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Sample records for pseudogene structural analysis

  1. Human von Willebrand factor gene and pseudogene: Structural analysis and differentiation by polymerase chain reaction

    SciTech Connect

    Mancuso, D.J.; Tuley, E.A.; Westfield, L.A.; Lester-Mancuso, T.L.; Sorace, J.M.; Sadler, J.E. ); Le Beau, M.M. )

    1991-01-01

    Structural analysis of the von Willebrand factor gene located on chromosome 12 is complicated by the presence of a partial unprocessed pseudogene on chromosome 22q11-13. The structures of the von Willebrand factor pseudogene and corresponding segment of the gene were determined, and methods were developed for the rapid differentiation of von Willebrand factor gene and pseudogene sequences. The pseudogene is 21-29 kilobases in length and corresponds to 12 exons (exons 23-34) of the von Willebrand factor gene. Approximately 21 kilobases of the gene and pseudogene were sequenced, including the 5{prime} boundary of the pseudogene. The 3{prime} boundary of the pseudogene lies within an 8-kb region corresponding to intron 34 of the gene. The presence of splice site and nonsense mutations suggests that the pseudogene cannot yield functional transcripts. The pseudogene has diverged {approximately}3.1{percent} in nucleotide sequence from the gene. This suggests a recent evolutionary origin {approximately}19-29 million years ago, near the time of divergence of humans and apes from monkeys. Several repetitive sequences were identified, including 4 Alu, one Line-1, and several short simple sequence repeats. Several of these simple repeats differ in length between the gene and pseudogene and provide useful markers for distinguishing these loci. Sequence differences between the gene and pseudogene were exploited to design oligonucleotide primers for use in the polymerase chain reaction to selectivity amplify sequences corresponding to exons 23-34 from either the von Willebrand factor gene or the pseudogene. This method is useful for the analysis of gene defects in patients with von Willebrand disease, without interference from homologous sequences in the pseudogene.

  2. Human mitochondrial transcription factor A (mtTFA): gene structure and characterization of related pseudogenes.

    PubMed

    Reyes, Aurelio; Mezzina, Maria; Gadaleta, Gemma

    2002-05-29

    Mitochondrial transcription factor A (mtTFA or Tfam) is a 25 kDa protein encoded by a nuclear gene and imported to mitochondria, where it functions as a key regulator of mammalian mitochondrial (mt) DNA transcription and replication. The coding sequence of the human mtTFA gene is reported in the literature and the sizes of few introns are known. In this paper we present the genomic structure of the human mtTFA gene along with the complete sequence of its six intronic regions. Three of the introns (I, III, VI) have been found to be less than 600 bp, while the other three were greater than 1.8 kb. In the course of this work, we discovered that, in addition to the active copy, different homologous sequences identified as processed pseudogenes psi h-mtTFA have been isolated and sequenced. Using an 'in silico' mapping approach we determined their locations on chromosomes 7, 11 and X. psi h-mtTFA locations are different from that of the gene, previously reported on chromosome 10. Transcription analysis by means of reverse transcriptase-polymerase chain reaction has shown that other than the RNA corresponding to the full-length transcript, an isoform lacking 96 bp is also present. Among the three sequenced pseudogenes only one of them located on chromosome 11 has been found to be transcribed in Jurkat cells under these culture conditions, even though transcription initiation and binding sites for different transcription factors have also been found upstream from the other two pseudogenes. PMID:12095695

  3. Structural characterization and chromosomal location of the mouse macrophage migration inhibitory factor gene and pseudogenes

    SciTech Connect

    Bozza, M.; Gerard, C.; Kolakowski, L.F. Jr.

    1995-06-10

    Macrophage migration inhibitory factor, MIF, is a cytokine released by T-lymphocytes, macrophages, and the pituitary gland that serves to integrate peripheral and central inflammatory responses. Ubiquitous expression and developmental regulation suggest that MIF may have additional roles outside of the immune system. Here we report the structure and chromosomal location of the mouse Mif gene and the partial characterization of five Mif pseudogenes. The mouse Mif gene spans less than 0.7 kb of chromosomal DNA and is composed of three exons. A comparison between the mouse and the human genes shows a similar gene structure and common regulatory elements in both promoter regions. The mouse Mif gene maps to the middle region of chromosome 10, between Bcr and S100b, which have been mapped to human chromosomes 22q11 and 21q22.3, respectively. The entire sequence of two pseudogenes demonstrates the absence of introns, the presence of the 5{prime} untranslated region of the cDNA, a 3{prime} poly(A) tail, and the lack of sequence similarity with untranscribed regions of the gene. The five pseudogenes are highly homologous to the cDNA, but contain a variable number of mutations that would produce mutated or truncated MIF-like proteins. Phylogenetic analyses of MIF genes and pseudogenes indicate several independent genetic events that can account for multiple genomic integrations. Three of the Mif pseudogenes were also mapped by interspecific backcross to chromosomes 1, 9, and 17. These results suggest that Mif pseudogenes originated by retrotransposition. 46 refs., 5 figs., 1 tab.

  4. Structure and functional evaluation of porcine NANOG that is a single-exon gene and has two pseudogenes.

    PubMed

    Yang, Fan; Zhang, Jinglong; Liu, Yajun; Cheng, De; Wang, Huayan

    2015-02-01

    Nanog plays an important role in maintaining the pluripotency of murine and human embryonic stem cells. However, the molecular features and transcriptional regulation of the NANOG gene have not been well investigated in pig. Here, we report, for the first time, that porcine NANOG is encoded by a single exon gene (SEG) mapped on chromosome 1 and has two daughter genes, one pseudogene NANOGP1 on chromosome 5 and one tandem duplicate on chromosome 1. The duplicated pseudogene NANOGP2 has high sequence similarity to NANOG, but does not encode a functional protein due to deletions and in-frame stop codons. The NANOGP1 contains four exons and three introns, but is short of the homeodomain sequence. Transcriptome analysis confirmed that NANOG mRNA in porcine iPS cells is transcribed from the SEG NANOG, but not from NANOGP1, because the NANOGP1 promoter is highly methylated, as confirmed by global DNA methylation analysis. The NANOG protein encoded by NANOG retains N, H, and C1/W/C2 domains. The H domain is required for nuclear translocation, while the C1/W/C2 domain ensures the NANOG regulatory function. Overexpression of NANOG in porcine embryonic fibroblasts promoted upregulation of its target genes SOX2, KLF4, and c-MYC. In conclusion, the functional porcine NANOG that is different in chromosomal structure from mouse and human genes is a single exon gene and encodes the functional NANOG protein that can be specifically regulated by OCT4/SOX2, and can promote the activation of target pluripotent factors in vivo. PMID:25542179

  5. Phylogenetic analysis and identification of pseudogenes reveal a progressive loss of zona pellucida genes during evolution of vertebrates.

    PubMed

    Goudet, Ghylène; Mugnier, Sylvie; Callebaut, Isabelle; Monget, Philippe

    2008-05-01

    Vertebrate eggs are surrounded by an extracellular matrix with similar functions and conserved individual components: the zona pellucida (ZP) glycoproteins. In mammals, chickens, frogs, and some fish species, we established an updated list of the ZP genes, studied the relationships within the ZP gene family using phylogenetic analysis, and identified ZP pseudogenes. Our study confirmed the classification of ZP genes in six subfamilies: ZPA/ZP2, ZPB/ZP4, ZPC/ZP3, ZP1, ZPAX, and ZPD. The identification of a Zpb pseudogene in the mouse genome, Zp1 pseudogenes in the dog and bovine genomes, and Zpax pseudogenes in the human, chimpanzee, macaque, and bovine genomes showed that the evolution of ZP genes mainly occurs by death of genes. Our study revealed that the extracellular matrix surrounding vertebrate eggs contains three to at least six ZP glycoproteins. Mammals can be classified in three categories. In the mouse, the ZP is composed of three ZP proteins (ZPA/ZP2, ZPC/ZP3, and ZP1). In dog, cattle and, putatively, pig, cat, and rabbit, the zona is composed of three ZP proteins (ZPA/ZP2, ZPB/ZP4, and ZPC/ZP3). In human, chimpanzee, macaque, and rat, the ZP is composed of four ZP proteins (ZPA/ZP2, ZPB/ZP4, ZPC/ZP3, and ZP1). Our review provides new directions to investigate the molecular basis of sperm-egg recognition, a mechanism which is not yet elucidated. PMID:18046012

  6. Structure of a human beta-actin-related pseudogene which lacks intervening sequences.

    PubMed Central

    Moos, M; Gallwitz, D

    1982-01-01

    From a human genomic library we have isolated and sequenced a beta-actin-related pseudogene (Hbeta Ac-psi l) which is free of intervening sequences. Several nucleotide insertions and deletions and translational stop codons generated within the protein-coding region indicate that this gene is functionless. PMID:6296793

  7. Mouse thymidine kinase: the promoter sequence and the gene and pseudogene structures in normal cells and in thymidine kinase deficient mutants.

    PubMed Central

    Seiser, C; Knöfler, M; Rudelstorfer, I; Haas, R; Wintersberger, E

    1989-01-01

    The mouse genome carries one gene and two pseudogenes for cytoplasmic thymidine kinase. The overall structure of these genes was determined with the help of cosmids and lambda phage clones and the upstream sequence containing the promoter was determined. The data allow an allocation of bands seen in the complex patterns of genomic Southern blots obtained from the DNA of wild type cells and of thymidine kinase deficient mutants to the gene as well as to the two pseudogenes. The much used LTK cell line was found to lack the entire gene but to retain the pseudogenes. Two other TK cell lines had DNA patterns indistinguishable from the wild type. Whereas the LTK line did not produce any TKmRNA, the two other mutants had normal amounts of TKmRNA but no cytoplasmic TK activity. Images PMID:2911464

  8. Comparative analysis of a putative tuberculosis-susceptibility gene, MC3R, and pseudogene sequences in cattle, African buffalo, hyena, rhinoceros and other African bovids and ruminants.

    PubMed

    Müller, A; Möller, M; Adams, L A; Warren, R M; Hoal, E G; van Helden, P D

    2012-01-01

    Studies in humans have suggested the possible involvement of melanocortin-3-receptor (MC3R) and other components of the central melanocortin system in host defense against mycobacteria. We report a genomic DNA nucleotide sequence highly homologous to human MC3R in several bovids and non-bovid African wildlife species. Nucleotide sequence analysis indicates that the orthologous genes of cattle and buffalo are highly homologous (89.4 and 90%, respectively) to the human MC3R gene. Sequence results also identified a typical non-functional, duplicated pseudogene, MC3RP, in 7 species from the family Bovidae. No pseudogene was found in animals outside Bovidae. The presence of the pseudogene in tuberculosis-susceptible species could have possible immunomodulatory effects on susceptibility to bovine tuberculosis infection, as well as a considerable influence on energy metabolism and food conversion efficiency. PMID:22286663

  9. Mutational analysis of a patient with mucopolysaccharidosis type VII, and identification of pseudogenes

    SciTech Connect

    Shipley, J.M.; Klinkenberg, M.; Wu, B.M.; Bachinsky, D.R.; Grubb, J.H.; Sly, W.S. )

    1993-03-01

    PCR of cDNA produced from patient fibroblasts allowed the authors to determine the paternal mutation in the first patient reported with [beta]-glucuronidase-deficiency mucopolysaccharidosis type VII (MPS VII). The G[r arrow]T transversion 1,881 bp downstream of the ATG translation initiation codon destroys an MboII restriction site and converts Trp627 to Cys (W627C). Digestion of genomic DNA PCR fragments with MboII indicated that the patient and the father were heterozygous for this missense mutation in exon 12. Failure to find cDNAs from patient RNA which did not contain this mutation suggested that the maternal mutation leads to greatly reduced synthesis or reduced stability of mRNA from the mutant allele. In order to identify the maternal mutation, it was necessary to analyze genomic sequences. This approach was complicated by the finding of multiple unprocessed pseudogenes and/or closely related genes. Using PCR with a panel of human/rodent hybrid cell lines, the authors found that these pseudogenes were present over chromosomes 5-7, 20, and 22 and the Y chromosome. Conditions were defined which allowed them to amplify and characterize genomic sequences for the true [beta]-glucuronidase gene despite this background of related sequences. The patient proved to be heterozygous for a second mutation, in which a C[r arrow]T transition introduces a termination codon (R356STOP) in exon 7. The mother was also heterozygous for this mutation. Expression of a cDNA containing the maternal mutation produced no enzyme activity, as expected. Expression of the paternal mutation in COS-7 cells produced a surprisingly high (65% of control) level of activity. However, activity was 13% of control in transiently transfected murine MPS VII cells. The level of activity of this mutant allele appears to correlate with the level of overexpression. 39 refs., 5 figs., 1 tab.

  10. The GENCODE pseudogene resource

    PubMed Central

    2012-01-01

    Background Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data. Results As part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. Based on their distribution, we develop simple statistical models for each type of activity, which we validate with large-scale RT-PCR-Seq experiments. Finally, we compare our pseudogenes with conservation and variation data from primate alignments and the 1000 Genomes project, producing lists of pseudogenes potentially under selection. Conclusions At one extreme, some pseudogenes possess conventional characteristics of functionality; these may represent genes that have recently died. On the other hand, we find interesting patterns of partial activity, which may suggest that dead genes are being resurrected as functioning non-coding RNAs. The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes. PMID:22951037

  11. Gene-pseudogene evolution: a probabilistic approach

    PubMed Central

    2015-01-01

    Over the last decade, methods have been developed for the reconstruction of gene trees that take into account the species tree. Many of these methods have been based on the probabilistic duplication-loss model, which describes how a gene-tree evolves over a species-tree with respect to duplication and losses, as well as extension of this model, e.g., the DLRS (Duplication, Loss, Rate and Sequence evolution) model that also includes sequence evolution under relaxed molecular clock. A disjoint, almost as recent, and very important line of research has been focused on non protein-coding, but yet, functional DNA. For instance, DNA sequences being pseudogenes in the sense that they are not translated, may still be transcribed and the thereby produced RNA may be functional. We extend the DLRS model by including pseudogenization events and devise an MCMC framework for analyzing extended gene families consisting of genes and pseudogenes with respect to this model, i.e., reconstructing gene-trees and identifying pseudogenization events in the reconstructed gene-trees. By applying the MCMC framework to biologically realistic synthetic data, we show that gene-trees as well as pseudogenization points can be inferred well. We also apply our MCMC framework to extended gene families belonging to the Olfactory Receptor and Zinc Finger superfamilies. The analysis indicate that both these super families contains very old pseudogenes, perhaps so old that it is reasonable to suspect that some are functional. In our analysis, the sub families of the Olfactory Receptors contains only lineage specific pseudogenes, while the sub families of the Zinc Fingers contains pseudogene lineages common to several species. PMID:26449131

  12. Analysis of Complete Genomes of Propionibacterium acnes Reveals a Novel Plasmid and Increased Pseudogenes in an Acne Associated Strain

    PubMed Central

    Fitz-Gibbon, Sorel; Tomida, Shuta; Li, Huiying

    2013-01-01

    The human skin harbors a diverse community of bacteria, including the Gram-positive, anaerobic bacterium Propionibacterium acnes. P. acnes has historically been linked to the pathogenesis of acne vulgaris, a common skin disease affecting over 80% of all adolescents in the US. To gain insight into potential P. acnes pathogenic mechanisms, we previously sequenced the complete genome of a P. acnes strain HL096PA1 that is highly associated with acne. In this study, we compared its genome to the first published complete genome KPA171202. HL096PA1 harbors a linear plasmid, pIMPLE-HL096PA1. This is the first described P. acnes plasmid. We also observed a five-fold increase of pseudogenes in HL096PA1, several of which encode proteins in carbohydrate transport and metabolism. In addition, our analysis revealed a few island-like genomic regions that are unique to HL096PA1 and a large genomic inversion spanning the ribosomal operons. Together, these findings offer a basis for understanding P. acnes virulent properties, host adaptation mechanisms, and its potential role in acne pathogenesis at the strain level. Furthermore, the plasmid identified in HL096PA1 may potentially provide a new opportunity for P. acnes genetic manipulation and targeted therapy against specific disease-associated strains. PMID:23762865

  13. Evolutionary direction of processed pseudogenes.

    PubMed

    Liu, Guoqing; Cui, Xiangjun; Li, Hong; Cai, Lu

    2016-08-01

    While some pseudogenes have been reported to play important roles in gene regulation, little is known about the possible relationship between pseudogene functions and evolutionary process of pseudogenes, or about the forces responsible for the pseudogene evolution. In this study, we characterized human processed pseudogenes in terms of evolutionary dynamics. Our results show that pseudogenes tend to evolve toward: lower GC content, strong dinucleotide bias, reduced abundance of transcription factor binding motifs and short palindromes, and decreased ability to form nucleosomes. We explored possible evolutionary forces that shaped the evolution pattern of pseudogenes, and concluded that mutations in pseudogenes are likely determined, at least partially, by neighbor-dependent mutational bias and recombination-associated selection. PMID:27333782

  14. Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P)

    PubMed Central

    Brown, Justin T; Lahey, Cora; Laosinchai-Wolf, Walairat; Hadd, Andrew G

    2006-01-01

    Background Gaucher disease is a potentially severe lysosomal storage disorder caused by mutations in the human glucocerebrosidase gene (GBA). We have developed a multiplexed genetic assay for eight diseases prevalent in the Ashkenazi population: Tay-Sachs, Gaucher type I, Niemann-Pick types A and B, mucolipidosis type IV, familial dysautonomia, Canavan, Bloom syndrome, and Fanconi anemia type C. This assay includes an allelic determination for GBA allele c.1448T>C (L444P). The goal of this study was to clinically evaluate this assay. Methods Biotinylated, multiplex PCR products were directly hybridized to capture probes immobilized on fluorescently addressed microspheres. After incubation with streptavidin-conjugated fluorophore, the reactions were analyzed by Luminex IS100. Clinical evaluations were conducted using de-identified patient DNA samples. Results We evaluated a multiplexed suspension array assay that includes wild-type and mutant genetic determinations for Gaucher disease allele c.1448T>C. Two percent of samples reported to be wild-type by conventional methods were observed to be c.1448T>C heterozygous using our assay. Sequence analysis suggested that this phenomenon was due to co-amplification of the functional gene and a paralogous pseudogene (ΨGBA) due to a polymorphism in the primer-binding site of the latter. Primers for the amplification of this allele were then repositioned to span an upstream deletion in the pseudogene, yielding a much longer amplicon. Although it is widely reported that long amplicons negatively impact amplification or detection efficiency in recently adopted multiplex techniques, this assay design functioned properly and resolved the occurrence of false heterozygosity. Conclusion Although previously available sequence information suggested GBA gene/pseudogene discrimination capabilities with a short amplified product, we identified common single-nucleotide polymorphisms in the pseudogene that required amplification of a

  15. Differentially-Expressed Pseudogenes in HIV-1 Infection

    PubMed Central

    Gupta, Aditi; Brown, C. Titus; Zheng, Yong-Hui; Adami, Christoph

    2015-01-01

    Not all pseudogenes are transcriptionally silent as previously thought. Pseudogene transcripts, although not translated, contribute to the non-coding RNA pool of the cell that regulates the expression of other genes. Pseudogene transcripts can also directly compete with the parent gene transcripts for mRNA stability and other cell factors, modulating their expression levels. Tissue-specific and cancer-specific differential expression of these “functional” pseudogenes has been reported. To ascertain potential pseudogene:gene interactions in HIV-1 infection, we analyzed transcriptomes from infected and uninfected T-cells and found that 21 pseudogenes are differentially expressed in HIV-1 infection. This is interesting because parent genes of one-third of these differentially-expressed pseudogenes are implicated in HIV-1 life cycle, and parent genes of half of these pseudogenes are involved in different viral infections. Our bioinformatics analysis identifies candidate pseudogene:gene interactions that may be of significance in HIV-1 infection. Experimental validation of these interactions would establish that retroviruses exploit this newly-discovered layer of host gene expression regulation for their own benefit. PMID:26426037

  16. Characterization of pseudogenes in members of the order Frankineae.

    PubMed

    Sur, Saubashya; Saha, Sangita; Tisa, Louis S; Bothra, Asim K; Sen, Arnab

    2013-11-01

    Pseudogenes are defined as non-functional relatives of genes whose protein-coding abilities are lost and are no longer expressed within cells. They are an outcome of accumulation of mutations within a gene whose end product is not essential for survival. Proper investigation of the procedure of pseudogenization is relevant for estimating occurrence of duplications in genomes. Frankineae houses an interesting group of microorganisms, carving a niche in the microbial world. This study was undertaken with the objective of determining the abundance of pseudogenes, understanding strength of purifying selection, investigating evidence of pseudogene expression, and analysing their molecular nature, their origin, evolution and deterioration patterns amongst domain families. Investigation revealed the occurrence of 956 core pFAM families sharing common characteristics indicating co-evolution. WD40, Rve_3, DDE_Tnp_IS240 and phage integrase core domains are larger families, having more pseudogenes, signifying a probability of harmful foreign genes being disabled within transposable elements. High selective pressure depicted that gene families rapidly duplicating and evolving undoubtedly facilitated creation of a number of pseudogenes in Frankineae. Codon usage analysis between protein-coding genes and pseudogenes indicated a wide degree of variation with respect to different factors. Moreover, the majority of pseudogenes were under the effect of purifying selection. Frankineae pseudogenes were under stronger selective constraints, indicating that they were functional for a very long time and became pseudogenes abruptly. The origin and deterioration of pseudogenes has been attributed to selection and mutational pressure acting upon sequences for adapting to stressed soil environments. PMID:24287652

  17. Characterization of human pseudogene-derived non-coding RNAs for functional potential.

    PubMed

    Guo, Xingyi; Lin, Mingyan; Rockowitz, Shira; Lachman, Herbert M; Zheng, Deyou

    2014-01-01

    Thousands of pseudogenes exist in the human genome and many are transcribed, but their functional potential remains elusive and understudied. To explore these issues systematically, we first developed a computational pipeline to identify transcribed pseudogenes from RNA-Seq data. Applying the pipeline to datasets from 16 distinct normal human tissues identified ∼ 3,000 pseudogenes that could produce non-coding RNAs in a manner of low abundance but high tissue specificity under normal physiological conditions. Cross-tissue comparison revealed that the transcriptional profiles of pseudogenes and their parent genes showed mostly positive correlations, suggesting that pseudogene transcription could have a positive effect on the expression of their parent genes, perhaps by functioning as competing endogenous RNAs (ceRNAs), as previously suggested and demonstrated with the PTEN pseudogene, PTENP1. Our analysis of the ENCODE project data also found many transcriptionally active pseudogenes in the GM12878 and K562 cell lines; moreover, it showed that many human pseudogenes produced small RNAs (sRNAs) and some pseudogene-derived sRNAs, especially those from antisense strands, exhibited evidence of interfering with gene expression. Further integrated analysis of transcriptomics and epigenomics data, however, demonstrated that trimethylation of histone 3 at lysine 9 (H3K9me3), a posttranslational modification typically associated with gene repression and heterochromatin, was enriched at many transcribed pseudogenes in a transcription-level dependent manner in the two cell lines. The H3K9me3 enrichment was more prominent in pseudogenes that produced sRNAs at pseudogene loci and their adjacent regions, an observation further supported by the co-enrichment of SETDB1 (a H3K9 methyltransferase), suggesting that pseudogene sRNAs may have a role in regional chromatin repression. Taken together, our comprehensive and systematic characterization of pseudogene transcription uncovers

  18. Characterization of Human Pseudogene-Derived Non-Coding RNAs for Functional Potential

    PubMed Central

    Guo, Xingyi; Lin, Mingyan; Rockowitz, Shira; Lachman, Herbert M.; Zheng, Deyou

    2014-01-01

    Thousands of pseudogenes exist in the human genome and many are transcribed, but their functional potential remains elusive and understudied. To explore these issues systematically, we first developed a computational pipeline to identify transcribed pseudogenes from RNA-Seq data. Applying the pipeline to datasets from 16 distinct normal human tissues identified ∼3,000 pseudogenes that could produce non-coding RNAs in a manner of low abundance but high tissue specificity under normal physiological conditions. Cross-tissue comparison revealed that the transcriptional profiles of pseudogenes and their parent genes showed mostly positive correlations, suggesting that pseudogene transcription could have a positive effect on the expression of their parent genes, perhaps by functioning as competing endogenous RNAs (ceRNAs), as previously suggested and demonstrated with the PTEN pseudogene, PTENP1. Our analysis of the ENCODE project data also found many transcriptionally active pseudogenes in the GM12878 and K562 cell lines; moreover, it showed that many human pseudogenes produced small RNAs (sRNAs) and some pseudogene-derived sRNAs, especially those from antisense strands, exhibited evidence of interfering with gene expression. Further integrated analysis of transcriptomics and epigenomics data, however, demonstrated that trimethylation of histone 3 at lysine 9 (H3K9me3), a posttranslational modification typically associated with gene repression and heterochromatin, was enriched at many transcribed pseudogenes in a transcription-level dependent manner in the two cell lines. The H3K9me3 enrichment was more prominent in pseudogenes that produced sRNAs at pseudogene loci and their adjacent regions, an observation further supported by the co-enrichment of SETDB1 (a H3K9 methyltransferase), suggesting that pseudogene sRNAs may have a role in regional chromatin repression. Taken together, our comprehensive and systematic characterization of pseudogene transcription uncovers a

  19. Evolutionary pathway of pseudogenization of globin genes, α5 and β5, in genus Oryzias.

    PubMed

    Maruyama, Kouichi; Wang, Bing; Ishikawa, Yuji; Yasumasu, Shigeki; Iuchi, Ichiro

    2015-09-01

    Hemoglobin transports oxygen in many organisms and consists of α- and β-globin chains. Previously, using molecular phylogenetic analysis, we proposed that both α- and β-globins of teleost could be classified into four groups. We also showed that the Hd-rR strain of medaka (Oryzias latipes) inhabiting southern Japan had all four groups of globin genes but that the α- and β-globin genes of group III were pseudogenized (α5(ψα), β5(ψβ)). Based on the small degree of nucleotide variations, the pseudogenization of β5 was assumed to have occurred at a relatively late stage of evolution. Here, we compared the α5(ψα)-β5(ψβ) of two other strains of O. latipes and found that both α5(ψα) and β5(ψβ) of the northern Japanese and Korean strains were pseudogenized similar to those of Hd-rR. In a Philippine population (Oryzias luzonensis), α5(ψα) was also pseudogenized, but the structure was different from that of O. latipes, and β5(ψβ) was almost deleted. Interestingly, an Indonesian population (Oryzias celebensis) had α5 and β5 genes that were deduced to be functional. Indeed, they were expressed from the young to adult development stages, and this expression pattern was consistent with the expression of α2 and ad.α1 in Hd-rR. Because α2 and ad.α1 in Hd-rR were assigned to groups I and II, respectively, we speculate that their expression patterns might be altered by pseudogenization of group III genes. These results provide a basis for further investigations of recruiting and changing expression patterns of one globin gene after pseudogenization of other globin genes during evolution. PMID:26199047

  20. A novel Q378X mutation exists in the transmembrane transporter protein ABCC6 and its pseudogene: implications for mutation analysis in pseudoxanthoma elasticum.

