07-01

RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics. Copyright © 2015 Elsevier Inc. All rights reserved.

Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.

PubMed

Kuroshu, Reginaldo M; Watanabe, Junichi; Sugano, Sumio; Morishita, Shinichi; Suzuki, Yutaka; Kasahara, Masahiro

2010-05-07

Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence approximately 800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only approximately US$3 per clone, demonstrating a significant advantage over previous approaches.

Development of advanced structural analysis methodologies for predicting widespread fatigue damage in aircraft structures

NASA Technical Reports Server (NTRS)

Harris, Charles E.; Starnes, James H., Jr.; Newman, James C., Jr.

1995-01-01

NASA is developing a 'tool box' that includes a number of advanced structural analysis computer codes which, taken together, represent the comprehensive fracture mechanics capability required to predict the onset of widespread fatigue damage. These structural analysis tools have complementary and specialized capabilities ranging from a finite-element-based stress-analysis code for two- and three-dimensional built-up structures with cracks to a fatigue and fracture analysis code that uses stress-intensity factors and material-property data found in 'look-up' tables or from equations. NASA is conducting critical experiments necessary to verify the predictive capabilities of the codes, and these tests represent a first step in the technology-validation and industry-acceptance processes. NASA has established cooperative programs with aircraft manufacturers to facilitate the comprehensive transfer of this technology by making these advanced structural analysis codes available to industry.

Long Non-Coding RNAs (lncRNAs) of Sea Cucumber: Large-Scale Prediction, Expression Profiling, Non-Coding Network Construction, and lncRNA-microRNA-Gene Interaction Analysis of lncRNAs in Apostichopus japonicus and Holothuria glaberrima During LPS Challenge and Radial Organ Complex Regeneration.

PubMed

Mu, Chuang; Wang, Ruijia; Li, Tianqi; Li, Yuqiang; Tian, Meilin; Jiao, Wenqian; Huang, Xiaoting; Zhang, Lingling; Hu, Xiaoli; Wang, Shi; Bao, Zhenmin

2016-08-01

Long non-coding RNA (lncRNA) structurally resembles mRNA but cannot be translated into protein. Although the systematic identification and characterization of lncRNAs have been increasingly reported in model species, information concerning non-model species is still lacking. Here, we report the first systematic identification and characterization of lncRNAs in two sea cucumber species: (1) Apostichopus japonicus during lipopolysaccharide (LPS) challenge and in heathy tissues and (2) Holothuria glaberrima during radial organ complex regeneration, using RNA-seq datasets and bioinformatics analysis. We identified A. japonicus and H. glaberrima lncRNAs that were differentially expressed during LPS challenge and radial organ complex regeneration, respectively. Notably, the predicted lncRNA-microRNA-gene trinities revealed that, in addition to targeting protein-coding transcripts, miRNAs might also target lncRNAs, thereby participating in a potential novel layer of regulatory interactions among non-coding RNA classes in echinoderms. Furthermore, the constructed coding-non-coding network implied the potential involvement of lncRNA-gene interactions during the regulation of several important genes (e.g., Toll-like receptor 1 [TLR1] and transglutaminase-1 [TGM1]) in response to LPS challenge and radial organ complex regeneration in sea cucumbers. Overall, this pioneer systematic identification, annotation, and characterization of lncRNAs in echinoderm pave the way for similar studies and future genetic, genomic, and evolutionary research in non-model species.

Coding of Class I and II aminoacyl-tRNA synthetases

PubMed Central

Carter, Charles W.

2018-01-01

SUMMARY The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene. Parallel experimental deconstructions of Class I and II synthetases reveal parallel losses in catalytic proficiency at two novel modular levels—protozymes and Urzymes—associated with the evolution of catalytic activity. Bi-directional coding supports an important unification of the proteome; affords a genetic relatedness metric—middle base-pairing frequencies in sense/antisense alignments—that probes more deeply into the evolutionary history of translation than do single multiple sequence alignments; and has facilitated the analysis of hitherto unknown coding relationships in tRNA sequences. Reconstruction of native synthetases by modular thermodynamic cycles facilitated by domain engineering emphasizes the subtlety associated with achieving high specificity, shedding new light on allosteric relationships in contemporary synthetases. Synthetase Urzyme structural biology suggests that they are catalytically active molten globules, broadening the potential manifold of polypeptide catalysts accessible to primitive genetic coding and motivating revisions of the origins of catalysis. Finally, bi-directional genetic coding of some of the oldest genes in the proteome places major limitations on the likelihood that any RNA World preceded the origins of coded proteins. PMID:28828732

The 2012 Ferrara seismic sequence: Regional crustal structure, earthquake sources, and seismic hazard

NASA Astrophysics Data System (ADS)

Malagnini, Luca; Herrmann, Robert B.; Munafò, Irene; Buttinelli, Mauro; Anselmi, Mario; Akinci, Aybige; Boschi, E.

2012-10-01

Inadequate seismic design codes can be dangerous, particularly when they underestimate the true hazard. In this study we use data from a sequence of moderate-sized earthquakes in northeast Italy to validate and test a regional wave propagation model which, in turn, is used to understand some weaknesses of the current design spectra. Our velocity model, while regionalized and somewhat ad hoc, is consistent with geophysical observations and the local geology. In the 0.02-0.1 Hz band, this model is validated by using it to calculate moment tensor solutions of 20 earthquakes (5.6 ≥ MW ≥ 3.2) in the 2012 Ferrara, Italy, seismic sequence. The seismic spectra observed for the relatively small main shock significantly exceeded the design spectra to be used in the area for critical structures. Observations and synthetics reveal that the ground motions are dominated by long-duration surface waves, which, apparently, the design codes do not adequately anticipate. In light of our results, the present seismic hazard assessment in the entire Pianura Padana, including the city of Milan, needs to be re-evaluated.

Chromosomal localization and partial genomic structure of the human peroxisome proliferator activated receptor-gamma (hPPAR gamma) gene.

PubMed

Beamer, B A; Negri, C; Yen, C J; Gavrilova, O; Rumberger, J M; Durcan, M J; Yarnall, D P; Hawkins, A L; Griffin, C A; Burns, D K; Roth, J; Reitman, M; Shuldiner, A R

1997-04-28

We determined the chromosomal localization and partial genomic structure of the coding region of the human PPAR gamma gene (hPPAR gamma), a nuclear receptor important for adipocyte differentiation and function. Sequence analysis and long PCR of human genomic DNA with primers that span putative introns revealed that intron positions and sizes of hPPAR gamma are similar to those previously determined for the mouse PPAR gamma gene[13]. Fluorescent in situ hybridization localized hPPAR gamma to chromosome 3, band 3p25. Radiation hybrid mapping with two independent primer pairs was consistent with hPPAR gamma being within 1.5 Mb of marker D3S1263 on 3p25-p24.2. These sequences of the intron/exon junctions of the 6 coding exons shared by hPPAR gamma 1 and hPPAR gamma 2 will facilitate screening for possible mutations. Furthermore, D3S1263 is a suitable polymorphic marker for linkage analysis to evaluate PPAR gamma's potential contribution to genetic susceptibility to obesity, lipoatrophy, insulin resistance, and diabetes.

Using cellular automata to generate image representation for biological sequences.

PubMed

Xiao, X; Shao, S; Ding, Y; Huang, Z; Chen, X; Chou, K-C

2005-02-01

A novel approach to visualize biological sequences is developed based on cellular automata (Wolfram, S. Nature 1984, 311, 419-424), a set of discrete dynamical systems in which space and time are discrete. By transforming the symbolic sequence codes into the digital codes, and using some optimal space-time evolvement rules of cellular automata, a biological sequence can be represented by a unique image, the so-called cellular automata image. Many important features, which are originally hidden in a long and complicated biological sequence, can be clearly revealed thru its cellular automata image. With biological sequences entering into databanks rapidly increasing in the post-genomic era, it is anticipated that the cellular automata image will become a very useful vehicle for investigation into their key features, identification of their function, as well as revelation of their "fingerprint". It is anticipated that by using the concept of the pseudo amino acid composition (Chou, K.C. Proteins: Structure, Function, and Genetics, 2001, 43, 246-255), the cellular automata image approach can also be used to improve the quality of predicting protein attributes, such as structural class and subcellular location.

Momentary Patterns of Covariation between Specific Affects and Interpersonal Behavior: Linking Relationship Science and Personality Assessment

PubMed Central

Ross, Jaclyn M.; Girard, Jeffrey M.; Wright, Aidan G.C.; Beeney, Joseph E.; Scott, Lori N.; Hallquist, Michael N.; Lazarus, Sophie A.; Stepp, Stephanie D.; Pilkonis, Paul A.

2016-01-01

Relationships are among the most salient factors affecting happiness and wellbeing for individuals and families. Relationship science has identified the study of dyadic behavioral patterns between couple members during conflict as an important window in to relational functioning with both short-term and long-term consequences. Several methods have been developed for the momentary assessment of behavior during interpersonal transactions. Among these, the most popular is the Specific Affect Coding System (SPAFF), which organizes social behavior into a set of discrete behavioral constructs. This study examines the interpersonal meaning of the SPAFF codes through the lens of interpersonal theory, which uses the fundamental dimensions of Dominance and Affiliation to organize interpersonal behavior. A sample of 67 couples completed a conflict task, which was video recorded and coded using SPAFF and a method for rating momentary interpersonal behavior, the Continuous Assessment of Interpersonal Dynamics (CAID). Actor partner interdependence models in a multilevel structural equation modeling framework were used to study the covariation of SPAFF codes and CAID ratings. Results showed that a number of SPAFF codes had clear interpersonal signatures, but many did not. Additionally, actor and partner effects for the same codes were strongly consistent with interpersonal theory’s principle of complementarity. Thus, findings reveal points of convergence and divergence in the two systems and provide support for central tenets of interpersonal theory. Future directions based on these initial findings are discussed. PMID:27148786

Momentary patterns of covariation between specific affects and interpersonal behavior: Linking relationship science and personality assessment.

PubMed

Ross, Jaclyn M; Girard, Jeffrey M; Wright, Aidan G C; Beeney, Joseph E; Scott, Lori N; Hallquist, Michael N; Lazarus, Sophie A; Stepp, Stephanie D; Pilkonis, Paul A

2017-02-01

Relationships are among the most salient factors affecting happiness and wellbeing for individuals and families. Relationship science has identified the study of dyadic behavioral patterns between couple members during conflict as an important window in to relational functioning with both short-term and long-term consequences. Several methods have been developed for the momentary assessment of behavior during interpersonal transactions. Among these, the most popular is the Specific Affect Coding System (SPAFF), which organizes social behavior into a set of discrete behavioral constructs. This study examines the interpersonal meaning of the SPAFF codes through the lens of interpersonal theory, which uses the fundamental dimensions of Dominance and Affiliation to organize interpersonal behavior. A sample of 67 couples completed a conflict task, which was video recorded and coded using SPAFF and a method for rating momentary interpersonal behavior, the Continuous Assessment of Interpersonal Dynamics (CAID). Actor partner interdependence models in a multilevel structural equation modeling framework were used to study the covariation of SPAFF codes and CAID ratings. Results showed that a number of SPAFF codes had clear interpersonal signatures, but many did not. Additionally, actor and partner effects for the same codes were strongly consistent with interpersonal theory's principle of complementarity. Thus, findings reveal points of convergence and divergence in the 2 systems and provide support for central tenets of interpersonal theory. Future directions based on these initial findings are discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

CELFE/NASTRAN Code for the Analysis of Structures Subjected to High Velocity Impact

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1978-01-01

CELFE (Coupled Eulerian Lagrangian Finite Element)/NASTRAN Code three-dimensional finite element code has the capability for analyzing of structures subjected to high velocity impact. The local response is predicted by CELFE and, for large problems, the far-field impact response is predicted by NASTRAN. The coupling of the CELFE code with NASTRAN (CELFE/NASTRAN code) and the application of the code to selected three-dimensional high velocity impact problems are described.

Error-correction coding for digital communications

NASA Astrophysics Data System (ADS)

Clark, G. C., Jr.; Cain, J. B.

This book is written for the design engineer who must build the coding and decoding equipment and for the communication system engineer who must incorporate this equipment into a system. It is also suitable as a senior-level or first-year graduate text for an introductory one-semester course in coding theory. Fundamental concepts of coding are discussed along with group codes, taking into account basic principles, practical constraints, performance computations, coding bounds, generalized parity check codes, polynomial codes, and important classes of group codes. Other topics explored are related to simple nonalgebraic decoding techniques for group codes, soft decision decoding of block codes, algebraic techniques for multiple error correction, the convolutional code structure and Viterbi decoding, syndrome decoding techniques, and sequential decoding techniques. System applications are also considered, giving attention to concatenated codes, coding for the white Gaussian noise channel, interleaver structures for coded systems, and coding for burst noise channels.

Design of convolutional tornado code

NASA Astrophysics Data System (ADS)

Zhou, Hui; Yang, Yao; Gao, Hongmin; Tan, Lu

2017-09-01

As a linear block code, the traditional tornado (tTN) code is inefficient in burst-erasure environment and its multi-level structure may lead to high encoding/decoding complexity. This paper presents a convolutional tornado (cTN) code which is able to improve the burst-erasure protection capability by applying the convolution property to the tTN code, and reduce computational complexity by abrogating the multi-level structure. The simulation results show that cTN code can provide a better packet loss protection performance with lower computation complexity than tTN code.

Analysis of the complete genome of the first Irkut virus isolate from China: comparison across the Lyssavirus genus.

PubMed

Liu, Ye; Li, Nan; Zhang, Shoufeng; Zhang, Fei; Lian, Hai; Wang, Ying; Zhang, Jinxia; Hu, Rongliang

2013-12-01

The genome of Irkut virus, isolate IRKV-THChina12, the first non-rabies lyssavirus from China (of bat origin), has been completely sequenced. In general, coding and non-coding regions of this viral genome are similar to those of other lyssaviruses. However, alignment of the deduced amino acid sequences of the structural proteins of IRKV-THChina12 with those of other lyssavirus representatives revealed significant variability between viral species. The nucleoprotein and matrix protein were found to be the most conserved, followed by the large protein, glycoprotein and phosphoprotein. Differences in the antigenic sites in glycoprotein may result in only partial protection of the available rabies biologics against Irkut virus, which is of particular concern for pre- and post-exposure rabies prophylaxis. Copyright © 2013 Elsevier Inc. All rights reserved.

Linear and Nonlinear Statistical Characterization of DNA

NASA Astrophysics Data System (ADS)

Norio Oiwa, Nestor; Goldman, Carla; Glazier, James

2002-03-01

We find spatial order in the distribution of protein-coding (including RNAs) and control segments of GenBank genomic sequences, irrespective of ATCG content. This is achieved by correlations, histograms, fractal dimensions and singularity spectra. Estimates of these quantities in complete nuclear genome indicate that coding sequences are long-range correlated and their disposition are self-similar (multifractal) for eukaryotes. These characteristics are absent in prokaryotes, where there are few noncoding sequences, suggesting the `junk' DNA play a relevant role to the genome structure and function. Concerning the genetic message of ATCG sequences, we build a random walk (Levy flight), using DNA symmetry arguments, where we associate A, T, C and G as left, right, down and up steps, respectively. Nonlinear analysis of mitochondrial DNA walks reveal multifractal pattern based on palindromic sequences, which fold in hairpins and loops.

Computational multispectral video imaging [Invited].

PubMed

Wang, Peng; Menon, Rajesh

2018-01-01

Multispectral imagers reveal information unperceivable to humans and conventional cameras. Here, we demonstrate a compact single-shot multispectral video-imaging camera by placing a micro-structured diffractive filter in close proximity to the image sensor. The diffractive filter converts spectral information to a spatial code on the sensor pixels. Following a calibration step, this code can be inverted via regularization-based linear algebra to compute the multispectral image. We experimentally demonstrated spectral resolution of 9.6 nm within the visible band (430-718 nm). We further show that the spatial resolution is enhanced by over 30% compared with the case without the diffractive filter. We also demonstrate Vis-IR imaging with the same sensor. Because no absorptive color filters are utilized, sensitivity is preserved as well. Finally, the diffractive filters can be easily manufactured using optical lithography and replication techniques.

Implementing Nepal's national building code—A case study in patience and persistence

USGS Publications Warehouse

Arendt, Lucy; Hortacsu, Ayse; Jaiswal, Kishor; Bevington, John; Shrestha, Surya; Lanning, Forrest; Mentor-William, Garmalia; Naeem, Ghazala; Thibert, Kate

2017-01-01

The April 2015 Gorkha Nepal earthquake revealed the relative effectiveness of the Nepal Standard, or national building code (NBC), and irregular compliance with it in different parts of Nepal. Much of the damage to more than half a million Nepal's residential structures may be attributed to the prevalence of owner-built or owner-supervised construction and the lack of owner and builder responsiveness to seismic risk and training in the appropriate means of complying with the NBC. To explain these circumstances, we review the protracted implementation of the NBC and the role played by one organization, the National Society for Earthquake Technology-Nepal (NSET), in the NBC's implementation. We also share observations on building code compliance made by individuals in Nepal participating in workshops led by the Earthquake Engineering Research Institute's 2014 class of Housner Fellows.

Genome-wide screening and identification of long noncoding RNAs and their interaction with protein coding RNAs in bladder urothelial cell carcinoma.

PubMed

Wang, Longxin; Fu, Dian; Qiu, Yongbin; Xing, Xiaoxiao; Xu, Feng; Han, Conghui; Xu, Xiaofeng; Wei, Zhifeng; Zhang, Zhengyu; Ge, Jingping; Cheng, Wen; Xie, Hai-Long

2014-07-10

To understand lncRNAs expression profiling and their potential functions in bladder cancer, we investigated the lncRNA and coding RNA expression on human bladder cancer and normal bladder tissues. Bioinformatic analysis revealed thousands of significantly differentially expressed lncRNAs and coding mRNA in bladder cancer relative to normal bladder tissue. Co-expression analysis revealed that 50% of lncRNAs and coding RNAs expressed in the same direction. A subset of lncRNAs might be involved in mTOR signaling, p53 signaling, cancer pathways. Our study provides a large scale of co-expression between lncRNA and coding RNAs in bladder cancer cells and lays biological basis for further investigation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Oblique shock structures formed during the ablation phase of aluminium wire array z-pinches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swadling, G. F.; Lebedev, S. V.; Niasse, N.

A series of experiments has been conducted in order to investigate the azimuthal structures formed by the interactions of cylindrically converging plasma flows during the ablation phase of aluminium wire array Z pinch implosions. These experiments were carried out using the 1.4 MA, 240 ns MAGPIE generator at Imperial College London. The main diagnostic used in this study was a two-colour, end-on, Mach-Zehnder imaging interferometer, sensitive to the axially integrated electron density of the plasma. The data collected in these experiments reveal the strongly collisional dynamics of the aluminium ablation streams. The structure of the flows is dominated by amore » dense network of oblique shock fronts, formed by supersonic collisions between adjacent ablation streams. An estimate for the range of the flow Mach number (M = 6.2-9.2) has been made based on an analysis of the observed shock geometry. Combining this measurement with previously published Thomson Scattering measurements of the plasma flow velocity by Harvey-Thompson et al.[Physics of Plasmas 19, 056303 (2012)] allowed us to place limits on the range of the ZT{sub e} of the plasma. The detailed and quantitative nature of the dataset lends itself well as a source for model validation and code verification exercises, as the exact shock geometry is sensitive to many of the plasma parameters. Comparison of electron density data produced through numerical modelling with the Gorgon 3D MHD code demonstrates that the code is able to reproduce the collisional dynamics observed in aluminium arrays reasonably well.« less

Definitions and codes for seral status and structure of vegetation.

Treesearch

Frederick C. Hall; Larry Bryant; Rod Clausnitzer; Kathy Geier-Hayes; Robert Keane; Jane Kertis; Ayn Shlisky; Robert Steel

1995-01-01

Definitions and codes for identifying vegetation seral status and structure are desired for land management planning, appraising wildlife habitat, and prescribing vegetation treatment. Codes are only presented; they are not a system for determining seral status or stand structure. Terms defined are climax, potential natural community (PNC), succession, seral status,...

Investigation of structural, electronic, elastic and optical properties of Cd{sub 1-x-y}Zn{sub x}Hg{sub y}Te alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamer, M., E-mail: mehmet.tamer@zirve.edu.tr

2016-06-15

Structural, optical and electronic properties and elastic constants of Cd1{sub -x-y}Zn{sub x} Hg{sub y}Te alloys have been studied by employing the commercial code Castep based on density functional theory. The generalized gradient approximation and local density approximation were utilized as exchange correlation. Using elastic constants for compounds, bulk modulus, band gap, Fermi energy and Kramers–Kronig relations, dielectric constants and the refractive index have been found through calculations. Apart from these, X-ray measurements revealed elastic constants and Vegard’s law. It is seen that results obtained from theory and experiments are all in agreement.

The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species.

PubMed

Chen, Caihui; Zheng, Yongjie; Liu, Sian; Zhong, Yongda; Wu, Yanfang; Li, Jiang; Xu, Li-An; Xu, Meng

2017-01-01

Cinnamomum camphora , a member of the Lauraceae family, is a valuable aromatic and timber tree that is indigenous to the south of China and Japan. All parts of Cinnamomum camphora have secretory cells containing different volatile chemical compounds that are utilized as herbal medicines and essential oils. Here, we reported the complete sequencing of the chloroplast genome of Cinnamomum camphora using illumina technology. The chloroplast genome of Cinnamomum camphora is 152,570 bp in length and characterized by a relatively conserved quadripartite structure containing a large single copy region of 93,705 bp, a small single copy region of 19,093 bp and two inverted repeat (IR) regions of 19,886 bp. Overall, the genome contained 123 coding regions, of which 15 were repeated in the IR regions. An analysis of chloroplast sequence divergence revealed that the small single copy region was highly variable among the different genera in the Lauraceae family. A total of 40 repeat structures and 83 simple sequence repeats were detected in both the coding and non-coding regions. A phylogenetic analysis indicated that Calycanthus is most closely related to Lauraceae , both being members of Laurales , which forms a sister group to Magnoliids . The complete sequence of the chloroplast of Cinnamomum camphora will aid in in-depth taxonomical studies of the Lauraceae family in the future. The genetic sequence information will also have valuable applications for chloroplast genetic engineering.

Mediator directs co-transcriptional heterochromatin assembly by RNA interference-dependent and -independent pathways.

PubMed

Oya, Eriko; Kato, Hiroaki; Chikashige, Yuji; Tsutsumi, Chihiro; Hiraoka, Yasushi; Murakami, Yota

2013-01-01

Heterochromatin at the pericentromeric repeats in fission yeast is assembled and spread by an RNAi-dependent mechanism, which is coupled with the transcription of non-coding RNA from the repeats by RNA polymerase II. In addition, Rrp6, a component of the nuclear exosome, also contributes to heterochromatin assembly and is coupled with non-coding RNA transcription. The multi-subunit complex Mediator, which directs initiation of RNA polymerase II-dependent transcription, has recently been suggested to function after initiation in processes such as elongation of transcription and splicing. However, the role of Mediator in the regulation of chromatin structure is not well understood. We investigated the role of Mediator in pericentromeric heterochromatin formation and found that deletion of specific subunits of the head domain of Mediator compromised heterochromatin structure. The Mediator head domain was required for Rrp6-dependent heterochromatin nucleation at the pericentromere and for RNAi-dependent spreading of heterochromatin into the neighboring region. In the latter process, Mediator appeared to contribute to efficient processing of siRNA from transcribed non-coding RNA, which was required for efficient spreading of heterochromatin. Furthermore, the head domain directed efficient transcription in heterochromatin. These results reveal a pivotal role for Mediator in multiple steps of transcription-coupled formation of pericentromeric heterochromatin. This observation further extends the role of Mediator to co-transcriptional chromatin regulation.

Whole-genome landscapes of major melanoma subtypes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayward, Nicholas K.; Wilmott, James S.; Waddell, Nicola

Melanoma of the skin is a common cancer only in Europeans, whereas it arises in internal body surfaces (mucosal sites) and on the hands and feet (acral sites) in people throughout the world. We report analysis of whole-genome sequences from cutaneous, acral and mucosal subtypes of melanoma. The heavily mutated landscape of coding and non-coding mutations in cutaneous melanoma resolved novel signatures of mutagenesis attributable to ultraviolet radiation. But, acral and mucosal melanomas were dominated by structural changes and mutation signatures of unknown aetiology, not previously identified in melanoma. The number of genes affected by recurrent mutations disrupting non-coding sequencesmore » was similar to that affected by recurrent mutations to coding sequences. Significantly mutated genes included BRAF, CDKN2A, NRAS and TP53 in cutaneous melanoma, BRAF, NRAS and NF1 in acral melanoma and SF3B1 in mucosal melanoma. Mutations affecting the TERT promoter were the most frequent of all; however, neither they nor ATRX mutations, which correlate with alternative telomere lengthening, were associated with greater telomere length. In most cases, melanomas had potentially actionable mutations, most in components of the mitogen-activated protein kinase and phosphoinositol kinase pathways. The whole-genome mutation landscape of melanoma reveals diverse carcinogenic processes across its subtypes, some unrelated to sun exposure, and extends potential involvement of the non-coding genome in its pathogenesis.« less

Whole-genome landscapes of major melanoma subtypes

DOE PAGES

Hayward, Nicholas K.; Wilmott, James S.; Waddell, Nicola; ...

2017-05-03

Melanoma of the skin is a common cancer only in Europeans, whereas it arises in internal body surfaces (mucosal sites) and on the hands and feet (acral sites) in people throughout the world. We report analysis of whole-genome sequences from cutaneous, acral and mucosal subtypes of melanoma. The heavily mutated landscape of coding and non-coding mutations in cutaneous melanoma resolved novel signatures of mutagenesis attributable to ultraviolet radiation. But, acral and mucosal melanomas were dominated by structural changes and mutation signatures of unknown aetiology, not previously identified in melanoma. The number of genes affected by recurrent mutations disrupting non-coding sequencesmore » was similar to that affected by recurrent mutations to coding sequences. Significantly mutated genes included BRAF, CDKN2A, NRAS and TP53 in cutaneous melanoma, BRAF, NRAS and NF1 in acral melanoma and SF3B1 in mucosal melanoma. Mutations affecting the TERT promoter were the most frequent of all; however, neither they nor ATRX mutations, which correlate with alternative telomere lengthening, were associated with greater telomere length. In most cases, melanomas had potentially actionable mutations, most in components of the mitogen-activated protein kinase and phosphoinositol kinase pathways. The whole-genome mutation landscape of melanoma reveals diverse carcinogenic processes across its subtypes, some unrelated to sun exposure, and extends potential involvement of the non-coding genome in its pathogenesis.« less

Wheat CBF gene family: identification of polymorphisms in the CBF coding sequence.

PubMed

Mohseni, Sara; Che, Hua; Djillali, Zakia; Dumont, Estelle; Nankeu, Joseph; Danyluk, Jean

2012-12-01

Expression of cold-regulated genes needed for protection against freezing stress is mediated, in part, by the CBF transcription factor family. Previous studies with temperate cereals suggested that the CBF gene family in wheat was large, and that CBF genes were at the base of an important low temperature tolerance trait. Therefore, the goal of our study was to identify the CBF repertoire in the freezing-tolerant hexaploid wheat cultivar Norstar, and then to examine if the coding region of CBF genes in two spring cultivars contain polymorphisms that could affect the protein sequence and structure. Our analyses reveal that hexaploid wheat contains a complex CBF family consisting of at least 65 CBF genes of which 60 are known to be expressed in the cultivar Norstar. They represent 27 paralogous genes with 1-3 homeologous copies for the A, B, and D genomes. The cultivar Norstar contains two pseudogenes and at least 24 additional proteins having sequences and (or) structures that deviate from the consensus in the conserved AP2 DNA-binding and (or) C-terminal activation-domains. This suggests that in cultivars such as Norstar, low temperature tolerance may be increased through breeding of additional optimal alleles. The examination of the CBF repertoire present in the two spring cultivars, Chinese Spring and Manitou, reveals that they have additional polymorphisms affecting conserved positions in these domains. Understanding the effects of these polymorphisms will provide additional information for the selection of optimum CBF alleles in Triticeae breeding programs.

Comparative Mitogenomics of the Assassin Bug Genus Peirates (Hemiptera: Reduviidae: Peiratinae) Reveal Conserved Mitochondrial Genome Organization of P. atromaculatus, P. fulvescens and P. turpis

PubMed Central

Zhao, Guangyu; Li, Hu; Zhao, Ping; Cai, Wanzhi

2015-01-01

In this study, we sequenced four new mitochondrial genomes and presented comparative mitogenomic analyses of five species in the genus Peirates (Hemiptera: Reduviidae). Mitochondrial genomes of these five assassin bugs had a typical set of 37 genes and retained the ancestral gene arrangement of insects. The A+T content, AT- and GC-skews were similar to the common base composition biases of insect mtDNA. Genomic size ranges from 15,702 bp to 16,314 bp and most of the size variation was due to length and copy number of the repeat unit in the putative control region. All of the control region sequences included large tandem repeats present in two or more copies. Our result revealed similarity in mitochondrial genomes of P. atromaculatus, P. fulvescens and P. turpis, as well as the highly conserved genomic-level characteristics of these three species, e.g., the same start and stop codons of protein-coding genes, conserved secondary structure of tRNAs, identical location and length of non-coding and overlapping regions, and conservation of structural elements and tandem repeat unit in control region. Phylogenetic analyses also supported a close relationship between P. atromaculatus, P. fulvescens and P. turpis, which might be recently diverged species. The present study indicates that mitochondrial genome has important implications on phylogenetics, population genetics and speciation in the genus Peirates. PMID:25689825

Orientation Dependence of the Deformation Microstructure of Ta-4%W after Cold-Rolling

NASA Astrophysics Data System (ADS)

Zhang, J.; Ma, G. Q.; Godfrey, A.; Shu, D. Y.; Chen, Q.; Wu, G. L.

2017-07-01

One of the common features of deformed face-centered cubic metals with medium to high stacking fault energy is the formation of geometrically necessary dislocation boundaries. The dislocation boundary arrangements in refractory metals with body-centered cubic crystal structure are, however, less well known. To address this issue a Ta-4%W alloy was cold rolled up to 70% in thickness in the present work. The resulting deformation microstructures were characterized by electron back-scattering diffraction and the dislocation boundary arrangements in each grain were revealed using sample-frame misorientation axis maps calculated using an in-house code. The maps were used to analyze the slip pattern of individual grains after rolling, revealing an orientation dependence of the slip pattern.

Comparative genomics reveals insights into avian genome evolution and adaptation

PubMed Central

Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

2015-01-01

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

A qualitative study of DRG coding practice in hospitals under the Thai Universal Coverage scheme.

PubMed

Pongpirul, Krit; Walker, Damian G; Winch, Peter J; Robinson, Courtland

2011-04-08

In the Thai Universal Coverage health insurance scheme, hospital providers are paid for their inpatient care using Diagnosis Related Group-based retrospective payment, for which quality of the diagnosis and procedure codes is crucial. However, there has been limited understandings on which health care professions are involved and how the diagnosis and procedure coding is actually done within hospital settings. The objective of this study is to detail hospital coding structure and process, and to describe the roles of key hospital staff, and other related internal dynamics in Thai hospitals that affect quality of data submitted for inpatient care reimbursement. Research involved qualitative semi-structured interview with 43 participants at 10 hospitals chosen to represent a range of hospital sizes (small/medium/large), location (urban/rural), and type (public/private). Hospital Coding Practice has structural and process components. While the structural component includes human resources, hospital committee, and information technology infrastructure, the process component comprises all activities from patient discharge to submission of the diagnosis and procedure codes. At least eight health care professional disciplines are involved in the coding process which comprises seven major steps, each of which involves different hospital staff: 1) Discharge Summarization, 2) Completeness Checking, 3) Diagnosis and Procedure Coding, 4) Code Checking, 5) Relative Weight Challenging, 6) Coding Report, and 7) Internal Audit. The hospital coding practice can be affected by at least five main factors: 1) Internal Dynamics, 2) Management Context, 3) Financial Dependency, 4) Resource and Capacity, and 5) External Factors. Hospital coding practice comprises both structural and process components, involves many health care professional disciplines, and is greatly varied across hospitals as a result of five main factors.

A qualitative study of DRG coding practice in hospitals under the Thai Universal Coverage Scheme

PubMed Central

2011-01-01

Background In the Thai Universal Coverage health insurance scheme, hospital providers are paid for their inpatient care using Diagnosis Related Group-based retrospective payment, for which quality of the diagnosis and procedure codes is crucial. However, there has been limited understandings on which health care professions are involved and how the diagnosis and procedure coding is actually done within hospital settings. The objective of this study is to detail hospital coding structure and process, and to describe the roles of key hospital staff, and other related internal dynamics in Thai hospitals that affect quality of data submitted for inpatient care reimbursement. Methods Research involved qualitative semi-structured interview with 43 participants at 10 hospitals chosen to represent a range of hospital sizes (small/medium/large), location (urban/rural), and type (public/private). Results Hospital Coding Practice has structural and process components. While the structural component includes human resources, hospital committee, and information technology infrastructure, the process component comprises all activities from patient discharge to submission of the diagnosis and procedure codes. At least eight health care professional disciplines are involved in the coding process which comprises seven major steps, each of which involves different hospital staff: 1) Discharge Summarization, 2) Completeness Checking, 3) Diagnosis and Procedure Coding, 4) Code Checking, 5) Relative Weight Challenging, 6) Coding Report, and 7) Internal Audit. The hospital coding practice can be affected by at least five main factors: 1) Internal Dynamics, 2) Management Context, 3) Financial Dependency, 4) Resource and Capacity, and 5) External Factors. Conclusions Hospital coding practice comprises both structural and process components, involves many health care professional disciplines, and is greatly varied across hospitals as a result of five main factors. PMID:21477310

Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii.

PubMed

Zhu, Yan; Chen, Longxian; Zhang, Chengjun; Hao, Pei; Jing, Xinyun; Li, Xuan

2017-01-25

Selaginella moellendorffii, a lycophyte, is a model plant to study the early evolution and development of vascular plants. As the first and only sequenced lycophyte to date, the genome of S. moellendorffii revealed many conserved genes and pathways, as well as specialized genes different from flowering plants. Despite the progress made, little is known about long noncoding RNAs (lncRNA) and the alternative splicing (AS) of coding genes in S. moellendorffii. Its coding gene models have not been fully validated with transcriptome data. Furthermore, it remains important to understand whether the regulatory mechanisms similar to flowering plants are used, and how they operate in a non-seed primitive vascular plant. RNA-sequencing (RNA-seq) was performed for three S. moellendorffii tissues, root, stem, and leaf, by constructing strand-specific RNA-seq libraries from RNA purified using RiboMinus isolation protocol. A total of 176 million reads (44 Gbp) were obtained from three tissue types, and were mapped to S. moellendorffii genome. By comparing with 22,285 existing gene models of S. moellendorffii, we identified 7930 high-confidence novel coding genes (a 35.6% increase), and for the first time reported 4422 lncRNAs in a lycophyte. Further, we refined 2461 (11.0%) of existing gene models, and identified 11,030 AS events (for 5957 coding genes) revealed for the first time for lycophytes. Tissue-specific gene expression with functional implication was analyzed, and 1031, 554, and 269 coding genes, and 174, 39, and 17 lncRNAs were identified in root, stem, and leaf tissues, respectively. The expression of critical genes for vascular development stages, i.e. formation of provascular cells, xylem specification and differentiation, and phloem specification and differentiation, was compared in S. moellendorffii tissues, indicating a less complex regulatory mechanism in lycophytes than in flowering plants. The results were further strengthened by the evolutionary trend of seven transcription factor families related to vascular development, which was observed among four representative species of seed and non-seed vascular plants, and nonvascular land and aquatic plants. The deep RNA-seq study of S. moellendorffii discovered extensive new gene contents, including novel coding genes, lncRNAs, AS events, and refined gene models. Compared to flowering vascular plants, S. moellendorffii displayed a less complexity in both gene structure, alternative splicing, and regulatory elements of vascular development. The study offered important insight into the evolution of vascular plants, and the regulation mechanism of vascular development in a non-seed plant.

PDR MODEL MAPPING OF OBSCURED H{sub 2} EMISSION AND THE LINE-OF-SIGHT STRUCTURE OF M17-SW

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheffer, Y.; Wolfire, M. G.

2013-09-01

We observed H{sub 2} line emission with Spitzer-IRS toward M17-SW and modeled the data with our photon-dominated region (PDR) code. Derived gas density values of up to few times 10{sup 7} cm{sup -3} indicate that H{sub 2} emission originates in high-density clumps. We discover that the PDR code can be utilized to map the amount of intervening extinction obscuring the H{sub 2} emission layers, and thus we obtain the radial profile of A{sub V} relative to the central ionizing cluster NGC 6618. The extinction has a positive radial gradient, varying between 15-47 mag over the projected distance of 0.9-2.5 pcmore » from the primary ionizer, CEN 1. These high extinction values are in good agreement with previous studies of A{sub V} toward stellar targets in M17-SW. The ratio of data to PDR model values is used to infer the global line-of-sight structure of the PDR surface, which is revealed to resemble a concave surface relative to NGC 6618. Such a configuration confirms that this PDR can be described as a bowl-shaped boundary of the central H II region in M17. The derived structure and physical conditions are important for interpreting the fine-structure and rotational line emission from the PDR.« less

First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications

PubMed Central

Chen, Zhi-Teng; Du, Yu-Zhou

2017-01-01

The complete mitochondrial genome (mitogenome) of Nemoura nankinensis (Plecoptera: Nemouridae) was sequenced as the first reported mitogenome from the family Nemouridae. The N. nankinensis mitogenome was the longest (16,602 bp) among reported plecopteran mitogenomes, and it contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. Most PCGs used standard ATN as start codons, and TAN as termination codons. All tRNA genes of N. nankinensis could fold into the cloverleaf secondary structures except for trnSer (AGN), whose dihydrouridine (DHU) arm was reduced to a small loop. There was also a large non-coding region (control region, CR) in the N. nankinensis mitogenome. The 1751 bp CR was the longest and had the highest A+T content (81.8%) among stoneflies. A large tandem repeat region, five potential stem-loop (SL) structures, four tRNA-like structures and four conserved sequence blocks (CSBs) were detected in the elongated CR. The presence of these tRNA-like structures in the CR has never been reported in other plecopteran mitogenomes. These novel features of the elongated CR in N. nankinensis may have functions associated with the process of replication and transcription. Finally, phylogenetic reconstruction suggested that Nemouridae was the sister-group of Capniidae. PMID:28475163

First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications.

PubMed

Chen, Zhi-Teng; Du, Yu-Zhou

2017-05-05

The complete mitochondrial genome (mitogenome) of Nemoura nankinensis (Plecoptera: Nemouridae) was sequenced as the first reported mitogenome from the family Nemouridae. The N. nankinensis mitogenome was the longest (16,602 bp) among reported plecopteran mitogenomes, and it contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. Most PCGs used standard ATN as start codons, and TAN as termination codons. All tRNA genes of N. nankinensis could fold into the cloverleaf secondary structures except for trnSer ( AGN ), whose dihydrouridine (DHU) arm was reduced to a small loop. There was also a large non-coding region (control region, CR) in the N. nankinensis mitogenome. The 1751 bp CR was the longest and had the highest A+T content (81.8%) among stoneflies. A large tandem repeat region, five potential stem-loop (SL) structures, four tRNA-like structures and four conserved sequence blocks (CSBs) were detected in the elongated CR. The presence of these tRNA-like structures in the CR has never been reported in other plecopteran mitogenomes. These novel features of the elongated CR in N. nankinensis may have functions associated with the process of replication and transcription. Finally, phylogenetic reconstruction suggested that Nemouridae was the sister-group of Capniidae.

The Complete Mitochondrial Genome of Mindarus keteleerifoliae (Insecta: Hemiptera: Aphididae) and Comparison with Other Aphididae Insects.

PubMed

Wang, Yuan; Chen, Jing; Jiang, Li-Yun; Qiao, Ge-Xia

2015-12-17

The mitogenome of Mindarus keteleerifoliae Zhang (Hemiptera: Aphididae) is a 15,199 bp circular molecule. The gene order and orientation of M. keteleerifoliae is similarly arranged to that of the ancestral insect of other aphid mitogenomes, and, a tRNA isomerism event maybe identified in the mitogenome of M. keteleerifoliae. The tRNA-Trp gene is coded in the J-strand and the same sequence in the N-strand codes for the tRNA-Ser gene. A similar phenomenon was also found in the mitogenome of Eriosoma lanigerum. However, whether tRNA isomers in aphids exist requires further study. Phylogenetic analyses, using all available protein-coding genes, support Mindarinae as the basal position of Aphididae. Two tribes of Aphidinae were recovered with high statistical significance. Characteristics of the M. keteleerifoliae mitogenome revealed distinct mitogenome structures and provided abundant phylogenetic signals, thus advancing our understanding of insect mitogenomic architecture and evolution. But, because only eight complete aphid mitogenomes, including M. keteleerifoliae, were published, future studies with larger taxon sampling sizes are necessary.

The bioelectric code: An ancient computational medium for dynamic control of growth and form.

PubMed

Levin, Michael; Martyniuk, Christopher J

2018-02-01

What determines large-scale anatomy? DNA does not directly specify geometrical arrangements of tissues and organs, and a process of encoding and decoding for morphogenesis is required. Moreover, many species can regenerate and remodel their structure despite drastic injury. The ability to obtain the correct target morphology from a diversity of initial conditions reveals that the morphogenetic code implements a rich system of pattern-homeostatic processes. Here, we describe an important mechanism by which cellular networks implement pattern regulation and plasticity: bioelectricity. All cells, not only nerves and muscles, produce and sense electrical signals; in vivo, these processes form bioelectric circuits that harness individual cell behaviors toward specific anatomical endpoints. We review emerging progress in reading and re-writing anatomical information encoded in bioelectrical states, and discuss the approaches to this problem from the perspectives of information theory, dynamical systems, and computational neuroscience. Cracking the bioelectric code will enable much-improved control over biological patterning, advancing basic evolutionary developmental biology as well as enabling numerous applications in regenerative medicine and synthetic bioengineering. Copyright © 2017 Elsevier B.V. All rights reserved.

Cloning and expression of a cDNA coding for catalase from zebrafish (Danio rerio).

PubMed

Ken, C F; Lin, C T; Wu, J L; Shaw, J F

2000-06-01

A full-length complementary DNA (cDNA) clone encoding a catalase was amplified by the rapid amplication of cDNA ends-polymerase chain reaction (RACE-PCR) technique from zebrafish (Danio rerio) mRNA. Nucleotide sequence analysis of this cDNA clone revealed that it comprised a complete open reading frame coding for 526 amino acid residues and that it had a molecular mass of 59 654 Da. The deduced amino acid sequence showed high similarity with the sequences of catalase from swine (86.9%), mouse (85.8%), rat (85%), human (83.7%), fruit fly (75.6%), nematode (71.1%), and yeast (58.6%). The amino acid residues for secondary structures are apparently conserved as they are present in other mammal species. Furthermore, the coding region of zebrafish catalase was introduced into an expression vector, pET-20b(+), and transformed into Escherichia coli expression host BL21(DE3)pLysS. A 60-kDa active catalase protein was expressed and detected by Coomassie blue staining as well as activity staining on polyacrylamide gel followed electrophoresis.

Conceptual Underpinnings of the Quality of Life in Neurological Disorders (Neuro-QoL): Comparisons of Core Sets for Stroke, Multiple Sclerosis, Spinal Cord Injury, and Traumatic Brain Injury.

PubMed

Wong, Alex W K; Lau, Stephen C L; Fong, Mandy W M; Cella, David; Lai, Jin-Shei; Heinemann, Allen W

2018-04-03

To determine the extent to which the content of the Quality of Life in Neurological Disorders (Neuro-QoL) covers the International Classification of Functioning, Disability and Health (ICF) Core Sets for multiple sclerosis (MS), stroke, spinal cord injury (SCI), and traumatic brain injury (TBI) using summary linkage indicators. Content analysis by linking content of the Neuro-QoL to corresponding ICF codes of each Core Set for MS, stroke, SCI, and TBI. Three academic centers. None. None. Four summary linkage indicators proposed by MacDermid et al were estimated to compare the content coverage between Neuro-QoL and the ICF codes of Core Sets for MS, stroke, MS, and TBI. Neuro-QoL represented 20% to 30% Core Set codes for different conditions in which more codes in Core Sets for MS (29%), stroke (28%), and TBI (28%) were covered than those for SCI in the long-term (20%) and early postacute (19%) contexts. Neuro-QoL represented nearly half of the unique Activity and Participation codes (43%-49%) and less than one third of the unique Body Function codes (12%-32%). It represented fewer Environmental Factors codes (2%-6%) and no Body Structures codes. Absolute linkage indicators found that at least 60% of Neuro-QoL items were linked to Core Set codes (63%-95%), but many items covered the same codes as revealed by unique linkage indicators (7%-13%), suggesting high concept redundancy among items. The Neuro-QoL links more closely to ICF Core Sets for stroke, MS, and TBI than to those for SCI, and primarily covers activity and participation ICF domains. Other instruments are needed to address concepts not measured by the Neuro-QoL when a comprehensive health assessment is needed. Copyright © 2018 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Combustion: Structural interaction in a viscoelastic material

NASA Technical Reports Server (NTRS)

Chang, T. Y.; Chang, J. P.; Kumar, M.; Kuo, K. K.

1980-01-01

The effect of interaction between combustion processes and structural deformation of solid propellant was considered. The combustion analysis was performed on the basis of deformed crack geometry, which was determined from the structural analysis. On the other hand, input data for the structural analysis, such as pressure distribution along the crack boundary and ablation velocity of the crack, were determined from the combustion analysis. The interaction analysis was conducted by combining two computer codes, a combustion analysis code and a general purpose finite element structural analysis code.

Pacific Northwest ecoclass codes for seral and potential natural communities.

Treesearch

Frederick C. Hall

1998-01-01

Lists codes for identification of potential natural communities (plant association, habitat types), their seral status, and vegetation structure in and around the Pacific Northwest. Codes are a six-digit alphanumeric system using the first letter of tree species, life-form, seral status, and structure so that most codes can be directly interpreted. Seven appendices...

Genomic cloning and chromosomal localization of HRY, the human homolog to the Drosophila segmentation gene, hairy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feder, J.N.; Jan, L.Y.; Jan, Y.N.

The Drosophila hairy gene encodes a basic helix- loop-helix protein that functions in at least two steps during Drosophila development: (1) during embryogenesis, when it partakes in the establishment of segments, and (2) during the larval stage, when it functions negatively in determining the pattern of sensory bristles on the adult fly. In the rat, a structurally homologous gene (RHL) behaves as an immediate-early gene in its response to growth factors and can, like that in Drosophila, suppress neuronal differentiation events. Here, the authors report the genomic cloning of the human hairy gene homolog (HRY). The coding region of themore » gene is contained within four exons. The predicted amino acid sequence reveals only four amino acid differences between the human and rat genes. Analysis of the DNA sequence 5[prime] to the coding region reveals a putatitve untranslated exon. To increase the value of the HRY gene as a genetic marker and to assess its potential involvement in genetic disorders, they sublocalized the locus to chromosome 3q28-q29 by fluorescence in situ hybridization. 34 refs., 4 figs., 1 tab.« less

A Case-by-Case Evolutionary Analysis of Four Imprinted Retrogenes

PubMed Central

McCole, Ruth B; Loughran, Noeleen B; Chahal, Mandeep; Fernandes, Luis P; Roberts, Roland G; Fraternali, Franca; O'Connell, Mary J; Oakey, Rebecca J

2011-01-01

Retroposition is a widespread phenomenon resulting in the generation of new genes that are initially related to a parent gene via very high coding sequence similarity. We examine the evolutionary fate of four retrogenes generated by such an event; mouse Inpp5f_v2, Mcts2, Nap1l5, and U2af1-rs1. These genes are all subject to the epigenetic phenomenon of parental imprinting. We first provide new data on the age of these retrogene insertions. Using codon-based models of sequence evolution, we show these retrogenes have diverse evolutionary trajectories, including divergence from the parent coding sequence under positive selection pressure, purifying selection pressure maintaining parent-retrogene similarity, and neutral evolution. Examination of the expression pattern of retrogenes shows an atypical, broad pattern across multiple tissues. Protein 3D structure modeling reveals that a positively selected residue in U2af1-rs1, not shared by its parent, may influence protein conformation. Our case-by-case analysis of the evolution of four imprinted retrogenes reveals that this interesting class of imprinted genes, while similar in regulation and sequence characteristics, follow very varied evolutionary paths. PMID:21166792

Using Multimedia to Reveal the Hidden Code of Everyday Behaviour to Children with Autistic Spectrum Disorders (ASDs)

ERIC Educational Resources Information Center

Doyle, Theresa; Arnedillo-Sanchez, Inmaculada

2011-01-01

This paper describes a framework which was developed for carers (teachers and parents) to help them create personalised social stories for children with autistic spectrum disorders (ASDs). It explores the social challenges experienced by individuals with ASDs and outlines an intervention aimed at revealing the hidden code that underpins social…

Sequence characterization of S100A8 gene reveals structural differences of protein and transcriptional factor binding sites in water buffalo and yak.

PubMed

Kathiravan, P; Goyal, S; Kataria, R S; Mishra, B P; Jayakumar, S; Joshi, B K

2011-01-01

The present study was undertaken to characterize the structure of S100A8 gene and its promoter in water buffalo and yak. Sequence data of 2.067 kb, 2.071 kb, and 2.052 kb with respect to complete S100A8 gene including 5' flanking region was generated in river buffalo, swamp buffalo, and yak, respectively. BLAST analysis of coding DNA sequences (CDS) of S100A8 gene revealed 95% homology of buffalo sequence with cattle, 85% with pig and horse, 83% with dog, 72-73% with murines, and around 79% with primates and humans. Phylogenetic analysis of predicted CDS revealed distinct clustering of murines, primates, and domestic animals with bovines and bubalines forming a subcluster among farm animals. In silico translation of predicted CDS revealed a sequence of 89 amino acids with 7 amino acid changes between cattle and buffalo and 2 changes between cattle and yak. The search for Pfam family revealed the N-terminal calcium binding domain and the noncanonical EF hand domain in the carboxy terminus, with more variations being observed in the N-terminal domain among different species. Two amino acid changes observed in carboxy terminal EF hand domain resulted in altered secondary structure of yak S100A8 protein. Analysis of S100A8 gene promoter revealed 14 putative motifs for transcriptional factor binding sites. Two putative motifs viz. C/EBP and v-Myb were found to be absent in swamp buffalo as compared to river buffalo and cattle. Differences in the structure of S100A8 protein and the transcriptional factor binding sites identified in the present study need to be analyzed further for their functional significance in yak and swamp buffalo respectively. Copyright © Taylor & Francis Group, LLC

Unitals and ovals of symmetric block designs in LDPC and space-time coding

NASA Astrophysics Data System (ADS)

Andriamanalimanana, Bruno R.

2004-08-01

An approach to the design of LDPC (low density parity check) error-correction and space-time modulation codes involves starting with known mathematical and combinatorial structures, and deriving code properties from structure properties. This paper reports on an investigation of unital and oval configurations within generic symmetric combinatorial designs, not just classical projective planes, as the underlying structure for classes of space-time LDPC outer codes. Of particular interest are the encoding and iterative (sum-product) decoding gains that these codes may provide. Various small-length cases have been numerically implemented in Java and Matlab for a number of channel models.

Ethical Issues and Codes of Ethics: Views of Adult Education Practitioners in Canada and the United States.

ERIC Educational Resources Information Center

Gordon, Wanda; Sork, Thomas J.

2001-01-01

Replicating an Indiana study, 261 responses from British Columbia adult educators revealed a high degree of support for codes of ethics and identified ethical dilemmas in practice. Half currently operated under a code. Responses to whether codes should have a regulatory function were mixed. (Contains 44 references.) (SK)

Bilayer Protograph Codes for Half-Duplex Relay Channels

NASA Technical Reports Server (NTRS)

Divsalar, Dariush; VanNguyen, Thuy; Nosratinia, Aria

2013-01-01

Direct to Earth return links are limited by the size and power of lander devices. A standard alternative is provided by a two-hops return link: a proximity link (from lander to orbiter relay) and a deep-space link (from orbiter relay to Earth). Although direct to Earth return links are limited by the size and power of lander devices, using an additional link and a proposed coding for relay channels, one can obtain a more reliable signal. Although significant progress has been made in the relay coding problem, existing codes must be painstakingly optimized to match to a single set of channel conditions, many of them do not offer easy encoding, and most of them do not have structured design. A high-performing LDPC (low-density parity-check) code for the relay channel addresses simultaneously two important issues: a code structure that allows low encoding complexity, and a flexible rate-compatible code that allows matching to various channel conditions. Most of the previous high-performance LDPC codes for the relay channel are tightly optimized for a given channel quality, and are not easily adapted without extensive re-optimization for various channel conditions. This code for the relay channel combines structured design and easy encoding with rate compatibility to allow adaptation to the three links involved in the relay channel, and furthermore offers very good performance. The proposed code is constructed by synthesizing a bilayer structure with a pro to graph. In addition to the contribution to relay encoding, an improved family of protograph codes was produced for the point-to-point AWGN (additive white Gaussian noise) channel whose high-rate members enjoy thresholds that are within 0.07 dB of capacity. These LDPC relay codes address three important issues in an integrative manner: low encoding complexity, modular structure allowing for easy design, and rate compatibility so that the code can be easily matched to a variety of channel conditions without extensive re-optimization. The main problem of half-duplex relay coding can be reduced to the simultaneous design of two codes at two rates and two SNRs (signal-to-noise ratios), such that one is a subset of the other. This problem can be addressed by forceful optimization, but a clever method of addressing this problem is via the bilayer lengthened (BL) LDPC structure. This method uses a bilayer Tanner graph to make the two codes while using a concept of "parity forwarding" with subsequent successive decoding that removes the need to directly address the issue of uneven SNRs among the symbols of a given codeword. This method is attractive in that it addresses some of the main issues in the design of relay codes, but it does not by itself give rise to highly structured codes with simple encoding, nor does it give rate-compatible codes. The main contribution of this work is to construct a class of codes that simultaneously possess a bilayer parity- forwarding mechanism, while also benefiting from the properties of protograph codes having an easy encoding, a modular design, and being a rate-compatible code.

Low Density Parity Check Codes: Bandwidth Efficient Channel Coding

NASA Technical Reports Server (NTRS)

Fong, Wai; Lin, Shu; Maki, Gary; Yeh, Pen-Shu

2003-01-01

Low Density Parity Check (LDPC) Codes provide near-Shannon Capacity performance for NASA Missions. These codes have high coding rates R=0.82 and 0.875 with moderate code lengths, n=4096 and 8176. Their decoders have inherently parallel structures which allows for high-speed implementation. Two codes based on Euclidean Geometry (EG) were selected for flight ASIC implementation. These codes are cyclic and quasi-cyclic in nature and therefore have a simple encoder structure. This results in power and size benefits. These codes also have a large minimum distance as much as d,,, = 65 giving them powerful error correcting capabilities and error floors less than lo- BER. This paper will present development of the LDPC flight encoder and decoder, its applications and status.

The Urtica dioica Agglutinin Is a Complex Mixture of Isolectins 1

PubMed Central

Van Damme, Els J. M.; Broekaert, Willem F.; Peumans, Willy J.

1988-01-01

Rhizomes of stinging nettle (Urtica dioica) contain a complex mixture of isolectins. Ion exchange chromatography with a high resolution fast protein liquid chromatography system revealed six isoforms which exhibit identical agglutination properties and carbohydrate-binding specificity and in addition have the same molecular structure and virtually identical biochemical properties. However, since the U. dioica agglutinin isolectins differ definitely with respect to their amino acid composition, it is likely that at least some of them are different polypeptides coded for by different genes. Images Fig. 3 PMID:16665952

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/. Supplementary data are available at Bioinformatics online.

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

PubMed Central

Lünse, Christina E.; Corbino, Keith A.; Ames, Tyler D.; Nelson, James W.; Roth, Adam; Perkins, Kevin R.; Sherlock, Madeline E.

2017-01-01

Abstract The discovery of structured non-coding RNAs (ncRNAs) in bacteria can reveal new facets of biology and biochemistry. Comparative genomics analyses executed by powerful computer algorithms have successfully been used to uncover many novel bacterial ncRNA classes in recent years. However, this general search strategy favors the discovery of more common ncRNA classes, whereas progressively rarer classes are correspondingly more difficult to identify. In the current study, we confront this problem by devising several methods to select subsets of intergenic regions that can concentrate these rare RNA classes, thereby increasing the probability that comparative sequence analysis approaches will reveal their existence. By implementing these methods, we discovered 224 novel ncRNA classes, which include ROOL RNA, an RNA class averaging 581 nt and present in multiple phyla, several highly conserved and widespread ncRNA classes with properties that suggest sophisticated biochemical functions and a multitude of putative cis-regulatory RNA classes involved in a variety of biological processes. We expect that further research on these newly found RNA classes will reveal additional aspects of novel biology, and allow for greater insights into the biochemistry performed by ncRNAs. PMID:28977401

Error floor behavior study of LDPC codes for concatenated codes design

NASA Astrophysics Data System (ADS)

Chen, Weigang; Yin, Liuguo; Lu, Jianhua

2007-11-01

Error floor behavior of low-density parity-check (LDPC) codes using quantized decoding algorithms is statistically studied with experimental results on a hardware evaluation platform. The results present the distribution of the residual errors after decoding failure and reveal that the number of residual error bits in a codeword is usually very small using quantized sum-product (SP) algorithm. Therefore, LDPC code may serve as the inner code in a concatenated coding system with a high code rate outer code and thus an ultra low error floor can be achieved. This conclusion is also verified by the experimental results.

APOLLO II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanchez, R.; Mondot, J.; Stankovski, Z.

1988-11-01

APOLLO II is a new, multigroup transport code under development at the Commissariat a l'Energie Atomique. The code has a modular structure and uses sophisticated software for data structuralization, dynamic memory management, data storage, and user macrolanguage. This paper gives an overview of the main methods used in the code for (a) multidimensional collision probability calculations, (b) leakage calculations, and (c) homogenization procedures. Numerical examples are given to demonstrate the potential of the modular structure of the code and the novel multilevel flat-flux representation used in the calculation of the collision probabilities.

Novel microscopy-based screening method reveals regulators of contact-dependent intercellular transfer

PubMed Central

Michael Frei, Dominik; Hodneland, Erlend; Rios-Mondragon, Ivan; Burtey, Anne; Neumann, Beate; Bulkescher, Jutta; Schölermann, Julia; Pepperkok, Rainer; Gerdes, Hans-Hermann; Kögel, Tanja

2015-01-01

Contact-dependent intercellular transfer (codeIT) of cellular constituents can have functional consequences for recipient cells, such as enhanced survival and drug resistance. Pathogenic viruses, prions and bacteria can also utilize this mechanism to spread to adjacent cells and potentially evade immune detection. However, little is known about the molecular mechanism underlying this intercellular transfer process. Here, we present a novel microscopy-based screening method to identify regulators and cargo of codeIT. Single donor cells, carrying fluorescently labelled endocytic organelles or proteins, are co-cultured with excess acceptor cells. CodeIT is quantified by confocal microscopy and image analysis in 3D, preserving spatial information. An siRNA-based screening using this method revealed the involvement of several myosins and small GTPases as codeIT regulators. Our data indicates that cellular protrusions and tubular recycling endosomes are important for codeIT. We automated image acquisition and analysis to facilitate large-scale chemical and genetic screening efforts to identify key regulators of codeIT. PMID:26271723

Cost-Effective Sequencing of Full-Length cDNA Clones Powered by a De Novo-Reference Hybrid Assembly

PubMed Central

Sugano, Sumio; Morishita, Shinichi; Suzuki, Yutaka

2010-01-01

Background Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. Methodology We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence ∼800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. Conclusions The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only ∼US$3 per clone, demonstrating a significant advantage over previous approaches. PMID:20479877

[Genetic diversity analysis of Andrographis paniculata in China based on SRAP and SNP].

PubMed

Chen, Rong; Wang, Xiao-Yun; Song, Yu-Ning; Zhu, Yun-feng; Wang, Peng-liang; Li, Min; Zhong, Guo-Yue

2014-12-01

In order to reveal genetic diversity of domestic Andrographis paniculata and its impact on quality, genetic backgrounds of 103 samples from 7 provinces in China were analyzed using SRAP marker and SNP marker. Genetic structures of the A. paniculata populations were estimated with Powermarker V 3.25 and Mega 6.0 software, and polymorphic SNPs were identified with CodonCode Aligner software. The results showed that the genetic distances of domestic A. paniculata germplasm ranged from 0. 01 to 0.09, and no polymorphic SNPs were discovered in coding sequence fragments of ent-copalyl diphosphate synthase. A. paniculata germplasm from various regions in China had poor genetic diversity. This phenomenon was closely related to strict self-fertilization and earlier introduction from the same origin. Therefore, genetic background had little impact on variable qualities of A. paniculata in domestic market. Mutation breeding, polyploid breeding and molecular breeding were proposed as promising strategies in germplasm innovation.

Gene encoding the human. beta. -hexosaminidase. beta. chain: Extensive homology of intron placement in the. alpha. - and. beta. -chain genes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Proia, R.L.

1988-03-01

Lysosomal {beta}-hexosaminidase is composed of two structurally similar chains, {alpha} and {beta}, that are the products of different genes. Mutations in either gene causing {beta}-hexosaminidase deficiency result in the lysosomal storage disease GM2-gangliosidosis. To enable the investigation of the molecular lesions in this disorder and to study the evolutionary relationship between the {alpha} and {beta} chains, the {beta}-chain gene was isolated, and its organization was characterized. The {beta}-chain coding region is divided into 14 exons distributed over {approx}40 kilobases of DNA. Comparison with the {alpha}-chain gene revealed that 12 of the 13 introns interrupt the coding regions at homologous positions.more » This extensive sharing of intron placement demonstrates that the {alpha} and {beta} chains evolved by way of the duplication of a common ancestor.« less

Coding of navigational affordances in the human visual system

PubMed Central

Epstein, Russell A.

2017-01-01

A central component of spatial navigation is determining where one can and cannot go in the immediate environment. We used fMRI to test the hypothesis that the human visual system solves this problem by automatically identifying the navigational affordances of the local scene. Multivoxel pattern analyses showed that a scene-selective region of dorsal occipitoparietal cortex, known as the occipital place area, represents pathways for movement in scenes in a manner that is tolerant to variability in other visual features. These effects were found in two experiments: One using tightly controlled artificial environments as stimuli, the other using a diverse set of complex, natural scenes. A reconstruction analysis demonstrated that the population codes of the occipital place area could be used to predict the affordances of novel scenes. Taken together, these results reveal a previously unknown mechanism for perceiving the affordance structure of navigable space. PMID:28416669

Discover mouse gene coexpression landscapes using dictionary learning and sparse coding.

PubMed

Li, Yujie; Chen, Hanbo; Jiang, Xi; Li, Xiang; Lv, Jinglei; Peng, Hanchuan; Tsien, Joe Z; Liu, Tianming

2017-12-01

Gene coexpression patterns carry rich information regarding enormously complex brain structures and functions. Characterization of these patterns in an unbiased, integrated, and anatomically comprehensive manner will illuminate the higher-order transcriptome organization and offer genetic foundations of functional circuitry. Here using dictionary learning and sparse coding, we derived coexpression networks from the space-resolved anatomical comprehensive in situ hybridization data from Allen Mouse Brain Atlas dataset. The key idea is that if two genes use the same dictionary to represent their original signals, then their gene expressions must share similar patterns, thereby considering them as "coexpressed." For each network, we have simultaneous knowledge of spatial distributions, the genes in the network and the extent a particular gene conforms to the coexpression pattern. Gene ontologies and the comparisons with published gene lists reveal biologically identified coexpression networks, some of which correspond to major cell types, biological pathways, and/or anatomical regions.

Repeated Evolution of the Pyrrolizidine Alkaloid–Mediated Defense System in Separate Angiosperm LineagesW⃞

PubMed Central

Reimann, Andreas; Nurhayati, Niknik; Backenköhler, Anita; Ober, Dietrich

2004-01-01

Species of several unrelated families within the angiosperms are able to constitutively produce pyrrolizidine alkaloids as a defense against herbivores. In pyrrolizidine alkaloid (PA) biosynthesis, homospermidine synthase (HSS) catalyzes the first specific step. HSS was recruited during angiosperm evolution from deoxyhypusine synthase (DHS), an enzyme involved in the posttranslational activation of eukaryotic initiation factor 5A. Phylogenetic analysis of 23 cDNA sequences coding for HSS and DHS of various angiosperm species revealed at least four independent recruitments of HSS from DHS: one within the Boraginaceae, one within the monocots, and two within the Asteraceae family. Furthermore, sequence analyses indicated elevated substitution rates within HSS-coding sequences after each gene duplication, with an increased level of nonsynonymous mutations. However, the contradiction between the polyphyletic origin of the first enzyme in PA biosynthesis and the structural identity of the final biosynthetic PA products needs clarification. PMID:15466410

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.

PubMed

Mayer, K; Schüller, C; Wambutt, R; Murphy, G; Volckaert, G; Pohl, T; Düsterhöft, A; Stiekema, W; Entian, K D; Terryn, N; Harris, B; Ansorge, W; Brandt, P; Grivell, L; Rieger, M; Weichselgartner, M; de Simone, V; Obermaier, B; Mache, R; Müller, M; Kreis, M; Delseny, M; Puigdomenech, P; Watson, M; Schmidtheini, T; Reichert, B; Portatelle, D; Perez-Alonso, M; Boutry, M; Bancroft, I; Vos, P; Hoheisel, J; Zimmermann, W; Wedler, H; Ridley, P; Langham, S A; McCullagh, B; Bilham, L; Robben, J; Van der Schueren, J; Grymonprez, B; Chuang, Y J; Vandenbussche, F; Braeken, M; Weltjens, I; Voet, M; Bastiaens, I; Aert, R; Defoor, E; Weitzenegger, T; Bothe, G; Ramsperger, U; Hilbert, H; Braun, M; Holzer, E; Brandt, A; Peters, S; van Staveren, M; Dirske, W; Mooijman, P; Klein Lankhorst, R; Rose, M; Hauf, J; Kötter, P; Berneiser, S; Hempel, S; Feldpausch, M; Lamberth, S; Van den Daele, H; De Keyser, A; Buysshaert, C; Gielen, J; Villarroel, R; De Clercq, R; Van Montagu, M; Rogers, J; Cronin, A; Quail, M; Bray-Allen, S; Clark, L; Doggett, J; Hall, S; Kay, M; Lennard, N; McLay, K; Mayes, R; Pettett, A; Rajandream, M A; Lyne, M; Benes, V; Rechmann, S; Borkova, D; Blöcker, H; Scharfe, M; Grimm, M; Löhnert, T H; Dose, S; de Haan, M; Maarse, A; Schäfer, M; Müller-Auer, S; Gabel, C; Fuchs, M; Fartmann, B; Granderath, K; Dauner, D; Herzl, A; Neumann, S; Argiriou, A; Vitale, D; Liguori, R; Piravandi, E; Massenet, O; Quigley, F; Clabauld, G; Mündlein, A; Felber, R; Schnabl, S; Hiller, R; Schmidt, W; Lecharny, A; Aubourg, S; Chefdor, F; Cooke, R; Berger, C; Montfort, A; Casacuberta, E; Gibbons, T; Weber, N; Vandenbol, M; Bargues, M; Terol, J; Torres, A; Perez-Perez, A; Purnelle, B; Bent, E; Johnson, S; Tacon, D; Jesse, T; Heijnen, L; Schwarz, S; Scholler, P; Heber, S; Francs, P; Bielke, C; Frishman, D; Haase, D; Lemcke, K; Mewes, H W; Stocker, S; Zaccaria, P; Bevan, M; Wilson, R K; de la Bastide, M; Habermann, K; Parnell, L; Dedhia, N; Gnoj, L; Schutz, K; Huang, E; Spiegel, L; Sehkon, M; Murray, J; Sheet, P; Cordes, M; Abu-Threideh, J; Stoneking, T; Kalicki, J; Graves, T; Harmon, G; Edwards, J; Latreille, P; Courtney, L; Cloud, J; Abbott, A; Scott, K; Johnson, D; Minx, P; Bentley, D; Fulton, B; Miller, N; Greco, T; Kemp, K; Kramer, J; Fulton, L; Mardis, E; Dante, M; Pepin, K; Hillier, L; Nelson, J; Spieth, J; Ryan, E; Andrews, S; Geisel, C; Layman, D; Du, H; Ali, J; Berghoff, A; Jones, K; Drone, K; Cotton, M; Joshu, C; Antonoiu, B; Zidanic, M; Strong, C; Sun, H; Lamar, B; Yordan, C; Ma, P; Zhong, J; Preston, R; Vil, D; Shekher, M; Matero, A; Shah, R; Swaby, I K; O'Shaughnessy, A; Rodriguez, M; Hoffmann, J; Till, S; Granat, S; Shohdy, N; Hasegawa, A; Hameed, A; Lodhi, M; Johnson, A; Chen, E; Marra, M; Martienssen, R; McCombie, W R

1999-12-16

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Visual Coding of Human Bodies: Perceptual Aftereffects Reveal Norm-Based, Opponent Coding of Body Identity

ERIC Educational Resources Information Center

Rhodes, Gillian; Jeffery, Linda; Boeing, Alexandra; Calder, Andrew J.

2013-01-01

Despite the discovery of body-selective neural areas in occipitotemporal cortex, little is known about how bodies are visually coded. We used perceptual adaptation to determine how body identity is coded. Brief exposure to a body (e.g., anti-Rose) biased perception toward an identity with opposite properties (Rose). Moreover, the size of this…

Invited Article: Relation between electric and magnetic field structures and their proton-beam images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kugland, N. L.; Ryutov, D. D.; Plechaty, C.

2012-10-15

Proton imaging is commonly used to reveal the electric and magnetic fields that are found in high energy density plasmas. Presented here is an analysis of this technique that is directed towards developing additional insight into the underlying physics. This approach considers: formation of images in the limits of weak and strong intensity variations; caustic formation and structure; image inversion to obtain line-integrated field characteristics; direct relations between images and electric or magnetic field structures in a plasma; imaging of sharp features such as Debye sheaths and shocks. Limitations on spatial and temporal resolution are assessed, and similarities with opticalmore » shadowgraphy are noted. Synthetic proton images are presented to illustrate the analysis. These results will be useful for quantitatively analyzing experimental proton imaging data and verifying numerical codes.« less

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

PubMed

Ding, Yiliang; Tang, Yin; Kwok, Chun Kit; Zhang, Yu; Bevilacqua, Philip C; Assmann, Sarah M

2014-01-30

RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

An Object-Oriented Approach to Writing Computational Electromagnetics Codes

NASA Technical Reports Server (NTRS)

Zimmerman, Martin; Mallasch, Paul G.

1996-01-01

Presently, most computer software development in the Computational Electromagnetics (CEM) community employs the structured programming paradigm, particularly using the Fortran language. Other segments of the software community began switching to an Object-Oriented Programming (OOP) paradigm in recent years to help ease design and development of highly complex codes. This paper examines design of a time-domain numerical analysis CEM code using the OOP paradigm, comparing OOP code and structured programming code in terms of software maintenance, portability, flexibility, and speed.

Code Analysis and Refactoring with Clang Tools, Version 0.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelley, Timothy M.

2016-12-23

Code Analysis and Refactoring with Clang Tools is a small set of example code that demonstrates techniques for applying tools distributed with the open source Clang compiler. Examples include analyzing where variables are used and replacing old data structures with standard structures.

Reassigning stop codons via translation termination: How a few eukaryotes broke the dogma.

PubMed

Alkalaeva, Elena; Mikhailova, Tatiana

2017-03-01

The genetic code determines how amino acids are encoded within mRNA. It is universal among the vast majority of organisms, although several exceptions are known. Variant genetic codes are found in ciliates, mitochondria, and numerous other organisms. All revealed genetic codes (standard and variant) have at least one codon encoding a translation stop signal. However, recently two new genetic codes with a reassignment of all three stop codons were revealed in studies examining the protozoa transcriptomes. Here, we discuss this finding and the recent studies of variant genetic codes in eukaryotes. We consider the possible molecular mechanisms allowing the use of certain codons as sense and stop signals simultaneously. The results obtained by studying these amazing organisms represent a new and exciting insight into the mechanism of stop codon decoding in eukaryotes. Also see the video abstract here. © 2017 WILEY Periodicals, Inc.

Atomistic structures of nano-engineered SiC and radiation-induced amorphization resistance

NASA Astrophysics Data System (ADS)

Imada, Kenta; Ishimaru, Manabu; Sato, Kazuhisa; Xue, Haizhou; Zhang, Yanwen; Shannon, Steven; Weber, William J.

2015-10-01

Nano-engineered 3C-SiC thin films, which possess columnar structures with high-density stacking faults and twins, were irradiated with 2 MeV Si ions at cryogenic and room temperatures. From cross-sectional transmission electron microscopy observations in combination with Monte Carlo simulations based on the Stopping and Range of Ions in Matter code, it was found that their amorphization resistance is six times greater than bulk crystalline SiC at room temperature. High-angle bright-field images taken by spherical aberration corrected scanning transmission electron microscopy revealed that the distortion of atomic configurations is localized near the stacking faults. The resultant strain field probably contributes to the enhancement of radiation tolerance of this material.

Nucleotide sequence and transcriptional start site of the Methylobacterium organophilum XX methanol dehydrogenase structural gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Machlin, S.M.; Hanson, R.S.

The nucleotide sequence of a cloned 2.5-kilobase-pair SmaI fragment containing the methanol dehydrogenase (MDH) structural gene from Methylobacterium organophilum XX was determined. A single open reading frame with a coding capacity of 626 amino acids (molecular weight, 66,000) was identified on one stand, and N-terminal sequencing of purified MDH revealed that 27 of these residues constituted a putative signal peptide. Primer extension mapping of in vivo transcripts indicated that the start of mRNA synthesis was 160 to 170 base pairs upstream of the ATG codon. Northern (RNA) blot analysis further demonstrated that the transcript was 2.1 kilobase pairs in lengthmore » and therefore appeared to encode only MDH.« less

Diagnostic analysis of observed and numerically simulated cloud and precipitation structures during pre-ERICA

NASA Technical Reports Server (NTRS)

Perkey, Donald J.; Doty, Kevin G.; Robertson, Franklin R.

1989-01-01

A preliminary 140-km simulation of a rapid cyclogenesis, using the Limited Area Mesoscale Prediction System (LAMPS) is discussed. A three-dimensional version of LAMPS used in the simulation is described, along with a trajectory model utilizing the three-hourly output history files from the LAMPS model. Preliminary integrations of the LAMPS code as well as passive microwave digital data from SSM/I aboard the DMSP satellite are used for exploring the evolving baroclinic structure and moisture field of the cyclone event. A trajectory analysis of the model histories reveals a significant role for preconditioning of the low-level upstream air, which is then drawn into the ascending warm conveyor belt ahead of the storm.

Data Sciences Summer Institute Topology Optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watts, Seth

DSSI_TOPOPT is a 2D topology optimization code that designs stiff structures made of a single linear elastic material and void space. The code generates a finite element mesh of a rectangular design domain on which the user specifies displacement and load boundary conditions. The code iteratively designs a structure that minimizes the compliance (maximizes the stiffness) of the structure under the given loading, subject to an upper bound on the amount of material used. Depending on user options, the code can evaluate the performance of a user-designed structure, or create a design from scratch. Output includes the finite element mesh,more » design, and visualizations of the design.« less

microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3' untranslated region: function in replication and influence of RNA secondary structure.

PubMed

Gerresheim, Gesche K; Dünnes, Nadia; Nieder-Röhrmann, Anika; Shalamova, Lyudmila A; Fricke, Markus; Hofacker, Ivo; Höner Zu Siederdissen, Christian; Marz, Manja; Niepmann, Michael

2017-02-01

We have analyzed the binding of the liver-specific microRNA-122 (miR-122) to three conserved target sites of hepatitis C virus (HCV) RNA, two in the non-structural protein 5B (NS5B) coding region and one in the 3' untranslated region (3'UTR). miR-122 binding efficiency strongly depends on target site accessibility under conditions when the range of flanking sequences available for the formation of local RNA secondary structures changes. Our results indicate that the particular sequence feature that contributes most to the correlation between target site accessibility and binding strength varies between different target sites. This suggests that the dynamics of miRNA/Ago2 binding not only depends on the target site itself but also on flanking sequence context to a considerable extent, in particular in a small viral genome in which strong selection constraints act on coding sequence and overlapping cis-signals and model the accessibility of cis-signals. In full-length genomes, single and combination mutations in the miR-122 target sites reveal that site 5B.2 is positively involved in regulating overall genome replication efficiency, whereas mutation of site 5B.3 showed a weaker effect. Mutation of the 3'UTR site and double or triple mutants showed no significant overall effect on genome replication, whereas in a translation reporter RNA, the 3'UTR target site inhibits translation directed by the HCV 5'UTR. Thus, the miR-122 target sites in the 3'-region of the HCV genome are involved in a complex interplay in regulating different steps of the HCV replication cycle.

The Particle Accelerator Simulation Code PyORBIT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorlov, Timofey V; Holmes, Jeffrey A; Cousineau, Sarah M

2015-01-01

The particle accelerator simulation code PyORBIT is presented. The structure, implementation, history, parallel and simulation capabilities, and future development of the code are discussed. The PyORBIT code is a new implementation and extension of algorithms of the original ORBIT code that was developed for the Spallation Neutron Source accelerator at the Oak Ridge National Laboratory. The PyORBIT code has a two level structure. The upper level uses the Python programming language to control the flow of intensive calculations performed by the lower level code implemented in the C++ language. The parallel capabilities are based on MPI communications. The PyORBIT ismore » an open source code accessible to the public through the Google Open Source Projects Hosting service.« less

Comparative genomics reveals insights into avian genome evolution and adaptation.

PubMed

Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M; Lee, Chul; Storz, Jay F; Antunes, Agostinho; Greenwold, Matthew J; Meredith, Robert W; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S; Gatesy, John; Hoffmann, Federico G; Opazo, Juan C; Håstad, Olle; Sawyer, Roger H; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A; Green, Richard E; O'Brien, Stephen J; Griffin, Darren; Johnson, Warren E; Haussler, David; Ryder, Oliver A; Willerslev, Eske; Graves, Gary R; Alström, Per; Fjeldså, Jon; Mindell, David P; Edwards, Scott V; Braun, Edward L; Rahbek, Carsten; Burt, David W; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D; Gilbert, M Thomas P; Wang, Jun

2014-12-12

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. Copyright © 2014, American Association for the Advancement of Science.

Two Perspectives on the Origin of the Standard Genetic Code

NASA Astrophysics Data System (ADS)

Sengupta, Supratim; Aggarwal, Neha; Bandhu, Ashutosh Vishwa

2014-12-01

The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other. We find that in the absence of horizontal gene transfer, natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. However, for certain probabilities of the horizontal transfer events, a universal code emerges having a structure that is consistent with the standard genetic code.

Integrated Composite Analyzer (ICAN): Users and programmers manual

NASA Technical Reports Server (NTRS)

Murthy, P. L. N.; Chamis, C. C.

1986-01-01

The use of and relevant equations programmed in a computer code designed to carry out a comprehensive linear analysis of multilayered fiber composites is described. The analysis contains the essential features required to effectively design structural components made from fiber composites. The inputs to the code are constituent material properties, factors reflecting the fabrication process, and composite geometry. The code performs micromechanics, macromechanics, and laminate analysis, including the hygrothermal response of fiber composites. The code outputs are the various ply and composite properties, composite structural response, and composite stress analysis results with details on failure. The code is in Fortran IV and can be used efficiently as a package in complex structural analysis programs. The input-output format is described extensively through the use of a sample problem. The program listing is also included. The code manual consists of two parts.

Just in time? Using QR codes for multi-professional learning in clinical practice.

PubMed

Jamu, Joseph Tawanda; Lowi-Jones, Hannah; Mitchell, Colin

2016-07-01

Clinical guidelines and policies are widely available on the hospital intranet or from the internet, but can be difficult to access at the required time and place. Clinical staff with smartphones could use Quick Response (QR) codes for contemporaneous access to relevant information to support the Just in Time Learning (JIT-L) paradigm. There are several studies that advocate the use of smartphones to enhance learning amongst medical students and junior doctors in UK. However, these participants are already technologically orientated. There are limited studies that explore the use of smartphones in nursing practice. QR Codes were generated for each topic and positioned at relevant locations on a medical ward. Support and training were provided for staff. Website analytics and semi-structured interviews were performed to evaluate the efficacy, acceptability and feasibility of using QR codes to facilitate Just in Time learning. Use was intermittently high but not sustained. Thematic analysis of interviews revealed a positive assessment of the Just in Time learning paradigm and context-sensitive clinical information. However, there were notable barriers to acceptance, including usability of QR codes and appropriateness of smartphone use in a clinical environment. The use of Just in Time learning for education and reference may be beneficial to healthcare professionals. However, alternative methods of access for less technologically literate users and a change in culture of mobile device use in clinical areas may be needed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optimal lightpath placement on a metropolitan-area network linked with optical CDMA local nets

NASA Astrophysics Data System (ADS)

Wang, Yih-Fuh; Huang, Jen-Fa

2008-01-01

A flexible optical metropolitan-area network (OMAN) [J.F. Huang, Y.F. Wang, C.Y. Yeh, Optimal configuration of OCDMA-based MAN with multimedia services, in: 23rd Biennial Symposium on Communications, Queen's University, Kingston, Canada, May 29-June 2, 2006, pp. 144-148] structured with OCDMA linkage is proposed to support multimedia services with multi-rate or various qualities of service. To prioritize transmissions in OCDMA, the orthogonal variable spreading factor (OVSF) codes widely used in wireless CDMA are adopted. In addition, for feasible multiplexing, unipolar OCDMA modulation [L. Nguyen, B. Aazhang, J.F. Young, All-optical CDMA with bipolar codes, IEEE Electron. Lett. 31 (6) (1995) 469-470] is used to generate the code selector of multi-rate OMAN, and a flexible fiber-grating-based system is used for the equipment on OCDMA-OVSF code. These enable an OMAN to assign suitable OVSF codes when creating different-rate lightpaths. How to optimally configure a multi-rate OMAN is a challenge because of displaced lightpaths. In this paper, a genetically modified genetic algorithm (GMGA) [L.R. Chen, Flexible fiber Bragg grating encoder/decoder for hybrid wavelength-time optical CDMA, IEEE Photon. Technol. Lett. 13 (11) (2001) 1233-1235] is used to preplan lightpaths in order to optimally configure an OMAN. To evaluate the performance of the GMGA, we compared it with different preplanning optimization algorithms. Simulation results revealed that the GMGA very efficiently solved the problem.

Structuring and coding in health care records: a qualitative analysis using diabetes as a case study.

PubMed

Robertson, Ann R R; Fernando, Bernard; Morrison, Zoe; Kalra, Dipak; Sheikh, Aziz

2015-03-27

Globally, diabetes mellitus presents a substantial and increasing burden to individuals, health care systems and society. Structuring and coding of information in the electronic health record underpin attempts to improve sharing and searching for information. Digital records for those with long-term conditions are expected to bring direct and secondary uses benefits, and potentially to support patient self-management. We sought to investigate if how and why records for adults with diabetes were structured and coded and to explore a range of UK stakeholders' perceptions of current practice in the National Health Service. We carried out a qualitative, theoretically informed case study of documenting health care information for diabetes in family practice and hospital settings in England, using semi-structured interviews, observations, systems demonstrations and documentary data. We conducted 22 interviews and four on-site observations. With respect to secondary uses - research, audit, public health and service planning - interviewees clearly articulated the benefits of highly structured and coded diabetes data and it was believed that benefits would expand through linkage to other datasets. Direct, more marginal, clinical benefits in terms of managing and monitoring diabetes and perhaps encouraging patient self-management were also reported. We observed marked differences in levels of record structuring and/or coding between family practices, where it was high, and the hospital. We found little evidence that structured and coded data were being exploited to improve information sharing between care settings. Using high levels of data structuring and coding in records for diabetes patients has the potential to be exploited more fully, and lessons might be learned from successful developments elsewhere in the UK. A first step would be for hospitals to attain levels of health information technology infrastructure and systems use commensurate with family practices.

Zebra: An advanced PWR lattice code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, L.; Wu, H.; Zheng, Y.

2012-07-01

This paper presents an overview of an advanced PWR lattice code ZEBRA developed at NECP laboratory in Xi'an Jiaotong Univ.. The multi-group cross-section library is generated from the ENDF/B-VII library by NJOY and the 361-group SHEM structure is employed. The resonance calculation module is developed based on sub-group method. The transport solver is Auto-MOC code, which is a self-developed code based on the Method of Characteristic and the customization of AutoCAD software. The whole code is well organized in a modular software structure. Some numerical results during the validation of the code demonstrate that this code has a good precisionmore » and a high efficiency. (authors)« less

RNA editing of non-coding RNA and its role in gene regulation.

PubMed

Daniel, Chammiran; Lagergren, Jens; Öhman, Marie

2015-10-01

It has for a long time been known that repetitive elements, particularly Alu sequences in human, are edited by the adenosine deaminases acting on RNA, ADAR, family. The functional interpretation of these events has been even more difficult than that of editing events in coding sequences, but today there is an emerging understanding of their downstream effects. A surprisingly large fraction of the human transcriptome contains inverted Alu repeats, often forming long double stranded structures in RNA transcripts, typically occurring in introns and UTRs of protein coding genes. Alu repeats are also common in other primates, and similar inverted repeats can frequently be found in non-primates, although the latter are less prone to duplex formation. In human, as many as 700,000 Alu elements have been identified as substrates for RNA editing, of which many are edited at several sites. In fact, recent advancements in transcriptome sequencing techniques and bioinformatics have revealed that the human editome comprises at least a hundred million adenosine to inosine (A-to-I) editing sites in Alu sequences. Although substantial additional efforts are required in order to map the editome, already present knowledge provides an excellent starting point for studying cis-regulation of editing. In this review, we will focus on editing of long stem loop structures in the human transcriptome and how it can effect gene expression. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting

PubMed Central

Firth, Andrew E; Atkins, John F

2009-01-01

Japanese encephalitis, West Nile, Usutu and Murray Valley encephalitis viruses form a tight subgroup within the larger Flavivirus genus. These viruses utilize a single-polyprotein expression strategy, resulting in ~10 mature proteins. Plotting the conservation at synonymous sites along the polyprotein coding sequence reveals strong conservation peaks at the very 5' end of the coding sequence, and also at the 5' end of the sequence encoding the NS2A protein. Such peaks are generally indicative of functionally important non-coding sequence elements. The second peak corresponds to a predicted stable pseudoknot structure whose biological importance is supported by compensatory mutations that preserve the structure. The pseudoknot is preceded by a conserved slippery heptanucleotide (Y CCU UUU), thus forming a classical stimulatory motif for -1 ribosomal frameshifting. We hypothesize, therefore, that the functional importance of the pseudoknot is to stimulate a portion of ribosomes to shift -1 nt into a short (45 codon), conserved, overlapping open reading frame, termed foo. Since cleavage at the NS1-NS2A boundary is known to require synthesis of NS2A in cis, the resulting transframe fusion protein is predicted to be NS1-NS2AN-term-FOO. We hypothesize that this may explain the origin of the previously identified NS1 'extension' protein in JEV-group flaviviruses, known as NS1'. PMID:19196463

Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree.

PubMed

Villela, Luciana Cristine Vasques; Alves, Anderson Luis; Varela, Eduardo Sousa; Yamagishi, Michel Eduardo Beleza; Giachetto, Poliana Fernanda; da Silva, Naiara Milagres Augusto; Ponzetto, Josi Margarete; Paiva, Samuel Rezende; Caetano, Alexandre Rodrigues

2017-02-01

The cachara (Pseudoplatystoma reticulatum) is a Neotropical freshwater catfish from family Pimelodidae (Siluriformes) native to Brazil. The species is of relative economic importance for local aquaculture production and basic biological information is under development to help boost efforts to domesticate and raise the species in commercial systems. The complete cachara mitochondrial genome was obtained by assembling Illumina RNA-seq data from pooled samples. The full mitogenome was found to be 16,576 bp in length, showing the same basic structure, order, and genetic organization observed in other Pimelodidae, with 13 protein-coding genes, 2 rNA genes, 22 trNAs, and a control region. Observed base composition was 24.63% T, 28.47% C, 31.45% A, and 15.44% G. With the exception of NAD6 and eight tRNAs, all of the observed mitochondrial genes were found to be coded on the H strand. A total of 107 SNPs were identified in P. reticulatum mtDNA, 67 of which were located in coding regions. Of these SNPs, 10 result in amino acid changes. Analysis of the obtained sequence with 94 publicly available full Siluriformes mitogenomes resulted in a phylogenetic tree that generally agreed with available phylogenetic proposals for the order. The first report of the complete Pseudoplatystoma reticulatum mitochondrial genome sequence revealed general gene organization, structure, content, and order similar to most vertebrates. Specific sequence and content features were observed and may have functional attributes which are now available for further investigation.

An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins.

PubMed

Yusufi, Faraaz Noor Khan; Park, Wonjun; Lee, May May; Lee, Dong-Yup

2009-01-01

Advances in high-throughput techniques have led to the creation of increasing amounts of glycome data. The storage and analysis of this data would benefit greatly from a compact notation for describing glycan structures that can be easily stored and interpreted by computers. Towards this end, we propose a fixed-length alpha-numeric code for representing N-linked glycan structures commonly found in secreted glycoproteins from mammalian cell cultures. This code, GlycoDigit, employs a pre-assigned alpha-numeric index to represent the monosaccharides attached in different branches to the core glycan structure. The present branch-centric representation allows us to visualize the structure while the numerical nature of the code makes it machine readable. In addition, a difference operator can be defined to quantitatively differentiate between glycan structures for further analysis. The usefulness and applicability of GlycoDigit were demonstrated by constructing and visualizing an N-linked glycosylation network.

Computational Infrastructure for Engine Structural Performance Simulation

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1997-01-01

Select computer codes developed over the years to simulate specific aspects of engine structures are described. These codes include blade impact integrated multidisciplinary analysis and optimization, progressive structural fracture, quantification of uncertainties for structural reliability and risk, benefits estimation of new technology insertion and hierarchical simulation of engine structures made from metal matrix and ceramic matrix composites. Collectively these codes constitute a unique infrastructure readiness to credibly evaluate new and future engine structural concepts throughout the development cycle from initial concept, to design and fabrication, to service performance and maintenance and repairs, and to retirement for cause and even to possible recycling. Stated differently, they provide 'virtual' concurrent engineering for engine structures total-life-cycle-cost.

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.

PubMed

Lim, Chun Shen; Brown, Chris M

2017-01-01

Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community.

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

PubMed Central

Lim, Chun Shen; Brown, Chris M.

2018-01-01

Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community. PMID:29354101

Comparison of three coding strategies for a low cost structure light scanner

NASA Astrophysics Data System (ADS)

Xiong, Hanwei; Xu, Jun; Xu, Chenxi; Pan, Ming

2014-12-01

Coded structure light is widely used for 3D scanning, and different coding strategies are adopted to suit for different goals. In this paper, three coding strategies are compared, and one of them is selected to implement a low cost structure light scanner under the cost of €100. To reach this goal, the projector and the video camera must be the cheapest, which will lead to some problems related to light coding. For a cheapest projector, complex intensity pattern can't be generated; even if it can be generated, it can't be captured by a cheapest camera. Based on Gray code, three different strategies are implemented and compared, called phase-shift, line-shift, and bit-shift, respectively. The bit-shift Gray code is the contribution of this paper, in which a simple, stable light pattern is used to generate dense(mean points distance<0.4mm) and accurate(mean error<0.1mm) results. The whole algorithm details and some example are presented in the papers.

Light element opacities of astrophysical interest from ATOMIC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colgan, J.; Kilcrease, D. P.; Magee, N. H. Jr.