    PubMed

    Cai, L; Lumsden, A; Guenther, U P; Neldner, S A; Zäch, S; Knoblauch, H; Ramesar, R; Hohl, D; Callen, D F; Neldner, K H; Lindpaintner, K; Richards, R I; Struk, B

    2001-09-01

    Pseudoxanthoma elasticum (PXE) is an inherited disorder of the elastic tissue with characteristic progressive calcification of elastic fibers in skin, eye, and the cardiovascular system. Recently mutations in the ABCC6 gene, encoding a transmembrane transporter protein, were identified as cause of the disease. Surprisingly, sequence and RFLP analysis for exon 9 with primers corresponding to flanking intronic sequence in diseased and haplotype negative members from all of our families and in a control population revealed either a homozygous or heterozygous state for the Q378X (1132C-->T) nonsense mutation in all individuals. With the publication of the genomic structure of the PXE locus we had identified the starting point of a large genomic segmental duplication within the locus in the cytogenetic interval defined by the Cy19 and Cy185 somatic cell hybrid breakpoints on chromosome 16p13.1. By means of somatic cell hybrid mapping we located this starting point telomeric to exon 10 of ABCC6. The duplication, however, does not include exon 10, but exons 1-9. These findings suggest that one or several copies of an ABCC6 pseudogene (psiABCC6) lie within this large segmental duplication. At least one copy contains exons 1-9 and maps to the chromosomal interval defined by the Cy163 and Cy11 breakpoints. Either this copy and/or an additional copy of psiABCC6 within Cy19-Cy183 carries the Q378X mutation that masks the correct identification of this nonsense mutation as being causative in pseudoxanthoma elasticum. Long-range PCR of exon 9 starting from sequence outside the genomic replication circumvents interference from the psiABCC6 DNA sequences and demonstrates that the Q378X mutation in the ABCC6 gene is associated with PXE in some families. These findings lead us to propose that gene conversion mechanisms from psiABCC6 to ABCC6 play a functional role in mutations causing PXE. PMID:11692167

  1. Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae).

    PubMed

    Mabuchi, Kohji; Miya, Masaki; Satoh, Takashi P; Westneat, Mark W; Nishida, Mutsumi

    2004-09-01

    Genomic size of animal mitochondrial DNA is usually minimized over time. Thus, when regional duplications occur, they are followed by a rapid elimination of redundant material. In contrast to this general view, we report here long-sustained tRNA pseudogenes in the mitochondrial genome (mitogenome) of teleost fishes of the family Scaridae (parrotfishes). During the course of a molecular phylogenetic study of the suborder Labroidei, we determined the complete nucleotide sequence of the mitogenome for a parrotfish, Chlorurus sordidus, and found a gene rearrangement accompanied by a tRNA pseudogene. In the typical gene order of vertebrates, a tRNA-gene cluster between ND1 and ND2 genes includes tRNA(Ile) (I), tRNA(Gln) (Q), and tRNA(Met) (M) genes in this order (IQM). However, in the mitogenome of the parrotfish, the tRNA(Met) gene was inserted between the tRNA(Ile) and the tRNA(Gln) genes, and the tRNA(Gln) gene was followed by a putative tRNA(Met) pseudogene (psiM). Such a tRNA gene rearrangement including a pseudogene (IMQpsiM) was found in all of the 10 examined species, representing 7 of the 10 currently recognized scarid genera. All sister groups examined (20 species of Labridae and a single species of Odacidae) had the typical gene order of vertebrate mitogenomes. Phylogenetic analysis of the tRNA(Met) genes and the resulting pseudogenes demonstrated that the ancestral tRNA(Met) gene was duplicated in a common ancestor of the parrotfish. Based on the fossil record, these results indicate that the pseudogenes have survived at least 14 million years. Most of the vertebrate mitochondrial gene rearrangements involving the IQM region have held the tRNA(Met) gene just upstream of the ND2 gene, and even in a few exceptional cases, including the present ones, the tRNA pseudogenes have been found in that position. In addition, most of these tRNA(Met) pseudogenes maintained clover-leaf secondary structures, with the remainder sustaining the clover-leaf structure in the

  2. Analysis of the CYP21A1P pseudogene: indication of mutational diversity and CYP21A2-like and duplicated CYP21A2 genes.

    PubMed

    Tsai, Li-Ping; Cheng, Ching-Feng; Chuang, Shu-Hua; Lee, Hsien-Hsiung

    2011-06-15

    The CYP21A1P gene downstream of the XA gene, carrying 15 deteriorated mutations, is a nonfunctional pseudogene that shares 98% nucleotide sequence homology with CYP21A2 located on chromosome 6p21.3. However, these mutations in the CYP21A1P gene are not totally involved in each individual. From our analysis of 100 healthy ethnic Chinese (i.e., Taiwanese) (n=200 chromosomes) using the polymerase chain reaction (PCR) products combined with an amplification-created restriction site (ACRS) method and DNA sequencing, we found that approximately 10% of CYP21A1P alleles (n=195 chromosomes) presented the CYP21A2 sequence; frequencies of P30, V281, Q318, and R356 in that locus were approximately 24%, 21%, 11%, and 34%, respectively, and approximately 90% of the CYP21A1P alleles had 15 mutated loci. In addition, approximately 2.5% (n=5 chromosomes) showed four haplotypes of the 3.7-kb TaqI-produced fragment of the CYP21A2-like gene and one duplicated CYP21A2 gene. We conclude that the pseudogene of the CYP21A1P mutation presents diverse variants. Moreover, the existence of the CYP21A2-like gene is more abundant than that of the duplicated CYP21A2 gene downstream of the XA gene and could not be distinguished from the CYP21A2-TNXB gene; thus, it may be misdiagnosed by previously established methods for congenital adrenal hyperplasia caused by a 21-hydroxylase deficiency. PMID:21324303

  3. A unique element resembling a processed pseudogene.

    PubMed

    Robins, A J; Wang, S W; Smith, T F; Wells, J R

    1986-01-01

    We describe a unique DNA element with structural features of a processed pseudogene but with important differences. It is located within an 8.4-kilobase pair region of chicken DNA containing five histone genes, but it is not related to these genes. The presence of terminal repeats, an open reading frame (and stop codon), polyadenylation/processing signal, and a poly(A) rich region about 20 bases 3' to this, together with a lack of 5' promoter motifs all suggest a processed pseudogene. However, no parent gene can be detected in the genome by Southern blotting experiments and, in addition, codon boundary values and mid-base correlations are not consistent with a protein coding region of a eukaryotic gene. The element was detected in DNA from different chickens and in peafowl, but not in quail, pheasant, or turkey. PMID:3941070

  4. HMGA1 pseudogenes as candidate proto-oncogenic competitive endogenous RNAs

    PubMed Central

    Esposito, Francesco; De Martino, Marco; Petti, Maria Grazia; Forzati, Floriana; Tornincasa, Mara; Federico, Antonella; Arra, Claudio; Pierantoni, Giovanna Maria; Fusco, Alfredo

    2014-01-01

    The High Mobility Group A (HMGA) are nuclear proteins that participate in the organization of nucleoprotein complexes involved in chromatin structure, replication and gene transcription. HMGA overexpression is a feature of human cancer and plays a causal role in cell transformation. Since non-coding RNAs and pseudogenes are now recognized to be important in physiology and disease, we investigated HMGA1 pseudogenes in cancer settings using bioinformatics analysis. Here we report the identification and characterization of two HMGA1 non-coding pseudogenes, HMGA1P6 and HMGA1P7. We show that their overexpression increases the levels of HMGA1 and other cancer-related proteins by inhibiting the suppression of their synthesis mediated by microRNAs. Consistently, embryonic fibroblasts from HMGA1P7-overexpressing transgenic mice displayed a higher growth rate and reduced susceptibility to senescence. Moreover, HMGA1P6 and HMGA1P7 were overexpressed in human anaplastic thyroid carcinomas, which are highly aggressive, but not in differentiated papillary carcinomas, which are less aggressive. Lastly, the expression of the HMGA1 pseudogenes was significantly correlated with HMGA1 protein levels thereby implicating HMGA1P overexpression in cancer progression. In conclusion, HMGA1P6 and HMGA1P7 are potential proto-oncogenic competitive endogenous RNAs. PMID:25268743

  5. [Peculiarities of phosphoglycerate kinase-1 pseudogene evolution in Schrenck salamander (Salamandrella schrenckii Strauch, 1870)].

    PubMed

    Malyarchuk, B A; Denisova, G A; Derenko, M V

    2013-07-01

    Processed copies of genes generally evolve in neutral mode as pseudogenes, however, some of them might be important sources of new functional genes. The psiPGK1 pseudogene has been discovered in Schrenck salamander (Salamandrella schrenckii, Amphibia, Caudata, Hynobiidae) via polymerase chain reaction used to amplify the phosphoglycerate kinase 1 gene (PGK1). This pseudogene is an intronless copy of PGK1 gene absent of exon 6. Analysis of psiPGK1 pseudogene polymorphism has demonstrated that it lacks mutations, which results in shifts in the stop codons and reading frames, as well as that the interspecies variation of this pseudogene was inconsistent with the neutral model of evolution. In addition, the pattern of phylogeographic differentiation of the psiPGK1 variants mainly coincides with that observed in mitochondrial DNA. These observations allow it to be suggested that the psiPGK1 pseudogene is a new functional gene in the Schrenck salamander. PMID:24450152

  6. Characterization of the multigene family encoding the mouse S16 ribosomal protein: strategy for distinguishing an expressed gene from its processed pseudogene counterparts by an analysis of total genomic DNA.

    PubMed Central

    Wagner, M; Perry, R P

    1985-01-01

    Two genes from the family encoding mouse ribosomal protein S16 were cloned, sequenced, and analyzed. One gene was found to be a processed pseudogene, i.e., a nonfunctional gene presumably derived from an mRNA intermediate. The other S16 gene contained introns and had exonic sequences identical to those of a cloned S16 cDNA. The expression of this gene was demonstrated by Northern blot analysis of nuclear poly(A)+ RNA with cDNA and unique sequence intron probes. Each S16 intron contains a well-preserved remnant of the TACTAAC motif, which is ubiquitous in yeast introns and known to play a critical role in intron splicing. A sequence comparison with two other mouse ribosomal protein genes analyzed in our laboratory, L30 and L32, revealed common structural features which might be involved in the control and coordination of ribosomal protein gene expression. These include the lack of a canonical TATA box in the -20 to -30 region and a remarkably similar 12-nucleotide pyrimidine sequence (CTTCCYTYYTC) that spans the cap site and is flanked by C + G-rich sequences. The nature of the other members of the S16 family was evaluated by three types of experiment: a DNase I sensitivity analysis to measure the extent of chromatin condensation; an analysis of the thermal stability of cDNA-gene hybrids to estimate the extent of divergence of each gene sequence from that of the expressed gene; and a restriction fragment analysis which distinguishes intron-containing genes from intronless processed genes. The results of these analyses show that all genes except the expressed S16 gene are in a condensed chromatin configuration associated with transcriptional quiescence; that most of the genes within the S16 family have sequences greater than 7% divergent from the expressed S16 gene; and that at least 7 of the 10 S16 genes lack introns. We conclude that the ribosomal protein S16 multigene family contains one expressed intron-containing gene and nine inactive pseudogenes, most or all

  7. Pseudogenes as an alternative source of natural antisense transcripts

    PubMed Central

    2010-01-01

    Background Naturally occurring antisense transcripts (NATs) are non-coding RNAs that may regulate the activity of sense transcripts to which they bind because of complementarity. NATs that are not located in the gene they regulate (trans-NATs) have better chances to evolve than cis-NATs, which is evident when the sense strand of the cis-NAT is part of a protein coding gene. However, the generation of a trans-NAT requires the formation of a relatively large region of complementarity to the gene it regulates. Results Pseudogene formation may be one evolutionary mechanism that generates trans-NATs to the parental gene. For example, this could occur if the parental gene is regulated by a cis-NAT that is copied as a trans-NAT in the pseudogene. To support this we identified human pseudogenes with a trans-NAT to the parental gene in their antisense strand by analysis of the database of expressed sequence tags (ESTs). We found that the mutations that appeared in these trans-NATs after the pseudogene formation do not show the flat distribution that would be expected in a non functional transcript. Instead, we found higher similarity to the parental gene in a region nearby the 3' end of the trans-NATs. Conclusions Our results do not imply a functional relation of the trans-NAT arising from pseudogenes over their respective parental genes but add evidence for it and stress the importance of duplication mechanisms of genetic material in the generation of non-coding RNAs. We also provide a plausible explanation for the large transcripts that can be found in the antisense strand of some pseudogenes. PMID:21047404

  8. Processed pseudogenes acquired somatically during cancer development.

    PubMed

    Cooke, Susanna L; Shlien, Adam; Marshall, John; Pipinikas, Christodoulos P; Martincorena, Inigo; Tubio, Jose M C; Li, Yilong; Menzies, Andrew; Mudie, Laura; Ramakrishna, Manasa; Yates, Lucy; Davies, Helen; Bolli, Niccolo; Bignell, Graham R; Tarpey, Patrick S; Behjati, Sam; Nik-Zainal, Serena; Papaemmanuil, Elli; Teixeira, Vitor H; Raine, Keiran; O'Meara, Sarah; Dodoran, Maryam S; Teague, Jon W; Butler, Adam P; Iacobuzio-Donahue, Christine; Santarius, Thomas; Grundy, Richard G; Malkin, David; Greaves, Mel; Munshi, Nikhil; Flanagan, Adrienne M; Bowtell, David; Martin, Sancha; Larsimont, Denis; Reis-Filho, Jorge S; Boussioutas, Alex; Taylor, Jack A; Hayes, Neil D; Janes, Sam M; Futreal, P Andrew; Stratton, Michael R; McDermott, Ultan; Campbell, Peter J

    2014-01-01

    Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5' truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context. PMID:24714652

  9. Processed pseudogenes acquired somatically during cancer development

    PubMed Central

    Cooke, Susanna L.; Shlien, Adam; Marshall, John; Pipinikas, Christodoulos P.; Martincorena, Inigo; Tubio, Jose M.C.; Li, Yilong; Menzies, Andrew; Mudie, Laura; Ramakrishna, Manasa; Yates, Lucy; Davies, Helen; Bolli, Niccolo; Bignell, Graham R.; Tarpey, Patrick S.; Behjati, Sam; Nik-Zainal, Serena; Papaemmanuil, Elli; Teixeira, Vitor H.; Raine, Keiran; O’Meara, Sarah; Dodoran, Maryam S.; Teague, Jon W.; Butler, Adam P.; Iacobuzio-Donahue, Christine; Santarius, Thomas; Grundy, Richard G.; Malkin, David; Greaves, Mel; Munshi, Nikhil; Flanagan, Adrienne M.; Bowtell, David; Martin, Sancha; Larsimont, Denis; Reis-Filho, Jorge S.; Boussioutas, Alex; Taylor, Jack A.; Hayes, Neil D.; Janes, Sam M.; Futreal, P. Andrew; Stratton, Michael R.; McDermott, Ultan; Campbell, Peter J.; Provenzano, Elena; van de Vijver, Marc; Richardson, Andrea L.; Purdie, Colin; Pinder, Sarah; Mac Grogan, Gaetan; Vincent-Salomon, Anne; Larsimont, Denis; Grabau, Dorthe; Sauer, Torill; Garred, Øystein; Ehinger, Anna; Van den Eynden, Gert G.; van Deurzen, C.H.M; Salgado, Roberto; Brock, Jane E.; Lakhani, Sunil R.; Giri, Dilip D.; Arnould, Laurent; Jacquemier, Jocelyne; Treilleux, Isabelle; Caldas, Carlos; Chin, Suet-Feung; Fatima, Aquila; Thompson, Alastair M.; Stenhouse, Alasdair; Foekens, John; Martens, John; Sieuwerts, Anieta; Brinkman, Arjen; Stunnenberg, Henk; Span, Paul N.; Sweep, Fred; Desmedt, Christine; Sotiriou, Christos; Thomas, Gilles; Broeks, Annegein; Langerod, Anita; Aparicio, Samuel; Simpson, Peter T.; van ’t Veer, Laura; Erla Eyfjörd, Jórunn; Hilmarsdottir, Holmfridur; Jonasson, Jon G.; Børresen-Dale, Anne-Lise; Lee, Ming Ta Michael; Wong, Bernice Huimin; Tan, Benita Kiat Tee; Hooijer, Gerrit K.J.

    2014-01-01

    Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5′ truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context. PMID:24714652

  10. Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome

    PubMed Central

    Milligan, Michael J.; Harvey, Erin; Yu, Albert; Morgan, Ashleigh L.; Smith, Daniela L.; Zhang, Eden; Berengut, Jonathan; Sivananthan, Jothini; Subramaniam, Radhini; Skoric, Aleksandra; Collins, Scott; Damski, Caio; Morris, Kevin V.; Lipovich, Leonard

    2016-01-01

    Pseudogenes are abundant in the human genome and had long been thought of purely as nonfunctional gene fossils. Recent observations point to a role for pseudogenes in regulating genes transcriptionally and post-transcriptionally in human cells. To computationally interrogate the network space of integrated pseudogene and long non-coding RNA regulation in the human transcriptome, we developed and implemented an algorithm to identify all long non-coding RNA (lncRNA) transcripts that overlap the genomic spans, and specifically the exons, of any human pseudogenes in either sense or antisense orientation. As inputs to our algorithm, we imported three public repositories of pseudogenes: GENCODE v17 (processed and unprocessed, Ensembl 72); Retroposed Pseudogenes V5 (processed only), and Yale Pseudo60 (processed and unprocessed, Ensembl 60); two public lncRNA catalogs: Broad Institute, GENCODE v17; NCBI annotated piRNAs; and NHGRI clinical variants. The data sets were retrieved from the UCSC Genome Database using the UCSC Table Browser. We identified 2277 loci containing exon-to-exon overlaps between pseudogenes, both processed and unprocessed, and long non-coding RNA genes. Of these loci we identified 1167 with Genbank EST and full-length cDNA support providing direct evidence of transcription on one or both strands with exon-to-exon overlaps. The analysis converged on 313 pseudogene-lncRNA exon-to-exon overlaps that were bidirectionally supported by both full-length cDNAs and ESTs. In the process of identifying transcribed pseudogenes, we generated a comprehensive, positionally non-redundant encyclopedia of human pseudogenes, drawing upon multiple, and formerly disparate public pseudogene repositories. Collectively, these observations suggest that pseudogenes are pervasively transcribed on both strands and are common drivers of gene regulation. PMID:27047535

  11. Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome.

    PubMed

    Milligan, Michael J; Harvey, Erin; Yu, Albert; Morgan, Ashleigh L; Smith, Daniela L; Zhang, Eden; Berengut, Jonathan; Sivananthan, Jothini; Subramaniam, Radhini; Skoric, Aleksandra; Collins, Scott; Damski, Caio; Morris, Kevin V; Lipovich, Leonard

    2016-01-01

    Pseudogenes are abundant in the human genome and had long been thought of purely as nonfunctional gene fossils. Recent observations point to a role for pseudogenes in regulating genes transcriptionally and post-transcriptionally in human cells. To computationally interrogate the network space of integrated pseudogene and long non-coding RNA regulation in the human transcriptome, we developed and implemented an algorithm to identify all long non-coding RNA (lncRNA) transcripts that overlap the genomic spans, and specifically the exons, of any human pseudogenes in either sense or antisense orientation. As inputs to our algorithm, we imported three public repositories of pseudogenes: GENCODE v17 (processed and unprocessed, Ensembl 72); Retroposed Pseudogenes V5 (processed only), and Yale Pseudo60 (processed and unprocessed, Ensembl 60); two public lncRNA catalogs: Broad Institute, GENCODE v17; NCBI annotated piRNAs; and NHGRI clinical variants. The data sets were retrieved from the UCSC Genome Database using the UCSC Table Browser. We identified 2277 loci containing exon-to-exon overlaps between pseudogenes, both processed and unprocessed, and long non-coding RNA genes. Of these loci we identified 1167 with Genbank EST and full-length cDNA support providing direct evidence of transcription on one or both strands with exon-to-exon overlaps. The analysis converged on 313 pseudogene-lncRNA exon-to-exon overlaps that were bidirectionally supported by both full-length cDNAs and ESTs. In the process of identifying transcribed pseudogenes, we generated a comprehensive, positionally non-redundant encyclopedia of human pseudogenes, drawing upon multiple, and formerly disparate public pseudogene repositories. Collectively, these observations suggest that pseudogenes are pervasively transcribed on both strands and are common drivers of gene regulation. PMID:27047535

  12. Differential Expression of OCT4 Pseudogenes in Pluripotent and Tumor Cell Lines

    PubMed Central

    Poursani, Ensieh M.; Mohammad Soltani, Bahram; Mowla, Seyed Javad

    2016-01-01

    Objective The human OCT4 gene, the most important pluripotency marker, can generate at least three different transcripts (OCT4A, OCT4B, and OCT4B1) by alternative splicing. OCT4A is the main isoform responsible for the stemness property of embryonic stem (ES) cells. There also exist eight processed OCT4 pseudogenes in the human genome with high homology to the OCT4A, some of which are transcribed in various cancers. Recent conflicting reports on OCT4 expression in tumor cells and tissues emphasize the need to discriminate the expression of OCT4A from other variants as well as OCT4 pseudogenes. Materials and Methods In this experimental study, DNA sequencing confirmed the authenticity of transcripts of OCT4 pseudogenes and their expression patterns were investigated in a panel of different human cell lines by reverse transcription-polymerase chain reaction (RT-PCR). Results Differential expression of OCT4 pseudogenes in various human cancer and pluripotent cell lines was observed. Moreover, the expression pattern of OCT4-pseudogene 3 (OCT4-pg3) followed that of OCT4A during neural differentiation of the pluripotent cell line of NTERA-2 (NT2). Although OCT4-pg3 was highly expressed in undifferentiated NT2 cells, its expression was rapidly down-regulated upon induction of neural differentiation. Analysis of protein expression of OCT4A, OCT4-pg1, OCT4-pg3, and OCT4-pg4 by Western blotting indicated that OCT4 pseudogenes cannot produce stable proteins. Consistent with a newly proposed competitive role of pseudogene microRNA docking sites, we detected miR-145 binding sites on all transcripts of OCT4 and OCT4 pseudogenes. Conclusion Our study suggests a potential coding-independent function for OCT4 pseudogenes during differentiation or tumorigenesis. PMID:27054116

  13. Mycobacterium leprae: genes, pseudogenes and genetic diversity

    PubMed Central

    Singh, Pushpendra; Cole, Stewart T

    2011-01-01

    Leprosy, which has afflicted human populations for millenia, results from infection with Mycobacterium leprae, an unculturable pathogen with an exceptionally long generation time. Considerable insight into the biology and drug resistance of the leprosy bacillus has been obtained from genomics. M. leprae has undergone reductive evolution and pseudogenes now occupy half of its genome. Comparative genomics of four different strains revealed remarkable conservation of the genome (99.995% identity) yet uncovered 215 polymorphic sites, mainly single nucleotide polymorphisms, and a handful of new pseudogenes. Mapping these polymorphisms in a large panel of strains defined 16 single nucleotide polymorphism-subtypes that showed strong geographical associations and helped retrace the evolution of M. leprae. PMID:21162636

  14. The IL-9 receptor gene (IL9R): Genomic structure, chromosomal localization in the pseudoautosomal region of the long arm of sex chromosomes, and identification of IL9R pseudogenes at 9qter, 10pter, 16pter, 18pter

    SciTech Connect

    Kermouni, A.; Godelaine, D.; Lurquin, C.; Szikora, J.P.

    1995-09-20

    Cosmids containing the human IL-9 receptor (R) gene (IL9R) have been isolated from a genomic library using the IL9R cDNA as a probe. We have shown that the human IL9R gene is composed of 11 exons and 10 introns, stretching over {approx} 17 kb, and is located within the pseudoautosomal region of the Xq and Yq chromosome, in the vicinity of the telomere. Analysis of the 5` flanking region revealed multiple transcription initiation sites as well as potential binding motifs for AP1, AP2, AP3, Sp1, and NF-kB, although this region lacks a TATA box. Using the human IL9R cosmid as a probe to perform fluorescence in situ hybridization, additional signals were identified in the subtelomeric regions of chromosomes 9q, 10p, 16p, and 18p. IL9R homologs located on chromosomes 9 and 18 were partially characterized, while those located on chromosomes 16 and 10 were completely sequenced. Although they are similiar to the IL9R gene ({approx} 90% identity), none of these copies encodes a functional receptor: none of them contains sequences homologous to the 5` flanking region or exon 1 of the IL9R gene, and the remaining ORFs have been inactivated by various point mutations and deletions. Taken together, our results indicate that the IL9R gene is located at Xq28 and Yq12, in the long arm pseudoautosomal region, and that four IL9R pseudogenes are located on 9q34, 10p15, 16p13.3 and 18p11.3, probably dispersed as the result of translocations during evolution. 42 refs., 6 figs., 3 tabs.

  15. How Many Processed Pseudogenes Are Accumulated in a Gene Family?

    PubMed Central

    Walsh, James Bruce

    1985-01-01

    A simple kinetic model is developed that describes the accumulation of processed pseudogenes in a functional gene family. Insertion of new pseudogenes occurs at rate ν per gene and is countered by spontaneous deletion (at rate δ per DNA segment) of segments containing processed pseudogenes. If there are k functional genes in a gene family, the equilibrium number of processed pseudogenes is k(ν/δ), and the percentage of functional genes in the gene family at equilibrium is 1/[1 + (ν/δ)]. ν/δ values estimated for five gene families ranged from 1.7 to 15. This fairly narrow range suggests that the rates of formation and deletion of processed pseudogenes may be positively correlated for these families. If δ is sufficiently large relative to the per nucleotide mutation rate µ (δ > 20µ), processed pseudogenes will show high homology with each other, even in the absence of gene conversion between pseudogenes. We argue that formation of processed pseudogenes may share common pathways with transposable elements and retroviruses, creating the potential for correlated responses in the evolution of processed pseudogenes due to direct selection for control of transposable elements and/or retroviruses. Finally, we discuss the nature of the selective forces that may act directly or indirectly to influence the evolution of processed pseudogenes. Anything produced by evolution is bound to be a bit of a mess—S. Brenner PMID:2408963

  16. Pseudogene-free amplification of HPRT1 in quantitative reverse transcriptase polymerase chain reaction.

    PubMed

    Valadan, Reza; Amjadi, Omolbanin; Tehrani, Mohsen; Rafiei, Alireza; Hedayatizadeh-Omran, Akbar; Alizadeh-Navaei, Reza

    2015-09-15

    Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) provides a powerful tool for precise gene expression analysis. The accuracy of the results highly depends on careful selection of a reference gene for data normalization. HPRT1 (hypoxanthine phosphoribosyl transferase 1) is a frequently used housekeeping gene for normalizing relative expression values. However, the existence of processed pseudogenes for HPRT1 might interfere with reliable results obtained in qRT-PCR due to amplification of unintended products. Here, we designed a primer pair for pseudogene-free amplification of HPRT1 in qRT-PCR. We demonstrate that this primer pair specifically amplified HPRT1 messenger RNA (mRNA) sequence while avoiding coamplification of the pseudogenes. PMID:26050630

  17. A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease

    PubMed Central

    Zuriaga, María Angeles; Mas-Coma, Santiago; Bargues, María Dolores

    2015-01-01

    A pseudogene, designated as "ps(5.8S+ITS-2)", paralogous to the 5.8S gene and internal transcribed spacer (ITS)-2 of the nuclear ribosomal DNA (rDNA), has been recently found in many triatomine species distributed throughout North America, Central America and northern South America. Among characteristics used as criteria for pseudogene verification, secondary structures and free energy are highlighted, showing a lower fit between minimum free energy, partition function and centroid structures, although in given cases the fit only appeared to be slightly lower. The unique characteristics of "ps(5.8S+ITS-2)" as a processed or retrotransposed pseudogenic unit of the ghost type are reviewed, with emphasis on its potential functionality compared to the functionality of genes and spacers of the normal rDNA operon. Besides the technical problem of the risk for erroneous sequence results, the usefulness of "ps(5.8S+ITS-2)" for specimen classification, phylogenetic analyses and systematic/taxonomic studies should be highlighted, based on consistence and retention index values, which in pseudogenic sequence trees were higher than in functional sequence trees. Additionally, intraindividual, interpopulational and interspecific differences in pseudogene amount and the fact that it is a pseudogene in the nuclear rDNA suggests a potential relationships with fitness, behaviour and adaptability of triatomine vectors and consequently its potential utility in Chagas disease epidemiology and control. PMID:25760450

  18. The cotton-top tamarin (Saguinus oedipus) has five beta-microseminoprotein genes, two of which are pseudogenes.

    PubMed

    Valtonen-André, Camilla; Lundwall, Ake

    2008-01-01

    beta-Microseminoprotein (MSP) is one of the most abundant proteins in human seminal plasma and is secreted from the prostate gland. Its evolution can be traced from primates down to nonvertebrate species such as amphioxus, despite substantial differences in the primary structure. Most mammals are known to have one single MSP gene, but we have previously shown that the cotton-top tamarin and the common marmoset-two New World monkeys-carry several MSP genes. In this study we continue our characterization of MSP genes in the cotton-top tamarin by presenting the full nucleotide sequence of the three previously identified genes, mspA, mspE, and mspJ. A promoter analysis using the luciferase reporter showed that mspE is as transcriptionally active as the single human MSP gene, whereas mspA and mspJ display no activity with this assay. Two novel MSP genes were also identified, mspB and mspH, both of which are pseudogenes. MspB has a frameshift mutation in the third exon resulting in a new C-terminus and premature stop of translation. MspH has the features of a processed pseudogene, originating from a transcript of mspE. It is integrated into the genome together with another processed pseudogene originating from a transcript of the nucleoporin gene NUP88. The MSP genes described in this study probably arose by phylogenetically rather late duplication or retrotransposition, suggesting that they are confined to a limited number of New World monkeys. PMID:18020964

  19. Not so pseudo anymore: pseudogenes as therapeutic targets

    PubMed Central

    Roberts, Thomas C; Morris, Kevin V

    2014-01-01

    Pseudogenes are junk DNA gene remnants generated by inactivating mutations or the loss of regulatory sequences, often following gene duplication or retrotransposition events. These pseudogenes have previously been considered to be molecular fossils derived from once-coding genes. In many cases, pseudogenes confer no observable selective advantage to the host organism and may be on a path towards removal from the genome. However, pseudogenes can also serve as raw material for the exaptation of novel functions, particularly in relation to the regulation of gene expression. Many pseudogenes are resurrected as noncoding RNA genes, which function in RNA-based gene regulatory circuits. As such, functional pseudogenes might simply be considered as ‘genes’. Here, we discuss the role of these pseudogene-derived RNAs as regulators of gene expression in the context of human disease. In particular, we consider the manipulation of pseudogene transcripts through the use of antisense oligonucleotides, siRNAs, aptamers or classical gene therapy approaches as novel pharmacological strategies. PMID:24279857

  20. The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons.

    PubMed

    Muro, Enrique M; Mah, Nancy; Moreno-Hagelsieb, Gabriel; Andrade-Navarro, Miguel A

    2011-03-01

    Almost 50 years following the discovery of the prokaryotic operon, the functional relevance of gene order within operons remains unclear. In this work, we take advantage of the eroded genome of Mycobacterium leprae to add evidence supporting the notion that functionally less important genes have a tendency to be located at the end of its operons. M. leprae's genome includes 1133 pseudogenes and 1614 protein-coding genes and can be compared with the close genome of M. tuberculosis. Assuming M. leprae's pseudogenes to represent dispensable genes, we have studied the position of these pseudogenes in the operons of M. leprae and of their orthologs in M. tuberculosis. We observed that both tend to be located in the 3' (downstream) half of the operon (P-values of 0.03 and 0.18, respectively). Analysis of pseudogenes in all available prokaryotic genomes confirms this trend (P-value of 7.1 × 10(-7)). In a complementary analysis, we found a significant tendency for essential genes to be located at the 5' (upstream) half of the operon (P-value of 0.006). Our work provides an indication that, in prokarya, functionally less important genes have a tendency to be located at the end of operons, while more relevant genes tend to be located toward operon starts. PMID:21051341

  1. The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons

    PubMed Central

    Muro, Enrique M.; Mah, Nancy; Moreno-Hagelsieb, Gabriel; Andrade-Navarro, Miguel A.

    2011-01-01

    Almost 50 years following the discovery of the prokaryotic operon, the functional relevance of gene order within operons remains unclear. In this work, we take advantage of the eroded genome of Mycobacterium leprae to add evidence supporting the notion that functionally less important genes have a tendency to be located at the end of its operons. M. leprae’s genome includes 1133 pseudogenes and 1614 protein-coding genes and can be compared with the close genome of M. tuberculosis. Assuming M. leprae’s pseudogenes to represent dispensable genes, we have studied the position of these pseudogenes in the operons of M. leprae and of their orthologs in M. tuberculosis. We observed that both tend to be located in the 3′ (downstream) half of the operon (P-values of 0.03 and 0.18, respectively). Analysis of pseudogenes in all available prokaryotic genomes confirms this trend (P-value of 7.1 × 10−7). In a complementary analysis, we found a significant tendency for essential genes to be located at the 5′ (upstream) half of the operon (P-value of 0.006). Our work provides an indication that, in prokarya, functionally less important genes have a tendency to be located at the end of operons, while more relevant genes tend to be located toward operon starts. PMID:21051341

  2. Structural Analysis

    NASA Technical Reports Server (NTRS)

    1991-01-01

    After an 800-foot-tall offshore oil recovery platform collapsed, the engineers at Engineering Dynamics, Inc., Kenner, LA, needed to learn the cause of the collapse, and analyze the proposed repairs. They used STAGSC-1, a NASA structural analysis program with geometric and nonlinear buckling analysis. The program allowed engineers to determine the deflected and buckling shapes of the structural elements. They could then view the proposed repairs under the pressure that caused the original collapse.

  3. Functional evidence of post-transcriptional regulation by pseudogenes.

    PubMed

    Muro, Enrique M; Mah, Nancy; Andrade-Navarro, Miguel A

    2011-11-01

    Pseudogenes have been mainly considered as functionless evolutionary relics since their discovery in 1977. However, multiple mechanisms of pseudogene functionality have been proposed both at the transcriptional and post-transcriptional level. This review focuses on the role of pseudogenes as post-transcriptional regulators. Two lines of research have recently presented strong evidence of their potential function as post-transcriptional regulators of the corresponding parental genes from which they originate. First, pseudogene genomic sequences can encode siRNAs. Second, pseudogene transcripts can act as indirect post-transcriptional regulators decoying ncRNA, in particular miRNAs that target the parental gene. This has been demonstrated for PTEN and KRAS, two genes involved in tumorigenesis. The role of pseudogenes in disease has not been proven and seems to be the next research landmark. In this review, we chronicle the events following the initial discovery of the 'useless' pseudogene to its breakthrough as a functional molecule with hitherto unbeknownst potential to influence human disease. PMID:21816204

  4. The human serotonin-7 receptor pseudogene: variation and chromosome location.

    PubMed Central

    Nam, D; Qian, I H; Kusumi, I; Ulpian, C; Tallerico, T; Liu, I S; Seeman, P

    1998-01-01

    We report a variation of the pseudogene for the serotonin-7 receptor in human DNA. Human genomic DNA was amplified, using the polymerase chain reaction method and degenerate oligonucleotide primers for serotonin receptor-like genes. A novel gene DNA sequence of 1325 bp was found. Based on nucleotides, this gene is 88% identical to the serotonin-7 receptor coding sequence. Compared with the previously known serotonin-7 receptor pseudogene, this pseudogene has 1 nucleotide deletion and 4 nucleotide mutations. The gene is located on human chromosome 12 at 12p12.3-p13.2. Images Fig. 1A PMID:9785699

  5. Pseudogene-expressed RNAs: a new frontier in cancers.

    PubMed

    Shi, Xuefei; Nie, Fengqi; Wang, Zhaoxia; Sun, Ming

    2016-02-01

    Over the past decade, the importance of non-protein-coding functional elements in the human genome has emerged from the water and been identified as a key revelation in post-genomic biology. Since the completion of the ENCODE (Encyclopedia of DNA Elements) and FANTOM (Functional Annotation of Mammals) project, tens of thousands of pseudogenes as well as numerous long non-coding RNA (lncRNA) genes were identified. However, while pseudogenes were initially regarded as non-functional relics littering the human genome during evolution, recent studies have revealed that they play critical roles at multiple levels in diverse physiological and pathological processes, especially in cancer through parental-gene-dependent or parental-gene-independent regulation. Herein, we review the current knowledge of pseudogenes and synthesize the nascent evidence for functional properties and regulatory modalities exerted by pseudogene-transcribed RNAs in human cancers and prospect the potential as molecular signatures in cancer reclassification and tailored therapy. PMID:26662308

  6. Genome-wide survey for biologically functional pseudogenes.

    PubMed

    Svensson, Orjan; Arvestad, Lars; Lagergren, Jens

    2006-05-01

    According to current estimates there exist about 20,000 pseudogenes in a mammalian genome. The vast majority of these are disabled and nonfunctional copies of protein-coding genes which, therefore, evolve neutrally. Recent findings that a Makorin1 pseudogene, residing on mouse Chromosome 5, is, indeed, in vivo vital and also evolutionarily preserved, encouraged us to conduct a genome-wide survey for other functional pseudogenes in human, mouse, and chimpanzee. We identify to our knowledge the first examples of conserved pseudogenes common to human and mouse, originating from one duplication predating the human-mouse species split and having evolved as pseudogenes since the species split. Functionality is one possible way to explain the apparently contradictory properties of such pseudogene pairs, i.e., high conservation and ancient origin. The hypothesis of functionality is tested by comparing expression evidence and synteny of the candidates with proper test sets. The tests suggest potential biological function. Our candidate set includes a small set of long-lived pseudogenes whose unknown potential function is retained since before the human-mouse species split, and also a larger group of primate-specific ones found from human-chimpanzee searches. Two processed sequences are notable, their conservation since the human-mouse split being as high as most protein-coding genes; one is derived from the protein Ataxin 7-like 3 (ATX7NL3), and one from the Spinocerebellar ataxia type 1 protein (ATX1). Our approach is comparative and can be applied to any pair of species. It is implemented by a semi-automated pipeline based on cross-species BLAST comparisons and maximum-likelihood phylogeny estimations. To separate pseudogenes from protein-coding genes, we use standard methods, utilizing in-frame disablements, as well as a probabilistic filter based on Ka/Ks ratios. PMID:16680195

  7. Processed Pseudogene Confounding Deletion/Duplication Assays for SMAD4.

    PubMed

    Millson, Alison; Lewis, Tracey; Pesaran, Tina; Salvador, David; Gillespie, Katrina; Gau, Chia-Ling; Pont-Kingdon, Genevieve; Lyon, Elaine; Bayrak-Toydemir, Pinar

    2015-09-01

    Mutations in SMAD4 have been associated with juvenile polyposis syndrome and combined juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome. SMAD4 is part of the SMAD gene family. To date, there has been no report in the literature of a SMAD4 pseudogene. An unusual SMAD4 duplication pattern was seen in multiple patient samples using two different duplication/deletion platforms: multiplex ligation-dependent probe amplification and chromosomal microarray. Follow-up confirmatory testing included real-time quantitative PCR and sequencing of an exon/exon junction, all results leading to the conclusion of the existence of a processed pseudogene. Examination of clinical results from two laboratories found a frequency of 0.26% (12 in 4672 cases) for this processed pseudogene. This is the first report of the presence of a processed pseudogene for SMAD4. We believe that knowledge of its existence is important for accurate interpretation of clinical diagnostic test results and for new assay designs. This study also indicates how a processed pseudogene may confound quantitative results, dependent on placement of probes and/or primers in a particular assay design, potentially leading to both false-positive and false-negative results. We also found that the SMAD4 processed pseudogene affects next-generation sequencing results by confounding the alignment of the sequences, resulting in erroneous variant calls. We recommend Sanger sequencing confirmation for SMAD4 variants. PMID:26165824

  8. Pseudogene-Expressed RNAs: Emerging Roles in Gene Regulation and Disease.

    PubMed

    Grandér, Dan; Johnsson, Per

    2016-01-01

    Pseudogenes have for long been considered as non-functional relics littering the human genome. Only now, it is becoming apparent that many pseudogenes are transcribed into long noncoding RNAs, some with proven biological functions. Here, we review the current knowledge of pseudogenes and their widespread functional properties with an emphasis on pseudogenes that have been functionally investigated in greater detail. Pseudogenes are emerging as a novel class of long noncoding RNAs functioning, for example, through microRNA sponging and chromatin remodeling. The examples discussed herein underline that pseudogene-encoded RNAs are important regulatory molecules involved in diseases such as cancer. PMID:25982975

  9. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

    PubMed Central

    Poliseno, Laura; Salmena, Leonardo; Zhang, Jiangwen; Carver, Brett; Haveman, William J.; Pandolfi, Pier Paolo

    2011-01-01

    The canonical role of messenger RNA (mRNA) is to deliver protein-coding information to sites of protein synthesis. However, given that microRNAs bind to RNAs, we hypothesized that RNAs possess a biological role in cancer cells that relies upon their ability to compete for microRNA binding and is independent of their protein-coding function. As a paradigm for the protein-coding-independent role of RNAs, we describe the functional relationship between the mRNAs produced by the PTEN tumour suppressor gene and its pseudogene (PTENP1) and the critical consequences of this interaction. We find that PTENP1 is biologically active as determined by its ability to regulate cellular levels of PTEN, and that it can exert a growth-suppressive role. We also show that PTENP1 locus is selectively lost in human cancer. We extend our analysis to other cancer-related genes that possess pseudogenes, such as oncogenic KRAS. Further, we demonstrate that the transcripts of protein coding genes such as PTEN are also biologically active. Together, these findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs. PMID:20577206

  10. Data supporting the design and evaluation of a universal primer pair for pseudogene-free amplification of HPRT1 in real-time PCR

    PubMed Central

    Valadan, Reza; Hedayatizadeh-Omran, Akbar; Alhosseini-Abyazani, Mahdyieh Naghavi; Amjadi, Omolbanin; Rafiei, Alireza; Tehrani, Mohsen; Alizadeh-Navaei, Reza

    2015-01-01

    Hypoxanthine-guanine phosphoribosyltransferase 1 (HPRT1) is a common housekeeping gene for sample normalization in the quantitative reverse transcriptase polymerase chain (qRT-PCR). However, co-amplification of HPRT1 pseudogenes may affect accurate results obtained in qRT-PCR. We designed a primer pair (HPSF) for pseudogene-free amplification of HPRT1 in qRT-PCR [1]. We showed specific amplification of HPRT1 mRNA in some common laboratory cell lines, including HeLa, NIH/3T3, CHO, BHK, COS-7 and VERO. This article provides data supporting the presence and location of HPRT1 pseudogenes within human and mouse genome, and the strategies used for designing primers that avoid the co-amplification of contaminating pseudogenes in qRT-PCR. In silico analysis of human genome showed three homologous sequences for HPRT1 on chromosomes 4, 5 and 11. The mRNA sequence of HPRT1 was aligned with the pseudogenes, and the primers were designed toward 5′ end of HPRT1 mRNA that was only specific to HPRT1 mRNA not to the pseudogenes. The standard curve plot generated by HPSF primers showed the correlation coefficient of 0.999 and the reaction efficiency of 99.5%. Our findings suggest that HPSF primers can be recommended as a candidate primer pair for accurate and reproducible qRT-PCR assays. PMID:26217821

  11. Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma.

    PubMed

    Chan, Wen-Ling; Yuo, Chung-Yee; Yang, Wen-Kuang; Hung, Shih-Ya; Chang, Ya-Sian; Chiu, Chien-Chih; Yeh, Kun-Tu; Huang, Hsien-Da; Chang, Jan-Gowth

    2013-04-01

    Pseudogenes, especially those that are transcribed, may not be mere genomic fossils, but their biological significance remains unclear. Postulating that in the human genome, as in animal models, pseudogenes may function as gene regulators through generation of endo-siRNAs (esiRNAs), antisense RNAs or RNA decoys, we performed bioinformatic and subsequent experimental tests to explore esiRNA-mediated mechanisms of pseudogene involvement in oncogenesis. A genome-wide survey revealed a partial retrotranscript pseudogene ψPPM1K containing inverted repeats capable of folding into hairpin structures that can be processed into two esiRNAs; these esiRNAs potentially target many cellular genes, including NEK8. In 41 paired surgical specimens, we found significantly reduced expression of two predicted ψPPM1K-specific esiRNAs, and the cognate gene PPM1K, in hepatocellular carcinoma compared with matched non-tumour tissues, whereas the expression of target gene NEK8 was increased in tumours. Additionally, NEK8 and PPM1K were downregulated in stably transfected ψPPM1K-overexpressing cells, but not in cells transfected with an esiRNA1-deletion mutant of ψPPM1K. Furthermore, expression of NEK8 in ψPPM1K-transfected cells demonstrated that NEK8 can counteract the growth inhibitory effects of ψPPM1K. These findings indicate that a transcribed pseudogene can exert tumour-suppressor activity independent of its parental gene by generation of esiRNAs that regulate human cell growth. PMID:23376929

  12. Progressive pseudogenization: vitamin C synthesis and its loss in bats.

    PubMed

    Cui, Jie; Pan, Yi-Hsuan; Zhang, Yijian; Jones, Gareth; Zhang, Shuyi

    2011-02-01

    For the past 50 years, it was believed that all bats, like humans and guinea pigs, did not synthesize vitamin C (Vc) because they lacked activity of L-gulonolactone oxidase (GULO) in their livers. Humans and guinea pigs lack the activity due to pseudogenization of GULO in their genomes, but there is no genetic evidence to show whether such loss in bats is caused by pseudogenization. Unexpectedly, our successful molecular cloning in one frugivorous bat (Rousettus leschenaultii) and one insectivorous bat (Hipposideros armiger) ascertains that no pseudogenization occurs in these species. Furthermore, we find normal GULO protein expression using bat-specific anti-GULO polyclonal antibodies in bats, evaluated by Western blotting. Most surprisingly, GULO activity assays reveal that these two bat species have retained the ability to synthesize Vc, but at low levels compared with the mouse. It is known that bats in the genus Pteropus have lost GULO activity. We then found that functional constraints acting on the GULO of Pteropus vampyrus (which lost its function) are relaxed. These results imply that the ability to synthesize Vc in bats has not been lost completely in species as previously thought. We also suggest that the evolution of bat GULO genes can be a good model to study genetic processes associated with loss-of-function. PMID:21037206

  13. The emerging role of pseudogene expressed non-coding RNAs in cellular functions

    PubMed Central

    Groen, Jessica N.; Capraro, David; Morris, Kevin V.

    2014-01-01

    A paradigm shift is sweeping modern day molecular biology following the realisation that large amounts of “junk” DNA”, thought initially to be evolutionary remnants, may actually be functional. Several recent studies support a functional role for pseudogene-expressed non-coding RNAs in regulating their protein-coding counterparts. Several hundreds of pseudogenes have been reported as transcribed into RNA in a large variety of tissues and tumours. Most studies have focused on pseudogenes expressed in the sense direction, but some reports suggest that pseudogenes can also be transcribed as antisense RNAs (asRNAs). A few examples of key regulatory genes, such as PTEN and OCT4, have in fact been reported to be under the regulation of pseudogene-expressed asRNAs. Here, we review what are known about pseudogene expressed non-coding RNA mediated gene regulation and their roles in the control of epigenetic states. PMID:24842102

  14. The major and minor chicken vitellogenin genes are each adjacent to partially deleted pseudogene copies of the other.

    PubMed Central

    Silva, R; Fischer, A H; Burch, J B

    1989-01-01

    The major chicken vitellogenin gene (VTGII) has previously been cloned and sequenced. We now report the isolation of genomic clones that encompass a minor chicken vitellogenin gene (VTGIII) which is also expressed in the liver in response to estradiol. Our analysis reveals that a pseudogene for VTGII (psi VTGII) lies 1,426 base pairs upstream of this VTGIII gene. A reevaluation of published sequence data reveals that the converse is also true, namely, that a pseudogene for VTGIII (psi VTGIII) lies 1,345 base pairs downstream of the VTGII gene. Our results show that a 335-base-pair deletion has removed the psi VTGIII promoter and cap site but left residual estrogen response element in a region where nuclease-hypersensitive sites have been reported to be induced in response to estradiol. Images PMID:2796998

  15. Genome-Wide Survey of Pseudogenes in 80 Fully Re-sequenced Arabidopsis thaliana Accessions

    PubMed Central

    Yao, Yongfang; Tian, Dacheng; Araki, Hitoshi; Yang, Sihai

    2012-01-01

    Pseudogenes (Ψs), including processed and non-processed Ψs, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life. However, systematic surveys of non-processed Ψs utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of Ψs within 80 fully re-sequenced Arabidopsis thaliana accessions, and 7546 genes, representing ∼28% of the genomic annotated open reading frames (ORFs), were found with disruptive mutations in at least one accession. The distribution of these Ψs on chromosomes showed a significantly negative correlation between Ψs/ORFs and their local gene densities, suggesting a higher proportion of Ψs in gene desert regions, e.g. near centromeres. On the other hand, compared with the non-Ψ loci, even the intact coding sequences (CDSs) in the Ψ loci were found to have shorter CDS length, fewer exon number and lower GC content. In addition, a significant functional bias against the null hypothesis was detected in the Ψs mainly involved in responses to environmental stimuli and biotic stress as reported, suggesting that they are likely important for adaptive evolution to rapidly changing environments by pseudogenization to accumulate successive mutations. PMID:23272162

  16. Multiple human D sub 5 dopamine receptor genes: A functional receptor and two pseudogenes

    SciTech Connect

    Grandy, D.K.; Yuan Zhang; Bouvier, C.; Qunyong Zhou; Johnson, R.A.; Allen, L.; Buck, K.; Bunzow, J.R.; Salon, J.; Civelli, O. )

    1991-10-15

    Three genes closely related to the D{sub 1} dopamine receptor were identified in the human genome. One of the genes lacks introns and encodes a functional human dopamine receptor, D{sub 5}, whose deduced amino acid sequence is 49% identical to that of the human D{sub 1} receptor. Compared with the human D{sub 1} dopamine receptor, the D{sub 5} receptor displayed a higher affinity for dopamine and was able to stimulate a biphasic rather than a monophasic intracellular accumulation of cAMP. Neither of the other two genes was able to direct the synthesis of a receptor. nucleotide sequence analysis revealed that these two genes are 98% identical to each other and 95% identical to the D{sub 5} sequence. Relative to the D{sub 5} sequence, both contain insertions and deletions that result in several in-frame termination codons. Premature termination of translation is the most likely explanation for the failure of these genes to produce receptors in COS-7 and 293 cells even though their messages are transcribed. The authors conclude that the two are pseudogenes. Blot hybridization experiments performed on rat genomic DNA suggest that there is one D{sub 5} gene in this species and that the pseudogenes may be the result of a relatively recent evolutionary event.

  17. Intron-exon organization of the active human protein S gene PS. alpha. and its pseudogene PS. beta. : Duplication and silencing during primate evolution

    SciTech Connect

    Ploos van Amstel, H.; Reitsma, P.H.; van der Logt, C.P.; Bertina, R.M. )

    1990-08-28

    The human protein S locus on chromosome 3 consists of two protein S genes, PS{alpha} and PS{beta}. Here the authors report the cloning and characterization of both genes. Fifteen exons of the PS{alpha} gene were identified that together code for protein S mRNA as derived from the reported protein S cDNAs. Analysis by primer extension of liver protein S mRNA, however, reveals the presence of two mRNA forms that differ in the length of their 5{prime}-noncoding region. Both transcripts contain a 5{prime}-noncoding region longer than found in the protein S cDNAs. The two products may arise from alternative splicing of an additional intron in this region or from the usage of two start sites for transcription. The intron-exon organization of the PS{alpha} gene fully supports the hypothesis that the protein S gene is the product of an evolutional assembling process in which gene modules coding for structural/functional protein units also found in other coagulation proteins have been put upstream of the ancestral gene of a steroid hormone binding protein. The PS{beta} gene is identified as a pseudogene. It contains a large variety of detrimental aberrations, viz., the absence of exon I, a splice site mutation, three stop codons, and a frame shift mutation. Overall the two genes PS{alpha} and PS{beta} show between their exonic sequences 96.5% homology. Southern analysis of primate DNA showed that the duplication of the ancestral protein S gene has occurred after the branching of the orangutan from the African apes. A nonsense mutation that is present in the pseudogene of man also could be identified in one of the two protein S genes of both chimpanzee and gorilla. This implicates that silencing of one of the two protein S genes must have taken place before the divergence of the three African apes.

  18. Salmonella Typhi shdA: pseudogene or allelic variant?

    PubMed

    Urrutia, I M; Fuentes, J A; Valenzuela, L M; Ortega, A P; Hidalgo, A A; Mora, G C

    2014-08-01

    ShdA from Salmonella Typhimurium (ShdASTm) is a large outer membrane protein that specifically recognizes and binds to fibronectin. ShdASTm is involved in the colonization of the cecum and the Peyer's patches of terminal ileum in mice. On the other hand, shdA gene from Salmonella Typhi (shdASTy) has been considered a pseudogene (i.e. a nonfunctional sequence of genomic DNA) due to the presence of deletions and mutations that gave rise to premature stop codons. In this work we show that, despite the deletions and mutations, shdASTy is fully functional. S. Typhi ΔshdA mutants presented an impaired adherence and invasion of HEp-2 pre-treated with TGF-β1, an inducer of fibronectin production. Moreover, shdA from S. Typhi and S. Typhimurium seem to be equivalent since shdASTm restored the adherence and invasion of S. Typhi ΔshdA mutant to wild type levels. In addition, anti-FLAG mAbs interfered with the adherence and invasion of the S. Typhi shdA-3xFLAG strain. Finally, shdASTy encodes a detectable protein when heterologously expressed in Escherichia coli DH5α. The data presented here show that shdASTy is not a pseudogene, but a different functional allele compared with shdASTm. PMID:24859062

  19. Nonlinear Structural Analysis

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Nonlinear structural analysis techniques for engine structures and components are addressed. The finite element method and boundary element method are discussed in terms of stress and structural analyses of shells, plates, and laminates.

  20. Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration.

    PubMed

    Douglas, Gavin M; Wilson, Michael D; Moses, Alan M

    2016-06-01

    Characteristics of pseudogene degeneration at the coding level are well-known, such as a shift toward neutral rates of nonsynonymous substitutions and gain of frameshift mutations. In contrast, degeneration of pseudogene transcriptional regulation is not well understood. Here, we test two predictions of regulatory degeneration along a pseudogenized lineage: 1) Decreased transcription factor (TF) binding and 2) accelerated evolution in putative cis-regulatory regions.We find evidence for decreased TF binding levels nearby two primate pseudogenes compared with functional liver genes. However, the majority of TF-bound sequences nearby pseudogenes do not show evidence for lineage-specific accelerated rates of evolution. We conclude that decreases in TF binding level could be a marker for regulatory degeneration, while sequence degeneration in primate cis-regulatory modules may be obscured by background rates of TF binding site turnover. PMID:26882985

  1. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes.