We present new calculations of local-thermodynamic-equilibrium (LTE) light element opacities from the Los Alamos ATOMIC code for systems of astrophysical interest. ATOMIC is a multi-purpose code that can generate LTE or non-LTE quantities of interest at various levels of approximation. Our calculations, which include fine-structure detail, represent a systematic improvement over previous Los Alamos opacity calculations using the LEDCOP legacy code. The ATOMIC code uses ab-initio atomic structure data computed from the CATS code, which is based on Cowan's atomic structure codes, and photoionization cross section data computed from the Los Alamos ionization code GIPPER. ATOMIC also incorporates a newmore » equation-of-state (EOS) model based on the chemical picture. ATOMIC incorporates some physics packages from LEDCOP and also includes additional physical processes, such as improved free-free cross sections and additional scattering mechanisms. Our new calculations are made for elements of astrophysical interest and for a wide range of temperatures and densities.« less

Manual for obscuration code with space station applications

NASA Technical Reports Server (NTRS)

Marhefka, R. J.; Takacs, L.

1986-01-01

The Obscuration Code, referred to as SHADOW, is a user-oriented computer code to determine the case shadow of an antenna in a complex environment onto the far zone sphere. The surrounding structure can be composed of multiple composite cone frustums and multiply sided flat plates. These structural pieces are ideal for modeling space station configurations. The means of describing the geometry input is compatible with the NEC-BASIC Scattering Code. In addition, an interactive mode of operation has been provided for DEC VAX computers. The first part of this document is a user's manual designed to give a description of the method used to obtain the shadow map, to provide an overall view of the operation of the computer code, to instruct a user in how to model structures, and to give examples of inputs and outputs. The second part is a code manual that details how to set up the interactive and non-interactive modes of the code and provides a listing and brief description of each of the subroutines.

The barriers to clinical coding in general practice: a literature review.

PubMed

de Lusignan, S

2005-06-01

Clinical coding is variable in UK general practice. The reasons for this remain undefined. This review explains why there are no readily available alternatives to recording structured clinical data and reviews the barriers to recording structured clinical data. Methods used included a literature review of bibliographic databases, university health informatics departments, and national and international medical informatics associations. The results show that the current state of development of computers and data processing means there is no practical alternative to coding data. The identified barriers to clinical coding are: the limitations of the coding systems and terminologies and the skill gap in their use; recording structured data in the consultation takes time and is distracting; the level of motivation of primary care professionals; and the priority within the organization. A taxonomy is proposed to describe the barriers to clinical coding. This can be used to identify barriers to coding and facilitate the development of strategies to overcome them.

Do plant cell walls have a code?

PubMed

Tavares, Eveline Q P; Buckeridge, Marcos S

2015-12-01

A code is a set of rules that establish correspondence between two worlds, signs (consisting of encrypted information) and meaning (of the decrypted message). A third element, the adaptor, connects both worlds, assigning meaning to a code. We propose that a Glycomic Code exists in plant cell walls where signs are represented by monosaccharides and phenylpropanoids and meaning is cell wall architecture with its highly complex association of polymers. Cell wall biosynthetic mechanisms, structure, architecture and properties are addressed according to Code Biology perspective, focusing on how they oppose to cell wall deconstruction. Cell wall hydrolysis is mainly focused as a mechanism of decryption of the Glycomic Code. Evidence for encoded information in cell wall polymers fine structure is highlighted and the implications of the existence of the Glycomic Code are discussed. Aspects related to fine structure are responsible for polysaccharide packing and polymer-polymer interactions, affecting the final cell wall architecture. The question whether polymers assembly within a wall display similar properties as other biological macromolecules (i.e. proteins, DNA, histones) is addressed, i.e. do they display a code? Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Structural reliability assessment capability in NESSUS

NASA Technical Reports Server (NTRS)

Millwater, H.; Wu, Y.-T.

1992-01-01

The principal capabilities of NESSUS (Numerical Evaluation of Stochastic Structures Under Stress), an advanced computer code developed for probabilistic structural response analysis, are reviewed, and its structural reliability assessed. The code combines flexible structural modeling tools with advanced probabilistic algorithms in order to compute probabilistic structural response and resistance, component reliability and risk, and system reliability and risk. An illustrative numerical example is presented.

Structural reliability assessment capability in NESSUS

NASA Astrophysics Data System (ADS)

Millwater, H.; Wu, Y.-T.

1992-07-01

The principal capabilities of NESSUS (Numerical Evaluation of Stochastic Structures Under Stress), an advanced computer code developed for probabilistic structural response analysis, are reviewed, and its structural reliability assessed. The code combines flexible structural modeling tools with advanced probabilistic algorithms in order to compute probabilistic structural response and resistance, component reliability and risk, and system reliability and risk. An illustrative numerical example is presented.

Structured FORTRAN Preprocessor

NASA Technical Reports Server (NTRS)

Flynn, J. A.; Lawson, C. L.; Van Snyder, W.; Tsitsivas, H. N.

1985-01-01

SFTRAN3 supports structured programing in FORTRAN environment. Language intended particularly to support two aspects of structured programing -- nestable single-entry control structures and modularization and top-down organization of code. Code designed and written using these SFTRAN3 facilities have fewer initial errors, easier to understand and less expensive to maintain and modify.

ESTEST: A Framework for the Verification and Validation of Electronic Structure Codes

NASA Astrophysics Data System (ADS)

Yuan, Gary; Gygi, Francois

2011-03-01

ESTEST is a verification and validation (V& V) framework for electronic structure codes that supports Qbox, Quantum Espresso, ABINIT, the Exciting Code and plans support for many more. We discuss various approaches to the electronic structure V& V problem implemented in ESTEST, that are related to parsing, formats, data management, search, comparison and analyses. Additionally, an early experiment in the distribution of V& V ESTEST servers among the electronic structure community will be presented. Supported by NSF-OCI 0749217 and DOE FC02-06ER25777.

Automated Discovery of Machine-Specific Code Improvements

DTIC Science & Technology

1984-12-01

operation of the source language. Additional analysis may reveal special features of the target architecture that may be exploited to generate efficient...Additional analysis may reveal special features of the target architecture that may be exploited to generate efficient code. Such analysis is optional...incorporate knowledge of the source language, but do not refer to features of the target machine. These early phases are sometimes referred to as the

Micromagnetic Code Development of Advanced Magnetic Structures Final Report CRADA No. TC-1561-98

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cerjan, Charles J.; Shi, Xizeng

The specific goals of this project were to: Further develop the previously written micromagnetic code DADIMAG (DOE code release number 980017); Validate the code. The resulting code was expected to be more realistic and useful for simulations of magnetic structures of specific interest to Read-Rite programs. We also planned to further the code for use in internal LLNL programs. This project complemented LLNL CRADA TC-840-94 between LLNL and Read-Rite, which allowed for simulations of the advanced magnetic head development completed under the CRADA. TC-1561-98 was effective concurrently with LLNL non-exclusive copyright license (TL-1552-98) to Read-Rite for DADIMAG Version 2 executablemore » code.« less

Reconstructing past occupational exposures: how reliable are women's reports of their partner's occupation?

PubMed

Tagiyeva, Nara; Semple, Sean; Devereux, Graham; Sherriff, Andrea; Henderson, John; Elias, Peter; Ayres, Jon G

2011-06-01

Most of the evidence on agreement between self- and proxy-reported occupational data comes from interview-based studies. The authors aimed to examine agreement between women's reports of their partner's occupation and their partner's own description using questionnaire-based data collected as a part of the prospective, population-based Avon Longitudinal Study of Parents and Children. Information on present occupation was self-reported by women's partners and proxy-reported by women through questionnaires administered at 8 and 21 months after the birth of a child. Job titles were coded to the Standard Occupational Classification (SOC2000) using software developed by the University of Warwick (Computer-Assisted Structured Coding Tool). The accuracy of proxy-report was expressed as percentage agreement and kappa coefficients for four-, three- and two-digit SOC2000 codes obtained in automatic and semiautomatic (manually improved) coding modes. Data from 6016 couples at 8 months and 5232 couples at 21 months postnatally were included in the analyses. The agreement between men's self-reported occupation and women's report of their partner's occupation in fully automatic coding mode at four-, three- and two-digit code level was 65%, 71% and 77% at 8 months and 68%, 73% and 76% at 21 months. The accuracy of agreement was slightly improved by semiautomatic coding of occupations: 73%/73%, 78%/77% and 83%/80% at 8/21 months respectively. While this suggests that women's description of their partners' occupation can be used as a valuable tool in epidemiological research where data from partners are not available, this study revealed no agreement between these young women and their partners at the two-digit level of SOC2000 coding in approximately one in five cases. Proxy reporting of occupation introduces a statistically significant degree of error in classification. The effects of occupational misclassification by proxy reporting in retrospective occupational epidemiological studies based on questionnaire data should be considered.

Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhati, Mugdha; Lee, Christopher; Nancarrow, Amy L.

2008-09-03

LIM-homeodomain (LIM-HD) transcription factors form a combinatorial 'LIM code' that contributes to the specification of cell types. In the ventral spinal cord, the binary LIM homeobox protein 3 (Lhx3)/LIM domain-binding protein 1 (Ldb1) complex specifies the formation of V2 interneurons. The additional expression of islet-1 (Isl1) in adjacent cells instead specifies the formation of motor neurons through assembly of a ternary complex in which Isl1 contacts both Lhx3 and Ldb1, displacing Lhx3 as the binding partner of Ldb1. However, little is known about how this molecular switch occurs. Here, we have identified the 30-residue Lhx3-binding domain on Isl1 (Isl1{sub LBD}).more » Although the LIM interaction domain of Ldb1 (Ldb1{sub LID}) and Isl1{sub LBD} share low levels of sequence homology, X-ray and NMR structures reveal that they bind Lhx3 in an identical manner, that is, Isl1{sub LBD} mimics Ldb1{sub LID}. These data provide a structural basis for the formation of cell type-specific protein-protein interactions in which unstructured linear motifs with diverse sequences compete to bind protein partners. The resulting alternate protein complexes can target different genes to regulate key biological events.« less

Isolation and sequencing of the gene encoding Sp23, a structural protein of spermatophore of the mealworm beetle, Tenebrio molitor.

PubMed

Feng, X; Happ, G M

1996-11-14

The cDNA for Sp23, a structural protein of the spermatophore of Tenebrio molitor, had been previously cloned and characterized (Paesen, G.C., Schwartz, M.B., Peferoen, M., Weyda, F. and Happ, G.M. (1992a) Amino acid sequence of Sp23, a structure protein of the spermatophore of the mealworm beetle, Tenebrio molitor. J. Biol. Chem. 257, 18852-18857). Using the labeled cDNA for Sp23 as a probe to screen a library of genomic DNA from Tenebrio molitor, we isolated a genomic clone for Sp23. A 5373-base pair (bp) restriction fragment containing the Sp23 gene was sequenced. The coding region is separated by a 55-bp intron which is located close to the translation start site. Three putative ecdysone response elements (EcRE) are identified in the 5' flanking region of the Sp23 gene. Comparison of the flanking regions of the Sp23 gene with those of the D-protein gene expressed in the accessory glands of Tenebrio reveals similar sequences present in the flanking regions of the two genes. The genomic organization of the coding region of the Sp23 gene shares similarities with that of the D-protein gene, three Drosophila accessory gland genes and two Drosophila 20-OH ecdysone-responsive genes.

Functional Equivalence Acceptance Testing of FUN3D for Entry Descent and Landing Applications

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.; Wood, William A.; Kleb, William L.; Alter, Stephen J.; Glass, Christopher E.; Padilla, Jose F.; Hammond, Dana P.; White, Jeffery A.

2013-01-01

The functional equivalence of the unstructured grid code FUN3D to the the structured grid code LAURA (Langley Aerothermodynamic Upwind Relaxation Algorithm) is documented for applications of interest to the Entry, Descent, and Landing (EDL) community. Examples from an existing suite of regression tests are used to demonstrate the functional equivalence, encompassing various thermochemical models and vehicle configurations. Algorithm modifications required for the node-based unstructured grid code (FUN3D) to reproduce functionality of the cell-centered structured code (LAURA) are also documented. Challenges associated with computation on tetrahedral grids versus computation on structured-grid derived hexahedral systems are discussed.

Computer analysis of protein functional sites projection on exon structure of genes in Metazoa.

PubMed

Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A

2015-01-01

Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and allow a better understanding of the emergence of biological diversity.

Burst Firing is a Neural Code in an Insect Auditory System

PubMed Central

Eyherabide, Hugo G.; Rokem, Ariel; Herz, Andreas V. M.; Samengo, Inés

2008-01-01

Various classes of neurons alternate between high-frequency discharges and silent intervals. This phenomenon is called burst firing. To analyze burst activity in an insect system, grasshopper auditory receptor neurons were recorded in vivo for several distinct stimulus types. The experimental data show that both burst probability and burst characteristics are strongly influenced by temporal modulations of the acoustic stimulus. The tendency to burst, hence, is not only determined by cell-intrinsic processes, but also by their interaction with the stimulus time course. We study this interaction quantitatively and observe that bursts containing a certain number of spikes occur shortly after stimulus deflections of specific intensity and duration. Our findings suggest a sparse neural code where information about the stimulus is represented by the number of spikes per burst, irrespective of the detailed interspike-interval structure within a burst. This compact representation cannot be interpreted as a firing-rate code. An information-theoretical analysis reveals that the number of spikes per burst reliably conveys information about the amplitude and duration of sound transients, whereas their time of occurrence is reflected by the burst onset time. The investigated neurons encode almost half of the total transmitted information in burst activity. PMID:18946533

Auditory Spatial Attention Representations in the Human Cerebral Cortex

PubMed Central

Kong, Lingqiang; Michalka, Samantha W.; Rosen, Maya L.; Sheremata, Summer L.; Swisher, Jascha D.; Shinn-Cunningham, Barbara G.; Somers, David C.

2014-01-01

Auditory spatial attention serves important functions in auditory source separation and selection. Although auditory spatial attention mechanisms have been generally investigated, the neural substrates encoding spatial information acted on by attention have not been identified in the human neocortex. We performed functional magnetic resonance imaging experiments to identify cortical regions that support auditory spatial attention and to test 2 hypotheses regarding the coding of auditory spatial attention: 1) auditory spatial attention might recruit the visuospatial maps of the intraparietal sulcus (IPS) to create multimodal spatial attention maps; 2) auditory spatial information might be encoded without explicit cortical maps. We mapped visuotopic IPS regions in individual subjects and measured auditory spatial attention effects within these regions of interest. Contrary to the multimodal map hypothesis, we observed that auditory spatial attentional modulations spared the visuotopic maps of IPS; the parietal regions activated by auditory attention lacked map structure. However, multivoxel pattern analysis revealed that the superior temporal gyrus and the supramarginal gyrus contained significant information about the direction of spatial attention. These findings support the hypothesis that auditory spatial information is coded without a cortical map representation. Our findings suggest that audiospatial and visuospatial attention utilize distinctly different spatial coding schemes. PMID:23180753

Reviewing the Challenges and Opportunities Presented by Code Switching and Mixing in Bangla

ERIC Educational Resources Information Center

Hasan, Md. Kamrul; Akhand, Mohd. Moniruzzaman

2015-01-01

This paper investigates the issues related to code-switching/code-mixing in an ESL context. Some preliminary data on Bangla-English code-switching/code-mixing has been analyzed in order to determine which structural pattern of code-switching/code-mixing is predominant in different social strata. This study also explores the relationship of…

Reviewing the Challenges and Opportunities Presented by Code Switching and Mixing in Bangla

ERIC Educational Resources Information Center

Hasan, Md. Kamrul; Akhand, Mohd. Moniruzzaman

2014-01-01

This paper investigates the issues related to code-switching/code-mixing in an ESL context. Some preliminary data on Bangla-English code-switching/code-mixing has been analyzed in order to determine which structural pattern of code-switching/code-mixing is predominant in different social strata. This study also explores the relationship of…

Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family

PubMed Central

Sinha, Sangita; Rappu, Pekka; Lange, S. C.; Mäntsälä, Pekka; Zalkin, Howard; Smith, Janet L.

1999-01-01

The yabJ gene in Bacillus subtilis is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The molecular mechanism of YabJ is unknown. YabJ is a member of a large, widely distributed family of proteins of unknown biochemical function. The 1.7-Å crystal structure of YabJ reveals a trimeric organization with extensive buried hydrophobic surface and an internal water-filled cavity. The most important finding in the structure is a deep, narrow cleft between subunits lined with nine side chains that are invariant among the 25 most similar homologs. This conserved site is proposed to be a binding or catalytic site for a ligand or substrate that is common to YabJ and other members of the YER057c/YjgF/UK114 family of proteins. PMID:10557275

Investigation of electronic structure and chemical bonding of intermetallic Pd2HfIn: An ab-initio study

NASA Astrophysics Data System (ADS)

Bano, Amreen; Gaur, N. K.

2018-05-01

Ab-initio calculations are carried out to study the electronic and chemical bonding properties of Intermetallic full Heusler compound Pd2HfIn which crystallizes in F-43m structure. All calculations are performed by using density functional theory (DFT) based code Quantum Espresso. Generalized gradient approximations (GGA) of Perdew- Burke- Ernzerhof (PBE) have been adopted for exchange-correlation potential. Calculated electronic band structure reveals the metallic character of the compound. From partial density of states (PDoS), we found the presence of relatively high intensity electronic states of 4d-Pd atom at Fermi level. We have found a pseudo-gap just abouve the Fermi level and N(E) at Fermi level is observed to be 0.8 states/eV, these finding indicates the existence of superconducting character in Pd2HfIn.

Characterizing RNA ensembles from NMR data with kinematic models

PubMed Central

Fonseca, Rasmus; Pachov, Dimitar V.; Bernauer, Julie; van den Bedem, Henry

2014-01-01

Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention. PMID:25114056

Systematically frameshifting by deletion of every 4th or 4th and 5th nucleotides during mitochondrial transcription: RNA self-hybridization regulates delRNA expression.

PubMed

Seligmann, Hervé

2016-01-01

In mitochondria, secondary structures punctuate post-transcriptional RNA processing. Recently described transcripts match the human mitogenome after systematic deletions of every 4th, respectively every 4th and 5th nucleotides, called delRNAs. Here I explore predicted stem-loop hairpin formation by delRNAs, and their associations with delRNA transcription and detected peptides matching their translation. Despite missing 25, respectively 40% of the nucleotides in the original sequence, del-transformed sequences form significantly more secondary structures than corresponding randomly shuffled sequences, indicating biological function, independently of, and in combination with, previously detected delRNA and thereof translated peptides. Self-hybridization decreases delRNA abundances, indicating downregulation. Systematic deletions of the human mitogenome reveal new, unsuspected coding and structural informations. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The puzzling structure in Saturn's outer B ring

NASA Astrophysics Data System (ADS)

Nicholson, Philip D.; Hedman, Matt; Buckingham, Rikley

2017-06-01

As first noted in Voyager images, the outer edge of Saturn's B ring is strongly perturbed by the 2:1 inner Lindblad resonance with Mimas (Porco \\etal\\ 1984). Cassini imaging and occultation data have revealed a more complex situation, where the expected resonantly-forced m=2 perturbation with an amplitude of 33~km is accompanied by freemodes with m=1, 2, 3, 4 and 5 (Spitale & Porco 2010, Nicholson \\etal\\ 2014a). To date, however, the structure immediately interior to the ring edge has not been examined carefully. We have compared optical depth profiles of the outer 1000~km of the B ring, using a large set of stellar occultations carried out since 2005 by the Cassini VIMS instrument. A search for wavelike structure, using a code written to search for hidden density waves (Hedman \\& Nicholson 2016), reveals a significant signature at a radius of ~117,150 km with a radial wavelength of ~110 km. This appears to be a trailing spiral with m=1 and a pattern speed equal to the local apsidal precession rate, $\\dpi\\simeq5.12\\dd$. Further searches for organized large-scale structure have revealed none with m=2 (as might have been expected), but several additional regions with significant m=1 variations and pattern speeds close to the local value of $\\dpi$. At present, it is unclear if these represent propagating spirals, standing waves, or perhaps features more akin to the eccentric ringlets often seen within gaps in the C ring and Cassini Division (Nicholson \\etal\\ 2014b, French \\etal\\ 2016). Comparisons of sets of profiles from 2008/9, 2012-14 and 2016 seem to show that these structures are changing over time.

The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

NASA Astrophysics Data System (ADS)

Štambuk, Nikola

The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

Computation of viscous blast wave flowfields

NASA Technical Reports Server (NTRS)

Atwood, Christopher A.

1991-01-01

A method to determine unsteady solutions of the Navier-Stokes equations was developed and applied. The structural finite-volume, approximately factored implicit scheme uses Newton subiterations to obtain the spatially and temporally second-order accurate time history of the interaction of blast-waves with stationary targets. The inviscid flux is evaluated using MacCormack's modified Steger-Warming flux or Roe flux difference splittings with total variation diminishing limiters, while the viscous flux is computed using central differences. The use of implicit boundary conditions in conjunction with a telescoping in time and space method permitted solutions to this strongly unsteady class of problems. Comparisons of numerical, analytical, and experimental results were made in two and three dimensions. These comparisons revealed accurate wave speed resolution with nonoscillatory discontinuity capturing. The purpose of this effort was to address the three-dimensional, viscous blast-wave problem. Test cases were undertaken to reveal these methods' weaknesses in three regimes: (1) viscous-dominated flow; (2) complex unsteady flow; and (3) three-dimensional flow. Comparisons of these computations to analytic and experimental results provided initial validation of the resultant code. Addition details on the numerical method and on the validation can be found in the appendix. Presently, the code is capable of single zone computations with selection of any permutation of solid wall or flow-through boundaries.

Diabetes Mellitus Coding Training for Family Practice Residents.

PubMed

Urse, Geraldine N

2015-07-01

Although physicians regularly use numeric coding systems such as the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) to describe patient encounters, coding errors are common. One of the most complicated diagnoses to code is diabetes mellitus. The ICD-9-CM currently has 39 separate codes for diabetes mellitus; this number will be expanded to more than 50 with the introduction of ICD-10-CM in October 2015. To assess the effect of a 1-hour focused presentation on ICD-9-CM codes on diabetes mellitus coding. A 1-hour focused lecture on the correct use of diabetes mellitus codes for patient visits was presented to family practice residents at Doctors Hospital Family Practice in Columbus, Ohio. To assess resident knowledge of the topic, a pretest and posttest were given to residents before and after the lecture, respectively. Medical records of all patients with diabetes mellitus who were cared for at the hospital 6 weeks before and 6 weeks after the lecture were reviewed and compared for the use of diabetes mellitus ICD-9 codes. Eighteen residents attended the lecture and completed the pretest and posttest. The mean (SD) percentage of correct answers was 72.8% (17.1%) for the pretest and 84.4% (14.6%) for the posttest, for an improvement of 11.6 percentage points (P≤.035). The percentage of total available codes used did not substantially change from before to after the lecture, but the use of the generic ICD-9-CM code for diabetes mellitus type II controlled (250.00) declined (58 of 176 [33%] to 102 of 393 [26%]) and the use of other codes increased, indicating a greater variety in codes used after the focused lecture. After a focused lecture on diabetes mellitus coding, resident coding knowledge improved. Review of medical record data did not reveal an overall change in the number of diabetic codes used after the lecture but did reveal a greater variety in the codes used.

The Pekin duck programmed death-ligand 1: cDNA cloning, genomic structure, molecular characterization and mRNA expression analysis.

PubMed

Yao, Q; Fischer, K P; Tyrrell, D L; Gutfreund, K S

2015-04-01

Programmed death ligand-1 (PD-L1) plays an important role in the attenuation of adaptive immune responses in higher vertebrates. Here, we describe the identification of the Pekin duck PD-L1 orthologue (duPD-L1) and its gene structure. The duPD-L1 cDNA encodes a 311-amino acid protein that has an amino acid identity of 78% and 42% with chicken and human PD-L1, respectively. Mapping of the duPD-L1 cDNA with duck genomic sequences revealed an exonic structure of its coding sequence similar to those of other vertebrates but lacked a noncoding exon 1. Homology modelling of the duPD-L1 extracellular domain was compatible with the tandem IgV-like and IgC-like IgSF domain structure of human PD-L1 (PDB ID: 3BIS). Residues known to be important for receptor binding of human PD-L1 were mostly conserved in duPD-L1 within the N-terminus and the G sheet, and partially conserved within the F sheet but not within sheets C and C'. DuPD-L1 mRNA was constitutively expressed in all tissues examined with highest expression levels in lung and spleen and very low levels of expression in muscle, kidney and brain. Mitogen stimulation of duck peripheral blood mononuclear cells transiently increased duPD-L1 mRNA expression. Our observations demonstrate evolutionary conservation of the exonic structure of its coding sequence, the extracellular domain structure and residues implicated in receptor binding, but the role of the longer cytoplasmic tail in avian PD-L1 proteins remains to be determined. © 2014 John Wiley & Sons Ltd.

Combining Thermal And Structural Analyses

NASA Technical Reports Server (NTRS)

Winegar, Steven R.

1990-01-01

Computer code makes programs compatible so stresses and deformations calculated. Paper describes computer code combining thermal analysis with structural analysis. Called SNIP (for SINDA-NASTRAN Interfacing Program), code provides interface between finite-difference thermal model of system and finite-element structural model when no node-to-element correlation between models. Eliminates much manual work in converting temperature results of SINDA (Systems Improved Numerical Differencing Analyzer) program into thermal loads for NASTRAN (NASA Structural Analysis) program. Used to analyze concentrating reflectors for solar generation of electric power. Large thermal and structural models needed to predict distortion of surface shapes, and SNIP saves considerable time and effort in combining models.

Evolution of Structure and Composition in Saturn's Rings Due to Ballistic Transport of Micrometeoroid Impact Ejecta

NASA Astrophysics Data System (ADS)

Estrada, P. R.; Durisen, R. H.; Cuzzi, J. N.

2014-04-01

We introduce improved numerical techniques for simulating the structural and compositional evolution of planetary rings due to micrometeoroid bombardment and subsequent ballistic transport of impact ejecta. Our current, robust code, which is based on the original structural code of [1] and on the pollution transport code of [3], is capable of modeling structural changes and pollution transport simultaneously over long times on both local and global scales. We provide demonstrative simulations to compare with, and extend upon previous work, as well as examples of how ballistic transport can maintain the observed structure in Saturn's rings using available Cassini occultation optical depth data.

Featured Image: Tests of an MHD Code

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2016-09-01

Creating the codes that are used to numerically model astrophysical systems takes a lot of work and a lot of testing! A new, publicly available moving-mesh magnetohydrodynamics (MHD) code, DISCO, is designed to model 2D and 3D orbital fluid motion, such as that of astrophysical disks. In a recent article, DISCO creator Paul Duffell (University of California, Berkeley) presents the code and the outcomes from a series of standard tests of DISCOs stability, accuracy, and scalability.From left to right and top to bottom, the test outputs shown above are: a cylindrical Kelvin-Helmholtz flow (showing off DISCOs numerical grid in 2D), a passive scalar in a smooth vortex (can DISCO maintain contact discontinuities?), a global look at the cylindrical Kelvin-Helmholtz flow, a Jupiter-mass planet opening a gap in a viscous disk, an MHD flywheel (a test of DISCOs stability), an MHD explosion revealing shock structures, an MHD rotor (a more challenging version of the explosion), a Flock 3D MRI test (can DISCO study linear growth of the magnetorotational instability in disks?), and a nonlinear 3D MRI test.Check out the gif below for a closer look at each of these images, or follow the link to the original article to see even more!CitationPaul C. Duffell 2016 ApJS 226 2. doi:10.3847/0067-0049/226/1/2

A toolbox of lectins for translating the sugar code: the galectin network in phylogenesis and tumors.

PubMed

Kaltner, H; Gabius, H-J

2012-04-01

Lectin histochemistry has revealed cell-type-selective glycosylation. It is under dynamic and spatially controlled regulation. Since their chemical properties allow carbohydrates to reach unsurpassed structural diversity in oligomers, they are ideal for high density information coding. Consequently, the concept of the sugar code assigns a functional dimension to the glycans of cellular glycoconjugates. Indeed, multifarious cell processes depend on specific recognition of glycans by their receptors (lectins), which translate the sugar-encoded information into effects. Duplication of ancestral genes and the following divergence of sequences account for the evolutionary dynamics in lectin families. Differences in gene number can even appear among closely related species. The adhesion/growth-regulatory galectins are selected as an instructive example to trace the phylogenetic diversification in several animals, most of them popular models in developmental and tumor biology. Chicken galectins are identified as a low-level-complexity set, thus singled out for further detailed analysis. The various operative means for establishing protein diversity among the chicken galectins are delineated, and individual characteristics in expression profiles discerned. To apply this galectin-fingerprinting approach in histopathology has potential for refining differential diagnosis and for obtaining prognostic assessments. On the grounds of in vitro work with tumor cells a strategically orchestrated co-regulation of galectin expression with presentation of cognate glycans is detected. This coordination epitomizes the far-reaching physiological significance of sugar coding.

Comparing Different Strategies in Directed Evolution of Enzyme Stereoselectivity: Single- versus Double-Code Saturation Mutagenesis.

PubMed

Sun, Zhoutong; Lonsdale, Richard; Li, Guangyue; Reetz, Manfred T

2016-10-04

Saturation mutagenesis at sites lining the binding pockets of enzymes constitutes a viable protein engineering technique for enhancing or inverting stereoselectivity. Statistical analysis shows that oversampling in the screening step (the bottleneck) increases astronomically as the number of residues in the randomization site increases, which is the reason why reduced amino acid alphabets have been employed, in addition to splitting large sites into smaller ones. Limonene epoxide hydrolase (LEH) has previously served as the experimental platform in these methodological efforts, enabling comparisons between single-code saturation mutagenesis (SCSM) and triple-code saturation mutagenesis (TCSM); these employ either only one or three amino acids, respectively, as building blocks. In this study the comparative platform is extended by exploring the efficacy of double-code saturation mutagenesis (DCSM), in which the reduced amino acid alphabet consists of two members, chosen according to the principles of rational design on the basis of structural information. The hydrolytic desymmetrization of cyclohexene oxide is used as the model reaction, with formation of either (R,R)- or (S,S)-cyclohexane-1,2-diol. DCSM proves to be clearly superior to the likewise tested SCSM, affording both R,R- and S,S-selective mutants. These variants are also good catalysts in reactions of further substrates. Docking computations reveal the basis of enantioselectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

PubMed

Giannozzi, Paolo; Baroni, Stefano; Bonini, Nicola; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Chiarotti, Guido L; Cococcioni, Matteo; Dabo, Ismaila; Dal Corso, Andrea; de Gironcoli, Stefano; Fabris, Stefano; Fratesi, Guido; Gebauer, Ralph; Gerstmann, Uwe; Gougoussis, Christos; Kokalj, Anton; Lazzeri, Michele; Martin-Samos, Layla; Marzari, Nicola; Mauri, Francesco; Mazzarello, Riccardo; Paolini, Stefano; Pasquarello, Alfredo; Paulatto, Lorenzo; Sbraccia, Carlo; Scandolo, Sandro; Sclauzero, Gabriele; Seitsonen, Ari P; Smogunov, Alexander; Umari, Paolo; Wentzcovitch, Renata M

2009-09-30

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Qualitative assessment of cause-of-injury coding in U.S. military hospitals: NATO standardization agreement (STANAG) 2050.

PubMed

Amoroso, P J; Smith, G S; Bell, N S

2000-04-01

Accurate injury cause data are essential for injury prevention research. U.S. military hospitals, unlike civilian hospitals, use the NATO STANAG system for cause-of-injury coding. Reported deficiencies in civilian injury cause data suggested a need to specifically evaluate the STANAG. The Total Army Injury and Health Outcomes Database (TAIHOD) was used to evaluate worldwide Army injury hospitalizations, especially STANAG Trauma, Injury, and Place of Occurrence coding. We conducted a review of hospital procedures at Tripler Army Medical Center (TAMC) including injury cause and intent coding, potential crossover between acute injuries and musculoskeletal conditions, and data for certain hospital patients who are not true admissions. We also evaluated the use of free-text injury comment fields in three hospitals. Army-wide review of injury records coding revealed full compliance with cause coding, although nonspecific codes appeared to be overused. A small but intensive single hospital records review revealed relatively poor intent coding but good activity and cause coding. Data on specific injury history were present on most acute injury records and 75% of musculoskeletal conditions. Place of Occurrence coding, although inherently nonspecific, was over 80% accurate. Review of text fields produced additional details of the injuries in over 80% of cases. STANAG intent coding specificity was poor, while coding of cause of injury was at least comparable to civilian systems. The strengths of military hospital data systems are an exceptionally high compliance with injury cause coding, the availability of free text, and capture of all population hospital records without regard to work-relatedness. Simple changes in procedures could greatly improve data quality.

Non-adiabatic Excited State Molecule Dynamics Modeling of Photochemistry and Photophysics of Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Tammie Renee; Tretiak, Sergei

2017-01-06

Understanding and controlling excited state dynamics lies at the heart of all our efforts to design photoactive materials with desired functionality. This tailor-design approach has become the standard for many technological applications (e.g., solar energy harvesting) including the design of organic conjugated electronic materials with applications in photovoltaic and light-emitting devices. Over the years, our team has developed efficient LANL-based codes to model the relevant photophysical processes following photoexcitation (spatial energy transfer, excitation localization/delocalization, and/or charge separation). The developed approach allows the non-radiative relaxation to be followed on up to ~10 ps timescales for large realistic molecules (hundreds of atomsmore » in size) in the realistic solvent dielectric environment. The Collective Electronic Oscillator (CEO) code is used to compute electronic excited states, and the Non-adiabatic Excited State Molecular Dynamics (NA-ESMD) code is used to follow the non-adiabatic dynamics on multiple coupled Born-Oppenheimer potential energy surfaces. Our preliminary NA-ESMD simulations have revealed key photoinduced mechanisms controlling competing interactions and relaxation pathways in complex materials, including organic conjugated polymer materials, and have provided a detailed understanding of photochemical products and intermediates and the internal conversion process during the initiation of energetic materials. This project will be using LANL-based CEO and NA-ESMD codes to model nonradiative relaxation in organic and energetic materials. The NA-ESMD and CEO codes belong to a class of electronic structure/quantum chemistry codes that require large memory, “long-queue-few-core” distribution of resources in order to make useful progress. The NA-ESMD simulations are trivially parallelizable requiring ~300 processors for up to one week runtime to reach a meaningful restart point.« less

Louder than words: power and conflict in interprofessional education articles, 1954–2013

PubMed Central

Paradis, Elise; Whitehead, Cynthia R

2015-01-01

Context Interprofessional education (IPE) aspires to enable collaborative practice. Current IPE offerings, although rapidly proliferating, lack evidence of efficacy and theoretical grounding. Objectives Our research aimed to explore the historical emergence of the field of IPE and to analyse the positioning of this academic field of inquiry. In particular, we sought to investigate the extent to which power and conflict – elements central to interprofessional care – figure in the IPE literature. Methods We used a combination of deductive and inductive automated coding and manual coding to explore the contents of 2191 articles in the IPE literature published between 1954 and 2013. Inductive coding focused on the presence and use of the sociological (rather than statistical) version of power, which refers to hierarchies and asymmetries among the professions. Articles found to be centrally about power were then analysed using content analysis. Results Publications on IPE have grown exponentially in the past decade. Deductive coding of identified articles showed an emphasis on students, learning, programmes and practice. Automated inductive coding of titles and abstracts identified 129 articles potentially about power, but manual coding found that only six articles put power and conflict at the centre. Content analysis of these six articles revealed that two provided tentative explorations of power dynamics, one skirted around this issue, and three explicitly theorised and integrated power and conflict. Conclusions The lack of attention to power and conflict in the IPE literature suggests that many educators do not foreground these issues. Education programmes are expected to transform individuals into effective collaborators, without heed to structural, organisational and institutional factors. In so doing, current constructions of IPE veil the problems that IPE attempts to solve. PMID:25800300

Building an ontology of pulmonary diseases with natural language processing tools using textual corpora.

PubMed

Baneyx, Audrey; Charlet, Jean; Jaulent, Marie-Christine

2007-01-01

Pathologies and acts are classified in thesauri to help physicians to code their activity. In practice, the use of thesauri is not sufficient to reduce variability in coding and thesauri are not suitable for computer processing. We think the automation of the coding task requires a conceptual modeling of medical items: an ontology. Our task is to help lung specialists code acts and diagnoses with software that represents medical knowledge of this concerned specialty by an ontology. The objective of the reported work was to build an ontology of pulmonary diseases dedicated to the coding process. To carry out this objective, we develop a precise methodological process for the knowledge engineer in order to build various types of medical ontologies. This process is based on the need to express precisely in natural language the meaning of each concept using differential semantics principles. A differential ontology is a hierarchy of concepts and relationships organized according to their similarities and differences. Our main research hypothesis is to apply natural language processing tools to corpora to develop the resources needed to build the ontology. We consider two corpora, one composed of patient discharge summaries and the other being a teaching book. We propose to combine two approaches to enrich the ontology building: (i) a method which consists of building terminological resources through distributional analysis and (ii) a method based on the observation of corpus sequences in order to reveal semantic relationships. Our ontology currently includes 1550 concepts and the software implementing the coding process is still under development. Results show that the proposed approach is operational and indicates that the combination of these methods and the comparison of the resulting terminological structures give interesting clues to a knowledge engineer for the building of an ontology.

Louder than words: power and conflict in interprofessional education articles, 1954-2013.

PubMed

Paradis, Elise; Whitehead, Cynthia R

2015-04-01

Interprofessional education (IPE) aspires to enable collaborative practice. Current IPE offerings, although rapidly proliferating, lack evidence of efficacy and theoretical grounding. Our research aimed to explore the historical emergence of the field of IPE and to analyse the positioning of this academic field of inquiry. In particular, we sought to investigate the extent to which power and conflict - elements central to interprofessional care - figure in the IPE literature. We used a combination of deductive and inductive automated coding and manual coding to explore the contents of 2191 articles in the IPE literature published between 1954 and 2013. Inductive coding focused on the presence and use of the sociological (rather than statistical) version of power, which refers to hierarchies and asymmetries among the professions. Articles found to be centrally about power were then analysed using content analysis. Publications on IPE have grown exponentially in the past decade. Deductive coding of identified articles showed an emphasis on students, learning, programmes and practice. Automated inductive coding of titles and abstracts identified 129 articles potentially about power, but manual coding found that only six articles put power and conflict at the centre. Content analysis of these six articles revealed that two provided tentative explorations of power dynamics, one skirted around this issue, and three explicitly theorised and integrated power and conflict. The lack of attention to power and conflict in the IPE literature suggests that many educators do not foreground these issues. Education programmes are expected to transform individuals into effective collaborators, without heed to structural, organisational and institutional factors. In so doing, current constructions of IPE veil the problems that IPE attempts to solve. © 2015 The Authors Medical Education Published by John Wiley & Sons Ltd.

Subspace-Aware Index Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kailkhura, Bhavya; Theagarajan, Lakshmi Narasimhan; Varshney, Pramod K.

In this paper, we generalize the well-known index coding problem to exploit the structure in the source-data to improve system throughput. In many applications (e.g., multimedia), the data to be transmitted may lie (or can be well approximated) in a low-dimensional subspace. We exploit this low-dimensional structure of the data using an algebraic framework to solve the index coding problem (referred to as subspace-aware index coding) as opposed to the traditional index coding problem which is subspace-unaware. Also, we propose an efficient algorithm based on the alternating minimization approach to obtain near optimal index codes for both subspace-aware and -unawaremore » cases. In conclusion, our simulations indicate that under certain conditions, a significant throughput gain (about 90%) can be achieved by subspace-aware index codes over conventional subspace-unaware index codes.« less

Subspace-Aware Index Codes

DOE PAGES

Kailkhura, Bhavya; Theagarajan, Lakshmi Narasimhan; Varshney, Pramod K.

2017-04-12

In this paper, we generalize the well-known index coding problem to exploit the structure in the source-data to improve system throughput. In many applications (e.g., multimedia), the data to be transmitted may lie (or can be well approximated) in a low-dimensional subspace. We exploit this low-dimensional structure of the data using an algebraic framework to solve the index coding problem (referred to as subspace-aware index coding) as opposed to the traditional index coding problem which is subspace-unaware. Also, we propose an efficient algorithm based on the alternating minimization approach to obtain near optimal index codes for both subspace-aware and -unawaremore » cases. In conclusion, our simulations indicate that under certain conditions, a significant throughput gain (about 90%) can be achieved by subspace-aware index codes over conventional subspace-unaware index codes.« less

GRID-seq reveals the global RNA-chromatin interactome

PubMed Central

Li, Xiao; Zhou, Bing; Chen, Liang; Gou, Lan-Tao; Li, Hairi; Fu, Xiang-Dong

2017-01-01

Higher eukaryotic genomes are bound by a large number of coding and non-coding RNAs, but approaches to comprehensively map the identity and binding sites of these RNAs are lacking. Here we report a method to in situ capture global RNA interactions with DNA by deep sequencing (GRID-seq), which enables the comprehensive identification of the entire repertoire of chromatin-interacting RNAs and their respective binding sites. In human, mouse and Drosophila cells, we detected a large set of tissue-specific coding and non-coding RNAs that are bound to active promoters and enhancers, especially super-enhancers. Assuming that most mRNA-chromatin interactions indicate the physical proximity of a promoter and an enhancer, we constructed a three-dimensional global connectivity map of promoters and enhancers, revealing transcription activity-linked genomic interactions in the nucleus. PMID:28922346

12 CFR Appendix G to Part 360 - Deposit-Customer Join File Structure

Code of Federal Regulations, 2010 CFR

2010-01-01

..._Code Relationship CodeThe code indicating how the customer is related to the account. Possible values... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Deposit-Customer Join File Structure G Appendix... GENERAL POLICY RESOLUTION AND RECEIVERSHIP RULES Pt. 360, App. G Appendix G to Part 360—Deposit-Customer...

Ensemble Weight Enumerators for Protograph LDPC Codes

NASA Technical Reports Server (NTRS)

Divsalar, Dariush

2006-01-01

Recently LDPC codes with projected graph, or protograph structures have been proposed. In this paper, finite length ensemble weight enumerators for LDPC codes with protograph structures are obtained. Asymptotic results are derived as the block size goes to infinity. In particular we are interested in obtaining ensemble average weight enumerators for protograph LDPC codes which have minimum distance that grows linearly with block size. As with irregular ensembles, linear minimum distance property is sensitive to the proportion of degree-2 variable nodes. In this paper the derived results on ensemble weight enumerators show that linear minimum distance condition on degree distribution of unstructured irregular LDPC codes is a sufficient but not a necessary condition for protograph LDPC codes.

Electronic and Thermoelectric Properties of Ternary Chalcohalide Semiconductors: First Principles Study

NASA Astrophysics Data System (ADS)

Khan, Wilayat; Hussain, Sajjad; Minar, Jan; Azam, Sikander

2018-02-01

Ternary chalcohalides have been widely utilized for different device applications. The thermoelectric properties of SbSI, SbSeI and SbSBr have been investigated by theoretical simulations, and the findings have been performed using BoltzTraP code, based on semi-classical Boltzmann transport theory. In this study, we simulated the electronic structures using the Englo-Vosko generalized gradient approximation employed in the WIEN2k program. From the electronic band structures, we found a combination of light and heavy bands around the Fermi level in the valence band, which strongly affect the effective masses of the carriers. The entire thermoelectric parameters, like the electrical, the electronic part of the thermal conductivities, the Seebeck coefficient and the power factor have been analysed as functions of temperature and chemical potential. The correlation between the effective masses and the thermoelectric properties is also included in the discussion because the effective mass reveals the mobility of the carriers which in turn affect the thermoelectric properties. The substitution of sulfur reveals high electrical conductivity and a smaller Seebeck coefficient based on effective mass leads to the increase in the power factor.

A graphically oriented specification language for automatic code generation. GRASP/Ada: A Graphical Representation of Algorithms, Structure, and Processes for Ada, phase 1

NASA Technical Reports Server (NTRS)

Cross, James H., II; Morrison, Kelly I.; May, Charles H., Jr.; Waddel, Kathryn C.

1989-01-01

The first phase of a three-phase effort to develop a new graphically oriented specification language which will facilitate the reverse engineering of Ada source code into graphical representations (GRs) as well as the automatic generation of Ada source code is described. A simplified view of the three phases of Graphical Representations for Algorithms, Structure, and Processes for Ada (GRASP/Ada) with respect to three basic classes of GRs is presented. Phase 1 concentrated on the derivation of an algorithmic diagram, the control structure diagram (CSD) (CRO88a) from Ada source code or Ada PDL. Phase 2 includes the generation of architectural and system level diagrams such as structure charts and data flow diagrams and should result in a requirements specification for a graphically oriented language able to support automatic code generation. Phase 3 will concentrate on the development of a prototype to demonstrate the feasibility of this new specification language.

Influence of the plasma environment on atomic structure using an ion-sphere model

DOE PAGES

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

2015-09-03

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Influence of the plasma environment on atomic structure using an ion-sphere model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Atomistic structures of nano-engineered SiC and radiation-induced amorphization resistance

DOE PAGES

Imada, Kenta; Ishimaru, Manabu; Sato, Kazuhisa; ...

2015-06-18

In this paper, nano-engineered 3C–SiC thin films, which possess columnar structures with high-density stacking faults and twins, were irradiated with 2 MeV Si ions at cryogenic and room temperatures. From cross-sectional transmission electron microscopy observations in combination with Monte Carlo simulations based on the Stopping and Range of Ions in Matter code, it was found that their amorphization resistance is six times greater than bulk crystalline SiC at room temperature. High-angle bright-field images taken by spherical aberration corrected scanning transmission electron microscopy revealed that the distortion of atomic configurations is localized near the stacking faults. Finally, the resultant strain fieldmore » probably contributes to the enhancement of radiation tolerance of this material.« less

Structural and functional partitioning of bread wheat chromosome 3B.

PubMed

Choulet, Frédéric; Alberti, Adriana; Theil, Sébastien; Glover, Natasha; Barbe, Valérie; Daron, Josquin; Pingault, Lise; Sourdille, Pierre; Couloux, Arnaud; Paux, Etienne; Leroy, Philippe; Mangenot, Sophie; Guilhot, Nicolas; Le Gouis, Jacques; Balfourier, Francois; Alaux, Michael; Jamilloux, Véronique; Poulain, Julie; Durand, Céline; Bellec, Arnaud; Gaspin, Christine; Safar, Jan; Dolezel, Jaroslav; Rogers, Jane; Vandepoele, Klaas; Aury, Jean-Marc; Mayer, Klaus; Berges, Hélène; Quesneville, Hadi; Wincker, Patrick; Feuillet, Catherine

2014-07-18

We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits. Copyright © 2014, American Association for the Advancement of Science.

"Rebuilding our community": hearing silenced voices on Aboriginal youth suicide.

PubMed

Walls, Melissa L; Hautala, Dane; Hurley, Jenna

2014-02-01

This paper brings forth the voices of adult Aboriginal First Nations community members who gathered in focus groups to discuss the problem of youth suicide on their reserves. Our approach emphasizes multilevel (e.g., individual, family, and broader ecological systems) factors viewed by participants as relevant to youth suicide. Wheaton's conceptualization of stressors and Evans-Campbell's multilevel classification of the impacts of historical trauma are used as theoretical and analytic guides. Thematic analysis of qualitative data transcripts revealed a highly complex intersection of stressors, traumas, and social problems seen by community members as underlying mechanisms influencing heightened levels of Aboriginal youth suicidality. Our multilevel coding approach revealed that suicidal behaviors were described by community members largely as a problem with deep historical and contemporary structural roots, as opposed to being viewed as individualized pathology.

Burner liner thermal-structural load modeling

NASA Technical Reports Server (NTRS)

Maffeo, R.

1986-01-01

The software package Transfer Analysis Code to Interface Thermal/Structural Problems (TRANCITS) was developed. The TRANCITS code is used to interface temperature data between thermal and structural analytical models. The use of this transfer module allows the heat transfer analyst to select the thermal mesh density and thermal analysis code best suited to solve the thermal problem and gives the same freedoms to the stress analyst, without the efficiency penalties associated with common meshes and the accuracy penalties associated with the manual transfer of thermal data.

A High Altitude Ionization Structure and Scintillation Model.

DTIC Science & Technology

1979-02-19

structure and convection model into an existing systems code. The purpose is to update estimates of the scintillation effects of the structuring of the...OSEC 37.2 Fig. 16. Isodensity contours of plasma density at t - 0 sec. The ini- tial destribution for NJNO is a gaus- sian in y, centered at y - 12.1 km...striations is a task for future work. 35 - . 5. IMPLEMENTATION INTO AN EXISTING CODE In any existing systems code that uses RANC phenomenology, there

X-Ray Crystal Structure of the passenger domain of Plasmid encoded toxin(Pet), an Autotransporter Enterotoxin from enteroaggregative Escherichia coli (EAEC)

PubMed Central

Meza-Aguilar, J. Domingo; Fromme, Petra; Torres-Larios, Alfredo; Mendoza-Hernández, Guillermo; Hernandez-Chiñas, Ulises; Monteros, Roberto A. Arreguin-Espinosa de los; Campos, Carlos A. Eslava; Fromme, Raimund

2014-01-01

Autotransporters (ATs) represent a superfamily of proteins produced by a variety of pathogenic bacteria, which include the pathogenic groups of Escherichia coli (E. coli) associated with gastrointestinal and urinary tract infections. We present the first X-ray structure of the passenger domain from the Plasmid-encoded toxin (Pet) a 100 kDa protein at 2.3 Å resolution which is a cause of acute diarrhea in both developing and industrialized countries. Pet is a cytoskeleton-altering toxin that induces loss of actin stress fibers. While Pet (pdb code: 4OM9) shows only a sequence identity of 50 % compared to the closest related protein sequence, extracellular serine protease plasmid (EspP) the structural features of both proteins are conserved. A closer structural look reveals that Pet contains a β-pleaded sheet at the sequence region of residues 181-190, the corresponding structural domain in EspP consists of a coiled loop. Secondary, the Pet passenger domain features a more pronounced beta sheet between residues 135-143 compared to the structure of EspP. PMID:24530907

Energy Spectral Behaviors of Communication Networks of Open-Source Communities

PubMed Central

Yang, Jianmei; Yang, Huijie; Liao, Hao; Wang, Jiangtao; Zeng, Jinqun

2015-01-01

Large-scale online collaborative production activities in open-source communities must be accompanied by large-scale communication activities. Nowadays, the production activities of open-source communities, especially their communication activities, have been more and more concerned. Take CodePlex C # community for example, this paper constructs the complex network models of 12 periods of communication structures of the community based on real data; then discusses the basic concepts of quantum mapping of complex networks, and points out that the purpose of the mapping is to study the structures of complex networks according to the idea of quantum mechanism in studying the structures of large molecules; finally, according to this idea, analyzes and compares the fractal features of the spectra in different quantum mappings of the networks, and concludes that there are multiple self-similarity and criticality in the communication structures of the community. In addition, this paper discusses the insights and application conditions of different quantum mappings in revealing the characteristics of the structures. The proposed quantum mapping method can also be applied to the structural studies of other large-scale organizations. PMID:26047331

Development and application of structural dynamics analysis capabilities

NASA Technical Reports Server (NTRS)

Heinemann, Klaus W.; Hozaki, Shig

1994-01-01

Extensive research activities were performed in the area of multidisciplinary modeling and simulation of aerospace vehicles that are relevant to NASA Dryden Flight Research Facility. The efforts involved theoretical development, computer coding, and debugging of the STARS code. New solution procedures were developed in such areas as structures, CFD, and graphics, among others. Furthermore, systems-oriented codes were developed for rendering the code truly multidisciplinary and rather automated in nature. Also, work was performed in pre- and post-processing of engineering analysis data.

A Novel Code System for Revealing Sources of Students' Difficulties with Stoichiometry

ERIC Educational Resources Information Center

Gulacar, Ozcan; Overton, Tina L.; Bowman, Charles R.; Fynewever, Herb

2013-01-01

A coding scheme is presented and used to evaluate solutions of seventeen students working on twenty five stoichiometry problems in a think-aloud protocol. The stoichiometry problems are evaluated as a series of sub-problems (e.g., empirical formulas, mass percent, or balancing chemical equations), and the coding scheme was used to categorize each…

Code Switching in English Language Teaching (ELT) Teaching Practice in Turkey: Student Teacher Practices, Beliefs and Identity

ERIC Educational Resources Information Center

Bilgin, Sezen Seymen

2016-01-01

Code switching involves the interplay of two languages and as well as serving linguistic functions, it has social and psychological implications. In the context of English language teaching, these psychological implications reveal themselves as teachers' thought processes. While the nature of code switching in language classrooms has been widely…

Teaching, Morality, and Responsibility: A Structuralist Analysis of a Teachers' Code of Conduct

ERIC Educational Resources Information Center

Shortt, Damien; Hallett, Fiona; Spendlove, David; Hardy, Graham; Barton, Amanda

2012-01-01

In this paper we conduct a Structuralist analysis of the General Teaching Council for England's "Code of Conduct and Practice for Registered Teachers" in order to reveal how teachers are required to fulfil an apparently impossible social role. The GTCE's "Code," we argue, may be seen as an attempt by a government agency to…

G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch.

PubMed

Kaplan, Oktay I; Berber, Burak; Hekim, Nezih; Doluca, Osman

2016-11-02

Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A case study examination of structure and function in a state health department chronic disease unit.

PubMed

Alongi, Jeanne

2015-04-01

I explored the structural and operational practices of the chronic disease prevention and control unit of a state health department and proposed a conceptual model of structure, function, and effectiveness for future study. My exploratory case study examined 7 elements of organizational structure and practice. My interviews with staff and external stakeholders of a single chronic disease unit yielded quantitative and qualitative data that I coded by perspective, process, relationship, and activity. I analyzed these for patterns and emerging themes. Chi-square analysis revealed significant correlations among collaboration with goal ambiguity, political support, and responsiveness, and evidence-based decisions with goal ambiguity and responsiveness. Although my study design did not permit conclusions about causality, my findings suggested that some elements of the model might facilitate effectiveness for chronic disease units and should be studied further. My findings might have important implications for identifying levers around which capacity can be built that may strengthen effectiveness.

A Case Study Examination of Structure and Function in a State Health Department Chronic Disease Unit

PubMed Central

2015-01-01

Objectives. I explored the structural and operational practices of the chronic disease prevention and control unit of a state health department and proposed a conceptual model of structure, function, and effectiveness for future study. Methods. My exploratory case study examined 7 elements of organizational structure and practice. My interviews with staff and external stakeholders of a single chronic disease unit yielded quantitative and qualitative data that I coded by perspective, process, relationship, and activity. I analyzed these for patterns and emerging themes. Results. Chi-square analysis revealed significant correlations among collaboration with goal ambiguity, political support, and responsiveness, and evidence-based decisions with goal ambiguity and responsiveness. Conclusions. Although my study design did not permit conclusions about causality, my findings suggested that some elements of the model might facilitate effectiveness for chronic disease units and should be studied further. My findings might have important implications for identifying levers around which capacity can be built that may strengthen effectiveness. PMID:25689211

Structured Light Based 3d Scanning for Specular Surface by the Combination of Gray Code and Phase Shifting

NASA Astrophysics Data System (ADS)

Zhang, Yujia; Yilmaz, Alper

2016-06-01

Surface reconstruction using coded structured light is considered one of the most reliable techniques for high-quality 3D scanning. With a calibrated projector-camera stereo system, a light pattern is projected onto the scene and imaged by the camera. Correspondences between projected and recovered patterns are computed in the decoding process, which is used to generate 3D point cloud of the surface. However, the indirect illumination effects on the surface, such as subsurface scattering and interreflections, will raise the difficulties in reconstruction. In this paper, we apply maximum min-SW gray code to reduce the indirect illumination effects of the specular surface. We also analysis the errors when comparing the maximum min-SW gray code and the conventional gray code, which justifies that the maximum min-SW gray code has significant superiority to reduce the indirect illumination effects. To achieve sub-pixel accuracy, we project high frequency sinusoidal patterns onto the scene simultaneously. But for specular surface, the high frequency patterns are susceptible to decoding errors. Incorrect decoding of high frequency patterns will result in a loss of depth resolution. Our method to resolve this problem is combining the low frequency maximum min-SW gray code and the high frequency phase shifting code, which achieves dense 3D reconstruction for specular surface. Our contributions include: (i) A complete setup of the structured light based 3D scanning system; (ii) A novel combination technique of the maximum min-SW gray code and phase shifting code. First, phase shifting decoding with sub-pixel accuracy. Then, the maximum min-SW gray code is used to resolve the ambiguity resolution. According to the experimental results and data analysis, our structured light based 3D scanning system enables high quality dense reconstruction of scenes with a small number of images. Qualitative and quantitative comparisons are performed to extract the advantages of our new combined coding method.

The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins.

PubMed

Ponce de Leon, Miguel; de Miranda, Antonio Basilio; Alvarez-Valin, Fernando; Carels, Nicolas

2014-01-01

For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a regularity (the codon structure) resulting from physicochemical constraints on proteins and thermodynamic constraints on ribosomal machinery. The physicochemical constraints on proteins mainly come from the hydropathy and molecular weight (MW) of secondary structures as well as the energy cost of amino acid synthesis. These constraints appear through a network of statistical correlations, such as (i) the cost of amino acid synthesis, which is in favor of a higher level of guanine in the first codon position, (ii) the constructive contribution of hydropathy alternation in proteins, (iii) the spatial organization of secondary structure in proteins according to solvent accessibility, (iv) the spatial organization of secondary structure according to amino acid hydropathy, (v) the statistical correlation of MW with protein secondary structures and their overall hydropathy, (vi) the statistical correlation of thymine in the second codon position with hydropathy and the energy cost of amino acid synthesis, and (vii) the statistical correlation of adenine in the second codon position with amino acid complexity and the MW of secondary protein structures. Amino acid physicochemical properties and functional constraints on proteins constitute a code that is translated into a purine bias within the coding DNA via tRNAs. In that sense, the Rrr pattern within coding DNA is the effect of information transfer on nucleotide composition from protein to DNA by selection according to the codon positions. Thus, coding DNA structure and ribosomal machinery co-evolved to minimize the energy cost of protein coding given the functional constraints on proteins.

Changes among Israeli Youth Movements: A Structural Analysis Based on Kahane's Code of Informality

ERIC Educational Resources Information Center

Cohen, Erik H.

2015-01-01

Multi-dimensional data analysis tools are applied to Reuven Kahane's data on the informality of youth organizations, yielding a graphic portrayal of Kahane's code of informality. This structure helps address questions of the whether the eight structural components exhaustively cover the field without redundancy. Further, the structure is used to…

24 CFR 578.75 - General operations.

Code of Federal Regulations, 2014 CFR

2014-04-01

... assistance under this part must meet State or local building codes, and in the absence of State or local building codes, the International Residential Code or International Building Code (as applicable to the type of structure) of the International Code Council. (2) Services provided with assistance under this...

24 CFR 578.75 - General operations.

Code of Federal Regulations, 2013 CFR

2013-04-01

... assistance under this part must meet State or local building codes, and in the absence of State or local building codes, the International Residential Code or International Building Code (as applicable to the type of structure) of the International Code Council. (2) Services provided with assistance under this...

Transcriptome-Wide Analysis of UTRs in Non-Small Cell Lung Cancer Reveals Cancer-Related Genes with SNV-Induced Changes on RNA Secondary Structure and miRNA Target Sites

PubMed Central

Novotny, Peter; Tang, Xiaojia; Kalari, Krishna R.; Gorodkin, Jan

2014-01-01

Traditional mutation assessment methods generally focus on predicting disruptive changes in protein-coding regions rather than non-coding regulatory regions like untranslated regions (UTRs) of mRNAs. The UTRs, however, are known to have many sequence and structural motifs that can regulate translational and transcriptional efficiency and stability of mRNAs through interaction with RNA-binding proteins and other non-coding RNAs like microRNAs (miRNAs). In a recent study, transcriptomes of tumor cells harboring mutant and wild-type KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) genes in patients with non-small cell lung cancer (NSCLC) have been sequenced to identify single nucleotide variations (SNVs). About 40% of the total SNVs (73,717) identified were mapped to UTRs, but omitted in the previous analysis. To meet this obvious demand for analysis of the UTRs, we designed a comprehensive pipeline to predict the effect of SNVs on two major regulatory elements, secondary structure and miRNA target sites. Out of 29,290 SNVs in 6462 genes, we predict 472 SNVs (in 408 genes) affecting local RNA secondary structure, 490 SNVs (in 447 genes) affecting miRNA target sites and 48 that do both. Together these disruptive SNVs were present in 803 different genes, out of which 188 (23.4%) were previously known to be cancer-associated. Notably, this ratio is significantly higher (one-sided Fisher's exact test p-value = 0.032) than the ratio (20.8%) of known cancer-associated genes (n = 1347) in our initial data set (n = 6462). Network analysis shows that the genes harboring disruptive SNVs were involved in molecular mechanisms of cancer, and the signaling pathways of LPS-stimulated MAPK, IL-6, iNOS, EIF2 and mTOR. In conclusion, we have found hundreds of SNVs which are highly disruptive with respect to changes in the secondary structure and miRNA target sites within UTRs. These changes hold the potential to alter the expression of known cancer genes or genes linked to cancer-associated pathways. PMID:24416147

Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites.

PubMed

Sabarinathan, Radhakrishnan; Wenzel, Anne; Novotny, Peter; Tang, Xiaojia; Kalari, Krishna R; Gorodkin, Jan

2014-01-01

Traditional mutation assessment methods generally focus on predicting disruptive changes in protein-coding regions rather than non-coding regulatory regions like untranslated regions (UTRs) of mRNAs. The UTRs, however, are known to have many sequence and structural motifs that can regulate translational and transcriptional efficiency and stability of mRNAs through interaction with RNA-binding proteins and other non-coding RNAs like microRNAs (miRNAs). In a recent study, transcriptomes of tumor cells harboring mutant and wild-type KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) genes in patients with non-small cell lung cancer (NSCLC) have been sequenced to identify single nucleotide variations (SNVs). About 40% of the total SNVs (73,717) identified were mapped to UTRs, but omitted in the previous analysis. To meet this obvious demand for analysis of the UTRs, we designed a comprehensive pipeline to predict the effect of SNVs on two major regulatory elements, secondary structure and miRNA target sites. Out of 29,290 SNVs in 6462 genes, we predict 472 SNVs (in 408 genes) affecting local RNA secondary structure, 490 SNVs (in 447 genes) affecting miRNA target sites and 48 that do both. Together these disruptive SNVs were present in 803 different genes, out of which 188 (23.4%) were previously known to be cancer-associated. Notably, this ratio is significantly higher (one-sided Fisher's exact test p-value = 0.032) than the ratio (20.8%) of known cancer-associated genes (n = 1347) in our initial data set (n = 6462). Network analysis shows that the genes harboring disruptive SNVs were involved in molecular mechanisms of cancer, and the signaling pathways of LPS-stimulated MAPK, IL-6, iNOS, EIF2 and mTOR. In conclusion, we have found hundreds of SNVs which are highly disruptive with respect to changes in the secondary structure and miRNA target sites within UTRs. These changes hold the potential to alter the expression of known cancer genes or genes linked to cancer-associated pathways.

SPAR improved structure-fluid dynamic analysis capability, phase 2

NASA Technical Reports Server (NTRS)

Pearson, M. L.

1984-01-01

An efficient and general method of analyzing a coupled dynamic system of fluid flow and elastic structures is investigated. The improvement of Structural Performance Analysis and Redesign (SPAR) code is summarized. All error codes are documented and the SPAR processor/subroutine cross reference is included.

Comparative Mitogenomics of Plant Bugs (Hemiptera: Miridae): Identifying the AGG Codon Reassignments between Serine and Lysine

PubMed Central

Wang, Pei; Song, Fan; Cai, Wanzhi

2014-01-01

Insect mitochondrial genomes are very important to understand the molecular evolution as well as for phylogenetic and phylogeographic studies of the insects. The Miridae are the largest family of Heteroptera encompassing more than 11,000 described species and of great economic importance. For better understanding the diversity and the evolution of plant bugs, we sequence five new mitochondrial genomes and present the first comparative analysis of nine mitochondrial genomes of mirids available to date. Our result showed that gene content, gene arrangement, base composition and sequences of mitochondrial transcription termination factor were conserved in plant bugs. Intra-genus species shared more conserved genomic characteristics, such as nucleotide and amino acid composition of protein-coding genes, secondary structure and anticodon mutations of tRNAs, and non-coding sequences. Control region possessed several distinct characteristics, including: variable size, abundant tandem repetitions, and intra-genus conservation; and was useful in evolutionary and population genetic studies. The AGG codon reassignments were investigated between serine and lysine in the genera Adelphocoris and other cimicomorphans. Our analysis revealed correlated evolution between reassignments of the AGG codon and specific point mutations at the antidocons of tRNALys and tRNASer(AGN). Phylogenetic analysis indicated that mitochondrial genome sequences were useful in resolving family level relationship of Cimicomorpha. Comparative evolutionary analysis of plant bug mitochondrial genomes allowed the identification of previously neglected coding genes or non-coding regions as potential molecular markers. The finding of the AGG codon reassignments between serine and lysine indicated the parallel evolution of the genetic code in Hemiptera mitochondrial genomes. PMID:24988409

The Validation of Macro and Micro Observations of Parent-Child Dynamics Using the Relationship Affect Coding System in Early Childhood.

PubMed

Dishion, Thomas J; Mun, Chung Jung; Tein, Jenn-Yun; Kim, Hanjoe; Shaw, Daniel S; Gardner, Frances; Wilson, Melvin N; Peterson, Jenene

2017-04-01

This study examined the validity of micro social observations and macro ratings of parent-child interaction in early to middle childhood. Seven hundred and thirty-one families representing multiple ethnic groups were recruited and screened as at risk in the context of Women, Infant, and Children (WIC) Nutritional Supplement service settings. Families were randomly assigned to the Family Checkup (FCU) intervention or the control condition at age 2 and videotaped in structured interactions in the home at ages 2, 3, 4, and 5. Parent-child interaction videotapes were micro-coded using the Relationship Affect Coding System (RACS) that captures the duration of two mutual dyadic states: positive engagement and coercion. Macro ratings of parenting skills were collected after coding the videotapes to assess parent use of positive behavior support and limit setting skills (or lack thereof). Confirmatory factor analyses revealed that the measurement model of macro ratings of limit setting and positive behavior support was not supported by the data, and thus, were excluded from further analyses. However, there was moderate stability in the families' micro social dynamics across early childhood and it showed significant improvements as a function of random assignment to the FCU. Moreover, parent-child dynamics were predictive of chronic behavior problems as rated by parents in middle childhood, but not emotional problems. We conclude with a discussion of the validity of the RACS and on methodological advantages of micro social coding over the statistical limitations of macro rating observations. Future directions are discussed for observation research in prevention science.

Probabilistic structural analysis methods for select space propulsion system components

NASA Technical Reports Server (NTRS)

Millwater, H. R.; Cruse, T. A.

1989-01-01

The Probabilistic Structural Analysis Methods (PSAM) project developed at the Southwest Research Institute integrates state-of-the-art structural analysis techniques with probability theory for the design and analysis of complex large-scale engineering structures. An advanced efficient software system (NESSUS) capable of performing complex probabilistic analysis has been developed. NESSUS contains a number of software components to perform probabilistic analysis of structures. These components include: an expert system, a probabilistic finite element code, a probabilistic boundary element code and a fast probability integrator. The NESSUS software system is shown. An expert system is included to capture and utilize PSAM knowledge and experience. NESSUS/EXPERT is an interactive menu-driven expert system that provides information to assist in the use of the probabilistic finite element code NESSUS/FEM and the fast probability integrator (FPI). The expert system menu structure is summarized. The NESSUS system contains a state-of-the-art nonlinear probabilistic finite element code, NESSUS/FEM, to determine the structural response and sensitivities. A broad range of analysis capabilities and an extensive element library is present.

Simulation of Weld Mechanical Behavior to Include Welding-Induced Residual Stress and Distortion: Coupling of SYSWELD and Abaqus Codes

DTIC Science & Technology

2015-11-01

induced residual stresses and distortions from weld simulations in the SYSWELD software code in structural Finite Element Analysis ( FEA ) simulations...performed in the Abaqus FEA code is presented. The translation of these results is accomplished using a newly developed Python script. Full details of...Local Weld Model in Structural FEA ....................................................15 CONCLUSIONS

Turbo Trellis Coded Modulation With Iterative Decoding for Mobile Satellite Communications

NASA Technical Reports Server (NTRS)

Divsalar, D.; Pollara, F.

1997-01-01

In this paper, analytical bounds on the performance of parallel concatenation of two codes, known as turbo codes, and serial concatenation of two codes over fading channels are obtained. Based on this analysis, design criteria for the selection of component trellis codes for MPSK modulation, and a suitable bit-by-bit iterative decoding structure are proposed. Examples are given for throughput of 2 bits/sec/Hz with 8PSK modulation. The parallel concatenation example uses two rate 4/5 8-state convolutional codes with two interleavers. The convolutional codes' outputs are then mapped to two 8PSK modulations. The serial concatenated code example uses an 8-state outer code with rate 4/5 and a 4-state inner trellis code with 5 inputs and 2 x 8PSK outputs per trellis branch. Based on the above mentioned design criteria for fading channels, a method to obtain he structure of the trellis code with maximum diversity is proposed. Simulation results are given for AWGN and an independent Rayleigh fading channel with perfect Channel State Information (CSI).

Accumulate repeat accumulate codes

NASA Technical Reports Server (NTRS)

Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

2004-01-01

In this paper we propose an innovative channel coding scheme called 'Accumulate Repeat Accumulate codes' (ARA). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes, thus belief propagation can be used for iterative decoding of ARA codes on a graph. The structure of encoder for this class can be viewed as precoded Repeat Accumulate (RA) code or as precoded Irregular Repeat Accumulate (IRA) code, where simply an accumulator is chosen as a precoder. Thus ARA codes have simple, and very fast encoder structure when they representing LDPC codes. Based on density evolution for LDPC codes through some examples for ARA codes, we show that for maximum variable node degree 5 a minimum bit SNR as low as 0.08 dB from channel capacity for rate 1/2 can be achieved as the block size goes to infinity. Thus based on fixed low maximum variable node degree, its threshold outperforms not only the RA and IRA codes but also the best known LDPC codes with the dame maximum node degree. Furthermore by puncturing the accumulators any desired high rate codes close to code rate 1 can be obtained with thresholds that stay close to the channel capacity thresholds uniformly. Iterative decoding simulation results are provided. The ARA codes also have projected graph or protograph representation that allows for high speed decoder implementation.

Probabilistic Structural Analysis Methods (PSAM) for select space propulsion system components

NASA Technical Reports Server (NTRS)

1991-01-01

The fourth year of technical developments on the Numerical Evaluation of Stochastic Structures Under Stress (NESSUS) system for Probabilistic Structural Analysis Methods is summarized. The effort focused on the continued expansion of the Probabilistic Finite Element Method (PFEM) code, the implementation of the Probabilistic Boundary Element Method (PBEM), and the implementation of the Probabilistic Approximate Methods (PAppM) code. The principal focus for the PFEM code is the addition of a multilevel structural dynamics capability. The strategy includes probabilistic loads, treatment of material, geometry uncertainty, and full probabilistic variables. Enhancements are included for the Fast Probability Integration (FPI) algorithms and the addition of Monte Carlo simulation as an alternate. Work on the expert system and boundary element developments continues. The enhanced capability in the computer codes is validated by applications to a turbine blade and to an oxidizer duct.

[Influence of "prehistory" of sequential movements of the right and the left hand on reproduction: coding of positions, movements and sequence structure].

PubMed

Bobrova, E V; Liakhovetskiĭ, V A; Borshchevskaia, E R

2011-01-01

The dependence of errors during reproduction of a sequence of hand movements without visual feedback on the previous right- and left-hand performance ("prehistory") and on positions in space of sequence elements (random or ordered by the explicit rule) was analyzed. It was shown that the preceding information about the ordered positions of the sequence elements was used during right-hand movements, whereas left-hand movements were performed with involvement of the information about the random sequence. The data testify to a central mechanism of the analysis of spatial structure of sequence elements. This mechanism activates movement coding specific for the left hemisphere (vector coding) in case of an ordered sequence structure and positional coding specific for the right hemisphere in case of a random sequence structure.

Nonlinear Transient Problems Using Structure Compatible Heat Transfer Code

NASA Technical Reports Server (NTRS)

Hou, Gene

2000-01-01

The report documents the recent effort to enhance a transient linear heat transfer code so as to solve nonlinear problems. The linear heat transfer code was originally developed by Dr. Kim Bey of NASA Largely and called the Structure-Compatible Heat Transfer (SCHT) code. The report includes four parts. The first part outlines the formulation of the heat transfer problem of concern. The second and the third parts give detailed procedures to construct the nonlinear finite element equations and the required Jacobian matrices for the nonlinear iterative method, Newton-Raphson method. The final part summarizes the results of the numerical experiments on the newly enhanced SCHT code.

Olfactory coding: giant inhibitory neuron governs sparse odor codes.

PubMed

Gupta, Nitin; Stopfer, Mark

2011-07-12

Electrophysiological investigations in locusts have revealed that the sparseness of odor representations, in the brain region expected to mediate olfactory learning, is shaped by a unique inhibitory neuron. Copyright © 2011 Elsevier Ltd. All rights reserved.

Dissipative structures in magnetorotational turbulence

NASA Astrophysics Data System (ADS)

Ross, Johnathan; Latter, Henrik N.

2018-07-01

Via the process of accretion, magnetorotational turbulence removes energy from a disc's orbital motion and transforms it into heat. Turbulent heating is far from uniform and is usually concentrated in small regions of intense dissipation, characterized by abrupt magnetic reconnection and higher temperatures. These regions are of interest because they might generate non-thermal emission, in the form of flares and energetic particles, or thermally process solids in protoplanetary discs. Moreover, the nature of the dissipation bears on the fundamental dynamics of the magnetorotational instability (MRI) itself: local simulations indicate that the large-scale properties of the turbulence (e.g. saturation levels and the stress-pressure relationship) depend on the short dissipative scales. In this paper we undertake a numerical study of how the MRI dissipates and the small-scale dissipative structures it employs to do so. We use the Godunov code RAMSES and unstratified compressible shearing boxes. Our simulations reveal that dissipation is concentrated in ribbons of strong magnetic reconnection that are significantly elongated in azimuth, up to a scale height. Dissipative structures are hence meso-scale objects, and potentially provide a route by which large scales and small scales interact. We go on to show how these ribbons evolve over time - forming, merging, breaking apart, and disappearing. Finally, we reveal important couplings between the large-scale density waves generated by the MRI and the small-scale structures, which may illuminate the stress-pressure relationship in MRI turbulence.

Distinct Mechanisms of Recognizing Endosomal Sorting Complex Required for Transport III (ESCRT-III) Protein IST1 by Different Microtubule Interacting and Trafficking (MIT) Domains*

PubMed Central

Guo, Emily Z.; Xu, Zhaohui

2015-01-01

The endosomal sorting complex required for transport (ESCRT) machinery is responsible for membrane remodeling in a number of biological processes including multivesicular body biogenesis, cytokinesis, and enveloped virus budding. In mammalian cells, efficient abscission during cytokinesis requires proper function of the ESCRT-III protein IST1, which binds to the microtubule interacting and trafficking (MIT) domains of VPS4, LIP5, and Spartin via its C-terminal MIT-interacting motif (MIM). Here, we studied the molecular interactions between IST1 and the three MIT domain-containing proteins to understand the structural basis that governs pairwise MIT-MIM interaction. Crystal structures of the three molecular complexes revealed that IST1 binds to the MIT domains of VPS4, LIP5, and Spartin using two different mechanisms (MIM1 mode versus MIM3 mode). Structural comparison revealed that structural features in both MIT and MIM contribute to determine the specific binding mechanism. Within the IST1 MIM sequence, two phenylalanine residues were shown to be important in discriminating MIM1 versus MIM3 binding. These observations enabled us to deduce a preliminary binding code, which we applied to provide CHMP2A, a protein that normally only binds the MIT domain in the MIM1 mode, the additional ability to bind the MIT domain of Spartin in the MIM3 mode. PMID:25657007

Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC).

PubMed

Neuhaus, Klaus; Landstorfer, Richard; Fellner, Lea; Simon, Svenja; Schafferhans, Andrea; Goldberg, Tatyana; Marx, Harald; Ozoline, Olga N; Rost, Burkhard; Kuster, Bernhard; Keim, Daniel A; Scherer, Siegfried

2016-02-24

Genomes of E. coli, including that of the human pathogen Escherichia coli O157:H7 (EHEC) EDL933, still harbor undetected protein-coding genes which, apparently, have escaped annotation due to their small size and non-essential function. To find such genes, global gene expression of EHEC EDL933 was examined, using strand-specific RNAseq (transcriptome), ribosomal footprinting (translatome) and mass spectrometry (proteome). Using the above methods, 72 short, non-annotated protein-coding genes were detected. All of these showed signals in the ribosomal footprinting assay indicating mRNA translation. Seven were verified by mass spectrometry. Fifty-seven genes are annotated in other enterobacteriaceae, mainly as hypothetical genes; the remaining 15 genes constitute novel discoveries. In addition, protein structure and function were predicted computationally and compared between EHEC-encoded proteins and 100-times randomly shuffled proteins. Based on this comparison, 61 of the 72 novel proteins exhibit predicted structural and functional features similar to those of annotated proteins. Many of the novel genes show differential transcription when grown under eleven diverse growth conditions suggesting environmental regulation. Three genes were found to confer a phenotype in previous studies, e.g., decreased cattle colonization. These findings demonstrate that ribosomal footprinting can be used to detect novel protein coding genes, contributing to the growing body of evidence that hypothetical genes are not annotation artifacts and opening an additional way to study their functionality. All 72 genes are taxonomically restricted and, therefore, appear to have evolved relatively recently de novo.

On codes with multi-level error-correction capabilities

NASA Technical Reports Server (NTRS)

Lin, Shu

1987-01-01

In conventional coding for error control, all the information symbols of a message are regarded equally significant, and hence codes are devised to provide equal protection for each information symbol against channel errors. However, in some occasions, some information symbols in a message are more significant than the other symbols. As a result, it is desired to devise codes with multilevel error-correcting capabilities. Another situation where codes with multi-level error-correcting capabilities are desired is in broadcast communication systems. An m-user broadcast channel has one input and m outputs. The single input and each output form a component channel. The component channels may have different noise levels, and hence the messages transmitted over the component channels require different levels of protection against errors. Block codes with multi-level error-correcting capabilities are also known as unequal error protection (UEP) codes. Structural properties of these codes are derived. Based on these structural properties, two classes of UEP codes are constructed.

New Tool Released for Engine-Airframe Blade-Out Structural Simulations

NASA Technical Reports Server (NTRS)

Lawrence, Charles

2004-01-01

Researchers at the NASA Glenn Research Center have enhanced a general-purpose finite element code, NASTRAN, for engine-airframe structural simulations during steady-state and transient operating conditions. For steady-state simulations, the code can predict critical operating speeds, natural modes of vibration, and forced response (e.g., cabin noise and component fatigue). The code can be used to perform static analysis to predict engine-airframe response and component stresses due to maneuver loads. For transient response, the simulation code can be used to predict response due to bladeoff events and subsequent engine shutdown and windmilling conditions. In addition, the code can be used as a pretest analysis tool to predict the results of the bladeout test required for FAA certification of new and derivative aircraft engines. Before the present analysis code was developed, all the major aircraft engine and airframe manufacturers in the United States and overseas were performing similar types of analyses to ensure the structural integrity of engine-airframe systems. Although there were many similarities among the analysis procedures, each manufacturer was developing and maintaining its own structural analysis capabilities independently. This situation led to high software development and maintenance costs, complications with manufacturers exchanging models and results, and limitations in predicting the structural response to the desired degree of accuracy. An industry-NASA team was formed to overcome these problems by developing a common analysis tool that would satisfy all the structural analysis needs of the industry and that would be available and supported by a commercial software vendor so that the team members would be relieved of maintenance and development responsibilities. Input from all the team members was used to ensure that everyone's requirements were satisfied and that the best technology was incorporated into the code. Furthermore, because the code would be distributed by a commercial software vendor, it would be more readily available to engine and airframe manufacturers, as well as to nonaircraft companies that did not previously have access to this capability.

Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia

PubMed Central

Wagner, Isaac D.; Varghese, Litty B.; Hemme, Christopher L.; Wiegel, Juergen

2013-01-01

Thermal environments have island-like characteristics and provide a unique opportunity to study population structure and diversity patterns of microbial taxa inhabiting these sites. Strains having ≥98% 16S rRNA gene sequence similarity to the obligately anaerobic Firmicutes Thermoanaerobacter uzonensis were isolated from seven geothermal springs, separated by up to 1600 m, within the Uzon Caldera (Kamchatka, Russian Far East). The intraspecies variation and spatial patterns of diversity for this taxon were assessed by multilocus sequence analysis (MLSA) of 106 strains. Analysis of eight protein-coding loci (gyrB, lepA, leuS, pyrG, recA, recG, rplB, and rpoB) revealed that all loci were polymorphic and that nucleotide substitutions were mostly synonymous. There were 148 variable nucleotide sites across 8003 bp concatenates of the protein-coding loci. While pairwise FST values indicated a small but significant level of genetic differentiation between most subpopulations, there was a negligible relationship between genetic divergence and spatial separation. Strains with the same allelic profile were only isolated from the same hot spring, occasionally from consecutive years, and single locus variant (SLV) sequence types were usually derived from the same spring. While recombination occurred, there was an “epidemic” population structure in which a particular T. uzonensis sequence type rose in frequency relative to the rest of the population. These results demonstrate spatial diversity patterns for an anaerobic bacterial species in a relative small geographic location and reinforce the view that terrestrial geothermal springs are excellent places to look for biogeographic diversity patterns regardless of the involved distances. PMID:23801987

Novel insights into the response of Atlantic salmon (Salmo salar) to Piscirickettsia salmonis: Interplay of coding genes and lncRNAs during bacterial infection.

PubMed

Valenzuela-Miranda, Diego; Gallardo-Escárate, Cristian

2016-12-01

Despite the high prevalence and impact to Chilean salmon aquaculture of the intracellular bacterium Piscirickettsia salmonis, the molecular underpinnings of host-pathogen interactions remain unclear. Herein, the interplay of coding and non-coding transcripts has been proposed as a key mechanism involved in immune response. Therefore, the aim of this study was to evidence how coding and non-coding transcripts are modulated during the infection process of Atlantic salmon with P. salmonis. For this, RNA-seq was conducted in brain, spleen, and head kidney samples, revealing different transcriptional profiles according to bacterial load. Additionally, while most of the regulated genes annotated for diverse biological processes during infection, a common response associated with clathrin-mediated endocytosis and iron homeostasis was present in all tissues. Interestingly, while endocytosis-promoting factors and clathrin inductions were upregulated, endocytic receptors were mainly downregulated. Furthermore, the regulation of genes related to iron homeostasis suggested an intracellular accumulation of iron, a process in which heme biosynthesis/degradation pathways might play an important role. Regarding the non-coding response, 918 putative long non-coding RNAs were identified, where 425 were newly characterized for S. salar. Finally, co-localization and co-expression analyses revealed a strong correlation between the modulations of long non-coding RNAs and genes associated with endocytosis and iron homeostasis. These results represent the first comprehensive study of putative interplaying mechanisms of coding and non-coding RNAs during bacterial infection in salmonids. Copyright © 2016 Elsevier Ltd. All rights reserved.

Argument structure hierarchy system and method for facilitating analysis and decision-making processes

DOEpatents

Janssen, Terry

2000-01-01

A system and method for facilitating decision-making comprising a computer program causing linkage of data representing a plurality of argument structure units into a hierarchical argument structure. Each argument structure unit comprises data corresponding to a hypothesis and its corresponding counter-hypothesis, data corresponding to grounds that provide a basis for inference of the hypothesis or its corresponding counter-hypothesis, data corresponding to a warrant linking the grounds to the hypothesis or its corresponding counter-hypothesis, and data corresponding to backing that certifies the warrant. The hierarchical argument structure comprises a top level argument structure unit and a plurality of subordinate level argument structure units. Each of the plurality of subordinate argument structure units comprises at least a portion of the grounds of the argument structure unit to which it is subordinate. Program code located on each of a plurality of remote computers accepts input from one of a plurality of contributors. Each input comprises data corresponding to an argument structure unit in the hierarchical argument structure and supports the hypothesis or its corresponding counter-hypothesis. A second programming code is adapted to combine the inputs into a single hierarchical argument structure. A third computer program code is responsive to the second computer program code and is adapted to represent a degree of support for the hypothesis and its corresponding counter-hypothesis in the single hierarchical argument structure.

Progressive Dictionary Learning with Hierarchical Predictive Structure for Scalable Video Coding.

PubMed

Dai, Wenrui; Shen, Yangmei; Xiong, Hongkai; Jiang, Xiaoqian; Zou, Junni; Taubman, David

2017-04-12

Dictionary learning has emerged as a promising alternative to the conventional hybrid coding framework. However, the rigid structure of sequential training and prediction degrades its performance in scalable video coding. This paper proposes a progressive dictionary learning framework with hierarchical predictive structure for scalable video coding, especially in low bitrate region. For pyramidal layers, sparse representation based on spatio-temporal dictionary is adopted to improve the coding efficiency of enhancement layers (ELs) with a guarantee of reconstruction performance. The overcomplete dictionary is trained to adaptively capture local structures along motion trajectories as well as exploit the correlations between neighboring layers of resolutions. Furthermore, progressive dictionary learning is developed to enable the scalability in temporal domain and restrict the error propagation in a close-loop predictor. Under the hierarchical predictive structure, online learning is leveraged to guarantee the training and prediction performance with an improved convergence rate. To accommodate with the stateof- the-art scalable extension of H.264/AVC and latest HEVC, standardized codec cores are utilized to encode the base and enhancement layers. Experimental results show that the proposed method outperforms the latest SHVC and HEVC simulcast over extensive test sequences with various resolutions.

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

DOE PAGES

Nik-Zainal, Serena; Davies, Helen; Staaf, Johan; ...

2016-05-02

Here, we analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, anothermore » with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.« less

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nik-Zainal, Serena; Davies, Helen; Staaf, Johan

Here, we analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, anothermore » with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.« less

Complete Mitochondrial Genome of Eruca sativa Mill. (Garden Rocket)

PubMed Central

Yang, Qing; Chang, Shengxin; Chen, Jianmei; Hu, Maolong; Guan, Rongzhan

2014-01-01

Eruca sativa (Cruciferae family) is an ancient crop of great economic and agronomic importance. Here, the complete mitochondrial genome of Eruca sativa was sequenced and annotated. The circular molecule is 247 696 bp long, with a G+C content of 45.07%, containing 33 protein-coding genes, three rRNA genes, and 18 tRNA genes. The Eruca sativa mitochondrial genome may be divided into six master circles and four subgenomic molecules via three pairwise large repeats, resulting in a more dynamic structure of the Eruca sativa mtDNA compared with other cruciferous mitotypes. Comparison with the Brassica napus MtDNA revealed that most of the genes with known function are conserved between these two mitotypes except for the ccmFN2 and rrn18 genes, and 27 point mutations were scattered in the 14 protein-coding genes. Evolutionary relationships analysis suggested that Eruca sativa is more closely related to the Brassica species and to Raphanus sativus than to Arabidopsis thaliana. PMID:25157569

Landscape of somatic mutations in 560 breast cancer whole genome sequences

PubMed Central

Nik-Zainal, Serena; Davies, Helen; Staaf, Johan; Ramakrishna, Manasa; Glodzik, Dominik; Zou, Xueqing; Martincorena, Inigo; Alexandrov, Ludmil B.; Martin, Sancha; Wedge, David C.; Van Loo, Peter; Ju, Young Seok; Smid, Marcel; Brinkman, Arie B; Morganella, Sandro; Aure, Miriam R.; Lingjærde, Ole Christian; Langerød, Anita; Ringnér, Markus; Ahn, Sung-Min; Boyault, Sandrine; Brock, Jane E.; Broeks, Annegien; Butler, Adam; Desmedt, Christine; Dirix, Luc; Dronov, Serge; Fatima, Aquila; Foekens, John A.; Gerstung, Moritz; Hooijer, Gerrit KJ; Jang, Se Jin; Jones, David R.; Kim, Hyung-Yong; King, Tari A.; Krishnamurthy, Savitri; Lee, Hee Jin; Lee, Jeong-Yeon; Li, Yilong; McLaren, Stuart; Menzies, Andrew; Mustonen, Ville; O’Meara, Sarah; Pauporté, Iris; Pivot, Xavier; Purdie, Colin A.; Raine, Keiran; Ramakrishnan, Kamna; Rodríguez-González, F. Germán; Romieu, Gilles; Sieuwerts, Anieta M.; Simpson, Peter T; Shepherd, Rebecca; Stebbings, Lucy; Stefansson, Olafur A; Teague, Jon; Tommasi, Stefania; Treilleux, Isabelle; Van den Eynden, Gert G.; Vermeulen, Peter; Vincent-Salomon, Anne; Yates, Lucy; Caldas, Carlos; van’t Veer, Laura; Tutt, Andrew; Knappskog, Stian; Tan, Benita Kiat Tee; Jonkers, Jos; Borg, Åke; Ueno, Naoto T; Sotiriou, Christos; Viari, Alain; Futreal, P. Andrew; Campbell, Peter J; Span, Paul N.; Van Laere, Steven; Lakhani, Sunil R; Eyfjord, Jorunn E.; Thompson, Alastair M.; Birney, Ewan; Stunnenberg, Hendrik G; van de Vijver, Marc J; Martens, John W.M.; Børresen-Dale, Anne-Lise; Richardson, Andrea L.; Kong, Gu; Thomas, Gilles; Stratton, Michael R.

2016-01-01

We analysed whole genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. 93 protein-coding cancer genes carried likely driver mutations. Some non-coding regions exhibited high mutation frequencies but most have distinctive structural features probably causing elevated mutation rates and do not harbour driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed 12 base substitution and six rearrangement signatures. Three rearrangement signatures, characterised by tandem duplications or deletions, appear associated with defective homologous recombination based DNA repair: one with deficient BRCA1 function; another with deficient BRCA1 or BRCA2 function; the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operative, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer. PMID:27135926

Experiences with explicit finite-difference schemes for complex fluid dynamics problems on STAR-100 and CYBER-203 computers

NASA Technical Reports Server (NTRS)

Kumar, A.; Rudy, D. H.; Drummond, J. P.; Harris, J. E.

1982-01-01

Several two- and three-dimensional external and internal flow problems solved on the STAR-100 and CYBER-203 vector processing computers are described. The flow field was described by the full Navier-Stokes equations which were then solved by explicit finite-difference algorithms. Problem results and computer system requirements are presented. Program organization and data base structure for three-dimensional computer codes which will eliminate or improve on page faulting, are discussed. Storage requirements for three-dimensional codes are reduced by calculating transformation metric data in each step. As a result, in-core grid points were increased in number by 50% to 150,000, with a 10% execution time increase. An assessment of current and future machine requirements shows that even on the CYBER-205 computer only a few problems can be solved realistically. Estimates reveal that the present situation is more storage limited than compute rate limited, but advancements in both storage and speed are essential to realistically calculate three-dimensional flow.

Structures of Neural Correlation and How They Favor Coding

PubMed Central

Franke, Felix; Fiscella, Michele; Sevelev, Maksim; Roska, Botond; Hierlemann, Andreas; da Silveira, Rava Azeredo

2017-01-01

Summary The neural representation of information suffers from “noise”—the trial-to-trial variability in the response of neurons. The impact of correlated noise upon population coding has been debated, but a direct connection between theory and experiment remains tenuous. Here, we substantiate this connection and propose a refined theoretical picture. Using simultaneous recordings from a population of direction-selective retinal ganglion cells, we demonstrate that coding benefits from noise correlations. The effect is appreciable already in small populations, yet it is a collective phenomenon. Furthermore, the stimulus-dependent structure of correlation is key. We develop simple functional models that capture the stimulus-dependent statistics. We then use them to quantify the performance of population coding, which depends upon interplays of feature sensitivities and noise correlations in the population. Because favorable structures of correlation emerge robustly in circuits with noisy, nonlinear elements, they will arise and benefit coding beyond the confines of retina. PMID:26796692

Development of structured ICD-10 and its application to computer-assisted ICD coding.