    PubMed

    Tam, Oliver H; Aravin, Alexei A; Stein, Paula; Girard, Angelique; Murchison, Elizabeth P; Cheloufi, Sihem; Hodges, Emily; Anger, Martin; Sachidanandam, Ravi; Schultz, Richard M; Hannon, Gregory J

    2008-05-22

    Pseudogenes populate the mammalian genome as remnants of artefactual incorporation of coding messenger RNAs into transposon pathways. Here we show that a subset of pseudogenes generates endogenous small interfering RNAs (endo-siRNAs) in mouse oocytes. These endo-siRNAs are often processed from double-stranded RNAs formed by hybridization of spliced transcripts from protein-coding genes to antisense transcripts from homologous pseudogenes. An inverted repeat pseudogene can also generate abundant small RNAs directly. A second class of endo-siRNAs may enforce repression of mobile genetic elements, acting together with Piwi-interacting RNAs. Loss of Dicer, a protein integral to small RNA production, increases expression of endo-siRNA targets, demonstrating their regulatory activity. Our findings indicate a function for pseudogenes in regulating gene expression by means of the RNA interference pathway and may, in part, explain the evolutionary pressure to conserve argonaute-mediated catalysis in mammals. PMID:18404147

  2. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

    PubMed Central

    Tam, Oliver H.; Aravin, Alexei A.; Stein, Paula; Girard, Angelique; Murchison, Elizabeth P.; Cheloufi, Sihem; Hodges, Emily; Anger, Martin; Sachidanandam, Ravi; Schultz, Richard M.; Hannon, Gregory J.

    2010-01-01

    Pseudogenes populate the mammalian genome as remnants of artefactual incorporation of coding messenger RNAs into transposon pathways1. Here we show that a subset of pseudogenes generates endogenous small interfering RNAs (endo-siRNAs) in mouse oocytes. These endo-siRNAs are often processed from double-stranded RNAs formed by hybridization of spliced transcripts from protein-coding genes to antisense transcripts from homologous pseudogenes. An inverted repeat pseudogene can also generate abundant small RNAs directly. A second class of endo-siRNAs may enforce repression of mobile genetic elements, acting together with Piwi-interacting RNAs. Loss of Dicer, a protein integral to small RNA production, increases expression of endo-siRNA targets, demonstrating their regulatory activity. Our findings indicate a function for pseudogenes in regulating gene expression by means of the RNA interference pathway and may, in part, explain the evolutionary pressure to conserve argonaute-mediated catalysis in mammals. PMID:18404147

  3. Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration

    PubMed Central

    Douglas, Gavin M.; Wilson, Michael D.; Moses, Alan M.

    2016-01-01

    Characteristics of pseudogene degeneration at the coding level are well-known, such as a shift toward neutral rates of nonsynonymous substitutions and gain of frameshift mutations. In contrast, degeneration of pseudogene transcriptional regulation is not well understood. Here, we test two predictions of regulatory degeneration along a pseudogenized lineage: 1) Decreased transcription factor (TF) binding and 2) accelerated evolution in putative cis-regulatory regions. We find evidence for decreased TF binding levels nearby two primate pseudogenes compared with functional liver genes. However, the majority of TF-bound sequences nearby pseudogenes do not show evidence for lineage-specific accelerated rates of evolution. We conclude that decreases in TF binding level could be a marker for regulatory degeneration, while sequence degeneration in primate cis-regulatory modules may be obscured by background rates of TF binding site turnover. PMID:26882985

  4. Determination of haploid DNA sequences in humans: application to the glucocerebrosidase pseudogene.

    PubMed

    Martínez-Arias, Rosa; Bertranpetit, Jaume; Comas, David

    2002-02-01

    Variation analyses in the human genome at the sequence level, especially human genetic population analysis and genetic epidemiology, are hampered by the difficulty to ascertain haplotypes on autosomal regions. We have designed a new methodological approach to obtain autosomal haploid sequences from diploid organisms. First, genotypes are unambiguously determined through long-range PCR and diploid DNA sequencing. Second, cloning the whole PCR-amplified segment and sequencing a single clone for those fragments that presented a heterozygous position discern the allelic phase. The second allele is deduced from the genotype, and the phase reconfirmed by sequencing a second clone. A hundred human chromosomes were analysed for a 5.4 kb encompassing the glucocerebrosidase pseudogene on human chromosome 1. Haplotypes were unambiguously ascertained for all samples. The manner to combine the used techniques makes this approach a novelty. Haploid sequences from diploid organisms are obtained in a less time consuming and more accurate manner than in other used procedures. PMID:12180141

  5. mRNA retroposition in human cells: processed pseudogene formation.

    PubMed Central

    Maestre, J; Tchénio, T; Dhellin, O; Heidmann, T

    1995-01-01

    Using a sensitive assay for detection of reverse transcription events, we demonstrate that human HeLa cells can 'retropose', i.e. reverse transcribe and integrate, the mRNA of a naive reporter gene, at a low but detectable frequency. Furthermore, we show that the retroposed copies have all the hallmarks of the processed pseudogenes naturally found in the mammalian genome: they lack intron and 5' promoter sequence, they have acquired a 3' poly(A) tail, and they are flanked by short repeats (< 15 bp) of target DNA sequence. These results demonstrate that human cells possess an endogenous reverse transcription activity, which is not restricted to transcripts of transposable elements, and which is likely to be involved in the formation, still ongoing, of a large fraction of the eukaryotic genome. Images PMID:8557053

  6. Transcriptional activity of the human pseudogene psi alpha globin compared with alpha globin, its functional gene counterpart.

    PubMed Central

    Whitelaw, E; Proudfoot, N J

    1983-01-01

    Transcriptional analysis of the human pseudogene psi alpha globin has revealed the following features: (1) The promoter with a 23 bp deletion between the CCAAT and ATA boxes is functional both in vitro and in vivo, 3 fold and 10 fold less efficient, respectively, than alpha. (2) Both the psi alpha and alpha globin gene promoters are active in the absence of transcriptional enhancers, either a gene-encoded or viral enhancer. (3) The mutated poly(A) addition signal in psi alpha (AATGAA) appears to be completely nonfunctional. This result provides an explanation for the absence of psi alpha transcripts in human erythroid cells. Images PMID:6316269

  7. Is Esterase-P Encoded by a Cryptic Pseudogene in Drosophila Melanogaster?

    PubMed Central

    Balakirev, E. S.; Ayala, F. J.

    1996-01-01

    We have amplified and sequenced the gene encoding Esterase-P (Est-P) in 10 strains of Drosophila melanogaster. Three premature termination codons occur in the coding region of the gene in two strains. This observation, together with other indirect evidence, leads us to propose that Est-P may be a pseudogene in D. melanogaster. Est-P would be a ``cryptic'' pseudogene, in the sense that it retains intact the coding sequence (without stop codons and other alterations usually observed in pseudogenes) in most D. melanogaster strains. We conjecture that the β-esterase cluster may consist in other Drosophila species of functional and nonfunctional genes. We also conjecture that the rarity of detected pseudogenes in Drosophila may be due to the difficulty of discovering them, because most of them are cryptic. PMID:8978040

  8. A New Family of Predicted Krüppel-Like Factor Genes and Pseudogenes in Placental Mammals

    PubMed Central

    Pei, Jimin; Grishin, Nick V.

    2013-01-01

    Krüppel-like factors (KLF) and specificity proteins (SP) constitute a family of zinc-finger-containing transcription factors that play important roles in a wide range of processes including differentiation and development of various tissues. The human genome possesses 17 KLF genes (KLF1–KLF17) and nine SP genes (SP1–SP9) with diverse functions. We used sequence similarity searches and gene synteny analysis to identify a new putative KLF gene/pseudogene named KLF18 that is present in most of the placental mammals with sequenced genomes. KLF18 is a chromosomal neighbor of the KLF17 gene and is likely a product of its duplication. Phylogenetic analyses revealed that mammalian predicted KLF18 proteins and KLF17 proteins experienced elevated rates of evolution and are grouped with KLF1/KLF2/KLF4 and non-mammalian KLF17. Predicted KLF18 proteins maintain conserved features in the zinc fingers of the SP/KLF family, while possessing repeats of a unique sequence motif in their N-terminal regions. No expression data have been reported for KLF18, suggesting that it either has highly restricted expression patterns and specialized functions, or could have become a pseudogene in extant placental mammals. Besides KLF18 genes/pseudogenes, we identified several KLF18-like genes such as Zfp352, Zfp352-like, and Zfp353 in the genomes of mouse and rat. These KLF18-like genes do not possess introns inside their coding regions, and gene expression data indicate that some of them may function in early embryonic development. They represent further expansions of KLF members in the murine lineage, most likely resulted from several events of retrotransposition and local gene duplication starting from an ancient spliced mRNA of KLF18. PMID:24244731

  9. Generalized Structured Component Analysis

    ERIC Educational Resources Information Center

    Hwang, Heungsun; Takane, Yoshio

    2004-01-01

    We propose an alternative method to partial least squares for path analysis with components, called generalized structured component analysis. The proposed method replaces factors by exact linear combinations of observed variables. It employs a well-defined least squares criterion to estimate model parameters. As a result, the proposed method…

  10. Expression of the human amylase genes: Recent origin of a salivary amylase promoter from an actin pseudogene

    SciTech Connect

    Samuelson, L.C.; Gumucio, D.L.; Meisler, M.H. ); Wiebauer, K. )

    1988-09-12

    The human genes encoding salivary amylase (AMY1) and pancreatic amylase (AMY2) are nearly identical in structure and sequence. The authors have used ribonuclease protection studies to identify the functional gene copies in this multigene family. Riboprobes derived from each gene were hybridized to RNA from human pancreas, parotid and liver. The sizes of the protected fragments demonstrated that both pancreatic genes are expressed in pancreas. One of the pancreatic genes, AMY2B, is also transcribed at a low level in liver, but not from the promoter used in pancreas. AMY1 transcripts were detected in parotid, but not in pancreas or liver. Unexpected fragments protected by liver RNA led to the discovery that the 5{prime} regions of the five human amylase genes contain a processed {gamma}-actin pseudogene. The promoter and start site for transcription of AMY1 are recently derived from the 3{prime} untranslated region of {gamma}-actin. In addition, insertion of an endogenous retrovirus has interrupted the {gamma}-actin pseudogene in four of the five amylase genes.

  11. Expression of the human amylase genes: recent origin of a salivary amylase promoter from an actin pseudogene.

    PubMed

    Samuelson, L C; Wiebauer, K; Gumucio, D L; Meisler, M H

    1988-09-12

    The human genes encoding salivary amylase (AMY1) and pancreatic amylase (AMY2) are nearly identical in structure and sequence. We have used ribonuclease protection studies to identify the functional gene copies in this multigene family. Riboprobes derived from each gene were hybridized to RNA from human pancreas, parotid and liver. The sizes of the protected fragments demonstrated that both pancreatic genes are expressed in pancreas. One of the pancreatic genes, AMY2B, is also transcribed at a low level in liver, but not from the promoter used in pancreas. AMY1 transcripts were detected in parotid, but not in pancreas or liver. Unexpected fragments protected by liver RNA led to the discovery that the 5' regions of the five human amylase genes contain a processed gamma-actin pseudogene. The promoter and start site for transcription of AMY1 are recently derived from the 3' untranslated region of gamma-actin. In addition, insertion of an endogenous retrovirus has interrupted the gamma-actin pseudogene in four of the five amylase genes. PMID:2458567

  12. pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes.

    PubMed

    Chan, Wen-Ling; Yang, Wen-Kuang; Huang, Hsien-Da; Chang, Jan-Gowth

    2013-01-01

    RNA interference (RNAi) is a gene silencing process within living cells, which is controlled by the RNA-induced silencing complex with a sequence-specific manner. In flies and mice, the pseudogene transcripts can be processed into short interfering RNAs (siRNAs) that regulate protein-coding genes through the RNAi pathway. Following these findings, we construct an innovative and comprehensive database to elucidate siRNA-mediated mechanism in human transcribed pseudogenes (TPGs). To investigate TPG producing siRNAs that regulate protein-coding genes, we mapped the TPGs to small RNAs (sRNAs) that were supported by publicly deep sequencing data from various sRNA libraries and constructed the TPG-derived siRNA-target interactions. In addition, we also presented that TPGs can act as a target for miRNAs that actually regulate the parental gene. To enable the systematic compilation and updating of these results and additional information, we have developed a database, pseudoMap, capturing various types of information, including sequence data, TPG and cognate annotation, deep sequencing data, RNA-folding structure, gene expression profiles, miRNA annotation and target prediction. As our knowledge, pseudoMap is the first database to demonstrate two mechanisms of human TPGs: encoding siRNAs and decoying miRNAs that target the parental gene. pseudoMap is freely accessible at http://pseudomap.mbc.nctu.edu.tw/. Database URL: http://pseudomap.mbc.nctu.edu.tw/ PMID:23396300

  13. Generation and reactivation of T-cell receptor A joining region pseudogenes in primates

    SciTech Connect

    Thiel, C.; Lanchbury, J.S.; Otting, N.

    1996-06-01

    Tandemly duplicated T-cell receptor (Tcr) AJ (J{alpha}) segments contribute significantly to TCRA chain junctional region diversity in mammals. Since only limited data exists on TCRA diversity in nonhuman primates, we examined the TCRAJ regions of 37 chimpanzee and 71 rhesus macaque TCRA cDNA clones derived from inverse polymerase chain reaction on peripheral blood mononuclear cell cDNA of healthy animals. Twenty-five different TCRAJ regions were characterized in the chimpanzee and 36 in the rhesus macaque. Each bears a close structural relationship to an equivalent human TCRAJ region. Conserved amino acid motifs are shared between all three species. There are indications that differences between nonhuman primates and humans exist in the generation of TCRAJ pseudogenes. The nucleotide and amino acid sequences of the various characterized TCRAJ of each species are reported and we compare our results to the available information on human genomic sequences. Although we provide evidence of dynamic processes modifying TCRAJ segments during primate evolution, their repertoire and primary structure appears to be relatively conserved. 21 refs., 2 figs.

  14. Analysis of Geological Structures

    NASA Astrophysics Data System (ADS)

    Price, Neville J.; Cosgrove, John W.

    1990-08-01

    A knowledge of structural geology is fundamental to understanding the processes by which the earth's crust has evolved. It is a subject of fundamental importance to students of geology, experienced field geologists and academic researchers as well as to petroleum and mining engineers. In contrast to many structural textbooks which dwell upon geometrical descriptions of geological structures, this book emphasises mechanical principles and the way in which they can be used to understand how and why a wide range of geological structures develop. Structures on all scales are considered but the emphasis of the book is on those that can be seen on the scale of hand specimen or outcrop. Drawing on their considerable teaching experience the authors present a coherent and lucid analysis of geological structures which will be welcomed by a wide variety of earth scientists.

  15. Probabilistic Structural Analysis Program

    NASA Technical Reports Server (NTRS)

    Pai, Shantaram S.; Chamis, Christos C.; Murthy, Pappu L. N.; Stefko, George L.; Riha, David S.; Thacker, Ben H.; Nagpal, Vinod K.; Mital, Subodh K.

    2010-01-01

    NASA/NESSUS 6.2c is a general-purpose, probabilistic analysis program that computes probability of failure and probabilistic sensitivity measures of engineered systems. Because NASA/NESSUS uses highly computationally efficient and accurate analysis techniques, probabilistic solutions can be obtained even for extremely large and complex models. Once the probabilistic response is quantified, the results can be used to support risk-informed decisions regarding reliability for safety-critical and one-of-a-kind systems, as well as for maintaining a level of quality while reducing manufacturing costs for larger-quantity products. NASA/NESSUS has been successfully applied to a diverse range of problems in aerospace, gas turbine engines, biomechanics, pipelines, defense, weaponry, and infrastructure. This program combines state-of-the-art probabilistic algorithms with general-purpose structural analysis and lifting methods to compute the probabilistic response and reliability of engineered structures. Uncertainties in load, material properties, geometry, boundary conditions, and initial conditions can be simulated. The structural analysis methods include non-linear finite-element methods, heat-transfer analysis, polymer/ceramic matrix composite analysis, monolithic (conventional metallic) materials life-prediction methodologies, boundary element methods, and user-written subroutines. Several probabilistic algorithms are available such as the advanced mean value method and the adaptive importance sampling method. NASA/NESSUS 6.2c is structured in a modular format with 15 elements.

  16. Using semantic web rules to reason on an ontology of pseudogenes

    PubMed Central

    Holford, Matthew E.; Khurana, Ekta; Cheung, Kei-Hoi; Gerstein, Mark

    2010-01-01

    Motivation: Recent years have seen the development of a wide range of biomedical ontologies. Notable among these is Sequence Ontology (SO) which offers a rich hierarchy of terms and relationships that can be used to annotate genomic data. Well-designed formal ontologies allow data to be reasoned upon in a consistent and logically sound way and can lead to the discovery of new relationships. The Semantic Web Rules Language (SWRL) augments the capabilities of a reasoner by allowing the creation of conditional rules. To date, however, formal reasoning, especially the use of SWRL rules, has not been widely used in biomedicine. Results: We have built a knowledge base of human pseudogenes, extending the existing SO framework to incorporate additional attributes. In particular, we have defined the relationships between pseudogenes and segmental duplications. We then created a series of logical rules using SWRL to answer research questions and to annotate our pseudogenes appropriately. Finally, we were left with a knowledge base which could be queried to discover information about human pseudogene evolution. Availability: The fully populated knowledge base described in this document is available for download from http://ontology.pseudogene.org. A SPARQL endpoint from which to query the dataset is also available at this location. Contact: matthew.holford@yale.edu; mark.gerstein@yale.edu PMID:20529940

  17. U6 snRNA Pseudogenes: Markers of Retrotransposition Dynamics in Mammals

    PubMed Central

    Doucet, Aurélien J.; Droc, Gaëtan; Siol, Oliver; Audoux, Jérôme; Gilbert, Nicolas

    2015-01-01

    Transposable elements comprise more than 45% of the human genome and long interspersed nuclear element 1 (LINE-1 or L1) is the only autonomous mobile element remaining active. Since its identification, it has been proposed that L1 contributes to the mobilization and amplification of other cellular RNAs and more recently, experimental demonstrations of this function has been described for many transcripts such as Alu, a nonautonomous mobile element, cellular mRNAs, or small noncoding RNAs. Detailed examination of the mobilization of various cellular RNAs revealed distinct pathways by which they could be recruited during retrotransposition; template choice or template switching. Here, by analyzing genomic structures and retrotransposition signatures associated with small nuclear RNA (snRNA) sequences, we identified distinct recruiting steps during the L1 retrotransposition cycle for the formation of snRNA-processed pseudogenes. Interestingly, some of the identified recruiting steps take place in the nucleus. Moreover, after comparison to other vertebrate genomes, we established that snRNA amplification by template switching is common to many LINE families from several LINE clades. Finally, we suggest that U6 snRNA copies can serve as markers of L1 retrotransposition dynamics in mammalian genomes. PMID:25761766

  18. Structural analysis of glucans

    PubMed Central

    Novak, Miroslav

    2014-01-01

    Glucans are most widespread polysaccharides in the nature. There is a large diversity in their molecular weight and configuration depending on the original source. According to the anomeric structure of glucose units it is possible to distinguish linear and branched α-, β- as well as mixed α,β-glucans with various glycoside bond positions and molecular masses. Isolation of glucans from raw sources needs removal of ballast compounds including proteins, lipids, polyphenols and other polysaccharides. Purity control of glucan fractions is necessary to evaluate the isolation and purification steps; more rigorous structural analyses of purified polysaccharides are required to clarify their structure. A set of spectroscopic, chemical and separation methods are used for this purpose. Among them, NMR spectroscopy is known as a powerful tool in structural analysis of glucans both in solution and in solid state. Along with chemolytic methods [methylation analysis (MA), periodate oxidation, partial chemical or enzymatic hydrolysis, etc.], correlation NMR experiments are able to determine the exact structure of tested polysaccharides. Vibration spectroscopic methods (FTIR, Raman) are sensitive to anomeric structure of glucans and can be used for purity control as well. Molecular weight distribution, homogeneity and branching of glucans can be estimated by size-exclusion chromatography (SEC), laser light scattering (LLS) and viscometry. PMID:25332993

  19. COI Structural Analysis Presentation

    NASA Technical Reports Server (NTRS)

    Cline, Todd; Stahl, H. Philip (Technical Monitor)

    2001-01-01

    This report discusses the structural analysis of the Next Generation Space Telescope Mirror System Demonstrator (NMSD) developed by Composite Optics Incorporated (COI) in support of the Next Generation Space Telescope (NGST) project. The mirror was submitted to Marshall Space Flight Center (MSFC) for cryogenic testing and evaluation. Once at MSFC, the mirror was lowered to approximately 40 K and the optical surface distortions were measured. Alongside this experiment, an analytical model was developed and used to compare to the test results. A NASTRAN finite element model was provided by COI and a thermal model was developed from it. Using the thermal model, steady state nodal temperatures were calculated based on the predicted environment of the large cryogenic test chamber at MSFC. This temperature distribution was applied in the structural analysis to solve for the deflections of the optical surface. Finally, these deflections were submitted for optical analysis and comparison to the interferometer test data.

  20. Noise-induced multistability in the regulation of cancer by genes and pseudogenes

    NASA Astrophysics Data System (ADS)

    Petrosyan, K. G.; Hu, Chin-Kun

    2016-07-01

    We extend a previously introduced model of stochastic gene regulation of cancer to a nonlinear case having both gene and pseudogene messenger RNAs (mRNAs) self-regulated. The model consists of stochastic Boolean genetic elements and possesses noise-induced multistability (multimodality). We obtain analytical expressions for probabilities for the case of constant but finite number of microRNA molecules which act as a noise source for the competing gene and pseudogene mRNAs. The probability distribution functions display both the global bistability regime as well as even-odd number oscillations for a certain range of model parameters. Statistical characteristics of the mRNA's level fluctuations are evaluated. The obtained results of the extended model advance our understanding of the process of stochastic gene and pseudogene expressions that is crucial in regulation of cancer.

  1. Design oriented structural analysis

    NASA Technical Reports Server (NTRS)

    Giles, Gary L.

    1994-01-01

    Desirable characteristics and benefits of design oriented analysis methods are described and illustrated by presenting a synoptic description of the development and uses of the Equivalent Laminated Plate Solution (ELAPS) computer code. ELAPS is a design oriented structural analysis method which is intended for use in the early design of aircraft wing structures. Model preparation is minimized by using a few large plate segments to model the wing box structure. Computational efficiency is achieved by using a limited number of global displacement functions that encompass all segments over the wing planform. Coupling with other codes is facilitated since the output quantities such as deflections and stresses are calculated as continuous functions over the plate segments. Various aspects of the ELAPS development are discussed including the analytical formulation, verification of results by comparison with finite element analysis results, coupling with other codes, and calculation of sensitivity derivatives. The effectiveness of ELAPS for multidisciplinary design application is illustrated by describing its use in design studies of high speed civil transport wing structures.

  2. Computational engine structural analysis

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Johns, R. H.

    1986-01-01

    A significant research activity at the NASA Lewis Research Center is the computational simulation of complex multidisciplinary engine structural problems. This simulation is performed using computational engine structural analysis (CESA) which consists of integrated multidisciplinary computer codes in conjunction with computer post-processing for problem-specific application. A variety of the computational simulations of specific cases are described in some detail in this paper. These case studies include: (1) aeroelastic behavior of bladed rotors, (2) high velocity impact of fan blades, (3) blade-loss transient response, (4) rotor/stator/squeeze-film/bearing interaction, (5) blade-fragment/rotor-burst containment, and (6) structural behavior of advanced swept turboprops. These representative case studies are selected to demonstrate the breath of the problems analyzed and the role of the computer including post-processing and graphical display of voluminous output data.

  3. Structural Analysis Made 'NESSUSary'

    NASA Technical Reports Server (NTRS)

    2005-01-01

    Everywhere you look, chances are something that was designed and tested by a computer will be in plain view. Computers are now utilized to design and test just about everything imaginable, from automobiles and airplanes to bridges and boats, and elevators and escalators to streets and skyscrapers. Computer-design engineering first emerged in the 1970s, in the automobile and aerospace industries. Since computers were in their infancy, however, architects and engineers during the time were limited to producing only designs similar to hand-drafted drawings. (At the end of 1970s, a typical computer-aided design system was a 16-bit minicomputer with a price tag of $125,000.) Eventually, computers became more affordable and related software became more sophisticated, offering designers the "bells and whistles" to go beyond the limits of basic drafting and rendering, and venture into more skillful applications. One of the major advancements was the ability to test the objects being designed for the probability of failure. This advancement was especially important for the aerospace industry, where complicated and expensive structures are designed. The ability to perform reliability and risk assessment without using extensive hardware testing is critical to design and certification. In 1984, NASA initiated the Probabilistic Structural Analysis Methods (PSAM) project at Glenn Research Center to develop analysis methods and computer programs for the probabilistic structural analysis of select engine components for current Space Shuttle and future space propulsion systems. NASA envisioned that these methods and computational tools would play a critical role in establishing increased system performance and durability, and assist in structural system qualification and certification. Not only was the PSAM project beneficial to aerospace, it paved the way for a commercial risk- probability tool that is evaluating risks in diverse, down- to-Earth application

  4. Structured Data in Structural Analysis Software

    NASA Technical Reports Server (NTRS)

    Kunz, Donald L.; Hopkins, Stewart

    1987-01-01

    This paper discusses the use of computer data structures in finite-element structural analysis programs. A number of data structure types that have been shown to be useful in such programs are introduced and described. A simple finite-element model is used to demonstrate how the given set of data structure types naturally lend themselves to developing software for the model. Different methods of implementing data structures in the context of a program are discussed.

  5. Multiple substitutions in the von Willebrand factor gene that mimic the pseudogene sequence

    SciTech Connect

    Eikenboom, J.C.; Brieet, E.; Reitsma, P.H.; Vink, T.; Sixma, J.J.

    1994-03-15

    The authors have analyzed a type IIB and a type I von Willebrand disease family for the presence of mutations in the region coding for the glycoprotein Ib binding domain of the von Willebrand factor. Since this sequence is also present in the highly homologous von Willebrand factor pseudogene, the authors have studied genomic DNA as well as cDNA, which was produced from RNA isolated from endothelial cells or platelets. In both families, they have detected multiple consecutive nucleotide substitutions in the 5{prime} end of exon 28 that result in a sequence identical to the von Willebrand factor pseudogene. These substitutions were also found in cDNA, which proves that they are present in the active gene. The occurrence of multiple adjacent substitutions that exactly reflect a part of the sequence of the von Willebrand factor pseudogene is difficult to reconcile with sequential single mutational events. They therefore hypothesize that each of these multiple substitutions arose from one recombinational event between gene and pseudogene. 34 refs., 4 figs., 2 tabs.

  6. Pseudogene CYP4Z2P 3′UTR promotes angiogenesis in breast cancer

    SciTech Connect

    Zheng, Lufeng; Li, Xiaoman; Gu, Yi; Ma, Yihua; Xi, Tao

    2014-10-24

    Highlights: • A new critical role of pseudogene CYP4Z2P 3′UTR in breast cancer is proposed. • We examine the level of pseudogene CYP4Z2P 3′UTR in breast cancer tissues. • The functions of CYP4Z2P 3′UTR and mechanism were studied. • The mechanism provides new insights for the breast cancer progression. - Abstract: Pseudogenes have long been marked as “false” genes, which are similar with real genes but have no apparent function. The 3′UTR is well-known to regulate gene expression post-transcriptionally. Our recent evidence, however, indicates novel functional roles of pseudogene CYP4Z2P 3′UTR (Z2P-UTR). We found that ectopic expression of Z2P-UTR in breast cancer cells significantly increased the expression of VEGF-A without affecting cell proliferation in vitro. Meanwhile, conditioned medium (CM) from Z2P-UTR overexpression cells enhanced proliferation, migration and tube formation of HUVEC, and promoted angiogenesis in ex vivo models. Also, CM increased the expression of VEGFR2 in HUVEC. Our data suggest that Z2P-UTR can promote breast cancer angiogenesis partly via paracrine pathway of VEGF-A/VEGFR2.