PubMed

Imai, Takeshi; Kajino, Masayuki; Sato, Megumi; Ohe, Kazuhiko

2010-01-01

This paper presents: (1) a framework of formal representation of ICD10, which functions as a bridge between ontological information and natural language expressions; and (2) a methodology to use formally described ICD10 for computer-assisted ICD coding. First, we analyzed and structurized the meanings of categories in 15 chapters of ICD10. Then we expanded the structured ICD10 (S-ICD10) by adding subordinate concepts and labels derived from Japanese Standard Disease Names. The information model to describe formal representation was refined repeatedly. The resultant model includes 74 types of semantic links. We also developed an ICD coding module based on S-ICD10 and a 'Coding Principle,' which achieved high accuracy (>70%) for four chapters. These results not only demonstrate the basic feasibility of our coding framework but might also inform the development of the information model for formal description framework in the ICD11 revision.

Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica.

PubMed

Fernandez-Valverde, Selene L; Calcino, Andrew D; Degnan, Bernard M

2015-05-15

The demosponge Amphimedon queenslandica is amongst the few early-branching metazoans with an assembled and annotated draft genome, making it an important species in the study of the origin and early evolution of animals. Current gene models in this species are largely based on in silico predictions and low coverage expressed sequence tag (EST) evidence. Amphimedon queenslandica protein-coding gene models are improved using deep RNA-Seq data from four developmental stages and CEL-Seq data from 82 developmental samples. Over 86% of previously predicted genes are retained in the new gene models, although 24% have additional exons; there is also a marked increase in the total number of annotated 3' and 5' untranslated regions (UTRs). Importantly, these new developmental transcriptome data reveal numerous previously unannotated protein-coding genes in the Amphimedon genome, increasing the total gene number by 25%, from 30,060 to 40,122. In general, Amphimedon genes have introns that are markedly smaller than those in other animals and most of the alternatively spliced genes in Amphimedon undergo intron-retention; exon-skipping is the least common mode of alternative splicing. Finally, in addition to canonical polyadenylation signal sequences, Amphimedon genes are enriched in a number of unique AT-rich motifs in their 3' UTRs. The inclusion of developmental transcriptome data has substantially improved the structure and composition of protein-coding gene models in Amphimedon queenslandica, providing a more accurate and comprehensive set of genes for functional and comparative studies. These improvements reveal the Amphimedon genome is comprised of a remarkably high number of tightly packed genes. These genes have small introns and there is pervasive intron retention amongst alternatively spliced transcripts. These aspects of the sponge genome are more similar unicellular opisthokont genomes than to other animal genomes.

The Complete Mitochondrial Genomes of Two Octopods Cistopus chinensis and Cistopus taiwanicus: Revealing the Phylogenetic Position of the Genus Cistopus within the Order Octopoda

PubMed Central

Cheng, Rubin; Zheng, Xiaodong; Ma, Yuanyuan; Li, Qi

2013-01-01

In the present study, we determined the complete mitochondrial DNA (mtDNA) sequences of two species of Cistopus, namely C. chinensis and C. taiwanicus, and conducted a comparative mt genome analysis across the class Cephalopoda. The mtDNA length of C. chinensis and C. taiwanicus are 15706 and 15793 nucleotides with an AT content of 76.21% and 76.5%, respectively. The sequence identity of mtDNA between C. chinensis and C. taiwanicus was 88%, suggesting a close relationship. Compared with C. taiwanicus and other octopods, C. chinensis encoded two additional tRNA genes, showing a novel gene arrangement. In addition, an unusual 23 poly (A) signal structure is found in the ATP8 coding region of C. chinensis. The entire genome and each protein coding gene of the two Cistopus species displayed notable levels of AT and GC skews. Based on sliding window analysis among Octopodiformes, ND1 and DN5 were considered to be more reliable molecular beacons. Phylogenetic analyses based on the 13 protein-coding genes revealed that C. chinensis and C. taiwanicus form a monophyletic group with high statistical support, consistent with previous studies based on morphological characteristics. Our results also indicated that the phylogenetic position of the genus Cistopus is closer to Octopus than to Amphioctopus and Callistoctopus. The complete mtDNA sequence of C. chinensis and C. taiwanicus represent the first whole mt genomes in the genus Cistopus. These novel mtDNA data will be important in refining the phylogenetic relationships within Octopodiformes and enriching the resource of markers for systematic, population genetic and evolutionary biological studies of Cephalopoda. PMID:24358345

Reliability-based criteria for load and resistance factor design code for wood bridges

Treesearch

Chris Eamon; Andrzej S. Nowak; Michael A. Ritter; Joe Murphy

2000-01-01

Recently AASHTO adopted a load and resistance factor design code for highway bridges. The new code provides a rational basis for the design of steel and concrete structures. However, the calibration was not done for wood bridges. Therefore, there is a need to fill this gap. The development of statistical models for wood bridge structures is discussed. Recent test...

An Amino Acid Code for β-sheet Packing Structure

PubMed Central

Joo, Hyun; Tsai, Jerry

2014-01-01

To understand the relationship between protein sequence and structure, this work extends the knob-socket model in an investigation of β-sheet packing. Over a comprehensive set of β-sheet folds, the contacts between residues were used to identify packing cliques: sets of residues that all contact each other. These packing cliques were then classified based on size and contact order. From this analysis, the 2 types of 4 residue packing cliques necessary to describe β-sheet packing were characterized. Both occur between 2 adjacent hydrogen bonded β-strands. First, defining the secondary structure packing within β-sheets, the combined socket or XY:HG pocket consists of 4 residues i,i+2 on one strand and j,j+2 on the other. Second, characterizing the tertiary packing between β-sheets, the knob-socket XY:H+B consists of a 3 residue XY:H socket (i,i+2 on one strand and j on the other) packed against a knob B residue (residue k distant in sequence). Depending on the packing depth of the knob B residue, 2 types of knob-sockets are found: side-chain and main-chain sockets. The amino acid composition of the pockets and knob-sockets reveal the sequence specificity of β-sheet packing. For β-sheet formation, the XY:HG pocket clearly shows sequence specificity of amino acids. For tertiary packing, the XY:H+B side-chain and main-chain sockets exhibit distinct amino acid preferences at each position. These relationships define an amino acid code for β-sheet structure and provide an intuitive topological mapping of β-sheet packing. PMID:24668690

Computer analysis of protein functional sites projection on exon structure of genes in Metazoa

PubMed Central

2015-01-01

Background Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. Results One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. Conclusions These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and allow a better understanding of the emergence of biological diversity. PMID:26693737

Good Trellises for IC Implementation of Viterbi Decoders for Linear Block Codes

NASA Technical Reports Server (NTRS)

Moorthy, Hari T.; Lin, Shu; Uehara, Gregory T.

1997-01-01

This paper investigates trellis structures of linear block codes for the integrated circuit (IC) implementation of Viterbi decoders capable of achieving high decoding speed while satisfying a constraint on the structural complexity of the trellis in terms of the maximum number of states at any particular depth. Only uniform sectionalizations of the code trellis diagram are considered. An upper-bound on the number of parallel and structurally identical (or isomorphic) subtrellises in a proper trellis for a code without exceeding the maximum state complexity of the minimal trellis of the code is first derived. Parallel structures of trellises with various section lengths for binary BCH and Reed-Muller (RM) codes of lengths 32 and 64 are analyzed. Next, the complexity of IC implementation of a Viterbi decoder based on an L-section trellis diagram for a code is investigated. A structural property of a Viterbi decoder called add-compare-select (ACS)-connectivity which is related to state connectivity is introduced. This parameter affects the complexity of wire-routing (interconnections within the IC). The effect of five parameters namely: (1) effective computational complexity; (2) complexity of the ACS-circuit; (3) traceback complexity; (4) ACS-connectivity; and (5) branch complexity of a trellis diagram on the very large scale integration (VISI) complexity of a Viterbi decoder is investigated. It is shown that an IC implementation of a Viterbi decoder based on a nonminimal trellis requires less area and is capable of operation at higher speed than one based on the minimal trellis when the commonly used ACS-array architecture is considered.

Good trellises for IC implementation of viterbi decoders for linear block codes

NASA Technical Reports Server (NTRS)

Lin, Shu; Moorthy, Hari T.; Uehara, Gregory T.

1996-01-01

This paper investigates trellis structures of linear block codes for the IC (integrated circuit) implementation of Viterbi decoders capable of achieving high decoding speed while satisfying a constraint on the structural complexity of the trellis in terms of the maximum number of states at any particular depth. Only uniform sectionalizations of the code trellis diagram are considered. An upper bound on the number of parallel and structurally identical (or isomorphic) subtrellises in a proper trellis for a code without exceeding the maximum state complexity of the minimal trellis of the code is first derived. Parallel structures of trellises with various section lengths for binary BCH and Reed-Muller (RM) codes of lengths 32 and 64 are analyzed. Next, the complexity of IC implementation of a Viterbi decoder based on an L-section trellis diagram for a code is investigated. A structural property of a Viterbi decoder called ACS-connectivity which is related to state connectivity is introduced. This parameter affects the complexity of wire-routing (interconnections within the IC). The effect of five parameters namely: (1) effective computational complexity; (2) complexity of the ACS-circuit; (3) traceback complexity; (4) ACS-connectivity; and (5) branch complexity of a trellis diagram on the VLSI complexity of a Viterbi decoder is investigated. It is shown that an IC implementation of a Viterbi decoder based on a non-minimal trellis requires less area and is capable of operation at higher speed than one based on the minimal trellis when the commonly used ACS-array architecture is considered.

The perceived organizational impact of the gender gap across a Canadian department of medicine and proposed strategies to combat it: a qualitative study.

PubMed

Pattani, Reena; Marquez, Christine; Dinyarian, Camellia; Sharma, Malika; Bain, Julie; Moore, Julia E; Straus, Sharon E

2018-04-10

Despite the gender parity existing in medical schools for over three decades, women remain underrepresented in academic medical centers, particularly in senior ranks and in leadership roles. This has consequences for patient care, education, research, and workplace culture within healthcare organizations. This study was undertaken to explore the perspectives of faculty members at a single department of medicine on the impact of the existing gender gap on organizational effectiveness and workplace culture, and to identify systems-based strategies to mitigate the gap. The study took place at a large university department of medicine in Toronto, Canada, with six affiliated hospitals. In this qualitative study, semi-structured individual interviews were conducted between May and September 2016 with full-time faculty members who held clinical and university-based appointments. Transcripts of the interviews were analyzed using thematic analysis. Three authors independently reviewed the transcripts to determine a preliminary list of codes and establish a coding framework. A modified audit consensus coding approach was applied; a single analyst reviewed all the transcripts and a second analyst audited 20% of the transcripts in each round of coding. Following each round, inter-rater reliability was determined, discrepancies were resolved through discussion, and modifications were made as needed to the coding framework. The analysis revealed faculty members' perceptions of the gender gap, potential contributing factors, organizational impacts, and possible solutions to bridge the gap. Of the 43 full-time faculty members who participated in the survey (29 of whom self-identified as female), most participants were aware of the existing gender gap within academic medicine. Participants described social exclusion, reinforced stereotypes, and unprofessional behaviors as consequences of the gap on organizational effectiveness and culture. They suggested improvements in (1) the processes for recruitment, hiring, and promotion; (2) inclusiveness of the work environment; (3) structures for mentorship; and (4) ongoing monitoring of the gap. The existing gender gap in academic medicine may have negative consequences for organizational effectiveness and workplace culture but many systems-based strategies to mitigate the gap exist. Although these solutions warrant rigorous evaluation, they are feasible to institute within most healthcare organizations immediately.

Numerical predictions of EML (electromagnetic launcher) system performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schnurr, N.M.; Kerrisk, J.F.; Davidson, R.F.

1987-01-01

The performance of an electromagnetic launcher (EML) depends on a large number of parameters, including the characteristics of the power supply, rail geometry, rail and insulator material properties, injection velocity, and projectile mass. EML system performance is frequently limited by structural or thermal effects in the launcher (railgun). A series of computer codes has been developed at the Los Alamos National Laboratory to predict EML system performance and to determine the structural and thermal constraints on barrel design. These codes include FLD, a two-dimensional electrostatic code used to calculate the high-frequency inductance gradient and surface current density distribution for themore » rails; TOPAZRG, a two-dimensional finite-element code that simultaneously analyzes thermal and electromagnetic diffusion in the rails; and LARGE, a code that predicts the performance of the entire EML system. Trhe NIKE2D code, developed at the Lawrence Livermore National Laboratory, is used to perform structural analyses of the rails. These codes have been instrumental in the design of the Lethality Test System (LTS) at Los Alamos, which has an ultimate goal of accelerating a 30-g projectile to a velocity of 15 km/s. The capabilities of the individual codes and the coupling of these codes to perform a comprehensive analysis is discussed in relation to the LTS design. Numerical predictions are compared with experimental data and presented for the LTS prototype tests.« less

Structural Code Considerations for Solar Rooftop Installations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dwyer, Stephen F.; Dwyer, Brian P.; Sanchez, Alfred

2014-12-01

Residential rooftop solar panel installations are limited in part by the high cost of structural related code requirements for field installation. Permitting solar installations is difficult because there is a belief among residential permitting authorities that typical residential rooftops may be structurally inadequate to support the additional load associated with a photovoltaic (PV) solar installation. Typical engineering methods utilized to calculate stresses on a roof structure involve simplifying assumptions that render a complex non-linear structure to a basic determinate beam. This method of analysis neglects the composite action of the entire roof structure, yielding a conservative analysis based on amore » rafter or top chord of a truss. Consequently, the analysis can result in an overly conservative structural analysis. A literature review was conducted to gain a better understanding of the conservative nature of the regulations and codes governing residential construction and the associated structural system calculations.« less

Simplified diagnostic coding sheet for computerized data storage and analysis in ophthalmology.

PubMed

Tauber, J; Lahav, M

1987-11-01

A review of currently-available diagnostic coding systems revealed that most are either too abbreviated or too detailed. We have compiled a simplified diagnostic coding sheet based on the International Coding and Diagnosis (ICD-9), which is both complete and easy to use in a general practice. The information is transferred to a computer, which uses the relevant (ICD-9) diagnoses as database and can be retrieved later for display of patients' problems or analysis of clinical data.

Nonlinear static and dynamic finite element analysis of an eccentrically loaded graphite-epoxy beam

NASA Technical Reports Server (NTRS)

Fasanella, Edwin L.; Jackson, Karen E.; Jones, Lisa E.

1991-01-01

The Dynamic Crash Analysis of Structures (DYCAT) and NIKE3D nonlinear finite element codes were used to model the static and implulsive response of an eccentrically loaded graphite-epoxy beam. A 48-ply unidirectional composite beam was tested under an eccentric axial compressive load until failure. This loading configuration was chosen to highlight the capabilities of two finite element codes for modeling a highly nonlinear, large deflection structural problem which has an exact solution. These codes are currently used to perform dynamic analyses of aircraft structures under impact loads to study crashworthiness and energy absorbing capabilities. Both beam and plate element models were developed to compare with the experimental data using the DYCAST and NIKE3D codes.

Leadership Class Configuration Interaction Code - Status and Opportunities

NASA Astrophysics Data System (ADS)

Vary, James

2011-10-01

With support from SciDAC-UNEDF (www.unedf.org) nuclear theorists have developed and are continuously improving a Leadership Class Configuration Interaction Code (LCCI) for forefront nuclear structure calculations. The aim of this project is to make state-of-the-art nuclear structure tools available to the entire community of researchers including graduate students. The project includes codes such as NuShellX, MFDn and BIGSTICK that run a range of computers from laptops to leadership class supercomputers. Codes, scripts, test cases and documentation have been assembled, are under continuous development and are scheduled for release to the entire research community in November 2011. A covering script that accesses the appropriate code and supporting files is under development. In addition, a Data Base Management System (DBMS) that records key information from large production runs and archived results of those runs has been developed (http://nuclear.physics.iastate.edu/info/) and will be released. Following an outline of the project, the code structure, capabilities, the DBMS and current efforts, I will suggest a path forward that would benefit greatly from a significant partnership between researchers who use the codes, code developers and the National Nuclear Data efforts. This research is supported in part by DOE under grant DE-FG02-87ER40371 and grant DE-FC02-09ER41582 (SciDAC-UNEDF).

The complete chloroplast genome sequence of strawberry (Fragaria  × ananassa Duch.) and comparison with related species of Rosaceae

PubMed Central

Cheng, Hui; Li, Jinfeng; Zhang, Hong; Cai, Binhua; Gao, Zhihong

2017-01-01

Compared with other members of the family Rosaceae, the chloroplast genomes of Fragaria species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of Fragaria species is needed. In this study, we sequenced the complete chloroplast genome of F. × ananassa ‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination of de novo assembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of the F. × ananassa ‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallest Fragaria chloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content in Fragaria, particularly among three octoploid strawberries which were F. × ananassa ‘Benihoppe’, F. chiloensis (GP33) and F. virginiana (O477). However, when the sequences of the coding and non-coding regions of F. × ananassa ‘Benihoppe’ were compared in detail with those of F. chiloensis (GP33) and F. virginiana (O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK, trnS-trnG, atpF-atpH, trnC-petN, trnT-psbD and trnP-psaJ) with a percentage of variable sites greater than 1% and no less than five parsimony-informative sites were identified and may be useful for phylogenetic analysis of the genus Fragaria. PMID:29038765

Fine Structure Processing improves speech perception as well as objective and subjective benefits in pediatric MED-EL COMBI 40+ users.

PubMed

Lorens, Artur; Zgoda, Małgorzata; Obrycka, Anita; Skarżynski, Henryk

2010-12-01

Presently, there are only few studies examining the benefits of fine structure information in coding strategies. Against this background, this study aims to assess the objective and subjective performance of children experienced with the C40+ cochlear implant using the CIS+ coding strategy who were upgraded to the OPUS 2 processor using FSP and HDCIS. In this prospective study, 60 children with more than 3.5 years of experience with the C40+ cochlear implant were upgraded to the OPUS 2 processor and fit and tested with HDCIS (Interval I). After 3 months of experience with HDCIS, they were fit with the FSP coding strategy (Interval II) and tested with all strategies (FSP, HDCIS, CIS+). After an additional 3-4 months, they were assessed on all three strategies and asked to choose their take-home strategy (Interval III). The children were tested using the Adaptive Auditory Speech Test which measures speech reception threshold (SRT) in quiet and noise at each test interval. The children were also asked to rate on a Visual Analogue Scale their satisfaction and coding strategy preference when listening to speech and a pop song. However, since not all tests could be performed at one single visit, some children were not able complete all tests at all intervals. At the study endpoint, speech in quiet showed a significant difference in SRT of 1.0 dB between FSP and HDCIS, with FSP performing better. FSP proved a better strategy compared with CIS+, showing lower SRT results of 5.2 dB. Speech in noise tests showed FSP to be significantly better than CIS+ by 0.7 dB, and HDCIS to be significantly better than CIS+ by 0.8 dB. Both satisfaction and coding strategy preference ratings also revealed that FSP and HDCIS strategies were better than CIS+ strategy when listening to speech and music. FSP was better than HDCIS when listening to speech. This study demonstrates that long-term pediatric users of the COMBI 40+ are able to upgrade to a newer processor and coding strategy without compromising their listening performance and even improving their performance with FSP after a short time of experience. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

A Coding Scheme for Analysing Problem-Solving Processes of First-Year Engineering Students

ERIC Educational Resources Information Center

Grigg, Sarah J.; Benson, Lisa C.

2014-01-01

This study describes the development and structure of a coding scheme for analysing solutions to well-structured problems in terms of cognitive processes and problem-solving deficiencies for first-year engineering students. A task analysis approach was used to assess students' problem solutions using the hierarchical structure from a…

Genome-wide characterization of pectin methyl esterase genes reveals members differentially expressed in tolerant and susceptible wheats in response to Fusarium graminearum.

PubMed

Zega, Alessandra; D'Ovidio, Renato

2016-11-01

Pectin methyl esterase (PME) genes code for enzymes that are involved in structural modifications of the plant cell wall during plant growth and development. They are also involved in plant-pathogen interaction. PME genes belong to a multigene family and in this study we report the first comprehensive analysis of the PME gene family in bread wheat (Triticum aestivum L.). Like in other species, the members of the TaPME family are dispersed throughout the genome and their encoded products retain the typical structural features of PMEs. qRT-PCR analysis showed variation in the expression pattern of TaPME genes in different tissues and revealed that these genes are mainly expressed in flowering spikes. In our attempt to identify putative TaPME genes involved in wheat defense, we revealed a strong variation in the expression of the TaPME following Fusarium graminearum infection, the causal agent of Fusarium head blight (FHB). Particularly interesting was the finding that the expression profile of some PME genes was markedly different between the FHB-resistant wheat cultivar Sumai3 and the FHB-susceptible cultivar Bobwhite, suggesting a possible involvement of these PME genes in FHB resistance. Moreover, the expression analysis of the TaPME genes during F. graminearum progression within the spike revealed those genes that responded more promptly to pathogen invasion. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerr, J.M.; Fisher, L.W.; Termine, J.D.

The authors have isolated and partially sequenced the human bone sialoprotein gene (IBSP). IBSP has been sublocalized by in situ hybridization to chromosome 4q38-q31 and is composed of six small exons (51 to 159 bp) and 1 large exon ([approximately]2.6 kb). The intron/exon junctions defined by sequence analysis are of class O, retaining an intact coding triplet. Sequence analysis of the 5[prime] upstream region revealed a TATAA (nucleotides -30 to-25 from the transcriptional start point) and a CCAAT (nucleotides -56 to-52) box, both in the reverse orientation. Intron 1 contains interesting structural elements composed of polypyrimidine repeats followed by amore » poly(AC)[sub n] tract. Both types of structural elements have been detected in promoter regions of other genes and have been implicated in transcriptional regulation. Several differences between the previously published cDNA sequence and the authors' sequence have been identified, most of which are contained within the untranslated exon 1. Three base revisions in the coding region include a G to T (Gly to Val, amino acid 195), T to C (Val to Ala, amino acid 268), and T to A (Glu to Asp, amino acid 270). In conclusion, the genomic organization and potential regulatory elements of human IBSP have been elucidated. 42 refs., 4 figs., 1 tab.« less

A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate

PubMed Central

Samuels, David C.; Boys, Richard J.; Henderson, Daniel A.; Chinnery, Patrick F.

2003-01-01

We applied a hidden Markov model segmentation method to the human mitochondrial genome to identify patterns in the sequence, to compare these patterns to the gene structure of mtDNA and to see whether these patterns reveal additional characteristics important for our understanding of genome evolution, structure and function. Our analysis identified three segmentation categories based upon the sequence transition probabilities. Category 2 segments corresponded to the tRNA and rRNA genes, with a greater strand-symmetry in these segments. Category 1 and 3 segments covered the protein- coding genes and almost all of the non-coding D-loop. Compared to category 1, the mtDNA segments assigned to category 3 had much lower guanine abundance. A comparison to two independent databases of mitochondrial mutations and polymorphisms showed that the high substitution rate of guanine in human mtDNA is largest in the category 3 segments. Analysis of synonymous mutations showed the same pattern. This suggests that this heterogeneity in the mutation rate is partly independent of respiratory chain function and is a direct property of the genome sequence itself. This has important implications for our understanding of mtDNA evolution and its use as a ‘molecular clock’ to determine the rate of population and species divergence. PMID:14530452

Molecular architecture of silk fibroin of Indian golden silkmoth, Antheraea assama.

PubMed

Gupta, Adarsh K; Mita, Kazuei; Arunkumar, Kallare P; Nagaraju, Javaregowda

2015-08-03

The golden silk spun by Indian golden silkmoth Antheraea assama, is regarded for its shimmering golden luster, tenacity and value as biomaterial. This report describes the gene coding for golden silk H-fibroin (AaFhc), its expression, full-length sequence and structurally important motifs discerning the underlying genetic and biochemical factors responsible for its much sought-after properties. The coding region, with biased isocodons, encodes highly repetitious crystalline core, flanked by a pair of 5' and 3' non-repetitious ends. AaFhc mRNA expression is strictly territorial, confined to the posterior silk gland, encoding a protein of size 230 kDa, which makes homodimers making the elementary structural units of the fibrous core of the golden silk. Characteristic polyalanine repeats that make tight β-sheet crystals alternate with non-polyalanine repeats that make less orderly antiparallel β-sheets, β-turns and partial α-helices. Phylogenetic analysis of the conserved N-terminal amorphous motif and the comparative analysis of the crystalline region with other saturniid H-fibroins reveal that AaFhc has longer, numerous and relatively uniform repeat motifs with lower serine content that assume tighter β-crystals and denser packing, which are speculated to be responsible for its acclaimed properties of higher tensile strength and higher refractive index responsible for golden luster.

A parallel and modular deformable cell Car-Parrinello code

NASA Astrophysics Data System (ADS)

Cavazzoni, Carlo; Chiarotti, Guido L.

1999-12-01

We have developed a modular parallel code implementing the Car-Parrinello [Phys. Rev. Lett. 55 (1985) 2471] algorithm including the variable cell dynamics [Europhys. Lett. 36 (1994) 345; J. Phys. Chem. Solids 56 (1995) 510]. Our code is written in Fortran 90, and makes use of some new programming concepts like encapsulation, data abstraction and data hiding. The code has a multi-layer hierarchical structure with tree like dependences among modules. The modules include not only the variables but also the methods acting on them, in an object oriented fashion. The modular structure allows easier code maintenance, develop and debugging procedures, and is suitable for a developer team. The layer structure permits high portability. The code displays an almost linear speed-up in a wide range of number of processors independently of the architecture. Super-linear speed up is obtained with a "smart" Fast Fourier Transform (FFT) that uses the available memory on the single node (increasing for a fixed problem with the number of processing elements) as temporary buffer to store wave function transforms. This code has been used to simulate water and ammonia at giant planet conditions for systems as large as 64 molecules for ˜50 ps.

A Simple Test of Class-Level Genetic Association Can Reveal Novel Cardiometabolic Trait Loci.

PubMed

Qian, Jing; Nunez, Sara; Reed, Eric; Reilly, Muredach P; Foulkes, Andrea S

2016-01-01

Characterizing the genetic determinants of complex diseases can be further augmented by incorporating knowledge of underlying structure or classifications of the genome, such as newly developed mappings of protein-coding genes, epigenetic marks, enhancer elements and non-coding RNAs. We apply a simple class-level testing framework, termed Genetic Class Association Testing (GenCAT), to identify protein-coding gene association with 14 cardiometabolic (CMD) related traits across 6 publicly available genome wide association (GWA) meta-analysis data resources. GenCAT uses SNP-level meta-analysis test statistics across all SNPs within a class of elements, as well as the size of the class and its unique correlation structure, to determine if the class is statistically meaningful. The novelty of findings is evaluated through investigation of regional signals. A subset of findings are validated using recently updated, larger meta-analysis resources. A simulation study is presented to characterize overall performance with respect to power, control of family-wise error and computational efficiency. All analysis is performed using the GenCAT package, R version 3.2.1. We demonstrate that class-level testing complements the common first stage minP approach that involves individual SNP-level testing followed by post-hoc ascribing of statistically significant SNPs to genes and loci. GenCAT suggests 54 protein-coding genes at 41 distinct loci for the 13 CMD traits investigated in the discovery analysis, that are beyond the discoveries of minP alone. An additional application to biological pathways demonstrates flexibility in defining genetic classes. We conclude that it would be prudent to include class-level testing as standard practice in GWA analysis. GenCAT, for example, can be used as a simple, complementary and efficient strategy for class-level testing that leverages existing data resources, requires only summary level data in the form of test statistics, and adds significant value with respect to its potential for identifying multiple novel and clinically relevant trait associations.

Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

NASA Astrophysics Data System (ADS)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

The STAGS computer code

NASA Technical Reports Server (NTRS)

Almroth, B. O.; Brogan, F. A.

1978-01-01

Basic information about the computer code STAGS (Structural Analysis of General Shells) is presented to describe to potential users the scope of the code and the solution procedures that are incorporated. Primarily, STAGS is intended for analysis of shell structures, although it has been extended to more complex shell configurations through the inclusion of springs and beam elements. The formulation is based on a variational approach in combination with local two dimensional power series representations of the displacement components. The computer code includes options for analysis of linear or nonlinear static stress, stability, vibrations, and transient response. Material as well as geometric nonlinearities are included. A few examples of applications of the code are presented for further illustration of its scope.

High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans.

PubMed

Lipovich, Leonard; Hou, Zhuo-Cheng; Jia, Hui; Sinkler, Christopher; McGowen, Michael; Sterner, Kirstin N; Weckle, Amy; Sugalski, Amara B; Pipes, Lenore; Gatti, Domenico L; Mason, Christopher E; Sherwood, Chet C; Hof, Patrick R; Kuzawa, Christopher W; Grossman, Lawrence I; Goodman, Morris; Wildman, Derek E

2016-02-01

The human brain and human cognitive abilities are strikingly different from those of other great apes despite relatively modest genome sequence divergence. However, little is presently known about the interspecies divergence in gene structure and transcription that might contribute to these phenotypic differences. To date, most comparative studies of gene structure in the brain have examined humans, chimpanzees, and macaque monkeys. To add to this body of knowledge, we analyze here the brain transcriptome of the western lowland gorilla (Gorilla gorilla gorilla), an African great ape species that is phylogenetically closely related to humans, but with a brain that is approximately one-third the size. Manual transcriptome curation from a sample of the planum temporale region of the neocortex revealed 12 protein-coding genes and one noncoding-RNA gene with exons in the gorilla unmatched by public transcriptome data from the orthologous human loci. These interspecies gene structure differences accounted for a total of 134 amino acids in proteins found in the gorilla that were absent from protein products of the orthologous human genes. Proteins varying in structure between human and gorilla were involved in immunity and energy metabolism, suggesting their relevance to phenotypic differences. This gorilla neocortical transcriptome comprises an empirical, not homology- or prediction-driven, resource for orthologous gene comparisons between human and gorilla. These findings provide a unique repository of the sequences and structures of thousands of genes transcribed in the gorilla brain, pointing to candidate genes that may contribute to the traits distinguishing humans from other closely related great apes. © 2015 Wiley Periodicals, Inc.

Performance Analysis of IEEE 802.11g TCM Waveforms Transmitted over a Channel with Pulse-Noise Interference

DTIC Science & Technology

2007-06-01

17 Table 2. Best (maximum free distance) rate r=2/3 punctured convolutional code ...Hamming distance between all pairs of non-zero paths. Table 2 lists the best rate r=2/3, punctured convolutional code information weight structure dB...Table 2. Best (maximum free distance) rate r=2/3 punctured convolutional code information weight structure. (From: [12]). K freed freeB

Probabilistic Structural Analysis Methods (PSAM) for select space propulsion systems components

NASA Technical Reports Server (NTRS)

1991-01-01

Summarized here is the technical effort and computer code developed during the five year duration of the program for probabilistic structural analysis methods. The summary includes a brief description of the computer code manuals and a detailed description of code validation demonstration cases for random vibrations of a discharge duct, probabilistic material nonlinearities of a liquid oxygen post, and probabilistic buckling of a transfer tube liner.

The identification and functional annotation of RNA structures conserved in vertebrates

PubMed Central

Seemann, Stefan E.; Mirza, Aashiq H.; Hansen, Claus; Bang-Berthelsen, Claus H.; Garde, Christian; Christensen-Dalsgaard, Mikkel; Torarinsson, Elfar; Yao, Zizhen; Workman, Christopher T.; Pociot, Flemming; Nielsen, Henrik; Tommerup, Niels; Ruzzo, Walter L.; Gorodkin, Jan

2017-01-01

Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved RNA structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ∼516,000 human genomic regions containing CRSs. We find that a substantial fraction of human–mouse CRS regions (1) colocalize consistently with binding sites of the same RNA binding proteins (RBPs) or (2) are transcribed in corresponding tissues. Additionally, a CaptureSeq experiment revealed expression of many of our CRS regions in human fetal brain, including 662 novel ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared expression and shared structure despite low abundance and low sequence identity. About 30,000 CRS regions are located near coding or long noncoding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3′ ends have significantly increased expression levels over their nonstructured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality. PMID:28487280

Influence of the plasma environment on atomic structure using an ion-sphere model

NASA Astrophysics Data System (ADS)

Belkhiri, Madeny; Fontes, Christopher J.; Poirier, Michel

2015-09-01

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22 +, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the multiconfiguration Dirac-Fock value of B. Saha and S. Fritzsche [J. Phys. B 40, 259 (2007), 10.1088/0953-4075/40/2/002]. Last, the present model is compared to experimental data in titanium measured on the terawatt Astra facility and provides values for electron temperature and density in agreement with the maria code.

Neural mechanisms underlying auditory feedback control of speech

PubMed Central

Reilly, Kevin J.; Guenther, Frank H.

2013-01-01

The neural substrates underlying auditory feedback control of speech were investigated using a combination of functional magnetic resonance imaging (fMRI) and computational modeling. Neural responses were measured while subjects spoke monosyllabic words under two conditions: (i) normal auditory feedback of their speech, and (ii) auditory feedback in which the first formant frequency of their speech was unexpectedly shifted in real time. Acoustic measurements showed compensation to the shift within approximately 135 ms of onset. Neuroimaging revealed increased activity in bilateral superior temporal cortex during shifted feedback, indicative of neurons coding mismatches between expected and actual auditory signals, as well as right prefrontal and Rolandic cortical activity. Structural equation modeling revealed increased influence of bilateral auditory cortical areas on right frontal areas during shifted speech, indicating that projections from auditory error cells in posterior superior temporal cortex to motor correction cells in right frontal cortex mediate auditory feedback control of speech. PMID:18035557

“Rebuilding our community”: Hearing silenced voices on Aboriginal youth suicide

PubMed Central

Walls, Melissa L.; Hautala, Dane; Hurley, Jenna

2014-01-01

This paper brings forth the voices of adult Aboriginal First Nations community members who gathered in focus groups to discuss the problem of youth suicide on their reserves. Our approach emphasizes multilevel (e.g., individual, family, and broader ecological systems) factors viewed by participants as relevant to youth suicide. Wheaton’s conceptualization of stressors (1994; 1999) and Evans-Campbell’s (2008) multilevel classification of the impacts of historical trauma are used as theoretical and analytic guides. Thematic analysis of qualitative data transcripts revealed a highly complex intersection of stressors, traumas, and social problems seen by community members as underlying mechanisms influencing heightened levels of Aboriginal youth suicidality. Our multilevel coding approach revealed that suicidal behaviors were described by community members largely as a problem with deep historical and contemporary structural roots as opposed to being viewed as individualized pathology. PMID:24097414

A Coded Structured Light System Based on Primary Color Stripe Projection and Monochrome Imaging

PubMed Central

Barone, Sandro; Paoli, Alessandro; Razionale, Armando Viviano

2013-01-01

Coded Structured Light techniques represent one of the most attractive research areas within the field of optical metrology. The coding procedures are typically based on projecting either a single pattern or a temporal sequence of patterns to provide 3D surface data. In this context, multi-slit or stripe colored patterns may be used with the aim of reducing the number of projected images. However, color imaging sensors require the use of calibration procedures to address crosstalk effects between different channels and to reduce the chromatic aberrations. In this paper, a Coded Structured Light system has been developed by integrating a color stripe projector and a monochrome camera. A discrete coding method, which combines spatial and temporal information, is generated by sequentially projecting and acquiring a small set of fringe patterns. The method allows the concurrent measurement of geometrical and chromatic data by exploiting the benefits of using a monochrome camera. The proposed methodology has been validated by measuring nominal primitive geometries and free-form shapes. The experimental results have been compared with those obtained by using a time-multiplexing gray code strategy. PMID:24129018

A coded structured light system based on primary color stripe projection and monochrome imaging.

PubMed

Barone, Sandro; Paoli, Alessandro; Razionale, Armando Viviano

2013-10-14

Coded Structured Light techniques represent one of the most attractive research areas within the field of optical metrology. The coding procedures are typically based on projecting either a single pattern or a temporal sequence of patterns to provide 3D surface data. In this context, multi-slit or stripe colored patterns may be used with the aim of reducing the number of projected images. However, color imaging sensors require the use of calibration procedures to address crosstalk effects between different channels and to reduce the chromatic aberrations. In this paper, a Coded Structured Light system has been developed by integrating a color stripe projector and a monochrome camera. A discrete coding method, which combines spatial and temporal information, is generated by sequentially projecting and acquiring a small set of fringe patterns. The method allows the concurrent measurement of geometrical and chromatic data by exploiting the benefits of using a monochrome camera. The proposed methodology has been validated by measuring nominal primitive geometries and free-form shapes. The experimental results have been compared with those obtained by using a time-multiplexing gray code strategy.

The MARS15-based FermiCORD code system for calculation of the accelerator-induced residual dose

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grebe, A.; Leveling, A.; Lu, T.

The FermiCORD code system, a set of codes based on MARS15 that calculates the accelerator-induced residual doses at experimental facilities of arbitrary configurations, has been developed. FermiCORD is written in C++ as an add-on to Fortran-based MARS15. The FermiCORD algorithm consists of two stages: 1) simulation of residual doses on contact with the surfaces surrounding the studied location and of radionuclide inventories in the structures surrounding those locations using MARS15, and 2) simulation of the emission of the nuclear decay gamma-quanta by the residuals in the activated structures and scoring the prompt doses of these gamma-quanta at arbitrary distances frommore » those structures. The FermiCORD code system has been benchmarked against similar algorithms based on other code systems and showed a good agreement. The code system has been applied for calculation of the residual dose of the target station for the Mu2e experiment and the results have been compared to approximate dosimetric approaches.« less

The MARS15-based FermiCORD code system for calculation of the accelerator-induced residual dose

NASA Astrophysics Data System (ADS)

Grebe, A.; Leveling, A.; Lu, T.; Mokhov, N.; Pronskikh, V.

2018-01-01

The FermiCORD code system, a set of codes based on MARS15 that calculates the accelerator-induced residual doses at experimental facilities of arbitrary configurations, has been developed. FermiCORD is written in C++ as an add-on to Fortran-based MARS15. The FermiCORD algorithm consists of two stages: 1) simulation of residual doses on contact with the surfaces surrounding the studied location and of radionuclide inventories in the structures surrounding those locations using MARS15, and 2) simulation of the emission of the nuclear decay γ-quanta by the residuals in the activated structures and scoring the prompt doses of these γ-quanta at arbitrary distances from those structures. The FermiCORD code system has been benchmarked against similar algorithms based on other code systems and against experimental data from the CERF facility at CERN, and FermiCORD showed reasonable agreement with these. The code system has been applied for calculation of the residual dose of the target station for the Mu2e experiment and the results have been compared to approximate dosimetric approaches.

Analysis of SMA Hybrid Composite Structures using Commercial Codes

NASA Technical Reports Server (NTRS)

Turner, Travis L.; Patel, Hemant D.

2004-01-01

A thermomechanical model for shape memory alloy (SMA) actuators and SMA hybrid composite (SMAHC) structures has been recently implemented in the commercial finite element codes MSC.Nastran and ABAQUS. The model may be easily implemented in any code that has the capability for analysis of laminated composite structures with temperature dependent material properties. The model is also relatively easy to use and requires input of only fundamental engineering properties. A brief description of the model is presented, followed by discussion of implementation and usage in the commercial codes. Results are presented from static and dynamic analysis of SMAHC beams of two types; a beam clamped at each end and a cantilevered beam. Nonlinear static (post-buckling) and random response analyses are demonstrated for the first specimen. Static deflection (shape) control is demonstrated for the cantilevered beam. Approaches for modeling SMAHC material systems with embedded SMA in ribbon and small round wire product forms are demonstrated and compared. The results from the commercial codes are compared to those from a research code as validation of the commercial implementations; excellent correlation is achieved in all cases.

Near Zone: Basic scattering code user's manual with space station applications

NASA Technical Reports Server (NTRS)

Marhefka, R. J.; Silvestro, J. W.

1989-01-01

The Electromagnetic Code - Basic Scattering Code, Version 3, is a user oriented computer code to analyze near and far zone patterns of antennas in the presence of scattering structures, to provide coupling between antennas in a complex environment, and to determine radiation hazard calculations at UHF and above. The analysis is based on uniform asymptotic techniques formulated in terms of the Uniform Geometrical Theory of Diffraction (UTD). Complicated structures can be simulated by arbitrarily oriented flat plates and an infinite ground plane that can be perfectly conducting or dielectric. Also, perfectly conducting finite elliptic cylinder, elliptic cone frustum sections, and finite composite ellipsoids can be used to model the superstructure of a ship, the body of a truck, and airplane, a satellite, etc. This manual gives special consideration to space station modeling applications. This is a user manual designed to give an overall view of the operation of the computer code, to instruct a user in how to model structures, and to show the validity of the code by comparing various computed results against measured and alternative calculations such as method of moments whenever available.

Concurrent credit portfolio losses

PubMed Central

Sicking, Joachim; Schäfer, Rudi

2018-01-01

We consider the problem of concurrent portfolio losses in two non-overlapping credit portfolios. In order to explore the full statistical dependence structure of such portfolio losses, we estimate their empirical pairwise copulas. Instead of a Gaussian dependence, we typically find a strong asymmetry in the copulas. Concurrent large portfolio losses are much more likely than small ones. Studying the dependences of these losses as a function of portfolio size, we moreover reveal that not only large portfolios of thousands of contracts, but also medium-sized and small ones with only a few dozens of contracts exhibit notable portfolio loss correlations. Anticipated idiosyncratic effects turn out to be negligible. These are troublesome insights not only for investors in structured fixed-income products, but particularly for the stability of the financial sector. JEL codes: C32, F34, G21, G32, H81. PMID:29425246

In situ X-ray probing reveals fingerprints of surface platinum oxide.

PubMed

Friebel, Daniel; Miller, Daniel J; O'Grady, Christopher P; Anniyev, Toyli; Bargar, John; Bergmann, Uwe; Ogasawara, Hirohito; Wikfeldt, Kjartan Thor; Pettersson, Lars G M; Nilsson, Anders

2011-01-07

In situ X-ray absorption spectroscopy (XAS) at the Pt L(3) edge is a useful probe for Pt-O interactions at polymer electrolyte membrane fuel cell (PEMFC) cathodes. We show that XAS using the high energy resolution fluorescence detection (HERFD) mode, applied to a well-defined monolayer Pt/Rh(111) sample where the bulk penetrating hard X-rays probe only surface Pt atoms, provides a unique sensitivity to structure and chemical bonding at the Pt-electrolyte interface. Ab initio multiple-scattering calculations using the FEFF code and complementary extended X-ray absorption fine structure (EXAFS) results indicate that the commonly observed large increase of the white-line at high electrochemical potentials on PEMFC cathodes originates from platinum oxide formation, whereas previously proposed chemisorbed oxygen-containing species merely give rise to subtle spectral changes.

[Cloning and sequence analysis of 55 K protein of egg drop syndrome virus].

PubMed

Zhu, L; Jin, Q; Zeng, L

1999-06-30

For understanding the characteristics of genomic structure of egg drop syndrome virus(EDSV). Nucleic acid was extracted using routine method from weak virulent strain AA-2 of EDSV isolated from Chinese sick hens. Construction of the whole genomic library was by hydrolysis with Hind III, strand encoding 55 K gene locating in Hind III--A segment was sequenced and analyzed. The open reading frame has a length of 1,014 nt and codes a polypeptide of 337 amino acids with molecular weight of 38,200. Analysis of the amino acid sequence revealed a homology from 25.5%-32.4% to the 55 K protein of human adenovirus types 2, 12, 40, canine adenovirus and fowl adenoviruses of group 1, whereas to ovine adenovirus is 46.4%. The genomic structure of EDSV has some relationship with adenoviruses.

Concurrent credit portfolio losses.

PubMed

Sicking, Joachim; Guhr, Thomas; Schäfer, Rudi

2018-01-01

We consider the problem of concurrent portfolio losses in two non-overlapping credit portfolios. In order to explore the full statistical dependence structure of such portfolio losses, we estimate their empirical pairwise copulas. Instead of a Gaussian dependence, we typically find a strong asymmetry in the copulas. Concurrent large portfolio losses are much more likely than small ones. Studying the dependences of these losses as a function of portfolio size, we moreover reveal that not only large portfolios of thousands of contracts, but also medium-sized and small ones with only a few dozens of contracts exhibit notable portfolio loss correlations. Anticipated idiosyncratic effects turn out to be negligible. These are troublesome insights not only for investors in structured fixed-income products, but particularly for the stability of the financial sector. JEL codes: C32, F34, G21, G32, H81.

Flow and Temperature Distribution Evaluation on Sodium Heated Large-sized Straight Double-wall-tube Steam Generator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kisohara, Naoyuki; Moribe, Takeshi; Sakai, Takaaki

2006-07-01

The sodium heated steam generator (SG) being designed in the feasibility study on commercialized fast reactor cycle systems is a straight double-wall-tube type. The SG is large sized to reduce its manufacturing cost by economics of scale. This paper addresses the temperature and flow multi-dimensional distributions at steady state to obtain the prospect of the SG. Large-sized heat exchanger components are prone to have non-uniform flow and temperature distributions. These phenomena might lead to tube buckling or tube to tube-sheet junction failure in straight tube type SGs, owing to tubes thermal expansion difference. The flow adjustment devices installed in themore » SG are optimized to prevent these issues, and the temperature distribution properties are uncovered by analysis methods. The analysis model of the SG consists of two parts, a sodium inlet distribution plenum (the plenum) and a heat transfer tubes bundle region (the bundle). The flow and temperature distributions in the plenum and the bundle are evaluated by the three-dimensional code 'FLUENT' and the two dimensional thermal-hydraulic code 'MSG', respectively. The MSG code is particularly developed for sodium heated SGs in JAEA. These codes have revealed that the sodium flow is distributed uniformly by the flow adjustment devices, and that the lateral tube temperature distributions remain within the allowable temperature range for the structural integrity of the tubes and the tube to tube-sheet junctions. (authors)« less

A Novel Approach to Synthesise a Dual-Mode Luminescent Composite Pigment for Uncloneable High-Security Codes to Combat Counterfeiting.