  7. Stem cell regulatory function mediated by expression of a novel mouse Oct4 pseudogene

    SciTech Connect

    Lin, Huey; Shabbir, Arsalan; Molnar, Merced; Lee, Techung . E-mail: chunglee@buffalo.edu

    2007-03-30

    Multiple pseudogenes have been proposed for embryonic stem (ES) cell-specific genes, and their abundance suggests that some of these potential pseudogenes may be functional. ES cell-specific expression of Oct4 regulates stem cell pluripotency and self-renewing state. Although Oct4 expression has been reported in adult tissues during gene reprogramming, the detected Oct4 signal might be contributed by Oct4 pseudogenes. Among the multiple Oct4 transcripts characterized here is a {approx}1 kb clone derived from P19 embryonal carcinoma stem cells, which shares a {approx}87% sequence homology with the parent Oct4 gene, and has the potential of encoding an 80-amino acid product (designated as Oct4P1). Adenoviral expression of Oct4P1 in mesenchymal stem cells promotes their proliferation and inhibits their osteochondral differentiation. These dual effects of Oct4P1 are reminiscent of the stem cell regulatory function of the parent Oct4, and suggest that Oct4P1 may be a functional pseudogene or a novel Oct4-related gene with a unique function in stem cells.

  8. Genomic organization of the murine G protein beta subunit genes and related processed pseudogenes.

    PubMed

    Kitanaka, J; Wang, X B; Kitanaka, N; Hembree, C M; Uhl, G R

    2001-12-01

    The functional significance of heterotrimeric guanine nucleotide binding protein (G protein) for the many physiological processes including the molecular mechanisms of drug addiction have been described. In investigating the changes of mRNA expression after acute psychostimulant administration, we previously identified a cDNA encoding a G protein beta1 subunit (Gbeta1) that was increased up to four-fold in certain brain regions after administration of psychostimulants. The mouse Gbeta1 gene (the mouse genetic symbol, GNB1) was mapped to chromosome 4, but little was known of its genetic features. To characterize the GNB1 gene further, we have cloned and analyzed the genomic structures of the mouse GNBI gene and its homologous sequences. The GNBI gene spans at least 50 kb, and consists of 12 exons and 11 introns. The exon/intron boundaries were determined and found to follow the GT/AG rule. Exons 3-11 encode the Gbeta1 protein, and the exon 2 is an alternative, resulting in putative two splicing variants. Although intron 11 is additional for GNBI compared with GNB2 and GNB3, the intron positions within the protein coding region of GNB1, GNB2 and GNB3 are identical, suggesting that GNB1 should have diverged from the ancestral gene family earlier than the genes for GNB2 and GNB3. We also found the 5'-truncated processed pseudogenes with 71-89% similarities to GNBI mRNA sequence, suggesting that the truncated cDNA copies, which have been reverse-transcribed from a processed mRNA for GNB1, might have been integrated into several new locations in the mouse genome. PMID:11913780

  9. Structural Analysis of Biodiversity

    PubMed Central

    Sirovich, Lawrence; Stoeckle, Mark Y.; Zhang, Yu

    2010-01-01

    Large, recently-available genomic databases cover a wide range of life forms, suggesting opportunity for insights into genetic structure of biodiversity. In this study we refine our recently-described technique using indicator vectors to analyze and visualize nucleotide sequences. The indicator vector approach generates correlation matrices, dubbed Klee diagrams, which represent a novel way of assembling and viewing large genomic datasets. To explore its potential utility, here we apply the improved algorithm to a collection of almost 17000 DNA barcode sequences covering 12 widely-separated animal taxa, demonstrating that indicator vectors for classification gave correct assignment in all 11000 test cases. Indicator vector analysis revealed discontinuities corresponding to species- and higher-level taxonomic divisions, suggesting an efficient approach to classification of organisms from poorly-studied groups. As compared to standard distance metrics, indicator vectors preserve diagnostic character probabilities, enable automated classification of test sequences, and generate high-information density single-page displays. These results support application of indicator vectors for comparative analysis of large nucleotide data sets and raise prospect of gaining insight into broad-scale patterns in the genetic structure of biodiversity. PMID:20195371

  10. Adaptive Gene Loss? Tracing Back the Pseudogenization of the Rabbit CCL8 Chemokine.

    PubMed

    van der Loo, Wessel; Magalhaes, Maria João; de Matos, Ana Lemos; Abrantes, Joana; Yamada, Fumio; Esteves, Pedro J

    2016-08-01

    Studies of the process of pseudogenization have widened our understanding of adaptive evolutionary change. In Rabbit, an alteration at the second extra-cellular loop of the CCR5 chemokine receptor was found to be associated with the pseudogenization of one of its prime ligands, the chemokine CCL8. This relationship has raised questions about the existence of a causal link between both events, which would imply adaptive gene loss. This hypothesis is evaluated here by tracing back the history of the genetic modifications underlying the chemokine pseudogenization. The obtained data indicate that mutations at receptor and ligand genes occurred after the lineage split of New World Leporids versus Old World Leporids and prior to the generic split of the of Old World species studied, which occurred an estimated 8-9 million years ago. More important, they revealed the emergence, before this zoographical split, of a "slippery" nucleotide motif (CCCCGGG) at the 3' region of CCL8-exon2. Such motives are liable of generating +1G or -1G frameshifts, which could, however, be overcome by "translesion" synthesis or somatic reversion. The CCL8 pseudogenization in the Old World lineage was apparently initiated by three synapomorphic point mutations at the exon2-intron2 boundary which provide at short range premature terminating codons, independently of the reading frame imposed by the slippery motif. The presence of this motif in New World Leporids might allow verifying this scenario. The importance of CCL8-CCR5 signaling in parasite-host interaction would suggest that the CCL8 knock-out in Old World populations might be related to changes in pathogenic environment. PMID:27306379

  11. Human Nanog pseudogene8 promotes the proliferation of gastrointestinal cancer cells

    SciTech Connect

    Uchino, Keita; Hirano, Gen; Hirahashi, Minako; Isobe, Taichi; Shirakawa, Tsuyoshi; Kusaba, Hitoshi; Baba, Eishi; Tsuneyoshi, Masazumi; Akashi, Koichi

    2012-09-10

    There is emerging evidence that human solid tumor cells originate from cancer stem cells (CSCs). In cancer cell lines, tumor-initiating CSCs are mainly found in the side population (SP) that has the capacity to extrude dyes such as Hoechst 33342. We found that Nanog is expressed specifically in SP cells of human gastrointestinal (GI) cancer cells. Nucleotide sequencing revealed that NanogP8 but not Nanog was expressed in GI cancer cells. Transfection of NanogP8 into GI cancer cell lines promoted cell proliferation, while its inhibition by anti-Nanog siRNA suppressed the proliferation. Immunohistochemical staining of primary GI cancer tissues revealed NanogP8 protein to be strongly expressed in 3 out of 60 cases. In these cases, NanogP8 was found especially in an infiltrative part of the tumor, in proliferating cells with Ki67 expression. These data suggest that NanogP8 is involved in GI cancer development in a fraction of patients, in whom it presumably acts by supporting CSC proliferation. -- Highlights: Black-Right-Pointing-Pointer Nanog maintains pluripotency by regulating embryonic stem cells differentiation. Black-Right-Pointing-Pointer Nanog is expressed in cancer stem cells of human gastrointestinal cancer cells. Black-Right-Pointing-Pointer Nucleotide sequencing revealed that Nanog pseudogene8 but not Nanog was expressed. Black-Right-Pointing-Pointer Nanog pseudogene8 promotes cancer stem cells proliferation. Black-Right-Pointing-Pointer Nanog pseudogene8 is involved in gastrointestinal cancer development.

  12. Assignment of an intron-containing human heat-shock protein gene (hsp90[beta], HSPCB) to chromosome 6 near TCTE1 (6p21) and two intronless pseudogenes to chromosomes 4 and 15 by polymerase chain reaction amplification from a panel of hybrid cell lines

    SciTech Connect

    Durkin, A.S.; Nierman, W.C.; Maglott, D.R. ); Vamvakopoulos, N.C. ); Zoghbi, H.Y. )

    1993-11-01

    We report here the successful application of designing primers from intronic sequences to map a structural hsp90[beta] gene to a unique human chromosome distinct from potential pseudogenes or rodent background. Also, by designing primers that bracket an intron and detecting products from intronless genes, we localized two hsp90[beta] pseudogenes to human chromosomes 4 and 15. PCR primers were designed from the published human hsp90[beta] DNA sequence from exon 11 (nucleotides 7066-7085, 7181-7198), intron A (1659-1678, 1722-1741), intron B (8109, 8170-8187), and exons 3 and 4 to amplify across intron C (3391-3412, 3731-3752).

  13. The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts.

    PubMed

    Xue, Jia-Yu; Liu, Yang; Li, Libo; Wang, Bin; Qiu, Yin-Long

    2010-02-01

    Plants have large and complex mitochondrial genomes in comparison to other eukaryotes. In bryophytes, the mitochondrial genomes exhibit a mixed mode of conservative and dynamic evolution. Here, we sequenced the complete mitochondrial genome from hornwort Phaeoceros laevis, to investigate the level of conservation in mitochondrial genome evolution within hornworts. The circular molecule consists of 209,482 base pairs and represents the largest known mitochondrial genome of bryophytes. It contains 30 protein genes, 3 rRNA genes, and 21 tRNA genes, with 34 cis-spliced group II introns disrupting 16 protein genes. There are 11 pseudogenes in this genome, and nine of them are shared with the other fully sequenced hornwort chondriome from Megaceros aenigmaticus, a distant relative of P. laevis. These pseudogenes were likely formed during an early stage of hornwort evolution. The two hornwort chondriomes differ by four inversions and translocations, seven genes, and four introns in the genome structure and organization. At the sequence level, they are very similar, with the identity values ranging mostly from 80 to 95% in intergenic spacers, introns, and exons. These data indicate that mitochondrial genome evolution in hornworts is less conservative than in liverworts, but has not reached the dynamic level as seen in seed plants. PMID:19998039

  14. Cloning and chromosomal localization of the human A{sub 2b} adenosine receptor gene (ADORA2B) and its pseudogene

    SciTech Connect

    Jacobson, M.A.; Johnson, R.G.; Luneau, C.J.

    1995-05-20

    To determine the chromosomal localization of the human A{sub 2b} adenosine receptor, the corresponding genomic clone was isolated and used as a probe for fluorescence in situ hybridization to metaphase chromosomes. Partial sequence analysis of the A{sub 2b} gene (ADORA2B) revealed an intron that interrupted the coding region corresponding to the second intracellular loop similar to that reported for A{sub 1} and A{sub 2a} adenosine receptor genes. A pseudogene for the A{sub 2b} receptor was also identified; it exhibited 79% identity to the A{sub 2b} adenosine receptor cDNA coding sequence and contained multiple deletions, point mutations, and frame shifts and two in-frame stops. These changes would result in the inability to encode a functional receptor. The genomic clones were utilized to localize the A{sub 2b} receptor to chromosome 17p12 and the A{sub 2b} pseudogene to chromosome 1q32. 15 refs., 1 fig.

  15. Phylogenetic timing of mutation and deletion events in the primate-specific serine hydroxymethyltransferase pseudogene HSHMT-{Psi}{sub c}

    SciTech Connect

    Dill-Devor, R.M.; Devor, E.J.

    1994-09-01

    We recently discovered a processed pseudogene which arose from the cytosolic isoforms of the pyridoxal-phosphate binding enzyme serine hydroxymethyltransferase (HSHMT-cyt). This pseudogene, which we have designated HSHMT-{Psi}{sub c}, is located on chromosome 1. Compared to the published HSHMT-cyt cDNA sequence, the 281 bp pseudogene PCR product on which we have concentrated displays an 11 bp deletion and nineteen separate single base substitutions. One of these introduces a stop signal that eliminates more than one-third of the coding region of the gene. Both the mitochondrial and cytosolic SHMT isoforms show a great deal of evolutionary conservation both at the amino acid and nucleotide sequence levels. For this reason we have attempted to amplify and sequence our 281 bp product in more than a dozen non-human primate and eleven non-primate mammalian species. Our results indicate that the pseudogene HSHMT-{Psi}{sub c} is present only in primate genomes. Further, a number of the mutations observed in the human sequence are unique to our species while others can be attributed to events occurring prior to the divergence of ancestral lines. Finally, the 11 bp deletion is found only among the apes, thus placing the deletion event at a time no longer than 25 million years ago. Similar phylogenetic timing can be assigned to other changes in the HSHMT-{Psi}{sub c} sequence, thus allowing us to present a reasonably detailed mutational history for this pseudogene.

  16. CODSTRAN - Composite durability structural analysis

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Smith, G. T.

    1978-01-01

    CODSTRAN (COmposite Durability STRucture ANalysis) a NASA Lewis Center computer program for the prediction of defect growth and fracture of composite structures when subjected to service loads is presented. Organization, capabilities and present status are discussed. Organizational aspects include executive, input, output, analysis and composite mechanics modules. Capabilities include: durability assessment of large structures and complex structural parts from composites, structural response due to static, cyclic, transient impact and thermal loads, and criteria for static, cyclic, and dynamic fracture. At the present state of development some of CODSTRAN's analysis capabilities include composite mechanics, static failures, and lamination residual stresses. An application in which CODSTRAN is used to predict the defect growth in a flat specimen, with a center through-slit under tension is studied. When completed, CODSTRAN will account for geometry and material nonlinearities, environmental effects as well as static, cyclic and dynamic fracture.

  17. An apomixis-linked ORC3-like pseudogene is associated with silencing of its functional homolog in apomictic Paspalum simplex.

    PubMed

    Siena, Lorena A; Ortiz, Juan Pablo A; Calderini, Ornella; Paolocci, Francesco; Cáceres, Maria E; Kaushal, Pankaj; Grisan, Simone; Pessino, Silvina C; Pupilli, Fulvio

    2016-03-01

    Apomixis in plants consists of asexual reproduction by seeds. Here we characterized at structural and functional levels an apomixis-linked sequence of Paspalum simplex homologous to subunit 3 of the ORIGIN RECOGNITION COMPLEX (ORC3). ORC is a multiprotein complex which controls DNA replication and cell differentiation in eukaryotes. Three PsORC3 copies were identified, each one characterized by a specific expression profile. Of these, PsORC3a, specific for apomictic genotypes, is a pseudogene that was poorly and constitutively expressed in all developmental stages of apomictic flowers, whereas PsORC3b, the putative functional gene in sexual flowers, showed a precise time-related regulation. Sense transcripts of PsORC3 were expressed in the female cell lineage of both apomictic and sexual reproductive phenotypes, and in aposporous initials. Although strong expression was detected in sexual early endosperm, no expression was present in the apomictic endosperm. Antisense PsORC3 transcripts were revealed exclusively in apomictic germ cell lineages. Defective orc3 mutants of rice and Arabidopsis showed normal female gametophytes although the embryo and endosperm were arrested at early phases of development. We hypothesize that PsORC3a is associated with the down-regulation of its functional homolog and with the development of apomictic endosperm which deviates from the canonical 2(maternal):1(paternal) genome ratio. PMID:26842983

  18. Regularized Generalized Structured Component Analysis

    ERIC Educational Resources Information Center

    Hwang, Heungsun

    2009-01-01

    Generalized structured component analysis (GSCA) has been proposed as a component-based approach to structural equation modeling. In practice, GSCA may suffer from multi-collinearity, i.e., high correlations among exogenous variables. GSCA has yet no remedy for this problem. Thus, a regularized extension of GSCA is proposed that integrates a ridge…

  19. A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation.

    PubMed Central

    Margolin, B S; Garrett-Engele, P W; Stevens, J N; Fritz, D Y; Garrett-Engele, C; Metzenberg, R L; Selker, E U

    1998-01-01

    In an analysis of 22 of the roughly 100 dispersed 5S rRNA genes in Neurospora crassa, a methylated 5S rRNA pseudogene, Psi63, was identified. We characterized the Psi63 region to better understand the control and function of DNA methylation. The 120-bp 5S rRNA-like region of Psi63 is interrupted by a 1.9-kb insertion that has characteristics of sequences that have been modified by repeat-induced point mutation (RIP). We found sequences related to this insertion in wild-type strains of N. crassa and other Neurospora species. Most showed evidence of RIP; but one, isolated from the N. crassa host of Psi63, showed no evidence of RIP. A deletion from near the center of this sequence apparently rendered it incapable of participating in RIP with the related full-length copies. The Psi63 insertion and the related sequences have features of transposons and are related to the Fot1 class of fungal transposable elements. Apparently Psi63 was generated by insertion of a previously unrecognized Neurospora transposable element into a 5S rRNA gene, followed by RIP. We name the resulting inactivated Neurospora transposon PuntRIP1 and the related sequence showing no evidence of RIP, but harboring a deletion that presumably rendered it defective for transposition, dPunt. PMID:9691037

  20. Phosphoglycerate kinase pseudogenes in the tammar wallaby and other macropodid marsupials.

    PubMed

    Cooper, D W; Holland, E A; Rudman, K; Donald, J A; Zehavi-Feferman, R; McKenzie, L M; Sinclair, A H; Spencer, J A; Graves, J A; Poole, W E

    1994-09-01

    Phosphoglycerate kinase (EC 2.7.2.3; PGK) exists in two forms in marsupials. PGK1 is an X-linked house-keeping enzyme, and PGK2 is a mainly testis-specific enzyme under autosomal control. We have used PGK1 probes derived from two closely related species of macropodid marsupials (kangaroos and wallabies) to demonstrate the existence of a large family of pseudogenes in the tammar wallaby (Macropus eugenii). Over 30 fragments are detectable after Taq digestion. We estimate that there are 25-30 copies per genome. Most are autosomally inherited and are apparently not closely linked. Only two restriction fragments that appeared to be sex linked could be detected. Varying degrees of hybridization of fragments to the probes suggest different levels of homology, and hence different ages of origin. The existence of two PGK1 homologous restriction fragments from the X and a large number from the autosomes was also demonstrated by somatic cell hybridization for two other macropodid species, the wallaroo (M. robustus) and the red kangaroo (M. rufus). These results are compared with those from human and mouse, and it is suggested that the propensity of PGK1 to form pseudogenes is an ancient (approximately 130 MYR BP) characteristic of mammals. The high level of polymorphism detected in the tammar makes these PGK1 probes potentially useful for measuring genetic variability in this species and other macropodids. PMID:8000135

  1. CODSTRAN: Composite durability structural analysis

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Smith, G. T.

    1978-01-01

    CODSTRAN (COmposite Durability STRuctural ANalysis) is an integrated computer program being developed for the prediction of defect growth and fracture of composite structures subjected to service loads and environments. CODSTRAN is briefly described with respect to organization, capabilities and present status. Application of CODSTRAN current capability to a flat composite laminate with a center slit which was subjected to axial tension loading predicted defect growth which is in good agreement with C-scan ultrasonic test records.

  2. Structural analysis of aligned RNAs.

    PubMed

    Voss, Björn

    2006-01-01

    The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de. PMID:17020924

  3. Structural Analysis of Communication Development.

    ERIC Educational Resources Information Center

    Conville, Richard L.

    This paper discusses the question of the legitimacy of applying structural analysis to actual human behavior and illustrates its legitimacy by using the reasoning in an essay by Paul Ricoeur. It then asks if the principles of communication development (obliqueness, exchange, and dying) derived from Helen Keller's experience of communication…

  4. Structural Analysis in the Classroom

    ERIC Educational Resources Information Center

    Gage, Nicholas A.; Lewis, Timothy J.

    2010-01-01

    The purpose of this article is to describe an applied method of assessing and manipulating environmental factors influencing student behavior. The assessment procedure is called structural analysis (SA) and can be a part of a functional behavioral assessment (FBA) process or a stand-alone set of procedures for teachers to use in their classrooms.…

  5. 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.

  6. False phylogenies on wood mice due to cryptic cytochrome-b pseudogene.

    PubMed

    Dubey, Sylvain; Michaux, Johan; Brünner, Harald; Hutterer, Rainer; Vogel, Peter

    2009-03-01

    The phylogeny and phylogeography of the Old World wood mice (subgenus Sylvaemus, genus Apodemus, Muridae) are well-documented. Nevertheless, the distributions of species, such as A. fulvipectus and A. ponticus remain dubious, as well as their phylogenetic relationships with A. sylvaticus. We analysed samples of Apodemus spp. across Europe using the mitochondrial cytochrome-b gene (cyt-b) and compared the DNA and amino-acid compositions of previously published sequences. The main result stemming from this study is the presence of a well-differentiated lineage of Sylvaemus including samples of various species (A. sylvaticus, A. fulvipectus, A. ponticus) from distant locations, which were revealed to be nuclear copies of the mitochondrial cyt-b. The presence of this cryptic pseudogene in published sequences is supported by different pathways. This has led to important errors in previous molecular trees and hence to partial misinterpretations in the phylogeny of Apodemus. PMID:19126432

  7. Expression of Dual-Specificity Phosphatase 5 Pseudogene 1 (DUSP5P1) in Tumor Cells

    PubMed Central

    Staege, Martin S.; Müller, Katja; Kewitz, Stefanie; Volkmer, Ines; Mauz-Körholz, Christine; Bernig, Toralf; Körholz, Dieter

    2014-01-01

    Sequencing of individual clones from a newly established cDNA library from the chemoresistant Hodgkin's lymphoma cell line L-1236 led to the isolation of a cDNA clone corresponding to a short sequence from chromosome 1. Reverse transcriptase-polymerase chain reaction indicated high expression of this sequence in Hodgkin's lymphoma derived cell lines but not in normal blood cells. Further characterization of this sequence and the surrounding genomic DNA revealed that this sequence is part of a human endogenous retrovirus locus. The sequence of this endogenous retrovirus is interrupted by a pseudogene of the dual specificity phosphatase 5 (DUSP5). Reverse transcriptase-polymerase chain reaction revealed high expression of this pseudogene (DUSP5P1) in HL cell lines but not in normal blood cells or Epstein-Barr virus-immortalized B cells. Cells from other tumor types (Burkitt's lymphoma, leukemia, neuroblastoma, Ewing sarcoma) also showed a higher DUSP5P1/DUSP5 ratio than normal cells. Furthermore, we observed that higher expression of DUSP5 in relation to DUSP5P1 correlated with the expression of the pro-apoptotic factor B cell leukemia/lymphoma 2-like 11 (BCL2L11) in peripheral blood cells and HL cells. Knock-down of DUSP5 in HL cells resulted in down-regulation of BCL2L11. Thus, the DUSP5/DUSP5P1 system could be responsible for regulation of BCL2L11 leading to inhibition of apoptosis in these tumor cells. PMID:24651368

  8. Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome

    SciTech Connect

    Romine, Margaret F.; Carlson, Timothy; Norbeck, Angela D.; McCue, Lee Ann; Lipton, Mary S.

    2008-05-01

    Shewanella oneidensis MR-1 is the first of 22 different Shewanella spp. whose genomes have been or are being sequenced and thus serves as the model organism for studying the functional repertoire of the Shewanella genus. The original MR-1 genome annotation revealed a large number of transposase genes and pseudogenes, indicating that many of the genome’s functions may be decaying. Comparative analyses of the sequenced Shewanella strains suggest that 209 genes in MR-1 have in-frame stop codons, frameshifts, or interruptions and/or are truncated and that 65 of the original pseudogene predictions were erroneous. Among the decaying functions are that of one of three chemotaxis clusters, type I pilus production, starch utilization, and nitrite respiration. Many of the mutations could be attributed to members of 41 different types of insertion sequence (IS) elements and three types of miniature inverted-repeat transposable elements identified here for the first time. The high copy numbers of individual mobile elements (up to 71) are expected to promote large-scale genome recombination events, as evidenced by the displacement of the algA promoter. The ability of MR-1 to acquire foreign genes via reactions catalyzed by both the integron integrase and the ISSod25-encoded integrases is suggested by the presence of attC sites and genes whose sequences are characteristic of other species downstream of each site. This large number of mobile elements and multiple potential sites for integrasemediated acquisition of foreign DNA indicate that the MR-1 genome is exceptionally dynamic, with many functions and regulatory control points in the process of decay or reinvention.

  9. Efficient Analysis of Complex Structures

    NASA Technical Reports Server (NTRS)

    Kapania, Rakesh K.

    2000-01-01

    Last various accomplishments achieved during this project are : (1) A Survey of Neural Network (NN) applications using MATLAB NN Toolbox on structural engineering especially on equivalent continuum models (Appendix A). (2) Application of NN and GAs to simulate and synthesize substructures: 1-D and 2-D beam problems (Appendix B). (3) Development of an equivalent plate-model analysis method (EPA) for static and vibration analysis of general trapezoidal built-up wing structures composed of skins, spars and ribs. Calculation of all sorts of test cases and comparison with measurements or FEA results. (Appendix C). (4) Basic work on using second order sensitivities on simulating wing modal response, discussion of sensitivity evaluation approaches, and some results (Appendix D). (5) Establishing a general methodology of simulating the modal responses by direct application of NN and by sensitivity techniques, in a design space composed of a number of design points. Comparison is made through examples using these two methods (Appendix E). (6) Establishing a general methodology of efficient analysis of complex wing structures by indirect application of NN: the NN-aided Equivalent Plate Analysis. Training of the Neural Networks for this purpose in several cases of design spaces, which can be applicable for actual design of complex wings (Appendix F).

  10. Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4)

    PubMed Central

    Key, Felix M.; Peter, Benjamin; Dennis, Megan Y.; Huerta-Sánchez, Emilia; Tang, Wei; Prokunina-Olsson, Ludmila; Nielsen, Rasmus; Andrés, Aida M.

    2014-01-01

    Interferon lambda 4 gene (IFNL4) encodes IFN-λ4, a new member of the IFN-λ family with antiviral activity. In humans IFNL4 open reading frame is truncated by a polymorphic frame-shift insertion that eliminates IFN-λ4 and turns IFNL4 into a polymorphic pseudogene. Functional IFN-λ4 has antiviral activity but the elimination of IFN-λ4 through pseudogenization is strongly associated with improved clearance of hepatitis C virus (HCV) infection. We show that functional IFN-λ4 is conserved and evolutionarily constrained in mammals and thus functionally relevant. However, the pseudogene has reached moderately high frequency in Africa, America, and Europe, and near fixation in East Asia. In fact, the pseudogenizing variant is among the 0.8% most differentiated SNPs between Africa and East Asia genome-wide. Its raise in frequency is associated with additional evidence of positive selection, which is strongest in East Asia, where this variant falls in the 0.5% tail of SNPs with strongest signatures of recent positive selection genome-wide. Using a new Approximate Bayesian Computation (ABC) approach we infer that the pseudogenizing allele appeared just before the out-of-Africa migration and was immediately targeted by moderate positive selection; selection subsequently strengthened in European and Asian populations resulting in the high frequency observed today. This provides evidence for a changing adaptive process that, by favoring IFN-λ4 inactivation, has shaped present-day phenotypic diversity and susceptibility to disease. PMID:25329461

  11. Structural analysis of vibroacoustical processes

    NASA Technical Reports Server (NTRS)

    Gromov, A. P.; Myasnikov, L. L.; Myasnikova, Y. N.; Finagin, B. A.

    1973-01-01

    The method of automatic identification of acoustical signals, by means of the segmentation was used to investigate noises and vibrations in machines and mechanisms, for cybernetic diagnostics. The structural analysis consists of presentation of a noise or vibroacoustical signal as a sequence of segments, determined by the time quantization, in which each segment is characterized by specific spectral characteristics. The structural spectrum is plotted as a histogram of the segments, also as a relation of the probability density of appearance of a segment to the segment type. It is assumed that the conditions of ergodic processes are maintained.

  12. Structured Functional Principal Component Analysis

    PubMed Central

    Shou, Haochang; Zipunnikov, Vadim; Crainiceanu, Ciprian M.; Greven, Sonja

    2015-01-01

    Summary Motivated by modern observational studies, we introduce a class of functional models that expand nested and crossed designs. These models account for the natural inheritance of the correlation structures from sampling designs in studies where the fundamental unit is a function or image. Inference is based on functional quadratics and their relationship with the underlying covariance structure of the latent processes. A computationally fast and scalable estimation procedure is developed for high-dimensional data. Methods are used in applications including high-frequency accelerometer data for daily activity, pitch linguistic data for phonetic analysis, and EEG data for studying electrical brain activity during sleep. PMID:25327216

  13. Structured functional principal component analysis.

    PubMed

    Shou, Haochang; Zipunnikov, Vadim; Crainiceanu, Ciprian M; Greven, Sonja

    2015-03-01

    Motivated by modern observational studies, we introduce a class of functional models that expand nested and crossed designs. These models account for the natural inheritance of the correlation structures from sampling designs in studies where the fundamental unit is a function or image. Inference is based on functional quadratics and their relationship with the underlying covariance structure of the latent processes. A computationally fast and scalable estimation procedure is developed for high-dimensional data. Methods are used in applications including high-frequency accelerometer data for daily activity, pitch linguistic data for phonetic analysis, and EEG data for studying electrical brain activity during sleep. PMID:25327216

  14. Uncertainty Analysis of Composite Structures

    NASA Technical Reports Server (NTRS)

    Noor, Ahmed K.; Starnes, James H., Jr.; Peters, Jeanne M.

    2000-01-01

    A two-phase approach and a computational procedure are presented for predicting the variability in the nonlinear response of composite structures associated with variations in the geometric and material parameters of the structure. In the first phase, hierarchical sensitivity analysis is used to identify the major parameters, which have the most effect on the response quantities of interest. In the second phase, the major parameters are taken to be fuzzy parameters, and a fuzzy set analysis is used to determine the range of variation of the response, associated with preselected variations in the major parameters. The effectiveness of the procedure is demonstrated by means of a numerical example of a cylindrical panel with four T-shaped stiffeners and a circular cutout.

  15. HOST structural analysis program overview

    NASA Technical Reports Server (NTRS)

    Thompson, Robert L.

    1986-01-01

    Hot-section components of aircraft gas turbine engines are subjected to severe thermal structural loading conditions, especially during the startup and takeoff portions of the engine cycle. The most severe and damaging stresses and strains are those induced by the steep thermal gradients induced during the startup transient. These transient stresses and strains are also the most difficult to predict, in part because the temperature gradients and distributions are not well known or readily predictable and, in part, because the cyclic elastic-viscoplastic behavior of the materials at these extremes of temperature and strain are not well known or readily predictable. A broad spectrum of structures related technology programs is underway to address these deficiencies at the basic as well as the applied level. The three key program elements in the HOST structural analysis program are computations, constitutive modeling, and experiments for each research activity. Also shown are tables summarizing each of the activities.

  16. Grid Stiffened Structure Analysis Tool

    NASA Technical Reports Server (NTRS)

    1999-01-01

    The Grid Stiffened Analysis Tool contract is contract performed by Boeing under NASA purchase order H30249D. The contract calls for a "best effort" study comprised of two tasks: (1) Create documentation for a composite grid-stiffened structure analysis tool, in the form of a Microsoft EXCEL spread sheet, that was developed by originally at Stanford University and later further developed by the Air Force, and (2) Write a program that functions as a NASTRAN pre-processor to generate an FEM code for grid-stiffened structure. In performing this contract, Task 1 was given higher priority because it enables NASA to make efficient use of a unique tool they already have; Task 2 was proposed by Boeing because it also would be beneficial to the analysis of composite grid-stiffened structures, specifically in generating models for preliminary design studies. The contract is now complete, this package includes copies of the user's documentation for Task 1 and a CD ROM & diskette with an electronic copy of the user's documentation and an updated version of the "GRID 99" spreadsheet.

  17. Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution.

    PubMed

    Sun, Yanxia; Moore, Michael J; Zhang, Shoujun; Soltis, Pamela S; Soltis, Douglas E; Zhao, Tingting; Meng, Aiping; Li, Xiaodong; Li, Jianqiang; Wang, Hengchang

    2016-03-01

    The grade of early-diverging eudicots includes five major lineages: Ranunculales, Trochodendrales, Buxales, Proteales and Sabiaceae. To examine the evolution of plastome structure in early-diverging eudicots, we determined the complete plastome sequences of eight previously unsequenced early-diverging eudicot taxa, Pachysandra terminalis (Buxaceae), Meliosma aff. cuneifolia (Sabiaceae), Sabia yunnanensis (Sabiaceae), Epimedium sagittatum (Berberidaceae), Euptelea pleiosperma (Eupteleaceae), Akebia trifoliata (Lardizabalaceae), Stephania japonica (Menispermaceae) and Papaver somniferum (Papaveraceae), and compared them to previously published plastomes of the early-diverging eudicots Buxus, Tetracentron, Trochodendron, Nelumbo, Platanus, Nandina, Megaleranthis, Ranunculus, Mahonia and Macadamia. All of the newly sequenced plastomes share the same 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes, except for that of Epimedium, in which infA is pseudogenized and clpP is highly divergent and possibly a pseudogene. The boundaries of the plastid Inverted Repeat (IR) were found to vary significantly across early-diverging eudicots; IRs ranged from 24.3 to 36.4kb in length and contained from 18 to 33 genes. Based on gene content, the IR was classified into six types, with shifts among types characterized by high levels of homoplasy. Reconstruction of ancestral IR gene content suggested that 18 genes were likely present in the IR region of the ancestor of eudicots. Maximum likelihood phylogenetic analysis of a 79-gene, 97-taxon data set that included all available early-diverging eudicots and representative sampling of remaining angiosperm diversity largely agreed with previous estimates of early-diverging eudicot relationships, but resolved Trochodendrales rather than Buxales as sister to Gunneridae, albeit with relatively weak bootstrap support, conflicting with what has been found for these three clades in most previous analyses. In addition, Proteales was

  18. Probabilistic methods for structural response analysis

    NASA Technical Reports Server (NTRS)

    Wu, Y.-T.; Burnside, O. H.; Cruse, T. A.

    1988-01-01

    This paper addresses current work to develop probabilistic structural analysis methods for integration with a specially developed probabilistic finite element code. The goal is to establish distribution functions for the structural responses of stochastic structures under uncertain loadings. Several probabilistic analysis methods are proposed covering efficient structural probabilistic analysis methods, correlated random variables, and response of linear system under stationary random loading.

  19. HOST structural analysis program overview

    NASA Technical Reports Server (NTRS)

    Johns, R. H.

    1983-01-01

    Hot section components of aircraft gas turbine engines are subjected to severe thermal structural loading conditions, especially during the start up and take off portions of the engine cycle. The most severe and damaging stresses and strains are those induced by the steep thermal gradients induced during the start up transient. These transient stresses and strains are also the most difficult to predict, in part because of the temperature gradients and distributions are not well known or readily predictable, and also because the cyclic elastic viscoplastic behavior of the materials at these extremes of temperature and strain are not well known or readily predictable. A broad spectrum of structures related technology programs is underway to address these deficiencies. One element of the structures program is developing improved time varying thermal mechanical load models for the entire engine mission cycle from start up to shutdown. Another major part of the program is the development of new and improved nonlinear 3-D finite elements and associated structural analysis programs, including the development of temporal elements with time dependent properties to account for creep effects in the materials and components.

  20. Analysis of DCC domain structure

    SciTech Connect

    Randrup, J.; Thews, R.L.

    1997-10-01

    Wavelet-type methods are employed for the analysis of pion field configurations that have been obtained by dynamical simulations in idealized scenarios relevant to the formation of disoriented chiral condensates. It is illustrated how the measurement of the isospin domain structure depends on the ability to zoom in on limited parts of the phase space, due to the interplay between the pion correlation length and the effective source geometry. The need for advanced analysis methods is underscored by the fact that the extracted neutral-fraction distribution would differ significantly from the ideal form, even under perfect experimental conditions, and, moreover, by the circumstance that thermal sources with suitably adjusted temperatures can lead to distributions that may be practically indistinguishable from those arising from DCC-type nonequilibrium evolutions. {copyright} {ital 1997} {ital The American Physical Society}

  1. Analysis of DCC domain structure

    SciTech Connect

    Randrup, J.; Thews, R.L.

    1997-05-07

    Wavelet-type methods are employed for the analysis of pion field configurations that have been obtained by dynamical simulations in idealized scenarios relevant to the formation of disoriented chiral condensates. It is illustrated how the measurement of the isospin domain structure depends on the ability to zoom in on limited parts of the phase space, due to the interplay between the pion correlation length and the effective source geometry. The need for advanced analysis methods is underscored by the fact that the extracted neutral-fraction distribution would differ significantly from the ideal form, even under perfect experimental conditions, and, moreover, by the circumstance that thermal sources with suitably adjusted temperatures can lead to distributions that may be practically indistinguishable from those arising from DCC-type nonequilibrium evolutions.

  2. Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5.

    PubMed

    Hawkins, Peter G; Morris, Kevin V

    2010-11-01

    Long non-coding RNAs (lncRNAs) have been shown to epigenetically regulate certain genes in human cells. Here we report evidence for the involvement of an antisense lncRNA in the transcriptional regulation of the pluripotency-associated factor Oct4. When an lncRNA antisense to Oct4-pseudogene 5 was suppressed, transcription of Oct4 and Oct4 pseudogenes 4 and 5 was observed to increase. This increase correlated with a loss of silent state epigenetic marks and the histone methyltransferase Ezh2 at the Oct4 promoter. We observed this lncRNA to interact with nucleolin and PURA, a 35 kD single-stranded DNA and RNA binding protein, and found that these proteins may act to negatively regulate this antisense transcript. PMID:21151833

  3. Association between prostate cancer in black Americans and an allele of the PADPRP pseudogene locus on chromosome 13

    SciTech Connect

    Doll, J.A.; Suarez, B.K.; Donis-Keller, H.

    1996-02-01

    Black American men have a higher incidence of cancer of the prostate (CAP), multiple myeloma, and lung cancer than do white American men. The basis for these differences no doubt includes environmental influences, because American blacks have also been found to have a higher incidence of CAP than do African blacks. However, genetic factors may play a role as well. For example, Lyn et al. reported an increase in the frequency of an allele of the poly(ADP-ribose) polymerase (PADPRP) pseudogene locus on chromosome 13 in black Americans with CAP, suggesting the presence of a disease-susceptibility locus. Since only nine CAP patients were studied, proof of the significance of the finding for the general population of black Americans will rely on independent replication of the result and studies with larger sample sizes. We have doubled the number of black American CAP patients studied at the PADPRP pseudogene locus on chromosome 13 and compared them with white Americans with CAP, along with reference samples. In addition, we have determined allele frequencies by using a larger number of white individuals, from the CEPH reference pedigree resource, and a larger number of black Americans than previously reported, which may reflect more accurately the allele frequencies in these populations. We also find a statistically significant association between an allele at the PADPRP pseudogene locus and CAP in black Americans; however, it is not the same allele reported by Lyn et al. Furthermore, we tested CAP tumor DNA for chromosome 13 PADPRP pseudogene region deletions. In contrast to the report of Bhatia et al., we found no evidence for deletions that would suggest the presence of a tumor-suppressor gene in this region of chromosome 13. 16 refs., 2 tabs.

  4. Progress in thermostructural analysis of space structures

    NASA Technical Reports Server (NTRS)

    Thornton, E. A.; Dechaumphai, P.; Mahaney, J.; Pandey, A. K.

    1982-01-01

    A finite element space structures research focused on the interdisciplinary problems of heating, thermal, and structural analysis is discussed. Slender member shadowing effects, and cable stiffened structures are described.

  5. Sequencing and comparative analysis of the gorilla MHC genomic sequence.

    PubMed

    Wilming, Laurens G; Hart, Elizabeth A; Coggill, Penny C; Horton, Roger; Gilbert, James G R; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC. PMID:23589541

  6. Two ethnic-specific polymorphisms in the human beta pseudogene of hemoglobin.

    PubMed

    Pompei, F; Ciminelli, B M; Modiano, G

    1998-08-01

    Two polymorphic sites, -107 C-->T and -100 G-->C with respect to the cap site of the human beta pseudogene of the hemoglobin gene, are described. They have been studied in five European, one Indian, two Asian, and two sub-Saharan African populations. The -107 C-->T site turned out to be polymorphic in all five European populations and the Indian population (pooled q = 0.142 +/- 0.018) and in the two Asian populations (pooled q = 0.073 +/- 0.025), but it was monomorphic in the two sub-Saharan populations. On the contrary, the -100 G-->C site was polymorphic in the two sub-Saharan samples (q = 0.093 +/- 0.024), but the variant allele was not found in any of the European, Indian, or Asian samples. Thus this only 8-bp-long stretch of DNA is informative for estimating the extent of genetic admixture in sub-Saharan Africans. PMID:9686479

  7. Heterogeneity of Human Neutrophil CD177 Expression Results from CD177P1 Pseudogene Conversion

    PubMed Central

    Liang, Rong; Ohnesorg, Thomas; Cho, Vicky; Abhayaratna, Walter P.; Gatenby, Paul A.; Perera, Chandima; Zhang, Yafei; Whittle, Belinda; Sinclair, Andrew; Goodnow, Christopher C.; Field, Matthew; Andrews, T. Daniel; Cook, Matthew C.

    2016-01-01

    Most humans harbor both CD177neg and CD177pos neutrophils but 1–10% of people are CD177null, placing them at risk for formation of anti-neutrophil antibodies that can cause transfusion-related acute lung injury and neonatal alloimmune neutropenia. By deep sequencing the CD177 locus, we catalogued CD177 single nucleotide variants and identified a novel stop codon in CD177null individuals arising from a single base substitution in exon 7. This is not a mutation in CD177 itself, rather the CD177null phenotype arises when exon 7 of CD177 is supplied entirely by the CD177 pseudogene (CD177P1), which appears to have resulted from allelic gene conversion. In CD177 expressing individuals the CD177 locus contains both CD177P1 and CD177 sequences. The proportion of CD177hi neutrophils in the blood is a heritable trait. Abundance of CD177hi neutrophils correlates with homozygosity for CD177 reference allele, while heterozygosity for ectopic CD177P1 gene conversion correlates with increased CD177neg neutrophils, in which both CD177P1 partially incorporated allele and paired intact CD177 allele are transcribed. Human neutrophil heterogeneity for CD177 expression arises by ectopic allelic conversion. Resolution of the genetic basis of CD177null phenotype identifies a method for screening for individuals at risk of CD177 isoimmunisation. PMID:27227454

  8. Heterogeneity of Human Neutrophil CD177 Expression Results from CD177P1 Pseudogene Conversion.

    PubMed

    Wu, Zuopeng; Liang, Rong; Ohnesorg, Thomas; Cho, Vicky; Lam, Wesley; Abhayaratna, Walter P; Gatenby, Paul A; Perera, Chandima; Zhang, Yafei; Whittle, Belinda; Sinclair, Andrew; Goodnow, Christopher C; Field, Matthew; Andrews, T Daniel; Cook, Matthew C

    2016-05-01

    Most humans harbor both CD177neg and CD177pos neutrophils but 1-10% of people are CD177null, placing them at risk for formation of anti-neutrophil antibodies that can cause transfusion-related acute lung injury and neonatal alloimmune neutropenia. By deep sequencing the CD177 locus, we catalogued CD177 single nucleotide variants and identified a novel stop codon in CD177null individuals arising from a single base substitution in exon 7. This is not a mutation in CD177 itself, rather the CD177null phenotype arises when exon 7 of CD177 is supplied entirely by the CD177 pseudogene (CD177P1), which appears to have resulted from allelic gene conversion. In CD177 expressing individuals the CD177 locus contains both CD177P1 and CD177 sequences. The proportion of CD177hi neutrophils in the blood is a heritable trait. Abundance of CD177hi neutrophils correlates with homozygosity for CD177 reference allele, while heterozygosity for ectopic CD177P1 gene conversion correlates with increased CD177neg neutrophils, in which both CD177P1 partially incorporated allele and paired intact CD177 allele are transcribed. Human neutrophil heterogeneity for CD177 expression arises by ectopic allelic conversion. Resolution of the genetic basis of CD177null phenotype identifies a method for screening for individuals at risk of CD177 isoimmunisation. PMID:27227454

  9. Finite element analysis of helicopter structures

    NASA Technical Reports Server (NTRS)

    Rich, M. J.

    1978-01-01

    Application of the finite element analysis is now being expanded to three dimensional analysis of mechanical components. Examples are presented for airframe, mechanical components, and composite structure calculations. Data are detailed on the increase of model size, computer usage, and the effect on reducing stress analysis costs. Future applications for use of finite element analysis for helicopter structures are projected.

  10. Probabilistic structural analysis methods of hot engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Hopkins, D. A.

    1989-01-01

    Development of probabilistic structural analysis methods for hot engine structures is a major activity at Lewis Research Center. Recent activities have focused on extending the methods to include the combined uncertainties in several factors on structural response. This paper briefly describes recent progress on composite load spectra models, probabilistic finite element structural analysis, and probabilistic strength degradation modeling. Progress is described in terms of fundamental concepts, computer code development, and representative numerical results.

  11. Probabilistic structural analysis methods development for SSME

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Hopkins, D. A.

    1988-01-01

    The development of probabilistic structural analysis methods is a major part of the SSME Structural Durability Program and consists of three program elements: composite load spectra, probabilistic finite element structural analysis, and probabilistic structural analysis applications. Recent progress includes: (1) the effects of the uncertainties of several factors on the HPFP blade temperature pressure and torque, (2) the evaluation of the cumulative distribution function of structural response variables based on assumed uncertainties on primitive structural variables, and (3) evaluation of the failure probability. Collectively, the results obtained demonstrate that the structural durability of critical SSME components can be probabilistically evaluated.

  12. Probabilistic structural analysis methods of hot engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Hopkins, D. A.

    1989-01-01

    Development of probabilistic structural analysis methods for hot engine structures at Lewis Research Center is presented. Three elements of the research program are: (1) composite load spectra methodology; (2) probabilistic structural analysis methodology; and (3) probabilistic structural analysis application. Recent progress includes: (1) quantification of the effects of uncertainties for several variables on high pressure fuel turbopump (HPFT) turbine blade temperature, pressure, and torque of the space shuttle main engine (SSME); (2) the evaluation of the cumulative distribution function for various structural response variables based on assumed uncertainties in primitive structural variables; and (3) evaluation of the failure probability. Collectively, the results demonstrate that the structural durability of hot engine structural components can be effectively evaluated in a formal probabilistic/reliability framework.

  13. Pseudogenization of the MCP-2/CCL8 chemokine gene in European rabbit (genus Oryctolagus), but not in species of Cottontail rabbit (Sylvilagus) and Hare (Lepus)

    PubMed Central

    2012-01-01

    Background Recent studies in human have highlighted the importance of the monocyte chemotactic proteins (MCP) in leukocyte trafficking and their effects in inflammatory processes, tumor progression, and HIV-1 infection. In European rabbit (Oryctolagus cuniculus) one of the prime MCP targets, the chemokine receptor CCR5 underwent a unique structural alteration. Until now, no homologue of MCP-2/CCL8a, MCP-3/CCL7 or MCP-4/CCL13 genes have been reported for this species. This is interesting, because at least the first two genes are expressed in most, if not all, mammals studied, and appear to be implicated in a variety of important chemokine ligand-receptor interactions. By assessing the Rabbit Whole Genome Sequence (WGS) data we have searched for orthologs of the mammalian genes of the MCP-Eotaxin cluster. Results We have localized the orthologs of these chemokine genes in the genome of European rabbit and compared them to those of leporid genera which do (i.e. Oryctolagus and Bunolagus) or do not share the CCR5 alteration with European rabbit (i.e. Lepus and Sylvilagus). Of the Rabbit orthologs of the CCL8, CCL7, and CCL13 genes only the last two were potentially functional, although showing some structural anomalies at the protein level. The ortholog of MCP-2/CCL8 appeared to be pseudogenized by deleterious nucleotide substitutions affecting exon1 and exon2. By analyzing both genomic and cDNA products, these studies were extended to wild specimens of four genera of the Leporidae family: Oryctolagus, Bunolagus, Lepus, and Sylvilagus. It appeared that the anomalies of the MCP-3/CCL7 and MCP-4/CCL13 proteins are shared among the different species of leporids. In contrast, whereas MCP-2/CCL8 was pseudogenized in every studied specimen of the Oryctolagus - Bunolagus lineage, this gene was intact in species of the Lepus - Sylvilagus lineage, and was, at least in Lepus, correctly transcribed. Conclusion The biological function of a gene was often revealed in situations of

  14. Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation

    PubMed Central

    Kondrashov, Fyodor A; Koonin, Eugene V; Morgunov, Igor G; Finogenova, Tatiana V; Kondrashova, Marie N

    2006-01-01

    Background The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in animal tissues has been reported. In order to clarify the status of the MS and ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic study. Results Using sequence similarity searches, we identified MS genes in arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in the numerous sequenced genomes of placental mammals. The regions of the placental mammals' genomes expected to code for malate synthase, as determined by comparison of the gene orders in vertebrate genomes, show clear similarity to the opossum MS sequence but contain stop codons, indicating that the MS gene became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable in animals other than the nematodes that possess a bifunctional, fused ICL-MS gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal gene transfer events that probably went in both directions between several bacterial and eukaryotic lineages. The strongest evidence was obtained for the acquisition of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the corresponding operonic organization by the common ancestor of the nematodes. Conclusion The distribution of the MS and ICL genes in animals suggests that either they encode alternative enzymes of the glyoxylate cycle that are not orthologous to the known MS and ICL or the animal MS acquired a new function that remains to be characterized. Regardless of the ultimate solution to this conundrum, the genes for the glyoxylate cycle enzymes present a remarkable variety of evolutionary events including unusual horizontal gene transfer from bacteria to animals. Reviewers Arcady Mushegian (Stowers Institute for Medical

  15. Distribution of nuclear mitochondrial pseudogenes in three pollinator fig wasps associated with Ficus pumila

    NASA Astrophysics Data System (ADS)

    Chen, Yan; Liu, Min; Compton, Stephen G.; Chen, Xiao-Yong

    2014-05-01

    Nuclear mitochondrial pseudogenes (NUMTs) are nuclear sequences transferred from mitochondrial genomes. Although widespread, their distribution patterns among populations or closely related species are rarely documented. We amplified and sequenced the mitochondrial cytochrome b (Cytb) gene to check for NUMTs in three fig wasp species that pollinate Ficus pumila (Wiebesia sp. 1, 2 and 3) in Southeastern China using direct and cloned sequencing. Unambiguous sequences (332) of 487 bp in length belonging to 33 haplotypes were found by direct sequencing. Their distribution was highly concordant with those of cytochrome c oxidase subunit I (COI). Obvious signs of co-amplification of NUMTs were indicated by their uneven distribution. NUMTs were observed in all individuals of 12 populations of Wiebesia sp. 3, and 13 individuals of three northern populations of Wiebesia sp. 1. Sequencing clones of potential co-amplification products confirmed that they were NUMTs. These NUMTs either clustered as NUMT clades basal to mtDNA Cytb clades (basal NUMTs), or together with Cytb haplotypes. Basal NUMTs had either stop codons or frame-shifting mutations resulting from deletion of a 106 bp fragment. In addition, no third codon or synonymous substitutions were detected within each NUMT clade. The phylogenetic tree indicated that basal NUMTs had been inserted into nuclei before divergence of the three species. No significant pairwise differences were detected in their ratios of third codon substitutions, suggesting that these NUMTs originated from one transfer event, with duplication in the nuclear genome resulting in the coexistence of the 381 bp copy. No significant substitution differences were detected between Cytb haplotypes and NUMTs that clustered with Cytb haplotypes. However, these NUMTs coexisted with Cytb haplotypes in multiple populations, suggesting that these NUMT haplotypes were recently inserted into the nuclear genome. Both basal and recently inserted NUMTs were rare

  16. The human L-threonine 3-dehydrogenase gene is an expressed pseudogene

    PubMed Central

    Edgar, Alasdair J

    2002-01-01

    Background L-threonine is an indispensable amino acid. One of the major L-threonine degradation pathways is the conversion of L-threonine via 2-amino-3-ketobutyrate to glycine. L-threonine dehydrogenase (EC 1.1.1.103) is the first enzyme in the pathway and catalyses the reaction: L-threonine + NAD+ = 2-amino-3-ketobutyrate + NADH. The murine and porcine L-threonine dehydrogenase genes (TDH) have been identified previously, but the human gene has not been identified. Results The human TDH gene is located at 8p23-22 and has 8 exons spanning 10 kb that would have been expected to encode a 369 residue ORF. However, 2 cDNA TDH transcripts encode truncated proteins of 157 and 230 residues. These truncated proteins are the result of 3 mutations within the gene. There is a SNP, A to G, present in the genomic DNA sequence of some individuals which results in the loss of the acceptor splice site preceding exon 4. The acceptor splice site preceding exon 6 was lost in all 23 individuals genotyped and there is an in-frame stop codon in exon 6 (CGA to TGA) resulting in arginine-214 being replaced by a stop codon. These truncated proteins would be non-functional since they have lost part of the NAD+ binding motif and the COOH terminal domain that is thought to be involved in binding L-threonine. TDH mRNA was present in all tissues examined. Conclusions The human L-threonine 3-dehydrogenase gene is an expressed pseudogene having lost the splice acceptor site preceding exon 6 and codon arginine-214 (CGA) is mutated to a stop codon (TGA). PMID:12361482

  17. Structure in Teaching Theory and Analysis.

    ERIC Educational Resources Information Center

    Anderson, O. Roger

    A theory of structure in teaching is presented and a system of analysis introduced which allows empirical investigation of verbal behavior in the classroom. Two kinds of structure are distinguished: "static" structure, defined as stable organized clusters of knowledge, and "kinetic" structure, defined as the sequential process of building up…

  18. Modeling, Analysis, and Optimization Issues for Large Space Structures

    NASA Technical Reports Server (NTRS)

    Pinson, L. D. (Compiler); Amos, A. K. (Compiler); Venkayya, V. B. (Compiler)

    1983-01-01

    Topics concerning the modeling, analysis, and optimization of large space structures are discussed including structure-control interaction, structural and structural dynamics modeling, thermal analysis, testing, and design.

  19. The first intron of human c-fms proto-oncogene contains a processed pseudogene (RPL7P) for ribosomal protein L7

    SciTech Connect

    Sapi, E.; Flick, M.B.; Kacinski, B.M.

    1994-08-01

    During sequence analysis of the first intron of the human c-fms oncogene, we identified an open reading frame encoding the ribosomal protein L7 (RPL7). The presence of this sequence within intron 1 of the c-fms gene was confirmed by Southern blot hybridization and by sequence analysis of two independent cosmid clones (cos2-e and cos1-22) that span the human genomic c-fms locus. The RPL7 sequence was detected in a region of sequence overlapped by the cos2-e and cos1-22 cosmid clones but oriented opposite to the c-fms gene. We demonstrate that the sequence is identical to the full-length RPL7 cDNA sequence, but lacks any recognizable introns, has a 30-bp poly(A) tail, and is bracketed by two perfect direct repeats of 14 bp. We also showed that despite the fact that the 5{prime} flanking region of the RPL7 sequence contains a potential TATA box upstream of an intact open reading frame, this pseudogene (RPL7P) is not actively transcribed. 28 refs., 4 figs.

  20. Genomic organization of the human gene (CA5) and pseudogene for mitochondrial carbonic anhydrase V and their localization to chromosomes 16q and 16p

    SciTech Connect

    Nagao, Yoshiro; Sly, W.S.; Batanian, J.R.