PubMed

Kanika; Kumar, Pawan; Singh, Satbir; Gupta, Bipin Kumar

2017-12-01

A strategy is demonstrated to protect valuable items, such as currency, pharmaceuticals, important documents, etc. against counterfeiting, by marking them with luminescent security codes. These luminescent security codes were printed by employing luminescent ink formulated from a cost effective dual-mode luminescent composite pigment of Gd 1.7 Yb 0.2 Er 0.1 O 3 and Zn 0.98 Mn 0.02 S phosphors using commercially available PVC Gold medium. In the composite, Gd 1.7 Yb 0.2 Er 0.1 O 3 and Zn 0.98 Mn 0.02 S account for upconversion and downconversion processes, respectively. The synthesis procedure of the composite involves the admixing of Gd 1.7 Yb 0.2 Er 0.1 O 3 nanorods and Zn 0.98 Mn 0.02 S phosphor, synthesised by hydrothermal and facile solid-state reaction methods, respectively. The structural, morphological, microstructural, and photoluminescent features of Gd 1.7 Yb 0.2 Er 0.1 O 3 nanorods, Zn 0.98 Mn 0.02 S phosphor and composite were characterised by using XRD, SEM, TEM, and photoluminescence (PL) techniques, respectively. The distribution of PL intensity of the printed pattern was examined by using confocal PL mapping microscopy. The obtained results reveal that security codes printed using ink formulated from this bi-luminescent composite pigment provide dual-stage security against counterfeiting. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hyper-responsivity to losses in the anterior insula during economic choice scales with depression severity.

PubMed

Engelmann, J B; Berns, G S; Dunlop, B W

2017-12-01

Commonly observed distortions in decision-making among patients with major depressive disorder (MDD) may emerge from impaired reward processing and cognitive biases toward negative events. There is substantial theoretical support for the hypothesis that MDD patients overweight potential losses compared with gains, though the neurobiological underpinnings of this bias are uncertain. Twenty-one unmedicated patients with MDD were compared with 25 healthy controls (HC) using functional magnetic resonance imaging (fMRI) together with an economic decision-making task over mixed lotteries involving probabilistic gains and losses. Region-of-interest analyses evaluated neural signatures of gain and loss coding within a core network of brain areas known to be involved in valuation (anterior insula, caudate nucleus, ventromedial prefrontal cortex). Usable fMRI data were available for 19 MDD and 23 HC subjects. Anterior insula signal showed negative coding of losses (gain > loss) in HC subjects consistent with previous findings, whereas MDD subjects demonstrated significant reversals in these associations (loss > gain). Moreover, depression severity further enhanced the positive coding of losses in anterior insula, ventromedial prefrontal cortex, and caudate nucleus. The hyper-responsivity to losses displayed by the anterior insula of MDD patients was paralleled by a reduced influence of gain, but not loss, stake size on choice latencies. Patients with MDD demonstrate a significant shift from negative to positive coding of losses in the anterior insula, revealing the importance of this structure in value-based decision-making in the context of emotional disturbances.

Open-Source Development of the Petascale Reactive Flow and Transport Code PFLOTRAN

NASA Astrophysics Data System (ADS)

Hammond, G. E.; Andre, B.; Bisht, G.; Johnson, T.; Karra, S.; Lichtner, P. C.; Mills, R. T.

2013-12-01

Open-source software development has become increasingly popular in recent years. Open-source encourages collaborative and transparent software development and promotes unlimited free redistribution of source code to the public. Open-source development is good for science as it reveals implementation details that are critical to scientific reproducibility, but generally excluded from journal publications. In addition, research funds that would have been spent on licensing fees can be redirected to code development that benefits more scientists. In 2006, the developers of PFLOTRAN open-sourced their code under the U.S. Department of Energy SciDAC-II program. Since that time, the code has gained popularity among code developers and users from around the world seeking to employ PFLOTRAN to simulate thermal, hydraulic, mechanical and biogeochemical processes in the Earth's surface/subsurface environment. PFLOTRAN is a massively-parallel subsurface reactive multiphase flow and transport simulator designed from the ground up to run efficiently on computing platforms ranging from the laptop to leadership-class supercomputers, all from a single code base. The code employs domain decomposition for parallelism and is founded upon the well-established and open-source parallel PETSc and HDF5 frameworks. PFLOTRAN leverages modern Fortran (i.e. Fortran 2003-2008) in its extensible object-oriented design. The use of this progressive, yet domain-friendly programming language has greatly facilitated collaboration in the code's software development. Over the past year, PFLOTRAN's top-level data structures were refactored as Fortran classes (i.e. extendible derived types) to improve the flexibility of the code, ease the addition of new process models, and enable coupling to external simulators. For instance, PFLOTRAN has been coupled to the parallel electrical resistivity tomography code E4D to enable hydrogeophysical inversion while the same code base can be used as a third-party library to provide hydrologic flow, energy transport, and biogeochemical capability to the community land model, CLM, part of the open-source community earth system model (CESM) for climate. In this presentation, the advantages and disadvantages of open source software development in support of geoscience research at government laboratories, universities, and the private sector are discussed. Since the code is open-source (i.e. it's transparent and readily available to competitors), the PFLOTRAN team's development strategy within a competitive research environment is presented. Finally, the developers discuss their approach to object-oriented programming and the leveraging of modern Fortran in support of collaborative geoscience research as the Fortran standard evolves among compiler vendors.

Codestream-Based Identification of JPEG 2000 Images with Different Coding Parameters

NASA Astrophysics Data System (ADS)

Watanabe, Osamu; Fukuhara, Takahiro; Kiya, Hitoshi

A method of identifying JPEG 2000 images with different coding parameters, such as code-block sizes, quantization-step sizes, and resolution levels, is presented. It does not produce false-negative matches regardless of different coding parameters (compression rate, code-block size, and discrete wavelet transform (DWT) resolutions levels) or quantization step sizes. This feature is not provided by conventional methods. Moreover, the proposed approach is fast because it uses the number of zero-bit-planes that can be extracted from the JPEG 2000 codestream by only parsing the header information without embedded block coding with optimized truncation (EBCOT) decoding. The experimental results revealed the effectiveness of image identification based on the new method.

The legumin gene family: structure of a B type gene of Vicia faba and a possible legumin gene specific regulatory element.

PubMed Central

Bäumlein, H; Wobus, U; Pustell, J; Kafatos, F C

1986-01-01

The field bean, Vicia faba L. var. minor, possesses two sub-families of 11 S legumin genes named A and B. We isolated from a genomic library a B-type gene (LeB4) and determined its primary DNA sequence. Gene LeB4 codes for a 484 amino acid residue prepropolypeptide, encompassing a signal peptide of 22 amino acid residues, an acidic, very hydrophilic alpha-chain of 281 residues and a basic, somewhat hydrophobic beta-chain of 181 residues. The latter two coding regions are immediately contiguous, but each is interrupted by a short intron. Type A legumin genes from soybean and pea are known to have introns in the same two positions, in addition to an extra intron (within the alpha-coding sequence). Sequence comparisons of legumin genes from these three plants revealed a highly conserved sequence element of at least 28 bp, centered at approximately 100 bp upstream of each cap site. The element is absent from the equivalent position of all non-legumin and other plant and fungal genes examined. We tentatively name this element "legumin box" and suggest that it may have a function in the regulation of legumin gene expression. PMID:3960730

Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics

PubMed Central

del Val, Coral; Rivas, Elena; Torres-Quesada, Omar; Toro, Nicolás; Jiménez-Zurdo, José I

2007-01-01

Bacterial small non-coding RNAs (sRNAs) are being recognized as novel widespread regulators of gene expression in response to environmental signals. Here, we present the first search for sRNA-encoding genes in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, performed by a genome-wide computational analysis of its intergenic regions. Comparative sequence data from eight related α-proteobacteria were obtained, and the interspecies pairwise alignments were scored with the programs eQRNA and RNAz as complementary predictive tools to identify conserved and stable secondary structures corresponding to putative non-coding RNAs. Northern experiments confirmed that eight of the predicted loci, selected among the original 32 candidates as most probable sRNA genes, expressed small transcripts. This result supports the combined use of eQRNA and RNAz as a robust strategy to identify novel sRNAs in bacteria. Furthermore, seven of the transcripts accumulated differentially in free-living and symbiotic conditions. Experimental mapping of the 5′-ends of the detected transcripts revealed that their encoding genes are organized in autonomous transcription units with recognizable promoter and, in most cases, termination signatures. These findings suggest novel regulatory functions for sRNAs related to the interactions of α-proteobacteria with their eukaryotic hosts. PMID:17971083

Application of Microgravity to the Assessment of Existing Structures and Structural Foundations.

DTIC Science & Technology

1988-04-29

UADGU Geophysique Francafse IUSRSU 6c. ADDRESS (City, State. and ZIP Code) 7b. ADDRESS (City, State, and ZIP Code) 20, Rue des Pavilions Box 65 92800...r (2.8 - 2.4) 286 AM~TCT f eldo f6 YOUOUVT 4. EXISTING STRUCTURES AND (U) CONPAGNIE DE PROSPECTION GEOPHYSIQUE FRANCAISE RUEIL-MALNAISO J LAKSHNRNRN

Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae.

PubMed

Redwan, R M; Saidin, A; Kumar, S V

2015-08-12

Pineapple (Ananas comosus var. comosus) is known as the king of fruits for its crown and is the third most important tropical fruit after banana and citrus. The plant, which is indigenous to South America, is the most important species in the Bromeliaceae family and is largely traded for fresh fruit consumption. Here, we report the complete chloroplast sequence of the MD-2 pineapple that was sequenced using the PacBio sequencing technology. In this study, the high error rate of PacBio long sequence reads of A. comosus's total genomic DNA were improved by leveraging on the high accuracy but short Illumina reads for error-correction via the latest error correction module from Novocraft. Error corrected long PacBio reads were assembled by using a single tool to produce a contig representing the pineapple chloroplast genome. The genome of 159,636 bp in length is featured with the conserved quadripartite structure of chloroplast containing a large single copy region (LSC) with a size of 87,482 bp, a small single copy region (SSC) with a size of 18,622 bp and two inverted repeat regions (IRA and IRB) each with the size of 26,766 bp. Overall, the genome contained 117 unique coding regions and 30 were repeated in the IR region with its genes contents, structure and arrangement similar to its sister taxon, Typha latifolia. A total of 35 repeats structure were detected in both the coding and non-coding regions with a majority being tandem repeats. In addition, 205 SSRs were detected in the genome with six protein-coding genes contained more than two SSRs. Comparative chloroplast genomes from the subclass Commelinidae revealed a conservative protein coding gene albeit located in a highly divergence region. Analysis of selection pressure on protein-coding genes using Ka/Ks ratio showed significant positive selection exerted on the rps7 gene of the pineapple chloroplast with P less than 0.05. Phylogenetic analysis confirmed the recent taxonomical relation among the member of commelinids which support the monophyly relationship between Arecales and Dasypogonaceae and between Zingiberales to the Poales, which includes the A. comosus. The complete sequence of the chloroplast of pineapple provides insights to the divergence of genic chloroplast sequences from the members of the subclass Commelinidae. The complete pineapple chloroplast will serve as a reference for in-depth taxonomical studies in the Bromeliaceae family when more species under the family are sequenced in the future. The genetic sequence information will also make feasible other molecular applications of the pineapple chloroplast for plant genetic improvement.

Design of neurophysiologically motivated structures of time-pulse coded neurons

NASA Astrophysics Data System (ADS)

Krasilenko, Vladimir G.; Nikolsky, Alexander I.; Lazarev, Alexander A.; Lobodzinska, Raisa F.

2009-04-01

The common methodology of biologically motivated concept of building of processing sensors systems with parallel input and picture operands processing and time-pulse coding are described in paper. Advantages of such coding for creation of parallel programmed 2D-array structures for the next generation digital computers which require untraditional numerical systems for processing of analog, digital, hybrid and neuro-fuzzy operands are shown. The optoelectronic time-pulse coded intelligent neural elements (OETPCINE) simulation results and implementation results of a wide set of neuro-fuzzy logic operations are considered. The simulation results confirm engineering advantages, intellectuality, circuit flexibility of OETPCINE for creation of advanced 2D-structures. The developed equivalentor-nonequivalentor neural element has power consumption of 10mW and processing time about 10...100us.

Individual Differences Reveal Correlates of Hidden Hearing Deficits

PubMed Central

Masud, Salwa; Mehraei, Golbarg; Verhulst, Sarah; Shinn-Cunningham, Barbara G.

2015-01-01

Clinical audiometry has long focused on determining the detection thresholds for pure tones, which depend on intact cochlear mechanics and hair cell function. Yet many listeners with normal hearing thresholds complain of communication difficulties, and the causes for such problems are not well understood. Here, we explore whether normal-hearing listeners exhibit such suprathreshold deficits, affecting the fidelity with which subcortical areas encode the temporal structure of clearly audible sound. Using an array of measures, we evaluated a cohort of young adults with thresholds in the normal range to assess both cochlear mechanical function and temporal coding of suprathreshold sounds. Listeners differed widely in both electrophysiological and behavioral measures of temporal coding fidelity. These measures correlated significantly with each other. Conversely, these differences were unrelated to the modest variation in otoacoustic emissions, cochlear tuning, or the residual differences in hearing threshold present in our cohort. Electroencephalography revealed that listeners with poor subcortical encoding had poor cortical sensitivity to changes in interaural time differences, which are critical for localizing sound sources and analyzing complex scenes. These listeners also performed poorly when asked to direct selective attention to one of two competing speech streams, a task that mimics the challenges of many everyday listening environments. Together with previous animal and computational models, our results suggest that hidden hearing deficits, likely originating at the level of the cochlear nerve, are part of “normal hearing.” PMID:25653371

A Scalable Architecture of a Structured LDPC Decoder

NASA Technical Reports Server (NTRS)

Lee, Jason Kwok-San; Lee, Benjamin; Thorpe, Jeremy; Andrews, Kenneth; Dolinar, Sam; Hamkins, Jon

2004-01-01

We present a scalable decoding architecture for a certain class of structured LDPC codes. The codes are designed using a small (n,r) protograph that is replicated Z times to produce a decoding graph for a (Z x n, Z x r) code. Using this architecture, we have implemented a decoder for a (4096,2048) LDPC code on a Xilinx Virtex-II 2000 FPGA, and achieved decoding speeds of 31 Mbps with 10 fixed iterations. The implemented message-passing algorithm uses an optimized 3-bit non-uniform quantizer that operates with 0.2dB implementation loss relative to a floating point decoder.

Inhibition of Pancreatic Cancer Cell Proliferation by LRH-1 Inhibitors

DTIC Science & Technology

2014-12-01

coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org [ PDB ID codes 4QJR (SF-1/PIP3) and 4QK4 (SF-1/PIP2)]. 1To whom...with Rfree/Rcryst values of 23/19% (Table S2). The structure was deposited with the PDB ID code 4QJR. SF 1/PIP3 (Fig. 1C) adopts the classic NR LBD...PIP2) was solved by molecular replacement, using PDB ID code 1YOW as the search model, and compared with the SF 1/PIP3 structure (Table S2). The

Local structure preserving sparse coding for infrared target recognition

PubMed Central

Han, Jing; Yue, Jiang; Zhang, Yi; Bai, Lianfa

2017-01-01

Sparse coding performs well in image classification. However, robust target recognition requires a lot of comprehensive template images and the sparse learning process is complex. We incorporate sparsity into a template matching concept to construct a local sparse structure matching (LSSM) model for general infrared target recognition. A local structure preserving sparse coding (LSPSc) formulation is proposed to simultaneously preserve the local sparse and structural information of objects. By adding a spatial local structure constraint into the classical sparse coding algorithm, LSPSc can improve the stability of sparse representation for targets and inhibit background interference in infrared images. Furthermore, a kernel LSPSc (K-LSPSc) formulation is proposed, which extends LSPSc to the kernel space to weaken the influence of the linear structure constraint in nonlinear natural data. Because of the anti-interference and fault-tolerant capabilities, both LSPSc- and K-LSPSc-based LSSM can implement target identification based on a simple template set, which just needs several images containing enough local sparse structures to learn a sufficient sparse structure dictionary of a target class. Specifically, this LSSM approach has stable performance in the target detection with scene, shape and occlusions variations. High performance is demonstrated on several datasets, indicating robust infrared target recognition in diverse environments and imaging conditions. PMID:28323824

Informational structure of genetic sequences and nature of gene splicing

NASA Astrophysics Data System (ADS)

Trifonov, E. N.

1991-10-01

Only about 1/20 of DNA of higher organisms codes for proteins, by means of classical triplet code. The rest of DNA sequences is largely silent, with unclear functions, if any. The triplet code is not the only code (message) carried by the sequences. There are three levels of molecular communication, where the same sequence ``talks'' to various bimolecules, while having, respectively, three different appearances: DNA, RNA and protein. Since the molecular structures and, hence, sequence specific preferences of these are substantially different, the original DNA sequence has to carry simultaneously three types of sequence patterns (codes, messages), thus, being a composite structure in which one had the same letter (nucleotide) is frequently involved in several overlapping codes of different nature. This multiplicity and overlapping of the codes is a unique feature of the Gnomic, language of genetic sequences. The coexisting codes have to be degenerate in various degrees to allow an optimal and concerted performance of all the encoded functions. There is an obvious conflict between the best possible performance of a given function and necessity to compromise the quality of a given sequence pattern in favor of other patterns. It appears that the major role of various changes in the sequences on their ``ontogenetic'' way from DNA to RNA to protein, like RNA editing and splicing, or protein post-translational modifications is to resolve such conflicts. New data are presented strongly indicating that the gene splicing is such a device to resolve the conflict between the code of DNA folding in chromatin and the triplet code for protein synthesis.

A Synchronization Algorithm and Implementation for High-Speed Block Codes Applications. Part 4

NASA Technical Reports Server (NTRS)

Lin, Shu; Zhang, Yu; Nakamura, Eric B.; Uehara, Gregory T.

1998-01-01

Block codes have trellis structures and decoders amenable to high speed CMOS VLSI implementation. For a given CMOS technology, these structures enable operating speeds higher than those achievable using convolutional codes for only modest reductions in coding gain. As a result, block codes have tremendous potential for satellite trunk and other future high-speed communication applications. This paper describes a new approach for implementation of the synchronization function for block codes. The approach utilizes the output of the Viterbi decoder and therefore employs the strength of the decoder. Its operation requires no knowledge of the signal-to-noise ratio of the received signal, has a simple implementation, adds no overhead to the transmitted data, and has been shown to be effective in simulation for received SNR greater than 2 dB.

Identification of Putative Nuclear Receptors and Steroidogenic Enzymes in Murray-Darling Rainbowfish (Melanotaenia fluviatilis) Using RNA-Seq and De Novo Transcriptome Assembly.

PubMed

Bain, Peter A; Papanicolaou, Alexie; Kumar, Anupama

2015-01-01

Murray-Darling rainbowfish (Melanotaenia fluviatilis [Castelnau, 1878]; Atheriniformes: Melanotaeniidae) is a small-bodied teleost currently under development in Australasia as a test species for aquatic toxicological studies. To date, efforts towards the development of molecular biomarkers of contaminant exposure have been hindered by the lack of available sequence data. To address this, we sequenced messenger RNA from brain, liver and gonads of mature male and female fish and generated a high-quality draft transcriptome using a de novo assembly approach. 149,742 clusters of putative transcripts were obtained, encompassing 43,841 non-redundant protein-coding regions. Deduced amino acid sequences were annotated by functional inference based on similarity with sequences from manually curated protein sequence databases. The draft assembly contained protein-coding regions homologous to 95.7% of the complete cohort of predicted proteins from the taxonomically related species, Oryzias latipes (Japanese medaka). The mean length of rainbowfish protein-coding sequences relative to their medaka homologues was 92.1%, indicating that despite the limited number of tissues sampled a large proportion of the total expected number of protein-coding genes was captured in the study. Because of our interest in the effects of environmental contaminants on endocrine pathways, we manually curated subsets of coding regions for putative nuclear receptors and steroidogenic enzymes in the rainbowfish transcriptome, revealing 61 candidate nuclear receptors encompassing all known subfamilies, and 41 putative steroidogenic enzymes representing all major steroidogenic enzymes occurring in teleosts. The transcriptome presented here will be a valuable resource for researchers interested in biomarker development, protein structure and function, and contaminant-response genomics in Murray-Darling rainbowfish.

THE McGill PLANAR HYDROGEN ATMOSPHERE CODE (McPHAC)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haakonsen, Christian Bernt; Turner, Monica L.; Tacik, Nick A.

2012-04-10

The McGill Planar Hydrogen Atmosphere Code (McPHAC) v1.1 calculates the hydrostatic equilibrium structure and emergent spectrum of an unmagnetized hydrogen atmosphere in the plane-parallel approximation, at surface gravities appropriate for neutron stars. McPHAC incorporates several improvements over previous codes for which tabulated model spectra are available: (1) Thomson scattering is treated anisotropically, which is shown to result in a 0.2%-3% correction in the emergent spectral flux across the 0.1-5 keV passband; (2) the McPHAC source code is made available to the community, allowing it to be scrutinized and modified by other researchers wishing to study or extend its capabilities; andmore » (3) the numerical uncertainty resulting from the discrete and iterative solution is studied as a function of photon energy, indicating that McPHAC is capable of producing spectra with numerical uncertainties <0.01%. The accuracy of the spectra may at present be limited to {approx}1%, but McPHAC enables researchers to study the impact of uncertain inputs and additional physical effects, thereby supporting future efforts to reduce those inaccuracies. Comparison of McPHAC results with spectra from one of the previous model atmosphere codes (NSA) shows agreement to {approx}<1% near the peaks of the emergent spectra. However, in the Wien tail a significant deficit of flux in the spectra of the previous model is revealed, determined to be due to the previous work not considering large enough optical depths at the highest photon frequencies. The deficit is most significant for spectra with T{sub eff} < 10{sup 5.6} K, though even there it may not be of much practical importance for most observations.« less

The McGill Planar Hydrogen Atmosphere Code (McPHAC)

NASA Astrophysics Data System (ADS)

Haakonsen, Christian Bernt; Turner, Monica L.; Tacik, Nick A.; Rutledge, Robert E.

2012-04-01

The McGill Planar Hydrogen Atmosphere Code (McPHAC) v1.1 calculates the hydrostatic equilibrium structure and emergent spectrum of an unmagnetized hydrogen atmosphere in the plane-parallel approximation, at surface gravities appropriate for neutron stars. McPHAC incorporates several improvements over previous codes for which tabulated model spectra are available: (1) Thomson scattering is treated anisotropically, which is shown to result in a 0.2%-3% correction in the emergent spectral flux across the 0.1-5 keV passband; (2) the McPHAC source code is made available to the community, allowing it to be scrutinized and modified by other researchers wishing to study or extend its capabilities; and (3) the numerical uncertainty resulting from the discrete and iterative solution is studied as a function of photon energy, indicating that McPHAC is capable of producing spectra with numerical uncertainties <0.01%. The accuracy of the spectra may at present be limited to ~1%, but McPHAC enables researchers to study the impact of uncertain inputs and additional physical effects, thereby supporting future efforts to reduce those inaccuracies. Comparison of McPHAC results with spectra from one of the previous model atmosphere codes (NSA) shows agreement to lsim1% near the peaks of the emergent spectra. However, in the Wien tail a significant deficit of flux in the spectra of the previous model is revealed, determined to be due to the previous work not considering large enough optical depths at the highest photon frequencies. The deficit is most significant for spectra with T eff < 105.6 K, though even there it may not be of much practical importance for most observations.

McPHAC: McGill Planar Hydrogen Atmosphere Code

NASA Astrophysics Data System (ADS)

Haakonsen, Christian Bernt; Turner, Monica L.; Tacik, Nick A.; Rutledge, Robert E.

2012-10-01

The McGill Planar Hydrogen Atmosphere Code (McPHAC) v1.1 calculates the hydrostatic equilibrium structure and emergent spectrum of an unmagnetized hydrogen atmosphere in the plane-parallel approximation at surface gravities appropriate for neutron stars. McPHAC incorporates several improvements over previous codes for which tabulated model spectra are available: (1) Thomson scattering is treated anisotropically, which is shown to result in a 0.2%-3% correction in the emergent spectral flux across the 0.1-5 keV passband; (2) the McPHAC source code is made available to the community, allowing it to be scrutinized and modified by other researchers wishing to study or extend its capabilities; and (3) the numerical uncertainty resulting from the discrete and iterative solution is studied as a function of photon energy, indicating that McPHAC is capable of producing spectra with numerical uncertainties <0.01%. The accuracy of the spectra may at present be limited to ~1%, but McPHAC enables researchers to study the impact of uncertain inputs and additional physical effects, thereby supporting future efforts to reduce those inaccuracies. Comparison of McPHAC results with spectra from one of the previous model atmosphere codes (NSA) shows agreement to lsim1% near the peaks of the emergent spectra. However, in the Wien tail a significant deficit of flux in the spectra of the previous model is revealed, determined to be due to the previous work not considering large enough optical depths at the highest photon frequencies. The deficit is most significant for spectra with T eff < 105.6 K, though even there it may not be of much practical importance for most observations.

Four Year-Olds Use Norm-Based Coding for Face Identity

ERIC Educational Resources Information Center

Jeffery, Linda; Read, Ainsley; Rhodes, Gillian

2013-01-01

Norm-based coding, in which faces are coded as deviations from an average face, is an efficient way of coding visual patterns that share a common structure and must be distinguished by subtle variations that define individuals. Adults and school-aged children use norm-based coding for face identity but it is not yet known if pre-school aged…

DNA as a Binary Code: How the Physical Structure of Nucleotide Bases Carries Information

ERIC Educational Resources Information Center

McCallister, Gary

2005-01-01

The DNA triplet code also functions as a binary code. Because double-ring compounds cannot bind to double-ring compounds in the DNA code, the sequence of bases classified simply as purines or pyrimidines can encode for smaller groups of possible amino acids. This is an intuitive approach to teaching the DNA code. (Contains 6 figures.)

Genetic Programming-based Phononic Bandgap Structure Design

DTIC Science & Technology

2011-09-01

derivative-based methods is that they require a good starting location to find the global minimum of a function. As can be seen from figure 2, there are many... FRANCHI CODE 7100 M H ORR CODE 7120 J A BUCARO CODE 7130 G J ORRIS 7140 J S PERKINS CODE 7140 S A CHIN BING CODE 7180 4555 OVERLOOK AVE SW WASHINGTON DC

17 CFR 17.03 - Delegation of authority to the Director of the Division of Market Oversight.

Code of Federal Regulations, 2010 CFR

2010-04-01

... information using the format, coding structure or electronic data transmission procedures otherwise required...) Pursuant to § 17.00(a), the authority to approve a format and coding structure other than that set forth in...

HITEMP Material and Structural Optimization Technology Transfer

NASA Technical Reports Server (NTRS)

Collier, Craig S.; Arnold, Steve (Technical Monitor)

2001-01-01

The feasibility of adding viscoelasticity and the Generalized Method of Cells (GMC) for micromechanical viscoelastic behavior into the commercial HyperSizer structural analysis and optimization code was investigated. The viscoelasticity methodology was developed in four steps. First, a simplified algorithm was devised to test the iterative time stepping method for simple one-dimensional multiple ply structures. Second, GMC code was made into a callable subroutine and incorporated into the one-dimensional code to test the accuracy and usability of the code. Third, the viscoelastic time-stepping and iterative scheme was incorporated into HyperSizer for homogeneous, isotropic viscoelastic materials. Finally, the GMC was included in a version of HyperSizer. MS Windows executable files implementing each of these steps is delivered with this report, as well as source code. The findings of this research are that both viscoelasticity and GMC are feasible and valuable additions to HyperSizer and that the door is open for more advanced nonlinear capability, such as viscoplasticity.

QR code based noise-free optical encryption and decryption of a gray scale image

NASA Astrophysics Data System (ADS)

Jiao, Shuming; Zou, Wenbin; Li, Xia

2017-03-01

In optical encryption systems, speckle noise is one major challenge in obtaining high quality decrypted images. This problem can be addressed by employing a QR code based noise-free scheme. Previous works have been conducted for optically encrypting a few characters or a short expression employing QR codes. This paper proposes a practical scheme for optically encrypting and decrypting a gray-scale image based on QR codes for the first time. The proposed scheme is compatible with common QR code generators and readers. Numerical simulation results reveal the proposed method can encrypt and decrypt an input image correctly.

Unraveling the molecular mechanisms of nitrogenase conformational protection against oxygen in diazotrophic bacteria.

PubMed

Lery, Letícia M S; Bitar, Mainá; Costa, Mauricio G S; Rössle, Shaila C S; Bisch, Paulo M

2010-12-22

G. diazotrophicus and A. vinelandii are aerobic nitrogen-fixing bacteria. Although oxygen is essential for the survival of these organisms, it irreversibly inhibits nitrogenase, the complex responsible for nitrogen fixation. Both microorganisms deal with this paradox through compensatory mechanisms. In A. vinelandii a conformational protection mechanism occurs through the interaction between the nitrogenase complex and the FeSII protein. Previous studies suggested the existence of a similar system in G. diazotrophicus, but the putative protein involved was not yet described. This study intends to identify the protein coding gene in the recently sequenced genome of G. diazotrophicus and also provide detailed structural information of nitrogenase conformational protection in both organisms. Genomic analysis of G. diazotrophicus sequences revealed a protein coding ORF (Gdia0615) enclosing a conserved "fer2" domain, typical of the ferredoxin family and found in A. vinelandii FeSII. Comparative models of both FeSII and Gdia0615 disclosed a conserved beta-grasp fold. Cysteine residues that coordinate the 2[Fe-S] cluster are in conserved positions towards the metallocluster. Analysis of solvent accessible residues and electrostatic surfaces unveiled an hydrophobic dimerization interface. Dimers assembled by molecular docking presented a stable behaviour and a proper accommodation of regions possibly involved in binding of FeSII to nitrogenase throughout molecular dynamics simulations in aqueous solution. Molecular modeling of the nitrogenase complex of G. diazotrophicus was performed and models were compared to the crystal structure of A. vinelandii nitrogenase. Docking experiments of FeSII and Gdia0615 with its corresponding nitrogenase complex pointed out in both systems a putative binding site presenting shape and charge complementarities at the Fe-protein/MoFe-protein complex interface. The identification of the putative FeSII coding gene in G. diazotrophicus genome represents a large step towards the understanding of the conformational protection mechanism of nitrogenase against oxygen. In addition, this is the first study regarding the structural complementarities of FeSII-nitrogenase interactions in diazotrophic bacteria. The combination of bioinformatic tools for genome analysis, comparative protein modeling, docking calculations and molecular dynamics provided a powerful strategy for the elucidation of molecular mechanisms and structural features of FeSII-nitrogenase interaction.

Protecting quantum memories using coherent parity check codes

NASA Astrophysics Data System (ADS)

Roffe, Joschka; Headley, David; Chancellor, Nicholas; Horsman, Dominic; Kendon, Viv

2018-07-01

Coherent parity check (CPC) codes are a new framework for the construction of quantum error correction codes that encode multiple qubits per logical block. CPC codes have a canonical structure involving successive rounds of bit and phase parity checks, supplemented by cross-checks to fix the code distance. In this paper, we provide a detailed introduction to CPC codes using conventional quantum circuit notation. We demonstrate the implementation of a CPC code on real hardware, by designing a [[4, 2, 2

Echoic Memory Interference and Comprehension in a Foreign Language.

ERIC Educational Resources Information Center

Greenberg, Seth N.; Roscoe, Suzanne

1988-01-01

Study of echoic memory interference among students in college introductory Spanish and German courses revealed that students with weaker listening comprehension skills depended more upon vulnerable sensory codes in echoic memory, while students with stronger comprehension relied on stable higher-order codes. (Author/CB)

Guidelines for development structured FORTRAN programs

NASA Technical Reports Server (NTRS)

Earnest, B. M.

1984-01-01

Computer programming and coding standards were compiled to serve as guidelines for the uniform writing of FORTRAN 77 programs at NASA Langley. Software development philosophy, documentation, general coding conventions, and specific FORTRAN coding constraints are discussed.

Capturing Snapshots of APE1 Processing DNA Damage

PubMed Central

Freudenthal, Bret D.; Beard, William A.; Cuneo, Matthew J.; Dyrkheeva, Nadezhda S.; Wilson, Samuel H.

2015-01-01

DNA apurinic-apyrimidinic (AP) sites are prevalent non-coding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA repair intermediate that is potentially cytotoxic. The molecular events of the incision reaction remain elusive due in part to limited structural information. We report multiple high-resolution human APE1:DNA structures that divulge novel features of the APE1 reaction, including the metal binding site, nucleophile, and arginine clamps that mediate product release. We also report APE1:DNA structures with a T:G mismatch 5′ to the AP-site, representing a clustered lesion occurring in methylated CpG dinucleotides. These reveal that APE1 molds the T:G mismatch into a unique Watson-Crick like geometry that distorts the active site reducing incision. These snapshots provide mechanistic clarity for APE1, while affording a rational framework to manipulate biological responses to DNA damage. PMID:26458045

Working memory as separable subsystems: a study with Portuguese primary school children.

PubMed

Campos, Isabel S; Almeida, Leandro S; Ferreira, Aristides I; Martinez, Luis F

2013-01-01

Although much research has been done to study the working memory structure in children in their first school years, the relation of cognitive constructs involved in this process remains uncertain. In particular, it is unclear whether working memory is a domain general construct that coordinates separate codes of verbal and visuospatial storage or whether it is a domain-specific construct with distinct resources of verbal and visuospatial information. This paper investigates the structure of working memory, by using the Working Memory Test Battery for Children (WMTB-C) and by doing confirmatory factor analyses (CFAs) on a sample of Portuguese children (n = 103) between 8 and 9 years of age. The results of the confirmatory factor analyses that provide the best fit of the data correspond to the model that includes Central Executive and Visuospatial Sketchpad in the same factor, co-varying with a Phonological Loop factor. Moreover, the traditional working memory tripartite structure--based on the Baddeley and Hitch Model--revealed good fit to the data.

The system-resonance approach in modeling genetic structures.

PubMed

Petoukhov, Sergey V

2016-01-01

The founder of the theory of resonance in structural chemistry Linus Pauling established the importance of resonance patterns in organization of living systems. Any living organism is a great chorus of coordinated oscillatory processes. From the formal point of view, biological organism is an oscillatory system with a great number of degrees of freedom. Such systems are studied in the theory of oscillations using matrix mathematics of their resonance characteristics. This study is devoted to a new approach for modeling genetically inherited structures and processes in living organisms using mathematical tools of the theory of resonances. This approach reveals hidden relationships in a number of genetic phenomena and gives rise to a new class of bio-mathematical models, which contribute to a convergence of biology with physics and informatics. In addition some relationships of molecular-genetic ensembles with mathematics of noise-immunity coding of information in modern communications technology are shown. Perspectives of applications of the phenomena of vibrational mechanics for modeling in biology are discussed. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Two-dimensional finite-element analyses of simulated rotor-fragment impacts against rings and beams compared with experiments

NASA Technical Reports Server (NTRS)

Stagliano, T. R.; Witmer, E. A.; Rodal, J. J. A.

1979-01-01

Finite element modeling alternatives as well as the utility and limitations of the two dimensional structural response computer code CIVM-JET 4B for predicting the transient, large deflection, elastic plastic, structural responses of two dimensional beam and/or ring structures which are subjected to rigid fragment impact were investigated. The applicability of the CIVM-JET 4B analysis and code for the prediction of steel containment ring response to impact by complex deformable fragments from a trihub burst of a T58 turbine rotor was studied. Dimensional analysis considerations were used in a parametric examination of data from engine rotor burst containment experiments and data from sphere beam impact experiments. The use of the CIVM-JET 4B computer code for making parametric structural response studies on both fragment-containment structure and fragment-deflector structure was illustrated. Modifications to the analysis/computation procedure were developed to alleviate restrictions.

Probabilistic Structural Analysis Methods (PSAM) for select space propulsion system components, part 2

NASA Technical Reports Server (NTRS)

1991-01-01

The technical effort and computer code enhancements performed during the sixth year of the Probabilistic Structural Analysis Methods program are summarized. Various capabilities are described to probabilistically combine structural response and structural resistance to compute component reliability. A library of structural resistance models is implemented in the Numerical Evaluations of Stochastic Structures Under Stress (NESSUS) code that included fatigue, fracture, creep, multi-factor interaction, and other important effects. In addition, a user interface was developed for user-defined resistance models. An accurate and efficient reliability method was developed and was successfully implemented in the NESSUS code to compute component reliability based on user-selected response and resistance models. A risk module was developed to compute component risk with respect to cost, performance, or user-defined criteria. The new component risk assessment capabilities were validated and demonstrated using several examples. Various supporting methodologies were also developed in support of component risk assessment.

Coordinated design of coding and modulation systems

NASA Technical Reports Server (NTRS)

Massey, J. L.; Ancheta, T.; Johannesson, R.; Lauer, G.; Lee, L.

1976-01-01

The joint optimization of the coding and modulation systems employed in telemetry systems was investigated. Emphasis was placed on formulating inner and outer coding standards used by the Goddard Spaceflight Center. Convolutional codes were found that are nearly optimum for use with Viterbi decoding in the inner coding of concatenated coding systems. A convolutional code, the unit-memory code, was discovered and is ideal for inner system usage because of its byte-oriented structure. Simulations of sequential decoding on the deep-space channel were carried out to compare directly various convolutional codes that are proposed for use in deep-space systems.

Role of a Dual Splicing and Amino Acid Code in Myopia, Cone Dysfunction and Cone Dystrophy Associated with L/M Opsin Interchange Mutations

PubMed Central

Greenwald, Scott H.; Kuchenbecker, James A.; Rowlan, Jessica S.; Neitz, Jay; Neitz, Maureen

2017-01-01

Purpose Human long (L) and middle (M) wavelength cone opsin genes are highly variable due to intermixing. Two L/M cone opsin interchange mutants, designated LIAVA and LVAVA, are associated with clinical diagnoses, including red-green color vision deficiency, blue cone monochromacy, cone degeneration, myopia, and Bornholm Eye Disease. Because the protein and splicing codes are carried by the same nucleotides, intermixing L and M genes can cause disease by affecting protein structure and splicing. Methods Genetically engineered mice were created to allow investigation of the consequences of altered protein structure alone, and the effects on cone morphology were examined using immunohistochemistry. In humans and mice, cone function was evaluated using the electroretinogram (ERG) under L/M- or short (S) wavelength cone isolating conditions. Effects of LIAVA and LVAVA genes on splicing were evaluated using a minigene assay. Results ERGs and histology in mice revealed protein toxicity for the LVAVA but not for the LIAVA opsin. Minigene assays showed that the dominant messenger RNA (mRNA) was aberrantly spliced for both variants; however, the LVAVA gene produced a small but significant amount of full-length mRNA and LVAVA subjects had correspondingly reduced ERG amplitudes. In contrast, the LIAVA subject had no L/M cone ERG. Conclusions Dramatic differences in phenotype can result from seemingly minor differences in genotype through divergent effects on the dual amino acid and splicing codes. Translational Relevance The mechanism by which individual mutations contribute to clinical phenotypes provides valuable information for diagnosis and prognosis of vision disorders associated with L/M interchange mutations, and it informs strategies for developing therapies. PMID:28516000

The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza.

PubMed

Qian, Jun; Song, Jingyuan; Gao, Huanhuan; Zhu, Yingjie; Xu, Jiang; Pang, Xiaohui; Yao, Hui; Sun, Chao; Li, Xian'en; Li, Chuyuan; Liu, Juyan; Xu, Haibin; Chen, Shilin

2013-01-01

Salvia miltiorrhiza is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of Salvia miltiorrhiza, the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,539 bp). It contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Four forward, three inverted and seven tandem repeats were detected in the Salvia miltiorrhiza cp genome. Simple sequence repeat (SSR) analysis among the 30 asterid cp genomes revealed that most SSRs are AT-rich, which contribute to the overall AT richness of these cp genomes. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the cp genomes. Entire cp genome comparison of Salvia miltiorrhiza and three other Lamiales cp genomes showed a high degree of sequence similarity and a relatively high divergence of intergenic spacers. Sequence divergence analysis discovered the ten most divergent and ten most conserved genes as well as their length variation, which will be helpful for phylogenetic studies in asterids. Our analysis also supports that both regional and functional constraints affect gene sequence evolution. Further, phylogenetic analysis demonstrated a sister relationship between Salvia miltiorrhiza and Sesamum indicum. The complete cp genome sequence of Salvia miltiorrhiza reported in this paper will facilitate population, phylogenetic and cp genetic engineering studies of this medicinal plant.

Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II

PubMed Central

Norman, Paul J.; Norberg, Steven J.; Guethlein, Lisbeth A.; Nemat-Gorgani, Neda; Royce, Thomas; Wroblewski, Emily E.; Dunn, Tamsen; Mann, Tobias; Alicata, Claudia; Hollenbach, Jill A.; Chang, Weihua; Shults Won, Melissa; Gunderson, Kevin L.; Abi-Rached, Laurent; Ronaghi, Mostafa; Parham, Peter

2017-01-01

The most polymorphic part of the human genome, the MHC, encodes over 160 proteins of diverse function. Half of them, including the HLA class I and II genes, are directly involved in immune responses. Consequently, the MHC region strongly associates with numerous diseases and clinical therapies. Notoriously, the MHC region has been intractable to high-throughput analysis at complete sequence resolution, and current reference haplotypes are inadequate for large-scale studies. To address these challenges, we developed a method that specifically captures and sequences the 4.8-Mbp MHC region from genomic DNA. For 95 MHC homozygous cell lines we assembled, de novo, a set of high-fidelity contigs and a sequence scaffold, representing a mean 98% of the target region. Included are six alternative MHC reference sequences of the human genome that we completed and refined. Characterization of the sequence and structural diversity of the MHC region shows the approach accurately determines the sequences of the highly polymorphic HLA class I and HLA class II genes and the complex structural diversity of complement factor C4A/C4B. It has also uncovered extensive and unexpected diversity in other MHC genes; an example is MUC22, which encodes a lung mucin and exhibits more coding sequence alleles than any HLA class I or II gene studied here. More than 60% of the coding sequence alleles analyzed were previously uncharacterized. We have created a substantial database of robust reference MHC haplotype sequences that will enable future population scale studies of this complicated and clinically important region of the human genome. PMID:28360230

Comparison of Model Calculations of Biological Damage from Exposure to Heavy Ions with Measurements

NASA Technical Reports Server (NTRS)

Kim, Myung-Hee Y.; Hada, Megumi; Cucinotta, Francis A.; Wu, Honglu

2014-01-01

The space environment consists of a varying field of radiation particles including high-energy ions, with spacecraft shielding material providing the major protection to astronauts from harmful exposure. Unlike low-LET gamma or X rays, the presence of shielding does not always reduce the radiation risks for energetic charged-particle exposure. Dose delivered by the charged particle increases sharply at the Bragg peak. However, the Bragg curve does not necessarily represent the biological damage along the particle path since biological effects are influenced by the track structures of both primary and secondary particles. Therefore, the ''biological Bragg curve'' is dependent on the energy and the type of the primary particle and may vary for different biological end points. Measurements of the induction of micronuclei (MN) have made across the Bragg curve in human fibroblasts exposed to energetic silicon and iron ions in vitro at two different energies, 300 MeV/nucleon and 1 GeV/nucleon. Although the data did not reveal an increased yield of MN at the location of the Bragg peak, the increased inhibition of cell progression, which is related to cell death, was found at the Bragg peak location. These results are compared to the calculations of biological damage using a stochastic Monte-Carlo track structure model, Galactic Cosmic Ray Event-based Risk Model (GERM) code (Cucinotta, et al., 2011). The GERM code estimates the basic physical properties along the passage of heavy ions in tissue and shielding materials, by which the experimental set-up can be interpreted. The code can also be used to describe the biophysical events of interest in radiobiology, cancer therapy, and space exploration. The calculation has shown that the severely damaged cells at the Bragg peak are more likely to go through reproductive death, the so called "overkill".

DRG benchmarking study establishes national coding norms.

PubMed

Vaul, J H

1998-05-01

With the increase in fraud and abuse investigations, healthcare financial managers should examine their organization's medical record coding procedures. The Federal government and third-party payers are looking specifically for improper billing of outpatient services, unbundling of procedures to increase payment, assigning higher-paying DRG codes for inpatient claims, and other abuses. A recent benchmarking study of Medicare Provider Analysis and Review (MEDPAR) data has established national norms for hospital coding and case mix based on DRGs and has revealed the majority of atypical coding cases fall into six DRG pairs. Organizations with a greater percentage of atypical cases--those more likely to be scrutinized by Federal investigators--will want to conduct suitable review and be sure appropriate documentation exists to justify the coding.

Parallel-vector computation for linear structural analysis and non-linear unconstrained optimization problems

NASA Technical Reports Server (NTRS)

Nguyen, D. T.; Al-Nasra, M.; Zhang, Y.; Baddourah, M. A.; Agarwal, T. K.; Storaasli, O. O.; Carmona, E. A.

1991-01-01

Several parallel-vector computational improvements to the unconstrained optimization procedure are described which speed up the structural analysis-synthesis process. A fast parallel-vector Choleski-based equation solver, pvsolve, is incorporated into the well-known SAP-4 general-purpose finite-element code. The new code, denoted PV-SAP, is tested for static structural analysis. Initial results on a four processor CRAY 2 show that using pvsolve reduces the equation solution time by a factor of 14-16 over the original SAP-4 code. In addition, parallel-vector procedures for the Golden Block Search technique and the BFGS method are developed and tested for nonlinear unconstrained optimization. A parallel version of an iterative solver and the pvsolve direct solver are incorporated into the BFGS method. Preliminary results on nonlinear unconstrained optimization test problems, using pvsolve in the analysis, show excellent parallel-vector performance indicating that these parallel-vector algorithms can be used in a new generation of finite-element based structural design/analysis-synthesis codes.

User's manual for Axisymmetric Diffuser Duct (ADD) code. Volume 1: General ADD code description

NASA Technical Reports Server (NTRS)

Anderson, O. L.; Hankins, G. B., Jr.; Edwards, D. E.