    1995-08-10

    Carbonic anhydrase V (CA V) is expressed in mitochondrial matrix in liver and several other tissues. It is of interest for its putative roles in providing bicarbonate to carbamoyl phosphate synthetase for ureagenesis and to pyruvate carboxylase for gluconeogenesis and its possible importance in explaining certain inherited metabolic disorders with hyperammonemia and hypoglycemia. Following the recent characterization of the cDNA for human CA V, we report the isolation of the human gene from two {lambda} genomic libraries and its characterization. The CA V gene (CA5) is approximately 50 kb long and contains 7 exons and 6 introns. The exon-intron boundaries are found in positions identical to those determined for the previously described CA II, CA III, and CA VII genes. Like the CA VII gene, CA5 does not contain typical TATA and CAAT promoter elements in the 5{prime} flanking region but does contain a TTTAA sequence 147 nucleotides upstream of the initiation codon. CA5 also contains a 12-bp GT-rich segment beginning 13 bp downstream of the polyadenylation signal in the 3{prime} untranslated region of exon 7. FISH analysis allowed CA5 to be assigned to chromosome 16q24.3. An unprocessed pseudogene containing sequence homologous to exons 3-7 and introns 3-6 was also isolated and was assigned by FISH analysis to chromosome 16p11.2-p12. 22 refs., 4 figs., 1 tab.

  1. Structural analysis considerations for wind turbine blades

    NASA Technical Reports Server (NTRS)

    Spera, D. A.

    1979-01-01

    Approaches to the structural analysis of wind turbine blade designs are reviewed. Specifications and materials data are discussed along with the analysis of vibrations, loads, stresses, and failure modes.

  2. Design sensitivity analysis of nonlinear structural response

    NASA Technical Reports Server (NTRS)

    Cardoso, J. B.; Arora, J. S.

    1987-01-01

    A unified theory is described of design sensitivity analysis of linear and nonlinear structures for shape, nonshape and material selection problems. The concepts of reference volume and adjoint structure are used to develop the unified viewpoint. A general formula for design sensitivity analysis is derived. Simple analytical linear and nonlinear examples are used to interpret various terms of the formula and demonstrate its use.

  3. Confirmation of the potential usefulness of two human beta globin pseudogene markers to estimate gene flows to and from sub-Saharan Africans.

    PubMed

    Ciminelli, Bianca Maria; Pompei, Fiorenza; Relucenti, Michela; Lum, J Koji; Simporé, Jacques; Spedini, Gabriella; Martínez-Labarga, Cristina; Pardo, Miguel G

    2002-04-01

    Two polymorphic sites, -107 and -100 with respect to the "cap" site of the human beta globin pseudogene, recently discovered in our laboratory, turned out to have an ethnically complementary distribution. The first site is polymorphic in Europeans, North Africans, Indians (Hindu), and Oriental Asians, and monomorphic in sub-Saharan Africans. Conversely, the second site is polymorphic in sub-Saharan African populations and monomorphic in the aforementioned populations. Here we report the gene frequencies of these two polymorphic sites in nine additional populations (Egyptians, Spaniards, Japanese, Chinese, Filipinos, Vietnamese, Africans from Togo and from Benin, and Pygmies), confirming their ethnospecificity and, through the analysis of these two markers in Oromo and Amhara of Ethiopia (two mixed populations), their usefulness in genetic admixture studies. Moreover, we studied another marker polymorphic in sub-Saharan African populations only, a TaqI restriction fragment length polymorphism located in the same region as the present markers, demonstrating the absence of linkage disequilibrium between it and the -100 site, so that we can exclude that the information they provide is redundant. PMID:12030652

  4. Of the Nine Cytidine Deaminase-Like Genes in Arabidopsis, Eight Are Pseudogenes and Only One Is Required to Maintain Pyrimidine Homeostasis in Vivo.

    PubMed

    Chen, Mingjia; Herde, Marco; Witte, Claus-Peter

    2016-06-01

    CYTIDINE DEAMINASE (CDA) catalyzes the deamination of cytidine to uridine and ammonia in the catabolic route of C nucleotides. The Arabidopsis (Arabidopsis thaliana) CDA gene family comprises nine members, one of which (AtCDA) was shown previously in vitro to encode an active CDA. A possible role in C-to-U RNA editing or in antiviral defense has been discussed for other members. A comprehensive bioinformatic analysis of plant CDA sequences, combined with biochemical functionality tests, strongly suggests that all Arabidopsis CDA family members except AtCDA are pseudogenes and that most plants only require a single CDA gene. Soybean (Glycine max) possesses three CDA genes, but only two encode functional enzymes and just one has very high catalytic efficiency. AtCDA and soybean CDAs are located in the cytosol. The functionality of AtCDA in vivo was demonstrated with loss-of-function mutants accumulating high amounts of cytidine but also CMP, cytosine, and some uridine in seeds. Cytidine hydrolysis in cda mutants is likely caused by NUCLEOSIDE HYDROLASE1 (NSH1) because cytosine accumulation is strongly reduced in a cda nsh1 double mutant. Altered responses of the cda mutants to fluorocytidine and fluorouridine indicate that a dual specific nucleoside kinase is involved in cytidine as well as uridine salvage. CDA mutants display a reduction in rosette size and have fewer leaves compared with the wild type, which is probably not caused by defective pyrimidine catabolism but by the accumulation of pyrimidine catabolism intermediates reaching toxic concentrations. PMID:27208239

  5. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.

    ERIC Educational Resources Information Center

    Chesick, John P.

    1989-01-01

    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  6. Computer applications for engineering/structural analysis

    NASA Astrophysics Data System (ADS)

    Zaslawsky, M.; Samaddar, S. K.

    1991-10-01

    Analysts and organizations have a tendency to lock themselves into specific codes with the obvious consequence of not addressing the real problem and thus reaching the wrong conclusion. This paper discusses the role of the analyst in selecting computer codes. The participation and support of a computation division in modifying the source program, configuration management, and pre- and post-processing of codes are among the subjects discussed. Specific examples illustrating the computer code selection process are described in the following problem areas: soil structure interaction, structural analysis of nuclear reactors, analysis of waste tanks where fluid structure interaction is important, analysis of equipment, structure-structure interaction, analysis of the operation of the superconductor supercollider which includes friction and transient temperature, and 3D analysis of the 10-meter telescope being built in Hawaii. Validation and verification of computer codes and their impact on the selection process are also discussed.

  7. Computer applications for engineering/structural analysis

    SciTech Connect

    Zaslawsky, M.; Samaddar, S.K.

    1991-01-01

    Analysts and organizations have a tendency to lock themselves into specific codes with the obvious consequences of not addressing the real problem and thus reaching the wrong conclusion. This paper discusses the role of the analyst in selecting computer codes. The participation and support of a computation division in modifying the source program, configuration management, and pre- and post-processing of codes are among the subjects discussed. Specific examples illustrating the computer code selection process are described in the following problem areas: soil structure interaction, structural analysis of nuclear reactors, analysis of waste tanks where fluid structure interaction is important, analysis of equipment, structure-structure interaction, analysis of the operation of the superconductor supercollider which includes friction and transient temperature, and 3D analysis of the 10-meter telescope being built in Hawaii. Validation and verification of computer codes and their impact on the selection process are also discussed.

  8. Modal analysis of jointed structures

    NASA Astrophysics Data System (ADS)

    Quinn, D. Dane

    2012-01-01

    Structural systems are often composed of multiple components joined together at localized interfaces. Compared to a corresponding monolithic system these interfaces are designed to have little influence on the load carrying capability of the system, and the resulting change in the overall system mass and stiffness is minimal. Hence, under nominal operating conditions the mode shapes and frequencies of the dominant structural modes are relatively insensitive to the presence of the interfaces. However, the energy dissipation in such systems is strongly dependent on the joints. The microslip that occurs at each interface couples together the structural modes of the system and introduces nonlinear damping into the system, effectively altering the observed damping of the structural modes, which can then significantly alter the amplitude of the response at the resonant modal frequencies. This work develops equations of motion for a jointed structure in terms of the structural modal coordinates and implements a reduced-order description of the microslip that occurs at the interface between components. The interface is incorporated into the modal description of the system through an existing decomposition of a series-series Iwan interface model and a continuum approximation for microslip of an elastic rod. The developed framework is illustrated on several examples, including a discrete three degree-of-freedom system as well as the longitudinal deformation of a continuum beam.

  9. Fast Approximate Analysis Of Modified Antenna Structure

    NASA Technical Reports Server (NTRS)

    Levy, Roy

    1991-01-01

    Abbreviated algorithms developed for fast approximate analysis of effects of modifications in supporting structures upon root-mean-square (rms) path-length errors of paraboloidal-dish antennas. Involves combination of methods of structural-modification reanalysis with new extensions of correlation analysis to obtain revised rms path-length error. Full finite-element analysis, usually requires computer of substantial capacity, necessary only to obtain responses of unmodified structure to known external loads and to selected self-equilibrating "indicator" loads. Responses used in shortcut calculations, which, although theoretically "exact", simple enough to be performed on hand-held calculator. Useful in design, design-sensitivity analysis, and parametric studies.

  10. Structural analysis techniqes for remote sensing

    NASA Technical Reports Server (NTRS)

    Shapiro, L. G.

    1982-01-01

    The structural analysis of remotely sensed imagery is defined and basic techniques for implementing the process are described. Structural analysis uses knowledge of the properties of an entity, its parts and their relationships, and the relationships in which it participates at a higher level to locate and recognize objects in a visual scene. The representation of structural knowledge, the development of algorithms for using the knowledge to help analyze an image, and techniques for storage and retrieval of relational models are addressed.

  11. Probabilistic structural analysis by extremum methods

    NASA Technical Reports Server (NTRS)

    Nafday, Avinash M.

    1990-01-01

    The objective is to demonstrate discrete extremum methods of structural analysis as a tool for structural system reliability evaluation. Specifically, linear and multiobjective linear programming models for analysis of rigid plastic frames under proportional and multiparametric loadings, respectively, are considered. Kinematic and static approaches for analysis form a primal-dual pair in each of these models and have a polyhedral format. Duality relations link extreme points and hyperplanes of these polyhedra and lead naturally to dual methods for system reliability evaluation.

  12. Inhibitory effect of RNA-mediated knockdown of zinc finger protein 91 pseudogene on pancreatic cancer cell growth and invasion

    PubMed Central

    Huang, Weiyi; Li, Ning; Hu, Jiong; Wang, Lei

    2016-01-01

    Worldwide, human pancreatic cancer is a rare malignancy with a poor prognosis. Long non-coding RNAs (lncRNAs) are known to have a crucial role in cancer occurrence and progression; however, the role of pseudogene-expressed lncRNAs, a major type of lncRNA, have not been thoroughly analyzed in cancer. Therefore, the present study focused on zinc finger protein 91 pseudogene (ZFP91-P). ZFP91-P expression was initially detected in two pancreatic cancer cell lines by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and the highest expression of ZFP91-P was found in the BXPC-3-H cell line. Subsequently, BXPC-3-H cells were transfected with ZFP91-P short hairpin RNA (shRNA) using a plasmid vector and termed shZFP91-P. Cells transfected with negative control plasmid vector were termed shCon. MTT and Transwell assays were performed to analyze the proliferation and migration of BXPC-3-H cells, respectively, and western blotting was used to detect epithelial-mesenchymal transition markers, including vimentin and β-catenin. The present study showed that depletion of ZFP91-P markedly decreased pancreatic cancer cell proliferation and inhibited cell migration capacity. In addition, the expression of β-catenin increased while vimentin expression decreased. The current findings suggest that high expression of ZFP91-P promotes the migration of BXPC-3-H cells and may be a novel marker for early diagnosis for pancreatic cancer. PMID:27446435

  13. Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

    PubMed Central

    Ji, Zhe; Song, Ruisheng; Regev, Aviv; Struhl, Kevin

    2015-01-01

    Using a new bioinformatic method to analyze ribosome profiling data, we show that 40% of lncRNAs and pseudogene RNAs expressed in human cells are translated. In addition, ~35% of mRNA coding genes are translated upstream of the primary protein-coding region (uORFs) and 4% are translated downstream (dORFs). Translated lncRNAs preferentially localize in the cytoplasm, whereas untranslated lncRNAs preferentially localize in the nucleus. The translation efficiency of cytoplasmic lncRNAs is nearly comparable to that of mRNAs, suggesting that cytoplasmic lncRNAs are engaged by the ribosome and translated. While most peptides generated from lncRNAs may be highly unstable byproducts without function, ~9% of the peptides are conserved in ORFs in mouse transcripts, as are 74% of pseudogene peptides, 24% of uORF peptides and 32% of dORF peptides. Analyses of synonymous and nonsynonymous substitution rates of these conserved peptides show that some are under stabilizing selection, suggesting potential functional importance. DOI: http://dx.doi.org/10.7554/eLife.08890.001 PMID:26687005

  14. Structural analysis of ultra-high speed aircraft structural components

    NASA Technical Reports Server (NTRS)

    Lenzen, K. H.; Siegel, W. H.

    1977-01-01

    The buckling characteristics of a hypersonic beaded skin panel were investigated under pure compression with boundary conditions similar to those found in a wing mounted condition. The primary phases of analysis reported include: (1) experimental testing of the panel to failure; (2) finite element structural analysis of the beaded panel with the computer program NASTRAN; and (3) summary of the semiclassical buckling equations for the beaded panel under purely compressive loads. A comparison of each of the analysis methods is also included.

  15. Modeling and structural analysis of honeycomb structure mirror

    NASA Astrophysics Data System (ADS)

    Li, Yeping

    2012-09-01

    In development of large-scale astronomical telescopes, some promising new technology and method such as honeycomb structure mirrors and silicon carbide mirrors are applied for primary mirrors. Especially in space telescopes, the mirror lightweight design is becoming the key technology and honeycomb structure mirrors are normally required more and more to reduce the cost and increase the feasibility of the telescopes system. In this paper, a parameter FEA model of a two meters honeycomb structure mirror has been built, by using the engineering analysis software ANSYS. Through this model, the structural analysis, thermal deformation analysis and the simulation active correction of low-order frequency aberration by the finite element method have been presented.

  16. Mass spectrometry for pectin structure analysis.

    PubMed

    Ralet, Marie-Christine; Lerouge, Patrice; Quéméner, Bernard

    2009-09-28

    Pectin are extremely complex biopolymers made up of different structural domains. Enzymatic degradation followed by purification and structural analysis of the degradation products proved to be efficient tools for the understanding of pectin fine structure, including covalent interactions between pectic structural domains or with other cell wall polysaccharides. Due to its high sensitivity, high throughput and capacity to analyze mixtures, mass spectrometry has gained more and more importance as a tool for oligosaccharides structural characterization in the past 10 years. This review will focus on the combined use of mass spectrometry and enzymatic digestion for pectins structural characterization. PMID:19058795

  17. Structural analysis consultation using artificial intelligence

    NASA Technical Reports Server (NTRS)

    Melosh, R. J.; Marcal, P. V.; Berke, L.

    1978-01-01

    The primary goal of consultation is definition of the best strategy to deal with a structural engineering analysis objective. The knowledge base to meet the need is designed to identify the type of numerical analysis, the needed modeling detail, and specific analysis data required. Decisions are constructed on the basis of the data in the knowledge base - material behavior, relations between geometry and structural behavior, measures of the importance of time and temperature changes - and user supplied specifics characteristics of the spectrum of analysis types, the relation between accuracy and model detail on the structure, its mechanical loadings, and its temperature states. Existing software demonstrated the feasibility of the approach, encompassing the 36 analysis classes spanning nonlinear, temperature affected, incremental analyses which track the behavior of structural systems.

  18. Static Nonlinear Analysis In Concrete Structures

    SciTech Connect

    Hemmati, Ali

    2008-07-08

    Push-over analysis is a simple and applied approach which can be used for estimation of demand responses influenced by earthquake stimulations. The analysis is non-linear static analysis of the structure affected under increasing lateral loads and specifying the displacement--load diagram or structure capacity curve, draw the curve the base shear values and lateral deflection on the roof level of the building will be used. However, for estimation of the real behavior of the structure against earthquake, the non-linear dynamic analysis approaches and various accelerographs should be applied. Of course it should be noted that this approach especially in relation with tall buildings is complex and time consuming. In the article, the different patterns of lateral loading in push-over analysis have been compared with non-linear dynamic analysis approach so that the results represented accordingly. The researches indicated the uniformly--distributed loading is closer to real status.

  19. NAPS: Network Analysis of Protein Structures.

    PubMed

    Chakrabarty, Broto; Parekh, Nita

    2016-07-01

    Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue-residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in Å) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein-protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/. PMID:27151201

  20. Constraints and restraints in crystal structure analysis

    PubMed Central

    Immirzi, Attilio

    2009-01-01

    The widely used restraint-based approach to structural analysis using diffraction data is critiqued. The convenience of using rigid constraints, through the use of internal coordinates, is discussed. PMID:22477768

  1. Semantic Antinomies and Deep Structure Analysis

    ERIC Educational Resources Information Center

    Zuber, Ryszard

    1975-01-01

    This article discusses constructions known as semantic antinomies, that is, the paradoxical results of false presuppositions, and how they can be dealt with by means of deep structure analysis. See FL 508 186 for availability. (CLK)

  2. Structural Dynamics and Data Analysis

    NASA Technical Reports Server (NTRS)

    Luthman, Briana L.

    2013-01-01

    This project consists of two parts, the first will be the post-flight analysis of data from a Delta IV launch vehicle, and the second will be a Finite Element Analysis of a CubeSat. Shock and vibration data was collected on WGS-5 (Wideband Global SATCOM- 5) which was launched on a Delta IV launch vehicle. Using CAM (CAlculation with Matrices) software, the data is to be plotted into Time History, Shock Response Spectrum, and SPL (Sound Pressure Level) curves. In this format the data is to be reviewed and compared to flight instrumentation data from previous flights of the same launch vehicle. This is done to ensure the current mission environments, such as shock, random vibration, and acoustics, are not out of family with existing flight experience. In family means the peaks on the SRS curve for WGS-5 are similar to the peaks from the previous flights and there are no major outliers. The curves from the data will then be compiled into a useful format so that is can be peer reviewed then presented before an engineering review board if required. Also, the reviewed data will be uploaded to the Engineering Review Board Information System (ERBIS) to archive. The second part of this project is conducting Finite Element Analysis of a CubeSat. In 2010, Merritt Island High School partnered with NASA to design, build and launch a CubeSat. The team is now called StangSat in honor of their mascot, the mustang. Over the past few years, the StangSat team has built a satellite and has now been manifested for flight on a SpaceX Falcon 9 launch in 2014. To prepare for the final launch, a test flight was conducted in Mojave, California. StangSat was launched on a Prospector 18D, a high altitude rocket made by Garvey Spacecraft Corporation, along with their sister satellite CP9 built by California Polytechnic University. However, StangSat was damaged during an off nominal landing and this project will give beneficial insights into what loads the CubeSat experienced during the crash

  3. Generalized Structured Component Analysis with Latent Interactions

    ERIC Educational Resources Information Center

    Hwang, Heungsun; Ho, Moon-Ho Ringo; Lee, Jonathan

    2010-01-01

    Generalized structured component analysis (GSCA) is a component-based approach to structural equation modeling. In practice, researchers may often be interested in examining the interaction effects of latent variables. However, GSCA has been geared only for the specification and testing of the main effects of variables. Thus, an extension of GSCA…

  4. Impact analysis of composite aircraft structures

    NASA Technical Reports Server (NTRS)

    Pifko, Allan B.; Kushner, Alan S.

    1993-01-01

    The impact analysis of composite aircraft structures is discussed. Topics discussed include: background remarks on aircraft crashworthiness; comments on modeling strategies for crashworthiness simulation; initial study of simulation of progressive failure of an aircraft component constructed of composite material; and research direction in composite characterization for impact analysis.

  5. Structural Analysis in a Conceptual Design Framework

    NASA Technical Reports Server (NTRS)

    Padula, Sharon L.; Robinson, Jay H.; Eldred, Lloyd B.

    2012-01-01

    Supersonic aircraft designers must shape the outer mold line of the aircraft to improve multiple objectives, such as mission performance, cruise efficiency, and sonic-boom signatures. Conceptual designers have demonstrated an ability to assess these objectives for a large number of candidate designs. Other critical objectives and constraints, such as weight, fuel volume, aeroelastic effects, and structural soundness, are more difficult to address during the conceptual design process. The present research adds both static structural analysis and sizing to an existing conceptual design framework. The ultimate goal is to include structural analysis in the multidisciplinary optimization of a supersonic aircraft. Progress towards that goal is discussed and demonstrated.

  6. Hot Flow Anomaly Structure Analysis

    NASA Astrophysics Data System (ADS)

    Shestakov, A.; Vaisberg, O. L.

    2010-12-01

    Hot Flow Anomaly observed on Interball-Tail on 03.14.1996 is investigated. The normal to the interplanetary current sheet interacting with bow shock was determined in assumption of tangential discontinuity. Calculated motional electric field was directed towards current sheet. The bow shock before HFA arrival to the spacecraft was quasi-perpendicular, and was quasi-parallel after HFA passage. Respectively, of the shocks, bracketing HFA, were quasi-perpendicular before HFA passage and quasi-parallel after it. With averaged velocity of plasma within the body of HFA and duration of HFA observation we determined its size in normal to the current sheet direction as ~ 2.5 RE. HFA consists of two regions separated by thin layer with different plasma characteristics. Convection of plasma within HFA, as observed along spacecraft trajectory by subtracting averaged velocity from observed velocities, show that plasma in each of two regions is moving from separating layer. It indicates that separating layer is the site of energy deposition from interaction of the solar wind with ions reflected from the shock. This is confirmed by analysis of ion velocity distributions in this layer.

  7. Structural-Thermal-Optical-Performance (STOP) Analysis

    NASA Technical Reports Server (NTRS)

    Bolognese, Jeffrey; Irish, Sandra

    2015-01-01

    The presentation will be given at the 26th Annual Thermal Fluids Analysis Workshop (TFAWS 2015) hosted by the Goddard Spaceflight Center (GSFC) Thermal Engineering Branch (Code 545). A STOP analysis is a multidiscipline analysis, consisting of Structural, Thermal and Optical Performance Analyses, that is performed for all space flight instruments and satellites. This course will explain the different parts of performing this analysis. The student will learn how to effectively interact with each discipline in order to accurately obtain the system analysis results.

  8. Pseudogenization of sopA and sopE2 is functionally linked and contributes to virulence of Salmonella enterica serovar Typhi.

    PubMed

    Valenzuela, L M; Hidalgo, A A; Rodríguez, L; Urrutia, I M; Ortega, A P; Villagra, N A; Paredes-Sabja, D; Calderón, I L; Gil, F; Saavedra, C P; Mora, G C; Fuentes, J A

    2015-07-01

    The difference in host range between Salmonella enterica serovar Typhimurium (S. Typhimurium) and S. enterica serovar Typhi (S. Typhi) can be partially attributed to pseudogenes. Pseudogenes are genomic segments homologous to functional genes that do not encode functional products due to the presence of genetic defects. S. Typhi lacks several protein effectors implicated in invasion or other important processes necessary for full virulence of S. Typhimurium. SopA and SopE2, effectors that have been lost by pseudogenization in S. Typhi, correspond to an ubiquitin ligase involved in cytokine production by infected cells, and to a guanine exchange factor necessary for invasion of epithelial cells, respectively. We hypothesized that sopA and/or sopE pseudogenization contributed to the virulence of S. Typhi. In this work, we found that S. Typhi expressing S. Typhimurium sopE2 exhibited a decreased invasion in different epithelial cell lines compared with S. Typhi WT. S. Typhimurium sopA completely abolished the hypo-invasive phenotype observed in S. Typhi expressing S. Typhimurium sopE2, suggesting that functional SopA and SopE2 participate concertedly in the invasion process. Finally, the expression of S. Typhimurium sopA and/or sopE2 in S. Typhi, determined changes in the secretion of IL-8 and IL-18 in infected epithelial cells. PMID:25913156

  9. A protein structure data and analysis system.

    PubMed

    Tian, Hao; Sunderraman, Rajshekhar; Weber, Irene; Wang, Haibin; Yang, Hong

    2005-01-01

    In this paper, we present the design and implementation of a protein structure data and analysis system that is only used in the lab for analyzing the proprietary data. It is capable of storing public protein data, such as the data in Protein Data Bank (PDB) [1], and life scientists' proprietary data. This toolkit is targeted at life scientists who want to maintain proprietary protein structure data (may be incomplete), to search and query publicly known protein structures and to compare their structure data with others. The comparison functions can be used to find structure differences between two proteins at atom level, especially in mutant versions of proteins. The system can also be used as a tool of choosing better protein structure template in new protein's tertiary structure prediction. The system is developed in Java and the protein data is stored in a relational database (Oracle 9i). PMID:17282836

  10. Seismic analysis of nuclear power plant structures

    NASA Technical Reports Server (NTRS)

    Go, J. C.

    1973-01-01

    Primary structures for nuclear power plants are designed to resist expected earthquakes of the site. Two intensities are referred to as Operating Basis Earthquake and Design Basis Earthquake. These structures are required to accommodate these seismic loadings without loss of their functional integrity. Thus, no plastic yield is allowed. The application of NASTRAN in analyzing some of these seismic induced structural dynamic problems is described. NASTRAN, with some modifications, can be used to analyze most structures that are subjected to seismic loads. A brief review of the formulation of seismic-induced structural dynamics is also presented. Two typical structural problems were selected to illustrate the application of the various methods of seismic structural analysis by the NASTRAN system.

  11. Simultaneous analysis and design. [in structural engineering

    NASA Technical Reports Server (NTRS)

    Haftka, R. T.

    1985-01-01

    Optimization techniques are increasingly being used for performing nonlinear structural analysis. The development of element by element (EBE) preconditioned conjugate gradient (CG) techniques is expected to extend this trend to linear analysis. Under these circumstances the structural design problem can be viewed as a nested optimization problem. There are computational benefits to treating this nested problem as a large single optimization problem. The response variables (such as displacements) and the structural parameters are all treated as design variables in a unified formulation which performs simultaneously the design and analysis. Two examples are used for demonstration. A seventy-two bar truss is optimized subject to linear stress constraints and a wing box structure is optimized subject to nonlinear collapse constraints. Both examples show substantial computational savings with the unified approach as compared to the traditional nested approach.

  12. Fuzzy finite element analysis of smart structures

    NASA Astrophysics Data System (ADS)

    Akpan, Unyime O.; Koko, Tamunoiyala S.; Orisamolu, Irewole R.; Gallant, B. Keith

    2000-06-01

    A fuzzy finite element based approach is developed for modelling smart structures with vague or imprecise uncertainties. Fuzzy sets are used to represent the uncertainties present in the piezoelectric, mechanical, thermal, and physical properties of the smart structure. In order to facilitate efficient computation, a sensitivity analysis procedure is used to streamline the number of input fuzzy variables, and the vertex fuzzy analysis technique is then used to compute the possibility distributions of the responses of the smart structural system. The methodology has been developed within the framework of the SMARTCOM computational tool for the design/analysis of smart composite structures. The methodology developed is found to be accurate and computationally efficient for solution of practical problems.

  13. Expression profile of COL2A1 and the pseudogene SLC6A10P predicts tumor recurrence in high-grade serous ovarian cancer.