1982-01-01

This User's Manual contains a complete description of the computer codes known as the AXISYMMETRIC DIFFUSER DUCT code or ADD code. It includes a list of references which describe the formulation of the ADD code and comparisons of calculation with experimental flows. The input/output and general use of the code is described in the first volume. The second volume contains a detailed description of the code including the global structure of the code, list of FORTRAN variables, and descriptions of the subroutines. The third volume contains a detailed description of the CODUCT code which generates coordinate systems for arbitrary axisymmetric ducts.

WDEC: A Code for Modeling White Dwarf Structure and Pulsations

NASA Astrophysics Data System (ADS)

Bischoff-Kim, Agnès; Montgomery, Michael H.

2018-05-01

The White Dwarf Evolution Code (WDEC), written in Fortran, makes models of white dwarf stars. It is fast, versatile, and includes the latest physics. The code evolves hot (∼100,000 K) input models down to a chosen effective temperature by relaxing the models to be solutions of the equations of stellar structure. The code can also be used to obtain g-mode oscillation modes for the models. WDEC has a long history going back to the late 1960s. Over the years, it has been updated and re-packaged for modern computer architectures and has specifically been used in computationally intensive asteroseismic fitting. Generations of white dwarf astronomers and dozens of publications have made use of the WDEC, although the last true instrument paper is the original one, published in 1975. This paper discusses the history of the code, necessary to understand why it works the way it does, details the physics and features in the code today, and points the reader to where to find the code and a user guide.

u-Constacyclic codes over F_p+u{F}_p and their applications of constructing new non-binary quantum codes

NASA Astrophysics Data System (ADS)

Gao, Jian; Wang, Yongkang

2018-01-01

Structural properties of u-constacyclic codes over the ring F_p+u{F}_p are given, where p is an odd prime and u^2=1. Under a special Gray map from F_p+u{F}_p to F_p^2, some new non-binary quantum codes are obtained by this class of constacyclic codes.

Development of a Simulink Library for the Design, Testing and Simulation of Software Defined GPS Radios. With Application to the Development of Parallel Correlator Structures

DTIC Science & Technology

2014-05-01

function Value = Select_Element(Index,Signal) %# eml Value = Signal(Index); Code Listing 1 Code for Selector Block 12 | P a g e 4.3...code for the Simulink function shiftedSignal = fcn(signal,Shift) %# eml shiftedSignal = circshift(signal,Shift); Code Listing 2 Code for CircShift

Distinct mechanisms of recognizing endosomal sorting complex required for transport III (ESCRT-III) protein IST1 by different microtubule interacting and trafficking (MIT) domains.

PubMed

Guo, Emily Z; Xu, Zhaohui

2015-03-27

The endosomal sorting complex required for transport (ESCRT) machinery is responsible for membrane remodeling in a number of biological processes including multivesicular body biogenesis, cytokinesis, and enveloped virus budding. In mammalian cells, efficient abscission during cytokinesis requires proper function of the ESCRT-III protein IST1, which binds to the microtubule interacting and trafficking (MIT) domains of VPS4, LIP5, and Spartin via its C-terminal MIT-interacting motif (MIM). Here, we studied the molecular interactions between IST1 and the three MIT domain-containing proteins to understand the structural basis that governs pairwise MIT-MIM interaction. Crystal structures of the three molecular complexes revealed that IST1 binds to the MIT domains of VPS4, LIP5, and Spartin using two different mechanisms (MIM1 mode versus MIM3 mode). Structural comparison revealed that structural features in both MIT and MIM contribute to determine the specific binding mechanism. Within the IST1 MIM sequence, two phenylalanine residues were shown to be important in discriminating MIM1 versus MIM3 binding. These observations enabled us to deduce a preliminary binding code, which we applied to provide CHMP2A, a protein that normally only binds the MIT domain in the MIM1 mode, the additional ability to bind the MIT domain of Spartin in the MIM3 mode. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Distinct Mechanisms of Recognizing Endosomal Sorting Complex Required for Transport III (ESCRT-III) Protein IST1 by Different Microtubule Interacting and Trafficking (MIT) Domains

DOE PAGES

Guo, Emily Z.; Xu, Zhaohui

2015-02-05

The endosomal sorting complex required for transport (ESCRT) machinery is responsible for membrane remodeling in a number of biological processes including multivesicular body biogenesis, cytokinesis, and enveloped virus budding. In mammalian cells, efficient abscission during cytokinesis requires proper function of the ESCRT-III protein IST1, which binds to the microtubule interacting and trafficking (MIT) domains of VPS4, LIP5, and Spartin via its C-terminal MIT-interacting motif (MIM). In this paper, we studied the molecular interactions between IST1 and the three MIT domain-containing proteins to understand the structural basis that governs pairwise MIT-MIM interaction. Crystal structures of the three molecular complexes revealed thatmore » IST1 binds to the MIT domains of VPS4, LIP5, and Spartin using two different mechanisms (MIM1 mode versus MIM3 mode). Structural comparison revealed that structural features in both MIT and MIM contribute to determine the specific binding mechanism. Within the IST1 MIM sequence, two phenylalanine residues were shown to be important in discriminating MIM1 versus MIM3 binding. Finally, these observations enabled us to deduce a preliminary binding code, which we applied to provide CHMP2A, a protein that normally only binds the MIT domain in the MIM1 mode, the additional ability to bind the MIT domain of Spartin in the MIM3 mode.« less

Evolutional dynamics of 45S and 5S ribosomal DNA in ancient allohexaploid Atropa belladonna.

PubMed

Volkov, Roman A; Panchuk, Irina I; Borisjuk, Nikolai V; Hosiawa-Baranska, Marta; Maluszynska, Jolanta; Hemleben, Vera

2017-01-23

Polyploid hybrids represent a rich natural resource to study molecular evolution of plant genes and genomes. Here, we applied a combination of karyological and molecular methods to investigate chromosomal structure, molecular organization and evolution of ribosomal DNA (rDNA) in nightshade, Atropa belladonna (fam. Solanaceae), one of the oldest known allohexaploids among flowering plants. Because of their abundance and specific molecular organization (evolutionarily conserved coding regions linked to variable intergenic spacers, IGS), 45S and 5S rDNA are widely used in plant taxonomic and evolutionary studies. Molecular cloning and nucleotide sequencing of A. belladonna 45S rDNA repeats revealed a general structure characteristic of other Solanaceae species, and a very high sequence similarity of two length variants, with the only difference in number of short IGS subrepeats. These results combined with the detection of three pairs of 45S rDNA loci on separate chromosomes, presumably inherited from both tetraploid and diploid ancestor species, example intensive sequence homogenization that led to substitution/elimination of rDNA repeats of one parent. Chromosome silver-staining revealed that only four out of six 45S rDNA sites are frequently transcriptionally active, demonstrating nucleolar dominance. For 5S rDNA, three size variants of repeats were detected, with the major class represented by repeats containing all functional IGS elements required for transcription, the intermediate size repeats containing partially deleted IGS sequences, and the short 5S repeats containing severe defects both in the IGS and coding sequences. While shorter variants demonstrate increased rate of based substitution, probably in their transition into pseudogenes, the functional 5S rDNA variants are nearly identical at the sequence level, pointing to their origin from a single parental species. Localization of the 5S rDNA genes on two chromosome pairs further supports uniparental inheritance from the tetraploid progenitor. The obtained molecular, cytogenetic and phylogenetic data demonstrate complex evolutionary dynamics of rDNA loci in allohexaploid species of Atropa belladonna. The high level of sequence unification revealed in 45S and 5S rDNA loci of this ancient hybrid species have been seemingly achieved by different molecular mechanisms.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adamek, Julian; Daverio, David; Durrer, Ruth

We present a new N-body code, gevolution , for the evolution of large scale structure in the Universe. Our code is based on a weak field expansion of General Relativity and calculates all six metric degrees of freedom in Poisson gauge. N-body particles are evolved by solving the geodesic equation which we write in terms of a canonical momentum such that it remains valid also for relativistic particles. We validate the code by considering the Schwarzschild solution and, in the Newtonian limit, by comparing with the Newtonian N-body codes Gadget-2 and RAMSES . We then proceed with a simulation ofmore » large scale structure in a Universe with massive neutrinos where we study the gravitational slip induced by the neutrino shear stress. The code can be extended to include different kinds of dark energy or modified gravity models and going beyond the usually adopted quasi-static approximation. Our code is publicly available.« less

Semantic enrichment of medical forms - semi-automated coding of ODM-elements via web services.

PubMed

Breil, Bernhard; Watermann, Andreas; Haas, Peter; Dziuballe, Philipp; Dugas, Martin

2012-01-01

Semantic interoperability is an unsolved problem which occurs while working with medical forms from different information systems or institutions. Standards like ODM or CDA assure structural homogenization but in order to compare elements from different data models it is necessary to use semantic concepts and codes on an item level of those structures. We developed and implemented a web-based tool which enables a domain expert to perform semi-automated coding of ODM-files. For each item it is possible to inquire web services which result in unique concept codes without leaving the context of the document. Although it was not feasible to perform a totally automated coding we have implemented a dialog based method to perform an efficient coding of all data elements in the context of the whole document. The proportion of codable items was comparable to results from previous studies.

National evaluation of the benefits and risks of greater structuring and coding of the electronic health record: exploratory qualitative investigation.

PubMed

Morrison, Zoe; Fernando, Bernard; Kalra, Dipak; Cresswell, Kathrin; Sheikh, Aziz

2014-01-01

We aimed to explore stakeholder views, attitudes, needs, and expectations regarding likely benefits and risks resulting from increased structuring and coding of clinical information within electronic health records (EHRs). Qualitative investigation in primary and secondary care and research settings throughout the UK. Data were derived from interviews, expert discussion groups, observations, and relevant documents. Participants (n=70) included patients, healthcare professionals, health service commissioners, policy makers, managers, administrators, systems developers, researchers, and academics. Four main themes arose from our data: variations in documentation practice; patient care benefits; secondary uses of information; and informing and involving patients. We observed a lack of guidelines, co-ordination, and dissemination of best practice relating to the design and use of information structures. While we identified immediate benefits for direct care and secondary analysis, many healthcare professionals did not see the relevance of structured and/or coded data to clinical practice. The potential for structured information to increase patient understanding of their diagnosis and treatment contrasted with concerns regarding the appropriateness of coded information for patients. The design and development of EHRs requires the capture of narrative information to reflect patient/clinician communication and computable data for administration and research purposes. Increased structuring and/or coding of EHRs therefore offers both benefits and risks. Documentation standards within clinical guidelines are likely to encourage comprehensive, accurate processing of data. As data structures may impact upon clinician/patient interactions, new models of documentation may be necessary if EHRs are to be read and authored by patients.

National evaluation of the benefits and risks of greater structuring and coding of the electronic health record: exploratory qualitative investigation

PubMed Central

Morrison, Zoe; Fernando, Bernard; Kalra, Dipak; Cresswell, Kathrin; Sheikh, Aziz

2014-01-01

Objective We aimed to explore stakeholder views, attitudes, needs, and expectations regarding likely benefits and risks resulting from increased structuring and coding of clinical information within electronic health records (EHRs). Materials and methods Qualitative investigation in primary and secondary care and research settings throughout the UK. Data were derived from interviews, expert discussion groups, observations, and relevant documents. Participants (n=70) included patients, healthcare professionals, health service commissioners, policy makers, managers, administrators, systems developers, researchers, and academics. Results Four main themes arose from our data: variations in documentation practice; patient care benefits; secondary uses of information; and informing and involving patients. We observed a lack of guidelines, co-ordination, and dissemination of best practice relating to the design and use of information structures. While we identified immediate benefits for direct care and secondary analysis, many healthcare professionals did not see the relevance of structured and/or coded data to clinical practice. The potential for structured information to increase patient understanding of their diagnosis and treatment contrasted with concerns regarding the appropriateness of coded information for patients. Conclusions The design and development of EHRs requires the capture of narrative information to reflect patient/clinician communication and computable data for administration and research purposes. Increased structuring and/or coding of EHRs therefore offers both benefits and risks. Documentation standards within clinical guidelines are likely to encourage comprehensive, accurate processing of data. As data structures may impact upon clinician/patient interactions, new models of documentation may be necessary if EHRs are to be read and authored by patients. PMID:24186957

Crystal Structures of SlyA Protein, a Master Virulence Regulator of Salmonella, in Free and DNA-bound States

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dolan, Kyle T.; Duguid, Erica M.; He, Chuan

2011-11-17

SlyA is a master virulence regulator that controls the transcription of numerous genes in Salmonella enterica. We present here crystal structures of SlyA by itself and bound to a high-affinity DNA operator sequence in the slyA gene. SlyA interacts with DNA through direct recognition of a guanine base by Arg-65, as well as interactions between conserved Arg-86 and the minor groove and a large network of non-base-specific contacts with the sugar phosphate backbone. Our structures, together with an unpublished structure of SlyA bound to the small molecule effector salicylate (Protein Data Bank code 3DEU), reveal that, unlike many other MarRmore » family proteins, SlyA dissociates from DNA without large conformational changes when bound to this effector. We propose that SlyA and other MarR global regulators rely more on indirect readout of DNA sequence to exert control over many genes, in contrast to proteins (such as OhrR) that recognize a single operator.« less

A Computer Oriented Scheme for Coding Chemicals in the Field of Biomedicine.

ERIC Educational Resources Information Center

Bobka, Marilyn E.; Subramaniam, J.B.

The chemical coding scheme of the Medical Coding Scheme (MCS), developed for use in the Comparative Systems Laboratory (CSL), is outlined and evaluated in this report. The chemical coding scheme provides a classification scheme and encoding method for drugs and chemical terms. Using the scheme complicated chemical structures may be expressed…

Structured Low-Density Parity-Check Codes with Bandwidth Efficient Modulation

NASA Technical Reports Server (NTRS)

Cheng, Michael K.; Divsalar, Dariush; Duy, Stephanie

2009-01-01

In this work, we study the performance of structured Low-Density Parity-Check (LDPC) Codes together with bandwidth efficient modulations. We consider protograph-based LDPC codes that facilitate high-speed hardware implementations and have minimum distances that grow linearly with block sizes. We cover various higher- order modulations such as 8-PSK, 16-APSK, and 16-QAM. During demodulation, a demapper transforms the received in-phase and quadrature samples into reliability information that feeds the binary LDPC decoder. We will compare various low-complexity demappers and provide simulation results for assorted coded-modulation combinations on the additive white Gaussian noise and independent Rayleigh fading channels.

Effects of GWAS-Associated Genetic Variants on lncRNAs within IBD and T1D Candidate Loci

PubMed Central

Brorsson, Caroline A.; Pociot, Flemming

2014-01-01

Long non-coding RNAs are a new class of non-coding RNAs that are at the crosshairs in many human diseases such as cancers, cardiovascular disorders, inflammatory and autoimmune disease like Inflammatory Bowel Disease (IBD) and Type 1 Diabetes (T1D). Nearly 90% of the phenotype-associated single-nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) lie outside of the protein coding regions, and map to the non-coding intervals. However, the relationship between phenotype-associated loci and the non-coding regions including the long non-coding RNAs (lncRNAs) is poorly understood. Here, we systemically identified all annotated IBD and T1D loci-associated lncRNAs, and mapped nominally significant GWAS/ImmunoChip SNPs for IBD and T1D within these lncRNAs. Additionally, we identified tissue-specific cis-eQTLs, and strong linkage disequilibrium (LD) signals associated with these SNPs. We explored sequence and structure based attributes of these lncRNAs, and also predicted the structural effects of mapped SNPs within them. We also identified lncRNAs in IBD and T1D that are under recent positive selection. Our analysis identified putative lncRNA secondary structure-disruptive SNPs within and in close proximity (+/−5 kb flanking regions) of IBD and T1D loci-associated candidate genes, suggesting that these RNA conformation-altering polymorphisms might be associated with diseased-phenotype. Disruption of lncRNA secondary structure due to presence of GWAS SNPs provides valuable information that could be potentially useful for future structure-function studies on lncRNAs. PMID:25144376

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

PubMed Central

Shabalina, Svetlana A.; Spiridonov, Nikolay A.; Kashina, Anna

2013-01-01

Messenger RNA is a key component of an intricate regulatory network of its own. It accommodates numerous nucleotide signals that overlap protein coding sequences and are responsible for multiple levels of regulation and generation of biological complexity. A wealth of structural and regulatory information, which mRNA carries in addition to the encoded amino acid sequence, raises the question of how these signals and overlapping codes are delineated along non-synonymous and synonymous positions in protein coding regions, especially in eukaryotes. Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides. The RNA level selection is acting on synonymous sites in both prokaryotes and eukaryotes and is more common than previously thought. Selection pressure on the coding gene regions follows three-nucleotide periodic pattern of nucleotide base-pairing in mRNA, which is imposed by the genetic code. Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles. Recent experimental evidence and analysis of mRNA structure and interspecies conservation suggest that there is an evolutionary tradeoff between selective pressure acting at the RNA and protein levels. Here we provide a comprehensive overview of the studies that define the role of silent positions in regulating RNA structure and processing that exert downstream effects on proteins and their functions. PMID:23293005

Lewis Structures Technology, 1988. Volume 2: Structural Mechanics

NASA Technical Reports Server (NTRS)

1988-01-01

Lewis Structures Div. performs and disseminates results of research conducted in support of aerospace engine structures. These results have a wide range of applicability to practitioners of structural engineering mechanics beyond the aerospace arena. The engineering community was familiarized with the depth and range of research performed by the division and its academic and industrial partners. Sessions covered vibration control, fracture mechanics, ceramic component reliability, parallel computing, nondestructive evaluation, constitutive models and experimental capabilities, dynamic systems, fatigue and damage, wind turbines, hot section technology (HOST), aeroelasticity, structural mechanics codes, computational methods for dynamics, structural optimization, and applications of structural dynamics, and structural mechanics computer codes.

A Proposal of Monitoring and Forecasting Method for Crustal Activity in and around Japan with 3-dimensional Heterogeneous Medium Using a Large-scale High-fidelity Finite Element Simulation

NASA Astrophysics Data System (ADS)

Hori, T.; Agata, R.; Ichimura, T.; Fujita, K.; Yamaguchi, T.; Takahashi, N.

2017-12-01

Recently, we can obtain continuous dense surface deformation data on land and partly on the sea floor, the obtained data are not fully utilized for monitoring and forecasting of crustal activity, such as spatio-temporal variation in slip velocity on the plate interface including earthquakes, seismic wave propagation, and crustal deformation. For construct a system for monitoring and forecasting, it is necessary to develop a physics-based data analysis system including (1) a structural model with the 3D geometry of the plate inter-face and the material property such as elasticity and viscosity, (2) calculation code for crustal deformation and seismic wave propagation using (1), (3) inverse analysis or data assimilation code both for structure and fault slip using (1) & (2). To accomplish this, it is at least necessary to develop highly reliable large-scale simulation code to calculate crustal deformation and seismic wave propagation for 3D heterogeneous structure. Unstructured FE non-linear seismic wave simulation code has been developed. This achieved physics-based urban earthquake simulation enhanced by 1.08 T DOF x 6.6 K time-step. A high fidelity FEM simulation code with mesh generator has also been developed to calculate crustal deformation in and around Japan with complicated surface topography and subducting plate geometry for 1km mesh. This code has been improved the code for crustal deformation and achieved 2.05 T-DOF with 45m resolution on the plate interface. This high-resolution analysis enables computation of change of stress acting on the plate interface. Further, for inverse analyses, waveform inversion code for modeling 3D crustal structure has been developed, and the high-fidelity FEM code has been improved to apply an adjoint method for estimating fault slip and asthenosphere viscosity. Hence, we have large-scale simulation and analysis tools for monitoring. We are developing the methods for forecasting the slip velocity variation on the plate interface. Although the prototype is for elastic half space model, we are applying it for 3D heterogeneous structure with the high-fidelity FE model. Furthermore, large-scale simulation codes for monitoring are being implemented on the GPU clusters and analysis tools are developing to include other functions such as examination in model errors.

The predominant circular form of avocado sunblotch viroid accumulates in planta as a free RNA adopting a rod-shaped secondary structure unprotected by tightly bound host proteins.

PubMed

López-Carrasco, Amparo; Flores, Ricardo

2017-07-01

Avocado sunblotch viroid (ASBVd), the type member of the family Avsunviroidae, replicates and accumulates in chloroplasts. Whether this minimal non-protein-coding circular RNA of 246-250 nt exists in vivo as a free nucleic acid or closely associated with host proteins remains unknown. To tackle this issue, the secondary structures of the monomeric circular (mc) (+) and (-) strands of ASBVd have been examined in silico by searching those of minimal free energy, and in vitro at single-nucleotide resolution by selective 2'-hydroxyl acylation analysed by primer extension (SHAPE). Both approaches resulted in predominant rod-like secondary structures without tertiary interactions, with the mc (+) RNA being more compact than its (-) counterpart as revealed by non-denaturing polyacryamide gel electrophoresis. Moreover, in vivo SHAPE showed that the mc ASBVd (+) form accumulates in avocado leaves as a free RNA adopting a similar rod-shaped conformation unprotected by tightly bound host proteins. Hence, the mc ASBVd (+) RNA behaves in planta like the previously studied mc (+) RNA of potato spindle tuber viroid, the type member of nuclear viroids (family Pospiviroidae), indicating that two different viroids replicating and accumulating in distinct subcellular compartments, have converged into a common structural solution. Circularity and compact secondary structures confer to these RNAs, and probably to all viroids, the intrinsic stability needed to survive in their natural habitats. However, in vivo SHAPE has not revealed the (possibly transient or loose) interactions of the mc ASBVd (+) RNA with two host proteins observed previously by UV irradiation of infected avocado leaves.

Interface requirements to couple thermal-hydraulic codes to severe accident codes: ATHLET-CD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trambauer, K.

1997-07-01

The system code ATHLET-CD is being developed by GRS in cooperation with IKE and IPSN. Its field of application comprises the whole spectrum of leaks and large breaks, as well as operational and abnormal transients for LWRs and VVERs. At present the analyses cover the in-vessel thermal-hydraulics, the early phases of core degradation, as well as fission products and aerosol release from the core and their transport in the Reactor Coolant System. The aim of the code development is to extend the simulation of core degradation up to failure of the reactor pressure vessel and to cover all physically reasonablemore » accident sequences for western and eastern LWRs including RMBKs. The ATHLET-CD structure is highly modular in order to include a manifold spectrum of models and to offer an optimum basis for further development. The code consists of four general modules to describe the reactor coolant system thermal-hydraulics, the core degradation, the fission product core release, and fission product and aerosol transport. Each general module consists of some basic modules which correspond to the process to be simulated or to its specific purpose. Besides the code structure based on the physical modelling, the code follows four strictly separated steps during the course of a calculation: (1) input of structure, geometrical data, initial and boundary condition, (2) initialization of derived quantities, (3) steady state calculation or input of restart data, and (4) transient calculation. In this paper, the transient solution method is briefly presented and the coupling methods are discussed. Three aspects have to be considered for the coupling of different modules in one code system. First is the conservation of masses and energy in the different subsystems as there are fluid, structures, and fission products and aerosols. Second is the convergence of the numerical solution and stability of the calculation. The third aspect is related to the code performance, and running time.« less

On the design of turbo codes

NASA Technical Reports Server (NTRS)

Divsalar, D.; Pollara, F.

1995-01-01

In this article, we design new turbo codes that can achieve near-Shannon-limit performance. The design criterion for random interleavers is based on maximizing the effective free distance of the turbo code, i.e., the minimum output weight of codewords due to weight-2 input sequences. An upper bound on the effective free distance of a turbo code is derived. This upper bound can be achieved if the feedback connection of convolutional codes uses primitive polynomials. We review multiple turbo codes (parallel concatenation of q convolutional codes), which increase the so-called 'interleaving gain' as q and the interleaver size increase, and a suitable decoder structure derived from an approximation to the maximum a posteriori probability decision rule. We develop new rate 1/3, 2/3, 3/4, and 4/5 constituent codes to be used in the turbo encoder structure. These codes, for from 2 to 32 states, are designed by using primitive polynomials. The resulting turbo codes have rates b/n (b = 1, 2, 3, 4 and n = 2, 3, 4, 5, 6), and include random interleavers for better asymptotic performance. These codes are suitable for deep-space communications with low throughput and for near-Earth communications where high throughput is desirable. The performance of these codes is within 1 dB of the Shannon limit at a bit-error rate of 10(exp -6) for throughputs from 1/15 up to 4 bits/s/Hz.

Accumulate-Repeat-Accumulate-Accumulate Codes

NASA Technical Reports Server (NTRS)

Divsalar, Dariush; Dolinar, Samuel; Thorpe, Jeremy

2007-01-01

Accumulate-repeat-accumulate-accumulate (ARAA) codes have been proposed, inspired by the recently proposed accumulate-repeat-accumulate (ARA) codes. These are error-correcting codes suitable for use in a variety of wireless data-communication systems that include noisy channels. ARAA codes can be regarded as serial turbolike codes or as a subclass of low-density parity-check (LDPC) codes, and, like ARA codes they have projected graph or protograph representations; these characteristics make it possible to design high-speed iterative decoders that utilize belief-propagation algorithms. The objective in proposing ARAA codes as a subclass of ARA codes was to enhance the error-floor performance of ARA codes while maintaining simple encoding structures and low maximum variable node degree.

A Comprehensive Approach to Convert a Radiology Department From Coding Based on International Classification of Diseases, Ninth Revision, to Coding Based on International Classification of Diseases, Tenth Revision.

PubMed

McBee, Morgan P; Laor, Tal; Pryor, Rebecca M; Smith, Rachel; Hardin, Judy; Ulland, Lisa; May, Sally; Zhang, Bin; Towbin, Alexander J

2018-02-01

The purpose of this study was to adapt our radiology reports to provide the documentation required for specific International Classification of Diseases, tenth rev (ICD-10) diagnosis coding. Baseline data were analyzed to identify the reports with the greatest number of unspecified ICD-10 codes assigned by computer-assisted coding software. A two-part quality improvement initiative was subsequently implemented. The first component involved improving clinical histories by utilizing technologists to obtain information directly from the patients or caregivers, which was then imported into the radiologist's report within the speech recognition software. The second component involved standardization of report terminology and creation of four different structured report templates to determine which yielded the fewest reports with an unspecified ICD-10 code assigned by an automated coding engine. In all, 12,077 reports were included in the baseline analysis. Of these, 5,151 (43%) had an unspecified ICD-10 code. The majority of deficient reports were for radiographs (n = 3,197; 62%). Inadequacies included insufficient clinical history provided and lack of detailed fracture descriptions. Therefore, the focus was standardizing terminology and testing different structured reports for radiographs obtained for fractures. At baseline, 58% of radiography reports contained a complete clinical history with improvement to >95% 8 months later. The total number of reports that contained an unspecified ICD-10 code improved from 43% at baseline to 27% at completion of this study (P < .0001). The number of radiology studies with a specific ICD-10 code can be improved through quality improvement methodology, specifically through the use of technologist-acquired clinical histories and structured reporting. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Quantum Stabilizer Codes Can Realize Access Structures Impossible by Classical Secret Sharing

NASA Astrophysics Data System (ADS)

Matsumoto, Ryutaroh

We show a simple example of a secret sharing scheme encoding classical secret to quantum shares that can realize an access structure impossible by classical information processing with limitation on the size of each share. The example is based on quantum stabilizer codes.

Investigating the structure preserving encryption of high efficiency video coding (HEVC)

NASA Astrophysics Data System (ADS)

Shahid, Zafar; Puech, William

2013-02-01

This paper presents a novel method for the real-time protection of new emerging High Efficiency Video Coding (HEVC) standard. Structure preserving selective encryption is being performed in CABAC entropy coding module of HEVC, which is significantly different from CABAC entropy coding of H.264/AVC. In CABAC of HEVC, exponential Golomb coding is replaced by truncated Rice (TR) up to a specific value for binarization of transform coefficients. Selective encryption is performed using AES cipher in cipher feedback mode on a plaintext of binstrings in a context aware manner. The encrypted bitstream has exactly the same bit-rate and is format complaint. Experimental evaluation and security analysis of the proposed algorithm is performed on several benchmark video sequences containing different combinations of motion, texture and objects.

Codes and standards for structural wood products and their use in the United States

Treesearch

David W. Green; Roland Hernandez

1998-01-01

The system of model building codes and voluntary product standards used in the United States for structural lumber and engineered wood products can appear complicated and confusing to those introduced to it for the first time. This paper is a discussion of the various types of structural wood products commonly used in U.S. residential and commercial construction and...

Nonlinear Computational Aeroelasticity: Formulations and Solution Algorithms

DTIC Science & Technology

2003-03-01

problem is proposed. Fluid-structure coupling algorithms are then discussed with some emphasis on distributed computing strategies. Numerical results...the structure and the exchange of structure motion to the fluid. The computational fluid dynamics code PFES is our finite element code for the numerical ...unstructured meshes). It was numerically demonstrated [1-3] that EBS can be less diffusive than SUPG [4-6] and the standard Finite Volume schemes

Exploring the inner parsecs of active galactic nuclei using near-infrared high resolution polarimetric simulations with MontAGN

NASA Astrophysics Data System (ADS)

Grosset, L.; Rouan, D.; Gratadour, D.; Pelat, D.; Orkisz, J.; Marin, F.; Goosmann, R.

2018-04-01

Aims: In this paper we aim to constrain the properties of dust structures in the central first parsecs of active galactic nuclei (AGN). Our goal is to study the required optical depth and composition of different dusty and ionised structures. Methods: We developed a radiative transfer code called Monte Carlo for Active Galactic Nuclei (MontAGN), which is optimised for polarimetric observations in the infrared. With both this code and STOKES, designed to be relevant from the hard X-ray band to near-infrared wavelengths, we investigate the polarisation emerging from a characteristic model of the AGN environment. For this purpose, we compare predictions of our models with previous infrared observations of NGC 1068, and try to reproduce several key polarisation patterns revealed by polarisation mapping. Results: We constrain the required dust structures and their densities. More precisely, we find that the electron density inside the ionisation cone is about 2.0 × 109 m-3. With structures constituted of spherical grains of constant density, we also highlight that the torus should be thicker than 20 in term of K-band optical depth to block direct light from the centre. It should also have a stratification in density: a less dense outer rim with an optical depth at 2.2 μm typically between 0.8 and 4 for observing the double scattering effect previously proposed. Conclusions: We bring constraints on the dust structures in the inner parsecs of an AGN model supposed to describe NGC 1068. When compared to observations, this leads to an optical depth of at least 20 in the Ks band for the torus of NGC 1068, corresponding to τV ≈ 170, which is within the range of current estimation based on observations. In the future, we will improve our study by including non-uniform dust structures and aligned elongated grains to constrain other possible interpretations of the observations.

Comparison of DAC and MONACO DSMC Codes with Flat Plate Simulation

NASA Technical Reports Server (NTRS)

Padilla, Jose F.

2010-01-01

Various implementations of the direct simulation Monte Carlo (DSMC) method exist in academia, government and industry. By comparing implementations, deficiencies and merits of each can be discovered. This document reports comparisons between DSMC Analysis Code (DAC) and MONACO. DAC is NASA's standard DSMC production code and MONACO is a research DSMC code developed in academia. These codes have various differences; in particular, they employ distinct computational grid definitions. In this study, DAC and MONACO are compared by having each simulate a blunted flat plate wind tunnel test, using an identical volume mesh. Simulation expense and DSMC metrics are compared. In addition, flow results are compared with available laboratory data. Overall, this study revealed that both codes, excluding grid adaptation, performed similarly. For parallel processing, DAC was generally more efficient. As expected, code accuracy was mainly dependent on physical models employed.

Heat transfer, thermal stress analysis and the dynamic behaviour of high power RF structures. [MARC and SUPERFISH codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

McKeown, J.; Labrie, J.P.

1983-08-01

A general purpose finite element computer code called MARC is used to calculate the temperature distribution and dimensional changes in linear accelerator rf structures. Both steady state and transient behaviour are examined with the computer model. Combining results from MARC with the cavity evaluation computer code SUPERFISH, the static and dynamic behaviour of a structure under power is investigated. Structure cooling is studied to minimize loss in shunt impedance and frequency shifts during high power operation. Results are compared with an experimental test carried out on a cw 805 MHz on-axis coupled structure at an energy gradient of 1.8 MeV/m.more » The model has also been used to compare the performance of on-axis and coaxial structures and has guided the mechanical design of structures suitable for average gradients in excess of 2.0 MeV/m at 2.45 GHz.« less

TEMPEST code simulations of hydrogen distribution in reactor containment structures. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trent, D.S.; Eyler, L.L.

The mass transport version of the TEMPEST computer code was used to simulate hydrogen distribution in geometric configurations relevant to reactor containment structures. Predicted results of Battelle-Frankfurt hydrogen distribution tests 1 to 6, and 12 are presented. Agreement between predictions and experimental data is good. Best agreement is obtained using the k-epsilon turbulence model in TEMPEST in flow cases where turbulent diffusion and stable stratification are dominant mechanisms affecting transport. The code's general analysis capabilities are summarized.

COGNATE: comparative gene annotation characterizer.

PubMed

Wilbrandt, Jeanne; Misof, Bernhard; Niehuis, Oliver

2017-07-17

The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization (e.g., Elliott TA, Gregory TR, Philos Trans Royal Soc B: Biol Sci 370:20140331, 2015). For example, testing the hypothesis that the total amount of coding sequences is a reliable measure of potential proteome diversity (Wang M, Kurland CG, Caetano-Anollés G, PNAS 108:11954, 2011) requires the application of standardized definitions of coding sequence and genes to create both comparable and comprehensive data sets and corresponding summary statistics. However, such standard definitions either do not exist or are not consistently applied. These circumstances call for a standard at the descriptive level using a minimum of parameters as well as an undeviating use of standardized terms, and for software that infers the required data under these strict definitions. The acquisition of a comprehensive, descriptive, and standardized set of parameters and summary statistics for genome publications and further analyses can thus greatly benefit from the availability of an easy to use standard tool. We developed a new open-source command-line tool, COGNATE (Comparative Gene Annotation Characterizer), which uses a given genome assembly and its annotation of protein-coding genes for a detailed description of the respective gene and genome structure parameters. Additionally, we revised the standard definitions of gene and genome structures and provide the definitions used by COGNATE as a working draft suggestion for further reference. Complete parameter lists and summary statistics are inferred using this set of definitions to allow down-stream analyses and to provide an overview of the genome and gene repertoire characteristics. COGNATE is written in Perl and freely available at the ZFMK homepage ( https://www.zfmk.de/en/COGNATE ) and on github ( https://github.com/ZFMK/COGNATE ). The tool COGNATE allows comparing genome assemblies and structural elements on multiples levels (e.g., scaffold or contig sequence, gene). It clearly enhances comparability between analyses. Thus, COGNATE can provide the important standardization of both genome and gene structure parameter disclosure as well as data acquisition for future comparative analyses. With the establishment of comprehensive descriptive standards and the extensive availability of genomes, an encompassing database will become possible.

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

PubMed

Lindblad-Toh, Kerstin; Wade, Claire M; Mikkelsen, Tarjei S; Karlsson, Elinor K; Jaffe, David B; Kamal, Michael; Clamp, Michele; Chang, Jean L; Kulbokas, Edward J; Zody, Michael C; Mauceli, Evan; Xie, Xiaohui; Breen, Matthew; Wayne, Robert K; Ostrander, Elaine A; Ponting, Chris P; Galibert, Francis; Smith, Douglas R; DeJong, Pieter J; Kirkness, Ewen; Alvarez, Pablo; Biagi, Tara; Brockman, William; Butler, Jonathan; Chin, Chee-Wye; Cook, April; Cuff, James; Daly, Mark J; DeCaprio, David; Gnerre, Sante; Grabherr, Manfred; Kellis, Manolis; Kleber, Michael; Bardeleben, Carolyne; Goodstadt, Leo; Heger, Andreas; Hitte, Christophe; Kim, Lisa; Koepfli, Klaus-Peter; Parker, Heidi G; Pollinger, John P; Searle, Stephen M J; Sutter, Nathan B; Thomas, Rachael; Webber, Caleb; Baldwin, Jennifer; Abebe, Adal; Abouelleil, Amr; Aftuck, Lynne; Ait-Zahra, Mostafa; Aldredge, Tyler; Allen, Nicole; An, Peter; Anderson, Scott; Antoine, Claudel; Arachchi, Harindra; Aslam, Ali; Ayotte, Laura; Bachantsang, Pasang; Barry, Andrew; Bayul, Tashi; Benamara, Mostafa; Berlin, Aaron; Bessette, Daniel; Blitshteyn, Berta; Bloom, Toby; Blye, Jason; Boguslavskiy, Leonid; Bonnet, Claude; Boukhgalter, Boris; Brown, Adam; Cahill, Patrick; Calixte, Nadia; Camarata, Jody; Cheshatsang, Yama; Chu, Jeffrey; Citroen, Mieke; Collymore, Alville; Cooke, Patrick; Dawoe, Tenzin; Daza, Riza; Decktor, Karin; DeGray, Stuart; Dhargay, Norbu; Dooley, Kimberly; Dooley, Kathleen; Dorje, Passang; Dorjee, Kunsang; Dorris, Lester; Duffey, Noah; Dupes, Alan; Egbiremolen, Osebhajajeme; Elong, Richard; Falk, Jill; Farina, Abderrahim; Faro, Susan; Ferguson, Diallo; Ferreira, Patricia; Fisher, Sheila; FitzGerald, Mike; Foley, Karen; Foley, Chelsea; Franke, Alicia; Friedrich, Dennis; Gage, Diane; Garber, Manuel; Gearin, Gary; Giannoukos, Georgia; Goode, Tina; Goyette, Audra; Graham, Joseph; Grandbois, Edward; Gyaltsen, Kunsang; Hafez, Nabil; Hagopian, Daniel; Hagos, Birhane; Hall, Jennifer; Healy, Claire; Hegarty, Ryan; Honan, Tracey; Horn, Andrea; Houde, Nathan; Hughes, Leanne; Hunnicutt, Leigh; Husby, M; Jester, Benjamin; Jones, Charlien; Kamat, Asha; Kanga, Ben; Kells, Cristyn; Khazanovich, Dmitry; Kieu, Alix Chinh; Kisner, Peter; Kumar, Mayank; Lance, Krista; Landers, Thomas; Lara, Marcia; Lee, William; Leger, Jean-Pierre; Lennon, Niall; Leuper, Lisa; LeVine, Sarah; Liu, Jinlei; Liu, Xiaohong; Lokyitsang, Yeshi; Lokyitsang, Tashi; Lui, Annie; Macdonald, Jan; Major, John; Marabella, Richard; Maru, Kebede; Matthews, Charles; McDonough, Susan; Mehta, Teena; Meldrim, James; Melnikov, Alexandre; Meneus, Louis; Mihalev, Atanas; Mihova, Tanya; Miller, Karen; Mittelman, Rachel; Mlenga, Valentine; Mulrain, Leonidas; Munson, Glen; Navidi, Adam; Naylor, Jerome; Nguyen, Tuyen; Nguyen, Nga; Nguyen, Cindy; Nguyen, Thu; Nicol, Robert; Norbu, Nyima; Norbu, Choe; Novod, Nathaniel; Nyima, Tenchoe; Olandt, Peter; O'Neill, Barry; O'Neill, Keith; Osman, Sahal; Oyono, Lucien; Patti, Christopher; Perrin, Danielle; Phunkhang, Pema; Pierre, Fritz; Priest, Margaret; Rachupka, Anthony; Raghuraman, Sujaa; Rameau, Rayale; Ray, Verneda; Raymond, Christina; Rege, Filip; Rise, Cecil; Rogers, Julie; Rogov, Peter; Sahalie, Julie; Settipalli, Sampath; Sharpe, Theodore; Shea, Terrance; Sheehan, Mechele; Sherpa, Ngawang; Shi, Jianying; Shih, Diana; Sloan, Jessie; Smith, Cherylyn; Sparrow, Todd; Stalker, John; Stange-Thomann, Nicole; Stavropoulos, Sharon; Stone, Catherine; Stone, Sabrina; Sykes, Sean; Tchuinga, Pierre; Tenzing, Pema; Tesfaye, Senait; Thoulutsang, Dawa; Thoulutsang, Yama; Topham, Kerri; Topping, Ira; Tsamla, Tsamla; Vassiliev, Helen; Venkataraman, Vijay; Vo, Andy; Wangchuk, Tsering; Wangdi, Tsering; Weiand, Michael; Wilkinson, Jane; Wilson, Adam; Yadav, Shailendra; Yang, Shuli; Yang, Xiaoping; Young, Geneva; Yu, Qing; Zainoun, Joanne; Zembek, Lisa; Zimmer, Andrew; Lander, Eric S

2005-12-08

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

Figuring Out Gas in Galaxies In Enzo (FOGGIE): Resolving the Inner Circumgalactic Medium

NASA Astrophysics Data System (ADS)

Corlies, Lauren; Peeples, Molly; Tumlinson, Jason; O'Shea, Brian; Smith, Britton

2018-01-01

Cosmological hydrodynamical simulations using every common numerical method have struggled to reproduce the multiphase nature of the circumgalactic medium (CGM) revealed by recent observations. However, to date, resolution in these simulations has been aimed at dense regions — the galactic disk and in-falling satellites — while the diffuse CGM never reaches comparable levels of refinement. Taking advantage of the flexible grid structure of the adaptive mesh refinement code Enzo, we force refinement in a region of the CGM of a Milky Way-like galaxy to the same spatial resolution as that of the disk. In this talk, I will present how the physical and structural distributions of the circumgalactic gas change dramatically as a function of the resolution alone. I will also show the implications these changes have for the observational properties of the gas in the context of the observations.

Brown Mycelial Mat as an Essential Morphological Structure of the Shiitake Medicinal Mushroom Lentinus edodes (Agaricomycetes).

PubMed

Vetchinkina, Elena; Gorshkov, Vladimir; Ageeva, Marina; Gogolev, Yuri; Nikitina, Valentina E

2017-01-01

We show here, to our knowledge for the first time, that the brown mycelial mat of the xylotrophic shiitake medicinal mushroom, Lentinus edodes, not only performs a protective function owing to significant changes in the ultrastructure (thickening of the cell wall, increased density, and pigmentation of the fungal hyphae) but also is a metabolically active stage in the development of the mushroom. The cells of this morphological structure exhibit repeated activation of expression of the genes lcc4, tir, exp1, chi, and exg1, coding for laccase, tyrosinase, a specific transcription factor, chitinase, and glucanase, which are required for fungal growth and morphogenesis. This study revealed the maximum activity of functionally important proteins with phenol oxidase and lectin activities, and the emergence of additional laccases, tyrosinases, and lectins, which are typical of only this stage of morphogenesis and have a regulatory function in the development and formation of fruiting bodies.

Categorical dimensions of human odor descriptor space revealed by non-negative matrix factorization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chennubhotla, Chakra; Castro, Jason

2013-01-01

In contrast to most other sensory modalities, the basic perceptual dimensions of olfaction remain un- clear. Here, we use non-negative matrix factorization (NMF) - a dimensionality reduction technique - to uncover structure in a panel of odor profiles, with each odor defined as a point in multi-dimensional descriptor space. The properties of NMF are favorable for the analysis of such lexical and perceptual data, and lead to a high-dimensional account of odor space. We further provide evidence that odor di- mensions apply categorically. That is, odor space is not occupied homogenously, but rather in a discrete and intrinsically clustered manner.more » We discuss the potential implications of these results for the neural coding of odors, as well as for developing classifiers on larger datasets that may be useful for predicting perceptual qualities from chemical structures.« less

Computational study of hydroxyapatite structures, properties and defects

NASA Astrophysics Data System (ADS)

Bystrov, V. S.; Coutinho, J.; Bystrova, A. V.; Dekhtyar, Yu D.; Pullar, R. C.; Poronin, A.; Palcevskis, E.; Dindune, A.; Alkan, B.; Durucan, C.; Paramonova, E. V.

2015-03-01

Hydroxyapatite (HAp) was studied from a first principle approach using the local density approximation (LDA) method in AIMPRO code, in combination with various quantum mechanical (QM) and molecular mechanical (MM) methods from HypemChem 7.5/8.0. The data obtained were used for studies of HAp structures, the physical properties of HAp (density of electronic states—DOS, bulk modulus etc) and defects in HAp. Computed data confirmed that HAp can co-exist in different phases—hexagonal and monoclinic. Ordered monoclinic structures, which could reveal piezoelectric properties, are of special interest. The data obtained allow us to characterize the properties of the following defects in HAp: O, H and OH vacancies; H and OH interstitials; substitutions of Ca by Mg, Sr, Mn or Se, and P by Si. These properties reveal the appearance of additional energy levels inside the forbidden zone, shifts of the top of the valence band or the bottom of the conduction band, and subsequent changes in the width of the forbidden zone. The data computed are compared with other known data, both calculated and experimental, such as alteration of the electron work functions under different influences of various defects and treatments, obtained by photoelectron emission. The obtained data are very useful, and there is an urgent need for such analysis of modified HAp interactions with living cells and tissues, improvement of implant techniques and development of new nanomedical applications.

Structure of a PE-PPE-EspG complex from Mycobacterium tuberculosis reveals molecular specificity of ESX protein secretion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ekiert, Damian C.; Cox, Jeffery S.

Nearly 10% of the coding capacity of the Mycobacterium tuberculosis genome is devoted to two highly expanded and enigmatic protein families called PE and PPE, some of which are important virulence/immunogenicity factors and are secreted during infection via a unique alternative secretory system termed "type VII." How PE-PPE proteins function during infection and how they are translocated to the bacterial surface through the five distinct type VII secretion systems [ESAT-6 secretion system (ESX)] of M. tuberculosis is poorly understood. Here in this paper, we report the crystal structure of a PE-PPE heterodimer bound to ESX secretion-associated protein G (EspG), whichmore » adopts a novel fold. This PE-PPE-EspG complex, along with structures of two additional EspGs, suggests that EspG acts as an adaptor that recognizes specific PE-PPE protein complexes via extensive interactions with PPE domains, and delivers them to ESX machinery for secretion. Surprisingly, secretion of most PE-PPE proteins in M. tuberculosis is likely mediated by EspG from the ESX-5 system, underscoring the importance of ESX-5 in mycobacterial pathogenesis. Furthermore, our results indicate that PE-PPE domains function as cis-acting targeting sequences that are read out by EspGs, revealing the molecular specificity for secretion through distinct ESX pathways.« less

Structure of a PE-PPE-EspG complex from Mycobacterium tuberculosis reveals molecular specificity of ESX protein secretion

DOE PAGES

Ekiert, Damian C.; Cox, Jeffery S.

2014-10-01

Nearly 10% of the coding capacity of the Mycobacterium tuberculosis genome is devoted to two highly expanded and enigmatic protein families called PE and PPE, some of which are important virulence/immunogenicity factors and are secreted during infection via a unique alternative secretory system termed "type VII." How PE-PPE proteins function during infection and how they are translocated to the bacterial surface through the five distinct type VII secretion systems [ESAT-6 secretion system (ESX)] of M. tuberculosis is poorly understood. Here in this paper, we report the crystal structure of a PE-PPE heterodimer bound to ESX secretion-associated protein G (EspG), whichmore » adopts a novel fold. This PE-PPE-EspG complex, along with structures of two additional EspGs, suggests that EspG acts as an adaptor that recognizes specific PE-PPE protein complexes via extensive interactions with PPE domains, and delivers them to ESX machinery for secretion. Surprisingly, secretion of most PE-PPE proteins in M. tuberculosis is likely mediated by EspG from the ESX-5 system, underscoring the importance of ESX-5 in mycobacterial pathogenesis. Furthermore, our results indicate that PE-PPE domains function as cis-acting targeting sequences that are read out by EspGs, revealing the molecular specificity for secretion through distinct ESX pathways.« less

Author Correction: Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

PubMed

Preissl, Sebastian; Fang, Rongxin; Huang, Hui; Zhao, Yuan; Raviram, Ramya; Gorkin, David U; Zhang, Yanxiao; Sos, Brandon C; Afzal, Veena; Dickel, Diane E; Kuan, Samantha; Visel, Axel; Pennacchio, Len A; Zhang, Kun; Ren, Bing

2018-03-01

In the version of this article initially published online, the accession code was given as GSE1000333. The correct code is GSE100033. The error has been corrected in the print, HTML and PDF versions of the article.

A Code of Ethics for Democratic Leadership

ERIC Educational Resources Information Center

Molina, Ricardo; Klinker, JoAnn Franklin

2012-01-01

Democratic leadership rests on sacred values, awareness, judgement, motivation and courage. Four turning points in a 38-year school administrator's career revealed decision-making in problematic moments stemmed from values in a personal and professional code of ethics. Reflection on practice and theory added vocabulary and understanding to make…

Coding Location: The View from Toddler Studies

ERIC Educational Resources Information Center

Huttenlocher, Janellen

2008-01-01

The ability to locate objects in the environment is adaptively important for mobile organisms. Research on location coding reveals that even toddlers have considerable spatial skill. Important information has been obtained using a disorientation task in which children watch a target object being hidden and are then blindfolded and rotated so they…

Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production

PubMed Central

2013-01-01

Background Microalgae are gaining importance as sustainable production hosts in the fields of biotechnology and bioenergy. A robust biomass accumulating strain of the genus Monoraphidium (SAG 48.87) was investigated in this work as a potential feedstock for biofuel production. The genome was sequenced, annotated, and key enzymes for triacylglycerol formation were elucidated. Results Monoraphidium neglectum was identified as an oleaginous species with favourable growth characteristics as well as a high potential for crude oil production, based on neutral lipid contents of approximately 21% (dry weight) under nitrogen starvation, composed of predominantly C18:1 and C16:0 fatty acids. Further characterization revealed growth in a relatively wide pH range and salt concentrations of up to 1.0% NaCl, in which the cells exhibited larger structures. This first full genome sequencing of a member of the Selenastraceae revealed a diploid, approximately 68 Mbp genome with a G + C content of 64.7%. The circular chloroplast genome was assembled to a 135,362 bp single contig, containing 67 protein-coding genes. The assembly of the mitochondrial genome resulted in two contigs with an approximate total size of 94 kb, the largest known mitochondrial genome within algae. 16,761 protein-coding genes were assigned to the nuclear genome. Comparison of gene sets with respect to functional categories revealed a higher gene number assigned to the category “carbohydrate metabolic process” and in “fatty acid biosynthetic process” in M. neglectum when compared to Chlamydomonas reinhardtii and Nannochloropsis gaditana, indicating a higher metabolic diversity for applications in carbohydrate conversions of biotechnological relevance. Conclusions The genome of M. neglectum, as well as the metabolic reconstruction of crucial lipid pathways, provides new insights into the diversity of the lipid metabolism in microalgae. The results of this work provide a platform to encourage the development of this strain for biotechnological applications and production concepts. PMID:24373495

Radiative transfer codes for atmospheric correction and aerosol retrieval: intercomparison study.

PubMed

Kotchenova, Svetlana Y; Vermote, Eric F; Levy, Robert; Lyapustin, Alexei

2008-05-01

Results are summarized for a scientific project devoted to the comparison of four atmospheric radiative transfer codes incorporated into different satellite data processing algorithms, namely, 6SV1.1 (second simulation of a satellite signal in the solar spectrum, vector, version 1.1), RT3 (radiative transfer), MODTRAN (moderate resolution atmospheric transmittance and radiance code), and SHARM (spherical harmonics). The performance of the codes is tested against well-known benchmarks, such as Coulson's tabulated values and a Monte Carlo code. The influence of revealed differences on aerosol optical thickness and surface reflectance retrieval is estimated theoretically by using a simple mathematical approach. All information about the project can be found at http://rtcodes.ltdri.org.

Radiative transfer codes for atmospheric correction and aerosol retrieval: intercomparison study

NASA Astrophysics Data System (ADS)

Kotchenova, Svetlana Y.; Vermote, Eric F.; Levy, Robert; Lyapustin, Alexei

2008-05-01

Results are summarized for a scientific project devoted to the comparison of four atmospheric radiative transfer codes incorporated into different satellite data processing algorithms, namely, 6SV1.1 (second simulation of a satellite signal in the solar spectrum, vector, version 1.1), RT3 (radiative transfer), MODTRAN (moderate resolution atmospheric transmittance and radiance code), and SHARM (spherical harmonics). The performance of the codes is tested against well-known benchmarks, such as Coulson's tabulated values and a Monte Carlo code. The influence of revealed differences on aerosol optical thickness and surface reflectance retrieval is estimated theoretically by using a simple mathematical approach. All information about the project can be found at http://rtcodes.ltdri.org.

Error Correcting Codes and Related Designs

DTIC Science & Technology

1990-09-30

Theory, IT-37 (1991), 1222-1224. 6. Codes and designs, existence and uniqueness, Discrete Math ., to appear. 7. (with R. Brualdi and N. Cai), Orphan...structure of the first order Reed-Muller codes, Discrete Math ., to appear. 8. (with J. H. Conway and N.J.A. Sloane), The binary self-dual codes of length up...18, 1988. 4. "Codes and Designs," Mathematics Colloquium, Technion, Haifa, Israel, March 6, 1989. 5. "On the Covering Radius of Codes," Discrete Math . Group

Standard interface files and procedures for reactor physics codes, version III

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carmichael, B.M.

Standards and procedures for promoting the exchange of reactor physics codes are updated to Version-III status. Standards covering program structure, interface files, file handling subroutines, and card input format are included. The implementation status of the standards in codes and the extension of the standards to new code areas are summarized. (15 references) (auth)

7 CFR Exhibit E to Subpart A of... - Voluntary National Model Building Codes

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 12 2013-01-01 2013-01-01 false Voluntary National Model Building Codes E Exhibit E... National Model Building Codes The following documents address the health and safety aspects of buildings and related structures and are voluntary national model building codes as defined in § 1924.4(h)(2) of...

7 CFR Exhibit E to Subpart A of... - Voluntary National Model Building Codes

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 12 2014-01-01 2013-01-01 true Voluntary National Model Building Codes E Exhibit E to... Model Building Codes The following documents address the health and safety aspects of buildings and related structures and are voluntary national model building codes as defined in § 1924.4(h)(2) of this...

7 CFR Exhibit E to Subpart A of... - Voluntary National Model Building Codes

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 12 2012-01-01 2012-01-01 false Voluntary National Model Building Codes E Exhibit E... National Model Building Codes The following documents address the health and safety aspects of buildings and related structures and are voluntary national model building codes as defined in § 1924.4(h)(2) of...

A phase code for memory could arise from circuit mechanisms in entorhinal cortex

PubMed Central

Hasselmo, Michael E.; Brandon, Mark P.; Yoshida, Motoharu; Giocomo, Lisa M.; Heys, James G.; Fransen, Erik; Newman, Ehren L.; Zilli, Eric A.

2009-01-01

Neurophysiological data reveals intrinsic cellular properties that suggest how entorhinal cortical neurons could code memory by the phase of their firing. Potential cellular mechanisms for this phase coding in models of entorhinal function are reviewed. This mechanism for phase coding provides a substrate for modeling the responses of entorhinal grid cells, as well as the replay of neural spiking activity during waking and sleep. Efforts to implement these abstract models in more detailed biophysical compartmental simulations raise specific issues that could be addressed in larger scale population models incorporating mechanisms of inhibition. PMID:19656654

Structural Analysis and Design Software

NASA Technical Reports Server (NTRS)

1997-01-01

Collier Research and Development Corporation received a one-of-a-kind computer code for designing exotic hypersonic aircraft called ST-SIZE in the first ever Langley Research Center software copyright license agreement. Collier transformed the NASA computer code into a commercial software package called HyperSizer, which integrates with other Finite Element Modeling and Finite Analysis private-sector structural analysis program. ST-SIZE was chiefly conceived as a means to improve and speed the structural design of a future aerospace plane for Langley Hypersonic Vehicles Office. Including the NASA computer code into HyperSizer has enabled the company to also apply the software to applications other than aerospace, including improved design and construction for offices, marine structures, cargo containers, commercial and military aircraft, rail cars, and a host of everyday consumer products.

DYNECHARM++: a toolkit to simulate coherent interactions of high-energy charged particles in complex structures

NASA Astrophysics Data System (ADS)

Bagli, Enrico; Guidi, Vincenzo

2013-08-01

A toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures, called DYNECHARM++ has been developed. The code has been written in C++ language taking advantage of this object-oriented programing method. The code is capable to evaluating the electrical characteristics of complex atomic structures and to simulate and track the particle trajectory within them. Calculation method of electrical characteristics based on their expansion in Fourier series has been adopted. Two different approaches to simulate the interaction have been adopted, relying on the full integration of particle trajectories under the continuum potential approximation and on the definition of cross-sections of coherent processes. Finally, the code has proved to reproduce experimental results and to simulate interaction of charged particles with complex structures.

Child Injury Deaths: Comparing Prevention Information from Two Coding Systems

PubMed Central

Schnitzer, Patricia G.; Ewigman, Bernard G.

2006-01-01

Objectives The International Classification of Disease (ICD) external cause of injury E-codes do not sufficiently identify injury circumstances amenable to prevention. The researchers developed an alternative classification system (B-codes) that incorporates behavioral and environmental factors, for use in childhood injury research, and compare the two coding systems in this paper. Methods All fatal injuries among children less than age five that occurred between January 1, 1992, and December 31, 1994, were classified using both B-codes and E-codes. Results E-codes identified the most common causes of injury death: homicide (24%), fires (21%), motor vehicle incidents (21%), drowning (10%), and suffocation (9%). The B-codes further revealed that homicides (51%) resulted from the child being shaken or struck by another person; many fires deaths (42%) resulted from children playing with matches or lighters; drownings (46%) usually occurred in natural bodies of water; and most suffocation deaths (68%) occurred in unsafe sleeping arrangements. Conclusions B-codes identify additional information with specific relevance for prevention of childhood injuries. PMID:15944169

Visual coding of human bodies: perceptual aftereffects reveal norm-based, opponent coding of body identity.

PubMed

Rhodes, Gillian; Jeffery, Linda; Boeing, Alexandra; Calder, Andrew J

2013-04-01

Despite the discovery of body-selective neural areas in occipitotemporal cortex, little is known about how bodies are visually coded. We used perceptual adaptation to determine how body identity is coded. Brief exposure to a body (e.g., anti-Rose) biased perception toward an identity with opposite properties (Rose). Moreover, the size of this aftereffect increased with adaptor extremity, as predicted by norm-based, opponent coding of body identity. A size change between adapt and test bodies minimized the effects of low-level, retinotopic adaptation. These results demonstrate that body identity, like face identity, is opponent coded in higher-level vision. More generally, they show that a norm-based multidimensional framework, which is well established for face perception, may provide a powerful framework for understanding body perception.

A Clustering-Based Approach to Enriching Code Foraging Environment.

PubMed

Niu, Nan; Jin, Xiaoyu; Niu, Zhendong; Cheng, Jing-Ru C; Li, Ling; Kataev, Mikhail Yu

2016-09-01

Developers often spend valuable time navigating and seeking relevant code in software maintenance. Currently, there is a lack of theoretical foundations to guide tool design and evaluation to best shape the code base to developers. This paper contributes a unified code navigation theory in light of the optimal food-foraging principles. We further develop a novel framework for automatically assessing the foraging mechanisms in the context of program investigation. We use the framework to examine to what extent the clustering of software entities affects code foraging. Our quantitative analysis of long-lived open-source projects suggests that clustering enriches the software environment and improves foraging efficiency. Our qualitative inquiry reveals concrete insights into real developer's behavior. Our research opens the avenue toward building a new set of ecologically valid code navigation tools.

DataRocket: Interactive Visualisation of Data Structures

NASA Astrophysics Data System (ADS)

Parkes, Steve; Ramsay, Craig

2010-08-01

CodeRocket is a software engineering tool that provides cognitive support to the software engineer for reasoning about a method or procedure and for documenting the resulting code [1]. DataRocket is a software engineering tool designed to support visualisation and reasoning about program data structures. DataRocket is part of the CodeRocket family of software tools developed by Rapid Quality Systems [2] a spin-out company from the Space Technology Centre at the University of Dundee. CodeRocket and DataRocket integrate seamlessly with existing architectural design and coding tools and provide extensive documentation with little or no effort on behalf of the software engineer. Comprehensive, abstract, detailed design documentation is available early on in a project so that it can be used for design reviews with project managers and non expert stakeholders. Code and documentation remain fully synchronised even when changes are implemented in the code without reference to the existing documentation. At the end of a project the press of a button suffices to produce the detailed design document. Existing legacy code can be easily imported into CodeRocket and DataRocket to reverse engineer detailed design documentation making legacy code more manageable and adding substantially to its value. This paper introduces CodeRocket. It then explains the rationale for DataRocket and describes the key features of this new tool. Finally the major benefits of DataRocket for different stakeholders are considered.

User's Guide for ENSAERO_FE Parallel Finite Element Solver

NASA Technical Reports Server (NTRS)

Eldred, Lloyd B.; Guruswamy, Guru P.

1999-01-01

A high fidelity parallel static structural analysis capability is created and interfaced to the multidisciplinary analysis package ENSAERO-MPI of Ames Research Center. This new module replaces ENSAERO's lower fidelity simple finite element and modal modules. Full aircraft structures may be more accurately modeled using the new finite element capability. Parallel computation is performed by breaking the full structure into multiple substructures. This approach is conceptually similar to ENSAERO's multizonal fluid analysis capability. The new substructure code is used to solve the structural finite element equations for each substructure in parallel. NASTRANKOSMIC is utilized as a front end for this code. Its full library of elements can be used to create an accurate and realistic aircraft model. It is used to create the stiffness matrices for each substructure. The new parallel code then uses an iterative preconditioned conjugate gradient method to solve the global structural equations for the substructure boundary nodes.

The Validation of Macro and Micro Observations of Parent–Child Dynamics Using the Relationship Affect Coding System in Early Childhood

PubMed Central

Mun, Chung Jung; Tein, Jenn-Yun; Kim, Hanjoe; Shaw, Daniel S.; Gardner, Frances; Wilson, Melvin N.; Peterson, Jenene

2018-01-01

This study examined the validity of micro social observations and macro ratings of parent–child interaction in early to middle childhood. Seven hundred and thirty-one families representing multiple ethnic groups were recruited and screened as at risk in the context of Women, Infant, and Children (WIC) Nutritional Supplement service settings. Families were randomly assigned to the Family Checkup (FCU) intervention or the control condition at age 2 and videotaped in structured interactions in the home at ages 2, 3, 4, and 5. Parent–child interaction videotapes were microcoded using the Relationship Affect Coding System (RACS) that captures the duration of two mutual dyadic states: positive engagement and coercion. Macro ratings of parenting skills were collected after coding the videotapes to assess parent use of positive behavior support and limit setting skills (or lack thereof). Confirmatory factor analyses revealed that the measurement model of macro ratings of limit setting and positive behavior support was not supported by the data, and thus, were excluded from further analyses. However, there was moderate stability in the families’ micro social dynamics across early childhood and it showed significant improvements as a function of random assignment to the FCU. Moreover, parent–child dynamics were predictive of chronic behavior problems as rated by parents in middle childhood, but not emotional problems. We conclude with a discussion of the validity of the RACS and on methodological advantages of micro social coding over the statistical limitations of macro rating observations. Future directions are discussed for observation research in prevention science. PMID:27620623

Underestimated prevalence of heart failure in hospital inpatients: a comparison of ICD codes and discharge letter information.

PubMed

Kaspar, Mathias; Fette, Georg; Güder, Gülmisal; Seidlmayer, Lea; Ertl, Maximilian; Dietrich, Georg; Greger, Helmut; Puppe, Frank; Störk, Stefan

2018-04-17

Heart failure is the predominant cause of hospitalization and amongst the leading causes of death in Germany. However, accurate estimates of prevalence and incidence are lacking. Reported figures originating from different information sources are compromised by factors like economic reasons or documentation quality. We implemented a clinical data warehouse that integrates various information sources (structured parameters, plain text, data extracted by natural language processing) and enables reliable approximations to the real number of heart failure patients. Performance of ICD-based diagnosis in detecting heart failure was compared across the years 2000-2015 with (a) advanced definitions based on algorithms that integrate various sources of the hospital information system, and (b) a physician-based reference standard. Applying these methods for detecting heart failure in inpatients revealed that relying on ICD codes resulted in a marked underestimation of the true prevalence of heart failure, ranging from 44% in the validation dataset to 55% (single year) and 31% (all years) in the overall analysis. Percentages changed over the years, indicating secular changes in coding practice and efficiency. Performance was markedly improved using search and permutation algorithms from the initial expert-specified query (F1 score of 81%) to the computer-optimized query (F1 score of 86%) or, alternatively, optimizing precision or sensitivity depending on the search objective. Estimating prevalence of heart failure using ICD codes as the sole data source yielded unreliable results. Diagnostic accuracy was markedly improved using dedicated search algorithms. Our approach may be transferred to other hospital information systems.

Application of golay complementary coded excitation schemes for non-destructive testing of sandwich structures

NASA Astrophysics Data System (ADS)

Arora, Vanita; Mulaveesala, Ravibabu

2017-06-01

In recent years, InfraRed Thermography (IRT) has become a widely accepted non-destructive testing technique to evaluate the structural integrity of composite sandwich structures due to its full-field, remote, fast and in-service inspection capabilities. This paper presents a novel infrared thermographic approach named as Golay complementary coded thermal wave imaging is presented to detect disbonds in a sandwich structure having face sheets from Glass/Carbon Fibre Reinforced (GFR/CFR) laminates and core of the wooden block.

Study of the Transition from MRI to Magnetic Turbulence via Parasitic Instability by a High-order MHD Simulation Code

NASA Astrophysics Data System (ADS)

Hirai, Kenichiro; Katoh, Yuto; Terada, Naoki; Kawai, Soshi

2018-02-01

Magnetic turbulence in accretion disks under ideal magnetohydrodynamic (MHD) conditions is expected to be driven by the magneto-rotational instability (MRI) followed by secondary parasitic instabilities. We develop a three-dimensional ideal MHD code that can accurately resolve turbulent structures, and carry out simulations with a net vertical magnetic field in a local shearing box disk model to investigate the role of parasitic instabilities in the formation process of magnetic turbulence. Our simulations reveal that a highly anisotropic Kelvin–Helmholtz (K–H) mode parasitic instability evolves just before the first peak in turbulent stress and then breaks large-scale shear flows created by MRI. The wavenumber of the enhanced parasitic instability is larger than the theoretical estimate, because the shear flow layers sometimes become thinner than those assumed in the linear analysis. We also find that interaction between antiparallel vortices caused by the K–H mode parasitic instability induces small-scale waves that break the shear flows. On the other hand, at repeated peaks in the nonlinear phase, anisotropic wavenumber spectra are observed only in the small wavenumber region and isotropic waves dominate at large wavenumbers unlike for the first peak. Restructured channel flows due to MRI at the peaks in nonlinear phase seem to be collapsed by the advection of small-scale shear structures into the restructured flow and resultant mixing.

GridMan: A grid manipulation system

NASA Technical Reports Server (NTRS)

Eiseman, Peter R.; Wang, Zhu

1992-01-01

GridMan is an interactive grid manipulation system. It operates on grids to produce new grids which conform to user demands. The input grids are not constrained to come from any particular source. They may be generated by algebraic methods, elliptic methods, hyperbolic methods, parabolic methods, or some combination of methods. The methods are included in the various available structured grid generation codes. These codes perform the basic assembly function for the various elements of the initial grid. For block structured grids, the assembly can be quite complex due to a large number of clock corners, edges, and faces for which various connections and orientations must be properly identified. The grid generation codes are distinguished among themselves by their balance between interactive and automatic actions and by their modest variations in control. The basic form of GridMan provides a much more substantial level of grid control and will take its input from any of the structured grid generation codes. The communication link to the outside codes is a data file which contains the grid or section of grid.

Analysis of SMA Hybrid Composite Structures in MSC.Nastran and ABAQUS

NASA Technical Reports Server (NTRS)

Turner, Travis L.; Patel, Hemant D.

2005-01-01

A thermoelastic constitutive model for shape memory alloy (SMA) actuators and SMA hybrid composite (SMAHC) structures was recently implemented in the commercial finite element codes MSC.Nastran and ABAQUS. The model may be easily implemented in any code that has the capability for analysis of laminated composite structures with temperature dependent material properties. The model is also relatively easy to use and requires input of only fundamental engineering properties. A brief description of the model is presented, followed by discussion of implementation and usage in the commercial codes. Results are presented from static and dynamic analysis of SMAHC beams of two types; a beam clamped at each end and a cantilever beam. Nonlinear static (post-buckling) and random response analyses are demonstrated for the first specimen. Static deflection (shape) control is demonstrated for the cantilever beam. Approaches for modeling SMAHC material systems with embedded SMA in ribbon and small round wire product forms are demonstrated and compared. The results from the commercial codes are compared to those from a research code as validation of the commercial implementations; excellent correlation is achieved in all cases.

VTOL in ground effect flows for closely spaced jets. [to predict pressure and upwash forces on aircraft structures

NASA Technical Reports Server (NTRS)

Migdal, D.; Hill, W. G., Jr.; Jenkins, R. C.

1979-01-01

Results of a series of in ground effect twin jet tests are presented along with flow models for closely spaced jets to help predict pressure and upwash forces on simulated aircraft surfaces. The isolated twin jet tests revealed unstable fountains over a range of spacings and jet heights, regions of below ambient pressure on the ground, and negative pressure differential in the upwash flow field. A separate computer code was developed for vertically oriented, incompressible jets. This model more accurately reflects fountain behavior without fully formed wall jets, and adequately predicts ground isobars, upwash dynamic pressure decay, and fountain lift force variation with height above ground.

The complete chloroplast genome of two Brassica species, Brassica nigra and B. Oleracea.

PubMed

Seol, Young-Joo; Kim, Kyunghee; Kang, Sang-Ho; Perumal, Sampath; Lee, Jonghoon; Kim, Chang-Kug

2017-03-01

The two Brassica species, Brassica nigra and Brassica oleracea, are important agronomic crops. The chloroplast genome sequences were generated by de novo assembly using whole genome next-generation sequences. The chloroplast genomes of B. nigra and B. oleracea were 153 633 bp and 153 366 bp in size, respectively, and showed conserved typical chloroplast structure. The both chloroplast genomes contained a total of 114 genes including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis revealed that B. oleracea is closely related to B. rapa and B. napus but B. nigra is more diverse than the neighbor species Raphanus sativus.

Wechsler Adult Intelligence Scale-Third Edition short form for index and IQ scores in a psychiatric population.

PubMed

Christensen, Bruce K; Girard, Todd A; Bagby, R Michael

2007-06-01

An eight-subtest short form (SF8) of the Wechsler Adult Intelligence Scale, Third Edition (WAIS-III), maintaining equal representation of each index factor, was developed for use with psychiatric populations. Data were collected from a mixed inpatient/outpatient sample (99 men and 101 women) referred for neuropsychological assessment. Psychometric analyses revealed an optimal SF8 comprising Vocabulary, Similarities, Arithmetic, Digit Span, Picture Completion, Matrix Reasoning, Digit Symbol Coding, and Symbol Search, scored by linear scaling. Expanding on previous short forms, the current SF8 maximizes the breadth of information and reduces administration time while maintaining the original WAIS-III factor structure. (c) 2007 APA, all rights reserved

Myotonia-related mutations in the distal C-terminus of ClC-1 and ClC-0 chloride channels affect the structure of a poly-proline helix

PubMed Central

Macías, María J.; Teijido, Oscar; Zifarelli, Giovanni; Martin, Pau; Ramirez-Espain, Ximena; Zorzano, Antonio; Palacín, Manuel; Pusch, Michael; Estévez, Raúl

2006-01-01

Myotonia is a state of hyperexcitability of skeletal-muscle fibres. Mutations in the ClC-1 Cl− channel cause recessive and dominant forms of this disease. Mutations have been described throughout the protein-coding region, including three sequence variations (A885P, R894X and P932L) in a distal C-terminal stretch of residues [CTD (C-terminal domain) region] that are not conserved between CLC proteins. We show that surface expression of these mutants is reduced in Xenopus oocytes compared with wild-type ClC-1. Functional, biochemical and NMR spectroscopy studies revealed that the CTD region encompasses a segment conserved in most voltage-dependent CLC channels that folds with a secondary structure containing a short type II poly-proline helix. We found that the myotonia-causing mutation A885P disturbs this structure by extending the poly-proline helix. We hypothesize that this structural modification results in the observed alteration of the common gate that acts on both pores of the channel. We provide the first experimental investigation of structural changes resulting from myotonia-causing mutations. PMID:17107341

Frequency- and Time-Domain Methods in Soil-Structure Interaction Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolisetti, Chandrakanth; Whittaker, Andrew S.; Coleman, Justin L.

2015-06-01

Soil-structure interaction (SSI) analysis in the nuclear industry is currently performed using linear codes that function in the frequency domain. There is a consensus that these frequency-domain codes give reasonably accurate results for low-intensity ground motions that result in almost linear response. For higher intensity ground motions, which may result in nonlinear response in the soil, structure or at the vicinity of the foundation, the adequacy of frequency-domain codes is unproven. Nonlinear analysis, which is only possible in the time domain, is theoretically more appropriate in such cases. These methods are available but are rarely used due to the largemore » computational requirements and a lack of experience with analysts and regulators. This paper presents an assessment of the linear frequency-domain code, SASSI, which is widely used in the nuclear industry, and the time-domain commercial finite-element code, LS-DYNA, for SSI analysis. The assessment involves benchmarking the SSI analysis procedure in LS-DYNA against SASSI for linearly elastic models. After affirming that SASSI and LS-DYNA result in almost identical responses for these models, they are used to perform nonlinear SSI analyses of two structures founded on soft soil. An examination of the results shows that, in spite of using identical material properties, the predictions of frequency- and time-domain codes are significantly different in the presence of nonlinear behavior such as gapping and sliding of the foundation.« less

Self-Taught Low-Rank Coding for Visual Learning.

PubMed

Li, Sheng; Li, Kang; Fu, Yun

2018-03-01

The lack of labeled data presents a common challenge in many computer vision and machine learning tasks. Semisupervised learning and transfer learning methods have been developed to tackle this challenge by utilizing auxiliary samples from the same domain or from a different domain, respectively. Self-taught learning, which is a special type of transfer learning, has fewer restrictions on the choice of auxiliary data. It has shown promising performance in visual learning. However, existing self-taught learning methods usually ignore the structure information in data. In this paper, we focus on building a self-taught coding framework, which can effectively utilize the rich low-level pattern information abstracted from the auxiliary domain, in order to characterize the high-level structural information in the target domain. By leveraging a high quality dictionary learned across auxiliary and target domains, the proposed approach learns expressive codings for the samples in the target domain. Since many types of visual data have been proven to contain subspace structures, a low-rank constraint is introduced into the coding objective to better characterize the structure of the given target set. The proposed representation learning framework is called self-taught low-rank (S-Low) coding, which can be formulated as a nonconvex rank-minimization and dictionary learning problem. We devise an efficient majorization-minimization augmented Lagrange multiplier algorithm to solve it. Based on the proposed S-Low coding mechanism, both unsupervised and supervised visual learning algorithms are derived. Extensive experiments on five benchmark data sets demonstrate the effectiveness of our approach.

Dyadic Coregulation and Deviant Talk in Adolescent Friendships: Interaction Patterns Associated With Problematic Substance Use in Early Adulthood

PubMed Central

Piehler, Timothy F.; Dishion, Thomas J.

2014-01-01

In a sample of 711 ethnically diverse adolescents, the observed interpersonal dynamics of dyadic adolescent friendship interactions were coded to predict early adulthood tobacco, alcohol, and marijuana use. Deviant discussion content within the interactions was coded along with dyadic coregulation (i.e., interpersonal coordination, attention synchrony). Structural equation modeling revealed that, as expected, deviant content in adolescent interactions at age 16–17 years was strongly predictive of problematic use of tobacco, alcohol, and marijuana at ages 22 and 23. Although dyadic coregulation was not directly predictive of early adulthood substance use, it did moderate the impact of deviant talk within the dyad on future alcohol and marijuana use. For these substances, high levels of dyadic coregulation increased the risk associated with high levels of deviant talk for problematic use in early adulthood. Results held when comparing across genders and across ethnic groups. The results suggest that these interpersonal dynamics are associated with developmental trajectories of risk for or resilience to peer influence processes. PMID:24188039

Dyadic coregulation and deviant talk in adolescent friendships: interaction patterns associated with problematic substance use in early adulthood.

PubMed

Piehler, Timothy F; Dishion, Thomas J

2014-04-01

In a sample of 711 ethnically diverse adolescents, the observed interpersonal dynamics of dyadic adolescent friendship interactions were coded to predict early adulthood tobacco, alcohol, and marijuana use. Deviant discussion content within the interactions was coded along with dyadic coregulation (i.e., interpersonal coordination, attention synchrony). Structural equation modeling revealed that, as expected, deviant content in adolescent interactions at age 16-17 years was strongly predictive of problematic use of tobacco, alcohol, and marijuana at ages 22 and 23. Although dyadic coregulation was not directly predictive of early adulthood substance use, it did moderate the impact of deviant talk within the dyad on future alcohol and marijuana use. For these substances, high levels of dyadic coregulation increased the risk associated with high levels of deviant talk for problematic use in early adulthood. Results held when comparing across genders and across ethnic groups. The results suggest that these interpersonal dynamics are associated with developmental trajectories of risk for or resilience to peer influence processes. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Lattice Boltzmann Simulation Optimization on Leading Multicore Platforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Samuel; Carter, Jonathan; Oliker, Leonid

2008-02-01

We present an auto-tuning approach to optimize application performance on emerging multicore architectures. The methodology extends the idea of search-based performance optimizations, popular in linear algebra and FFT libraries, to application-specific computational kernels. Our work applies this strategy to a lattice Boltzmann application (LBMHD) that historically has made poor use of scalar microprocessors due to its complex data structures and memory access patterns. We explore one of the broadest sets of multicore architectures in the HPC literature, including the Intel Clovertown, AMD Opteron X2, Sun Niagara2, STI Cell, as well as the single core Intel Itanium2. Rather than hand-tuning LBMHDmore » for each system, we develop a code generator that allows us identify a highly optimized version for each platform, while amortizing the human programming effort. Results show that our auto-tuned LBMHD application achieves up to a 14x improvement compared with the original code. Additionally, we present detailed analysis of each optimization, which reveal surprising hardware bottlenecks and software challenges for future multicore systems and applications.« less

Lattice Boltzmann simulation optimization on leading multicore platforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, S.; Carter, J.; Oliker, L.

2008-01-01

We present an auto-tuning approach to optimize application performance on emerging multicore architectures. The methodology extends the idea of searchbased performance optimizations, popular in linear algebra and FFT libraries, to application-specific computational kernels. Our work applies this strategy to a lattice Boltzmann application (LBMHD) that historically has made poor use of scalar microprocessors due to its complex data structures and memory access patterns. We explore one of the broadest sets of multicore architectures in the HPC literature, including the Intel Clovertown, AMD Opteron X2, Sun Niagara2, STI Cell, as well as the single core Intel Itanium2. Rather than hand-tuning LBMHDmore » for each system, we develop a code generator that allows us identify a highly optimized version for each platform, while amortizing the human programming effort. Results show that our autotuned LBMHD application achieves up to a 14 improvement compared with the original code. Additionally, we present detailed analysis of each optimization, which reveal surprising hardware bottlenecks and software challenges for future multicore systems and applications.« less

The flaA locus of Bacillus subtilis is part of a large operon coding for flagellar structures, motility functions, and an ATPase-like polypeptide.

PubMed Central

Albertini, A M; Caramori, T; Crabb, W D; Scoffone, F; Galizzi, A

1991-01-01

We cloned and sequenced 8.3 kb of Bacillus subtilis DNA corresponding to the flaA locus involved in flagellar biosynthesis, motility, and chemotaxis. The DNA sequence revealed the presence of 10 complete and 2 incomplete open reading frames. Comparison of the deduced amino acid sequences to data banks showed similarities of nine of the deduced products to a number of proteins of Escherichia coli and Salmonella typhimurium for which a role in flagellar functioning has been directly demonstrated. In particular, the sequence data suggest that the flaA operon codes for the M-ring protein, components of the motor switch, and the distal part of the basal-body rod. The gene order is remarkably similar to that described for region III of the enterobacterial flagellar regulon. One of the open reading frames was translated into a protein with 48% amino acid identity to S. typhimurium FliI and 29% identity to the beta subunit of E. coli ATP synthase. PMID:1828465

The Complete Mitochondrial Genome of the Land Snail Cornu aspersum (Helicidae: Mollusca): Intra-Specific Divergence of Protein-Coding Genes and Phylogenetic Considerations within Euthyneura

PubMed Central

Gaitán-Espitia, Juan Diego; Nespolo, Roberto F.; Opazo, Juan C.

2013-01-01

The complete sequences of three mitochondrial genomes from the land snail Cornu aspersum were determined. The mitogenome has a length of 14050 bp, and it encodes 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. It also includes nine small intergene spacers, and a large AT-rich intergenic spacer. The intra-specific divergence analysis revealed that COX1 has the lower genetic differentiation, while the most divergent genes were NADH1, NADH3 and NADH4. With the exception of Euhadra herklotsi, the structural comparisons showed the same gene order within the family Helicidae, and nearly identical gene organization to that found in order Pulmonata. Phylogenetic reconstruction recovered Basommatophora as polyphyletic group, whereas Eupulmonata and Pulmonata as paraphyletic groups. Bayesian and Maximum Likelihood analyses showed that C. aspersum is a close relative of Cepaea nemoralis, and with the other Helicidae species form a sister group of Albinaria caerulea, supporting the monophyly of the Stylommatophora clade. PMID:23826260

The cDNA-derived amino acid sequence of hemoglobin II from Lucina pectinata.

PubMed

Torres-Mercado, Elineth; Renta, Jessicca Y; Rodríguez, Yolanda; López-Garriga, Juan; Cadilla, Carmen L

2003-11-01

Hemoglobin II from the clam Lucina pectinata is an oxygen-reactive protein with a unique structural organization in the heme pocket involving residues Gln65 (E7), Tyr30 (B10), Phe44 (CD1), and Phe69 (E11). We employed the reverse transcriptase-polymerase chain reaction (RT-PCR) and methods to synthesize various cDNA(HbII). An initial 300-bp cDNA clone was amplified from total RNA by RT-PCR using degenerate oligonucleotides. Gene-specific primers derived from the HbII-partial cDNA sequence were used to obtain the 5' and 3' ends of the cDNA by RACE. The length of the HbII cDNA, estimated from overlapping clones, was approximately 2114 bases. Northern blot analysis revealed that the mRNA size of HbII agrees with the estimated size using cDNA data. The coding region of the full-length HbII cDNA codes for 151 amino acids. The calculated molecular weight of HbII, including the heme group and acetylated N-terminal residue, is 17,654.07 Da.

Polyspecific pyrrolysyl-tRNA synthetases from directed evolution.

PubMed

Guo, Li-Tao; Wang, Yane-Shih; Nakamura, Akiyoshi; Eiler, Daniel; Kavran, Jennifer M; Wong, Margaret; Kiessling, Laura L; Steitz, Thomas A; O'Donoghue, Patrick; Söll, Dieter

2014-11-25

Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA(Pyl) have emerged as ideal translation components for genetic code innovation. Variants of the enzyme facilitate the incorporation >100 noncanonical amino acids (ncAAs) into proteins. PylRS variants were previously selected to acylate N(ε)-acetyl-Lys (AcK) onto tRNA(Pyl). Here, we examine an N(ε)-acetyl-lysyl-tRNA synthetase (AcKRS), which is polyspecific (i.e., active with a broad range of ncAAs) and 30-fold more efficient with Phe derivatives than it is with AcK. Structural and biochemical data reveal the molecular basis of polyspecificity in AcKRS and in a PylRS variant [iodo-phenylalanyl-tRNA synthetase (IFRS)] that displays both enhanced activity and substrate promiscuity over a chemical library of 313 ncAAs. IFRS, a product of directed evolution, has distinct binding modes for different ncAAs. These data indicate that in vivo selections do not produce optimally specific tRNA synthetases and suggest that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids.

Molecular analysis of Toxoplasma gondii Surface Antigen 1 (SAG1) gene cloned from Toxoplasma gondii DNA isolated from Javanese acute toxoplasmosis

NASA Astrophysics Data System (ADS)

Haryati, Sri; Agung Prasetyo, Afiono; Sari, Yulia; Dharmawan, Ruben

2018-05-01

Toxoplasma gondii Surface Antigen 1 (SAG1) is often used as a diagnostic tool due to its immunodominant-specific as antigen. However, data of the Toxoplasma gondii SAG1 protein from Indonesian isolate is limited. To study the protein, genomic DNA was isolated from a Javanese acute toxoplasmosis blood samples patient. A complete coding sequence of Toxoplasma gondii SAG1 was cloned and inserted into an Escherichia coli expression plasmid and sequenced. The sequencing results were subjected to bioinformatics analysis. The Toxoplasma gondii SAG1 complete coding sequences were successfully cloned. Physicochemical analysis revealed the 336 aa of SAG1 had 34.7 kDa of weight. The isoelectric point and aliphatic index were 8.4 and 78.4, respectively. The N-terminal methionine half-life in Escherichia coli was more than 10 hours. The antigenicity, secondary structure, and identification of the HLA binding motifs also had been discussed. The results of this study would contribute information about Toxoplasma gondii SAG1 and benefits for further works willing to develop diagnostic and therapeutic strategies against the parasite.

Polyspecific pyrrolysyl-tRNA synthetases from directed evolution

PubMed Central

Guo, Li-Tao; Wang, Yane-Shih; Nakamura, Akiyoshi; Eiler, Daniel; Kavran, Jennifer M.; Wong, Margaret; Kiessling, Laura L.; Steitz, Thomas A.; O’Donoghue, Patrick; Söll, Dieter

2014-01-01

Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNAPyl have emerged as ideal translation components for genetic code innovation. Variants of the enzyme facilitate the incorporation >100 noncanonical amino acids (ncAAs) into proteins. PylRS variants were previously selected to acylate Nε-acetyl-Lys (AcK) onto tRNAPyl. Here, we examine an Nε-acetyl-lysyl-tRNA synthetase (AcKRS), which is polyspecific (i.e., active with a broad range of ncAAs) and 30-fold more efficient with Phe derivatives than it is with AcK. Structural and biochemical data reveal the molecular basis of polyspecificity in AcKRS and in a PylRS variant [iodo-phenylalanyl-tRNA synthetase (IFRS)] that displays both enhanced activity and substrate promiscuity over a chemical library of 313 ncAAs. IFRS, a product of directed evolution, has distinct binding modes for different ncAAs. These data indicate that in vivo selections do not produce optimally specific tRNA synthetases and suggest that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids. PMID:25385624

Applied ethics: Have we lost a crucial opportunity?

PubMed

Kerkhoff, Thomas R; Hanson, Stephanie L

2015-11-01

Comments on the article, "Guidelines for competency development and measurement in rehabilitation psychology postdoctoral training," by Stiers et al. (see record 2014-55195-001). A review of the recent publication of Stiers et al., a well-organized distillation of the functional competencies required of practitioners of Rehabilitation Psychology that evolved from the Baltimore Consensus Conference (Stiers et al., 2012), revealed a potentially important omission in the section labeled Structured Observations of Competencies in Assessment and Intervention (Table 4, p. 117). Throughout the subsections regarding Knowledge, Skills/Abilities, and Attitudes/ Values, indirect reference to the American Psychological Association (APA) Ethical Principles of Psychologists and Code of Conduct (APA, 2010) is evident without formal citation of the Code. The concepts operationalized in the APA ethical principles suffuse the content of this section of the competencies, but without direct reference to those principles. The remainder of the tables (5-7, pp. 188 -120) include explicit inclusion of knowledge of ethics in the contexts of demonstrating competencies in consultation, research and evaluation, teaching and supervision, and management and administration. (c) 2015 APA, all rights reserved).

RNA Relics and Origin of Life

PubMed Central

Demongeot, Jacques; Glade, Nicolas; Moreira, Andrés; Vial, Laurent

2009-01-01

A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells. PMID:20111682

Crystal structures of two Bordetella pertussis periplasmic receptors contribute to defining a novel pyroglutamic acid binding DctP subfamily.

PubMed

Rucktooa, Prakash; Antoine, Rudy; Herrou, Julien; Huvent, Isabelle; Locht, Camille; Jacob-Dubuisson, Françoise; Villeret, Vincent; Bompard, Coralie

2007-06-29

Gram-negative bacteria have developed several different transport systems for solute uptake. One of these, the tripartite ATP independent periplasmic transport system (TRAP-T), makes use of an extracytoplasmic solute receptor (ESR) which captures specific solutes with high affinity and transfers them to their partner permease complex located in the bacterial inner membrane. We hereby report the structures of DctP6 and DctP7, two such ESRs from Bordetella pertussis. These two proteins display a high degree of sequence and structural similarity and possess the "Venus flytrap" fold characteristic of ESRs, comprising two globular alpha/beta domains hinged together to form a ligand binding cleft. DctP6 and DctP7 both show a closed conformation due to the presence of one pyroglutamic acid molecule bound by highly conserved residues in their respective ligand binding sites. BLAST analyses have revealed that the DctP6 and DctP7 residues involved in ligand binding are strictly present in a number of predicted TRAP-T ESRs from other bacteria. In most cases, the genes encoding these TRAP-T systems are located in the vicinity of a gene coding for a pyroglutamic acid metabolising enzyme. Both the high degree of conservation of these ligand binding residues and the genomic context of these TRAP-T-coding operons in a number of bacterial species, suggest that DctP6 and DctP7 constitute the prototypes of a novel TRAP-T DctP subfamily involved in pyroglutamic acid transport.

The identification and functional annotation of RNA structures conserved in vertebrates.

PubMed

Seemann, Stefan E; Mirza, Aashiq H; Hansen, Claus; Bang-Berthelsen, Claus H; Garde, Christian; Christensen-Dalsgaard, Mikkel; Torarinsson, Elfar; Yao, Zizhen; Workman, Christopher T; Pociot, Flemming; Nielsen, Henrik; Tommerup, Niels; Ruzzo, Walter L; Gorodkin, Jan

2017-08-01

Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved RNA structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ∼516,000 human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (1) colocalize consistently with binding sites of the same RNA binding proteins (RBPs) or (2) are transcribed in corresponding tissues. Additionally, a CaptureSeq experiment revealed expression of many of our CRS regions in human fetal brain, including 662 novel ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared expression and shared structure despite low abundance and low sequence identity. About 30,000 CRS regions are located near coding or long noncoding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their nonstructured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality. © 2017 Seemann et al.; Published by Cold Spring Harbor Laboratory Press.

Unit cell geometry of multiaxial preforms for structural composites

NASA Technical Reports Server (NTRS)

Ko, Frank; Lei, Charles; Rahman, Anisur; Du, G. W.; Cai, Yun-Jia

1993-01-01

The objective of this study is to investigate the yarn geometry of multiaxial preforms. The importance of multiaxial preforms for structural composites is well recognized by the industry but, to exploit their full potential, engineering design rules must be established. This study is a step in that direction. In this work the preform geometry for knitted and braided preforms was studied by making a range of well designed samples and studying them by photo microscopy. The structural geometry of the preforms is related to the processing parameters. Based on solid modeling and B-spline methodology a software package is developed. This computer code enables real time structural representations of complex fiber architecture based on the rule of preform manufacturing. The code has the capability of zooming and section plotting. These capabilities provide a powerful means to study the effect of processing variables on the preform geometry. the code also can be extended to an auto mesh generator for downstream structural analysis using finite element method. This report is organized into six sections. In the first section the scope and background of this work is elaborated. In section two the unit cell geometries of braided and multi-axial warp knitted preforms is discussed. The theoretical frame work of yarn path modeling and solid modeling is presented in section three. The thin section microscopy carried out to observe the structural geometry of the preforms is the subject in section four. The structural geometry is related to the processing parameters in section five. Section six documents the implementation of the modeling techniques into the computer code MP-CAD. A user manual for the software is also presented here. The source codes and published papers are listed in the Appendices.