    PubMed

    Ganapathi, Mahrukh K; Jones, Wendell D; Sehouli, Jalid; Michener, Chad M; Braicu, Ioana E; Norris, Eric J; Biscotti, Charles V; Vaziri, Susan A J; Ganapathi, Ram N

    2016-02-01

    Tumor recurrence, following initial response to adjuvant chemotherapy, is a major problem in women with high-grade serous ovarian cancer (HGSOC). Microarray analysis of primary tumors has identified genes that may be useful in risk stratification/overall survival, but are of limited value in predicting the >70% rate for tumor recurrence. In this study, we performed RNA-Seq analysis of primary and recurrent HGSOC to first identify unique differentially expressed genes. From this dataset, we selected 21 archetypical coding genes and one noncoding RNA, based on statistically significant differences in their expression profile between tumors, for validation by qPCR in a larger cohort of 110 ovarian tumors (71 primary and 39 recurrent) and for testing association of specific genes with time-to-recurrence (TTR). Kaplan-Meier tests revealed that high expression of collagen type II, alpha 1 (COL2A1) was associated with delayed TTR (HR = 0.47, 95% CI: 0.27-0.82, p = 0.008), whereas low expression of the pseudogene, solute carrier family 6 member 10 (SLC6A10P), was associated with longer TTR (HR = 0.53, 95% CI: 0.30-0.93, p = 0.027). Notably, TTR was significantly delayed for tumors that simultaneously highly expressed COL2A1 and lowly expressed SLC6A10P (HR = 0.21, 95% CI: 0.082-0.54, p = 0.0011), an estimated median of 95 months as compared to an estimated median of 16 months for subjects expressing other levels of COL2A1 and SLC6A10P. Thus, evaluating expression levels of COL2A1 and SLC6A10P at primary surgery could be beneficial for clinically managing recurrence of HGSOC. PMID:26311224

  14. Static structural analysis of shell-type structures

    NASA Technical Reports Server (NTRS)

    Baker, E. H.; Cappelli, A. P.; Kovalevsky, L.; Rish, F. L.; Verrette, R. M.

    1968-01-01

    Shell analysis manual provides methods for determining static deflections and internal load and stress distributions in shells under various loading conditions, and methods of analyzing static instability of shell structures. Also included are methods for determining the lightest shell wall for various constructions.

  15. Probabilistic structural analysis computer code (NESSUS)

    NASA Technical Reports Server (NTRS)

    Shiao, Michael C.

    1988-01-01

    Probabilistic structural analysis has been developed to analyze the effects of fluctuating loads, variable material properties, and uncertain analytical models especially for high performance structures such as SSME turbopump blades. The computer code NESSUS (Numerical Evaluation of Stochastic Structure Under Stress) was developed to serve as a primary computation tool for the characterization of the probabilistic structural response due to the stochastic environments by statistical description. The code consists of three major modules NESSUS/PRE, NESSUS/FEM, and NESSUS/FPI. NESSUS/PRE is a preprocessor which decomposes the spatially correlated random variables into a set of uncorrelated random variables using a modal analysis method. NESSUS/FEM is a finite element module which provides structural sensitivities to all the random variables considered. NESSUS/FPI is Fast Probability Integration method by which a cumulative distribution function or a probability density function is calculated.

  16. FTH1P3, a Novel H-Ferritin Pseudogene Transcriptionally Active, Is Ubiquitously Expressed and Regulated during Cell Differentiation.

    PubMed

    Di Sanzo, Maddalena; Aversa, Ilenia; Santamaria, Gianluca; Gagliardi, Monica; Panebianco, Mariafranca; Biamonte, Flavia; Zolea, Fabiana; Faniello, Maria Concetta; Cuda, Giovanni; Costanzo, Francesco

    2016-01-01

    Ferritin, the major iron storage protein, performs its essential functions in the cytoplasm, nucleus and mitochondria. The variable assembly of 24 subunits of the Heavy (H) and Light (L) type composes the cytoplasmic molecule. In humans, two distinct genes code these subunits, both belonging to complex multigene families. Until now, one H gene has been identified with the coding sequence interrupted by three introns and more than 20 intronless copies widely dispersed on different chromosomes. Two of the intronless genes are actively transcribed in a tissue-specific manner. Herein, we report that FTH1P3, another intronless pseudogene, is transcribed. FTH1P3 transcript was detected in several cell lines and tissues, suggesting that its transcription is ubiquitary, as it happens for the parental ferritin H gene. Moreover, FTH1P3 expression is positively regulated during the cell differentiation process. PMID:26982978

  17. FTH1P3, a Novel H-Ferritin Pseudogene Transcriptionally Active, Is Ubiquitously Expressed and Regulated during Cell Differentiation

    PubMed Central

    Di Sanzo, Maddalena; Aversa, Ilenia; Santamaria, Gianluca; Gagliardi, Monica; Panebianco, Mariafranca; Biamonte, Flavia; Zolea, Fabiana; Faniello, Maria Concetta

    2016-01-01

    Ferritin, the major iron storage protein, performs its essential functions in the cytoplasm, nucleus and mitochondria. The variable assembly of 24 subunits of the Heavy (H) and Light (L) type composes the cytoplasmic molecule. In humans, two distinct genes code these subunits, both belonging to complex multigene families. Until now, one H gene has been identified with the coding sequence interrupted by three introns and more than 20 intronless copies widely dispersed on different chromosomes. Two of the intronless genes are actively transcribed in a tissue-specific manner. Herein, we report that FTH1P3, another intronless pseudogene, is transcribed. FTH1P3 transcript was detected in several cell lines and tissues, suggesting that its transcription is ubiquitary, as it happens for the parental ferritin H gene. Moreover, FTH1P3 expression is positively regulated during the cell differentiation process. PMID:26982978

  18. Thermal-Structural Analysis of Sunshield Membranes

    NASA Technical Reports Server (NTRS)

    Johnston, John; Parrish, Keith

    2003-01-01

    Future large infrared space telescopes, such as the James Webb Space Telescope (JWST), will require deployable sunshields to provide passive cooling for optics and instruments. Deployable sunshield structures for such applications typically consist of multiple thin-film membrane layers supported by deployable booms. The mechanical design of the sunshield must accommodate thermal strains due to layer-to-layer temperature differences as well as potentially large in-plane temperature gradients within individual film layers. This paper describes a thermal-structural analysis for predicting the stress state in a thin-film membrane subject to both mechanical thermal loads that could aid in the mechanical design of future sunshield structures. First the temperature field predicted by a thermal analysis is mapped to a structural finite element model, and then the structural response is predicted using a nonlinear static analysis. The structural model uses membrane elements in conjunction with a tension field material model to predict the response of the thin-film membrane layer. The tension field material model accounts for no-compression behavior associated with wrinkling and slackness. This approach was used to study the problem of a single membrane layer from the NASA reference concept for the JWST sunshield. Results from the analysis show that the membrane can experience a loss of tensile preload due to the presence of an in-plane temperature gradient representative of the cold-side layer temperature distribution predicted for the reference concept JWST.

  19. Analysis of flexible structures under lateral impact

    SciTech Connect

    Ramirez, D. F.; Razavi, H.

    2012-07-01

    Three methods for analysis of flexible structures under lateral impact are presented. The first proposed method (Method A) consists of: (1) modifying an available deceleration on a rigid target with conservation principles to account for structural flexibility; and (2) transient nonlinear analysis of the structure with the corrected forcing function. The second proposed method (Method B) is similar to Method A in obtaining the forcing function but it solves the equations of motion of an idealized two-degree-of-freedom system instead of directly using conservation principles. The last method simply provides the maximum force in the structure using the conservation of energy and linear momentum. A coupled simulation is also performed in LS-DYNA and compared against the proposed methods. A case study is presented to illustrate the applicability of all three methods and the LS-DYNA simulation. (authors)

  20. Structural analysis for a 40-story building

    NASA Technical Reports Server (NTRS)

    Hua, L.

    1972-01-01

    NASTRAN was chosen as the principal analytical tool for structural analysis of the Illinois Center Plaza Hotel Building in Chicago, Illinois. The building is a 40-story, reinforced concrete structure utilizing a monolithic slab-column system. The displacements, member stresses, and foundation loads due to wind load, live load, and dead load were obtained through a series of NASTRAN runs. These analyses and the input technique are described.

  1. Structural analysis of FAST reflector supporting system

    NASA Astrophysics Data System (ADS)

    Luo, Y. F.; Deng, C. G.; Li, G. Q.; He, Y. M.

    According to the deformation and movement requirements of the FAST reflector, a multi-purpose analysis, including the load-bearing behavior, deformation, construction costs of the reflector supporting structure and its model, is presented in this paper. The advantages and disadvantages of steel and aluminum alloy structures are also discussed and compared through detailed design calculations under load-bearing capacity and normal working conditions.

  2. Improving transient analysis technology for aircraft structures

    NASA Technical Reports Server (NTRS)

    Melosh, R. J.; Chargin, Mladen

    1989-01-01

    Aircraft dynamic analyses are demanding of computer simulation capabilities. The modeling complexities of semi-monocoque construction, irregular geometry, high-performance materials, and high-accuracy analysis are present. At issue are the safety of the passengers and the integrity of the structure for a wide variety of flight-operating and emergency conditions. The technology which supports engineering of aircraft structures using computer simulation is examined. Available computer support is briefly described and improvement of accuracy and efficiency are recommended. Improved accuracy of simulation will lead to a more economical structure. Improved efficiency will result in lowering development time and expense.

  3. Simplified method for nonlinear structural analysis

    NASA Technical Reports Server (NTRS)

    Kaufman, A.

    1983-01-01

    A simplified inelastic analysis computer program was developed for predicting the stress-strain history of a thermomechanically cycled structure from an elastic solution. The program uses an iterative and incremental procedure to estimate the plastic strains from the material stress-strain properties and a simulated plasticity hardening model. The simplified method was exercised on a number of problems involving uniaxial and multiaxial loading, isothermal and nonisothermal conditions, and different materials and plasticity models. Good agreement was found between these analytical results and nonlinear finite element solutions for these problems. The simplified analysis program used less than 1 percent of the CPU time required for a nonlinear finite element analysis.

  4. Experimental modal analysis. [for vibrating structures

    NASA Technical Reports Server (NTRS)

    Allemang, R. J.

    1983-01-01

    Experimental modal analysis is extremely important with regard to verification of analytical models, identification of vibration and acoustic problems, and structural modification and sensitivity analysis. With the expanding access of the testing environment to computational power, the complexity of existing approaches, as well as the development of new approaches, to the estimation of modal parameters has grown tremendously. Currently, the state of the art in experimental modal analysis involves methods that can be grouped in four categories: forced normal mode excitation method, frequency response function method, damped complex exponential function method, and mathematical input-output model methods. The theoretical basis of each of these general approaches, with appropriate references, is reviewed briefly.

  5. Structural reliability analysis and seismic risk assessment

    SciTech Connect

    Hwang, H.; Reich, M.; Shinozuka, M.

    1984-01-01

    This paper presents a reliability analysis method for safety evaluation of nuclear structures. By utilizing this method, it is possible to estimate the limit state probability in the lifetime of structures and to generate analytically the fragility curves for PRA studies. The earthquake ground acceleration, in this approach, is represented by a segment of stationary Gaussian process with a zero mean and a Kanai-Tajimi Spectrum. All possible seismic hazard at a site represented by a hazard curve is also taken into consideration. Furthermore, the limit state of a structure is analytically defined and the corresponding limit state surface is then established. Finally, the fragility curve is generated and the limit state probability is evaluated. In this paper, using a realistic reinforced concrete containment as an example, results of the reliability analysis of the containment subjected to dead load, live load and ground earthquake acceleration are presented and a fragility curve for PRA studies is also constructed.

  6. Turbine blade nonlinear structural and life analysis

    NASA Technical Reports Server (NTRS)

    Mcknight, R. L.; Laflen, J. H.; Halford, G. R.; Kaufman, A.

    1982-01-01

    The utility of advanced structural analysis and life prediction techniques was evaluated for the life assessment of a commercial air-cooled turbine blade with a history of tip cracking. Three dimensional, nonlinear finite element structural analyses were performed for the blade tip region. The computed strain-temperature history of the critical location was imposed on a uniaxial strain controlled test specimen to evaluate the validity of the structural analysis method. Experimental results indicated higher peak stresses and greater stress relaxation than the analytical predictions. Life predictions using the Strainrange Partitioning and Frequency Modified approaches predicted 1200 to 4420 cycles and 2700 cycles to crack initiation, respectively, compared to an observed life of 3000 cycles.

  7. Out of plane analysis for composite structures

    NASA Technical Reports Server (NTRS)

    Paul, P. C.; Saff, C. R.; Sanger, Kenneth B.; Mahler, M. A.; Kan, Han Pin; Kautz, Edward F.

    1990-01-01

    Simple two dimensional analysis techniques were developed to aid in the design of strong joints for integrally stiffened/bonded composite structures subjected to out of plane loads. It was found that most out of plane failures were due to induced stresses arising from rapid changes in load path direction or geometry, induced stresses due to changes in geometry caused by buckling, or direct stresses produced by fuel pressure or bearing loads. While the analysis techniques were developed to address a great variety of out of plane loading conditions, they were primarily derived to address the conditions described above. The methods were developed and verified using existing element test data. The methods were demonstrated using the data from a test failure of a high strain wingbox that was designed, built, and tested under a previous program. Subsequently, a set of design guidelines were assembled to assist in the design of safe, strong integral composite structures using the analysis techniques developed.

  8. Economic Evaluation of Computerized Structural Analysis

    NASA Technical Reports Server (NTRS)

    Fortin, P. E.

    1985-01-01

    This completed effort involved a technical and economic study of the capabilities of computer programs in the area of structural analysis. The applicability of the programs to NASA projects and to other users was studied. The applications in other industries was explored including both research and development and applied areas. The costs of several alternative analysis programs were compared. A literature search covered applicable technical literature including journals, trade publications and books. In addition to the literature search, several commercial companies that have developed computerized structural analysis programs were contacted and their technical brochures reviewed. These programs include SDRC I-DEAS, MSC/NASTRAN, SCADA, SUPERSAP, NISA/DISPLAY, STAAD-III, MICAS, GTSTRUDL, and STARS. These programs were briefly reviewed as applicable to NASA projects.

  9. Integrated Structural Analysis and Test Program

    NASA Technical Reports Server (NTRS)

    Kaufman, Daniel

    2005-01-01

    An integrated structural-analysis and structure-testing computer program is being developed in order to: Automate repetitive processes in testing and analysis; Accelerate pre-test analysis; Accelerate reporting of tests; Facilitate planning of tests; Improve execution of tests; Create a vibration, acoustics, and shock test database; and Integrate analysis and test data. The software package includes modules pertaining to sinusoidal and random vibration, shock and time replication, acoustics, base-driven modal survey, and mass properties and static/dynamic balance. The program is commanded by use of ActiveX controls. There is minimal need to generate command lines. Analysis or test files are selected by opening a Windows Explorer display. After selecting the desired input file, the program goes to a so-called analysis data process or test data process, depending on the type of input data. The status of the process is given by a Windows status bar, and when processing is complete, the data are reported in graphical, tubular, and matrix form.

  10. Uncertain structural dynamics of aircraft panels and fuzzy structures analysis

    NASA Astrophysics Data System (ADS)

    Sparrow, Victor W.; Buehrle, Ralph D.

    2002-11-01

    Aircraft fuselage panels, seemingly simple structures, are actually complex because of the uncertainty of the attachments of the frame stiffeners and longitudinal stringers. It is clearly important to understand the dynamics of these panels because of the subsequent radiation into the passenger cabin, even when complete information is not available for all portions of the finite-element model. Over the last few years a fuzzy structures analysis (FSA) approach has been undertaken at Penn State and NASA Langley to quantify the uncertainty in modeling aircraft panels. A new MSC.Nastran [MSC.Software Corp. (Santa Ana, CA)] Direct Matrix Abstraction Program (DMAP) code was written and tested [AIAA paper 2001-1320, 42nd AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conf., Seattle, WA, 16 April 2001] and was applied to simple fuselage panel models [J. Acoust. Soc. Am. 109, 2410(A) (2001)]. Recently the work has focused on understanding the dynamics of a realistic aluminum fuselage panel, typical of today's aircraft construction. This presentation will provide an overview of the research and recent results will be given for the fuselage panel. Comparison between experiments and the FSA results will be shown for different fuzzy input parameters. [Work supported by NASA Research Cooperative Agreement NCC-1-382.

  11. Stochastic Simulation Tool for Aerospace Structural Analysis

    NASA Technical Reports Server (NTRS)

    Knight, Norman F.; Moore, David F.

    2006-01-01

    Stochastic simulation refers to incorporating the effects of design tolerances and uncertainties into the design analysis model and then determining their influence on the design. A high-level evaluation of one such stochastic simulation tool, the MSC.Robust Design tool by MSC.Software Corporation, has been conducted. This stochastic simulation tool provides structural analysts with a tool to interrogate their structural design based on their mathematical description of the design problem using finite element analysis methods. This tool leverages the analyst's prior investment in finite element model development of a particular design. The original finite element model is treated as the baseline structural analysis model for the stochastic simulations that are to be performed. A Monte Carlo approach is used by MSC.Robust Design to determine the effects of scatter in design input variables on response output parameters. The tool was not designed to provide a probabilistic assessment, but to assist engineers in understanding cause and effect. It is driven by a graphical-user interface and retains the engineer-in-the-loop strategy for design evaluation and improvement. The application problem for the evaluation is chosen to be a two-dimensional shell finite element model of a Space Shuttle wing leading-edge panel under re-entry aerodynamic loading. MSC.Robust Design adds value to the analysis effort by rapidly being able to identify design input variables whose variability causes the most influence in response output parameters.

  12. Coupled Aerodynamic-Thermal-Structural (CATS) Analysis

    NASA Technical Reports Server (NTRS)

    1995-01-01

    Coupled Aerodynamic-Thermal-Structural (CATS) Analysis is a focused effort within the Numerical Propulsion System Simulation (NPSS) program to streamline multidisciplinary analysis of aeropropulsion components and assemblies. Multidisciplinary analysis of axial-flow compressor performance has been selected for the initial focus of this project. CATS will permit more accurate compressor system analysis by enabling users to include thermal and mechanical effects as an integral part of the aerodynamic analysis of the compressor primary flowpath. Thus, critical details, such as the variation of blade tip clearances and the deformation of the flowpath geometry, can be more accurately modeled and included in the aerodynamic analyses. The benefits of this coupled analysis capability are (1) performance and stall line predictions are improved by the inclusion of tip clearances and hot geometries, (2) design alternatives can be readily analyzed, and (3) higher fidelity analysis by researchers in various disciplines is possible. The goals for this project are a 10-percent improvement in stall margin predictions and a 2:1 speed-up in multidisciplinary analysis times. Working cooperatively with Pratt & Whitney, the Lewis CATS team defined the engineering processes and identified the software products necessary for streamlining these processes. The basic approach is to integrate the aerodynamic, thermal, and structural computational analyses by using data management and Non-Uniform Rational B-Splines (NURBS) based data mapping. Five software products have been defined for this task: (1) a primary flowpath data mapper, (2) a two-dimensional data mapper, (3) a database interface, (4) a blade structural pre- and post-processor, and (5) a computational fluid dynamics code for aerothermal analysis of the drum rotor. Thus far (1) a cooperative agreement has been established with Pratt & Whitney, (2) a Primary Flowpath Data Mapper has been prototyped and delivered to General Electric

  13. Structural analysis of light aircraft using NASTRAN

    NASA Technical Reports Server (NTRS)

    Wilkinson, M. T.; Bruce, A. C.

    1973-01-01

    An application of NASTRAN to the structural analysis of light aircraft was conducted to determine the cost effectiveness. A model of the Baby Ace D model homebuilt aircraft was used. The NASTRAN model of the aircraft consists of 193 grid points connected by 352 structural members. All members are either rod or beam elements, including bending of unsymmetrical cross sections and torsion of noncircular cross sections. The aerodynamic loads applied to the aircraft were in accordance with FAA regulations governing the utility category aircraft.

  14. Music Structure Analysis from Acoustic Signals

    NASA Astrophysics Data System (ADS)

    Dannenberg, Roger B.; Goto, Masataka

    Music is full of structure, including sections, sequences of distinct musical textures, and the repetition of phrases or entire sections. The analysis of music audio relies upon feature vectors that convey information about music texture or pitch content. Texture generally refers to the average spectral shape and statistical fluctuation, often reflecting the set of sounding instruments, e.g., strings, vocal, or drums. Pitch content reflects melody and harmony, which is often independent of texture. Structure is found in several ways. Segment boundaries can be detected by observing marked changes in locally averaged texture.

  15. Analysis of Open TEM-Waveguide Structures

    NASA Astrophysics Data System (ADS)

    Rambousky, R.; Garbe, H.

    This work belongs to a research project on the analysis and characterization of higher order modes occurring in open TEM-waveguide structures. An open TEM waveguide, derived from a conventional GTEM cell by removing the sidewalls, is investigated. The intrinsic resonances of the electromagnetic field occurring in the test volume of the waveguide are analyzed in frequency domain by computer simulation and measurement. This resonance behavior is compared to that of more simplified wire models, describing just the planar septum of the original TEM waveguide. The influence of the number of wires used in the wire model is investigated with respect to the resonant behavior. The use of wire structures is a prerequisite for application of transmission-line super theory (TLST) for further analysis.

  16. Structure analysis for plane geometry figures

    NASA Astrophysics Data System (ADS)

    Feng, Tianxiao; Lu, Xiaoqing; Liu, Lu; Li, Keqiang; Tang, Zhi

    2013-12-01

    As there are increasing numbers of digital documents for education purpose, we realize that there is not a retrieval application for mathematic plane geometry images. In this paper, we propose a method for retrieving plane geometry figures (PGFs), which often appear in geometry books and digital documents. First, detecting algorithms are applied to detect common basic geometry shapes from a PGF image. Based on all basic shapes, we analyze the structural relationships between two basic shapes and combine some of them to a compound shape to build the PGF descriptor. Afterwards, we apply matching function to retrieve candidate PGF images with ranking. The great contribution of the paper is that we propose a structure analysis method to better describe the spatial relationships in such image composed of many overlapped shapes. Experimental results demonstrate that our analysis method and shape descriptor can obtain good retrieval results with relatively high effectiveness and efficiency.

  17. Study of galaxy structures by correlation analysis

    SciTech Connect

    Salvador-Sole, E.; Sanroma, M. )

    1989-10-01

    In a previous paper the authors presented a new method that makes it possible to infer the surface number density profile of galaxies in groups and clusters. This method is based on the correlation analysis of galaxy positions in a plate and applies to radially symmetric systems with uncorrelated positions of their particles. Here it is shown that, under these same assumptions, the method makes it possible to obtain the surface density profile of any additive positive property, as well as other related quantities, such as the line-of-sight velocity dispersion of galaxies. Moreover, the method can deal not only with structures that are radially symmetric but also with ones that are elliptically symmetric and axisymmetric. Finally, it is shown that the analogous method in one dimension makes it possible to obtain another important profile for the analysis of galaxy structures, namely, the line-of-sight velocity distribution. 5 refs.

  18. Combination of structural reliability and interval analysis

    NASA Astrophysics Data System (ADS)

    Qiu, Zhiping; Yang, Di; Elishakoff, Isaac

    2008-02-01

    In engineering applications, probabilistic reliability theory appears to be presently the most important method, however, in many cases precise probabilistic reliability theory cannot be considered as adequate and credible model of the real state of actual affairs. In this paper, we developed a hybrid of probabilistic and non-probabilistic reliability theory, which describes the structural uncertain parameters as interval variables when statistical data are found insufficient. By using the interval analysis, a new method for calculating the interval of the structural reliability as well as the reliability index is introduced in this paper, and the traditional probabilistic theory is incorporated with the interval analysis. Moreover, the new method preserves the useful part of the traditional probabilistic reliability theory, but removes the restriction of its strict requirement on data acquisition. Example is presented to demonstrate the feasibility and validity of the proposed theory.

  19. To Be or Not to Be a Pseudogene: A Molecular Epidemiological Approach to the mclx Genes and Its Impact in Tuberculosis

    PubMed Central

    Mendes, Marta Vaz; van Soolingen, Dick; Correia-Neves, Margarida

    2015-01-01

    Tuberculosis presents a myriad of symptoms, progression routes and propagation patterns not yet fully understood. Whereas for a long time research has focused solely on the patient immunity and overall susceptibility, it is nowadays widely accepted that the genetic diversity of its causative agent, Mycobacterium tuberculosis, plays a key role in this dynamic. This study focuses on a particular family of genes, the mclxs (Mycobacterium cyclase/LuxR-like genes), which codify for a particular and nearly mycobacterial-exclusive combination of protein domains. mclxs genes were found to be pseudogenized by frameshift-causing insertion(s)/deletion(s) in a considerable number of M. tuberculosis complex strains and clinical isolates. To discern the functional implications of the pseudogenization, we have analysed the pattern of frameshift-causing mutations in a group of M. tuberculosis isolates while taking into account their microbial-, patient- and disease-related traits. Our logistic regression-based analyses have revealed disparate effects associated with the transcriptional inactivation of two mclx genes. In fact, mclx2 (Rv1358) pseudogenization appears to be primarily driven by the microbial phylogenetic background, being mainly related to the Euro-American (EAm) lineage; on the other hand, mclx3 (Rv2488c) presents a higher tendency for pseudogenization among isolates from patients born on the Western Pacific area, and from isolates causing extra-pulmonary infections. These results contribute to the overall knowledge on the biology of M. tuberculosis infection, whereas at the same time launch the necessary basis for the functional assessment of these so far overlooked genes. PMID:26035295

  20. Human haematopoietic stem cells express Oct4 pseudogenes and lack the ability to initiate Oct4 promoter-driven gene expression.

    PubMed

    Redshaw, Zoe; Strain, Alastair J

    2010-01-01

    The transcription factor Oct4 is well defined as a key regulator of embryonic stem (ES) cell pluripotency. In recent years, the role of Oct4 has purportedly extended to the self renewal and maintenance of multipotency in adult stem cell (ASC) populations. This profile has arisen mainly from reports utilising reverse transcription-polymerase chain reaction (RT-PCR) based methodologies and has since come under scrutiny following the discovery that many developmental genes have multiple pseudogenes associated with them. Six known pseudogenes exist for Oct4, all of which exhibit very high sequence homology (three >97%), and for this reason the generation of artefacts may have contributed to false identification of Oct4 in somatic cell populations. While ASC lack a molecular blueprint of transcription factors proposed to be involved with 'stemness' as described for ES cells, it is not unreasonable to assume that similar gene patterns may exist. The focus of this work was to corroborate reports that Oct4 is involved in the regulation of ASC self-renewal and differentiation, using a combination of methodologies to rule out pseudogene interference. Haematopoietic stem cells (HSC) derived from human umbilical cord blood (UCB) and various differentiated cell lines underwent RT-PCR, product sequencing and transfection studies using an Oct4 promoter-driven reporter. In summary, only the positive control expressed Oct4, with all other cell types expressing a variety of Oct4 pseudogenes. Somatic cells were incapable of utilising an exogenous Oct4 promoter construct, leading to the conclusion that Oct4 does not appear involved in the multipotency of human HSC from UCB. PMID:20356403

  1. Coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures

    NASA Technical Reports Server (NTRS)

    Mcknight, R. L.; Huang, H.; Hartle, M.

    1992-01-01

    Accomplishments are described for the third years effort of a 5-year program to develop a methodology for coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures. These accomplishments include: (1) structural analysis capability specialized for graded composite structures including large deformation and deformation position eigenanalysis technologies; (2) a thermal analyzer specialized for graded composite structures; (3) absorption of electromagnetic waves by graded composite structures; and (4) coupled structural thermal/electromagnetic analysis of graded composite structures.

  2. Structural analysis at aircraft conceptual design stage

    NASA Astrophysics Data System (ADS)

    Mansouri, Reza

    In the past 50 years, computers have helped by augmenting human efforts with tremendous pace. The aircraft industry is not an exception. Aircraft industry is more than ever dependent on computing because of a high level of complexity and the increasing need for excellence to survive a highly competitive marketplace. Designers choose computers to perform almost every analysis task. But while doing so, existing effective, accurate and easy to use classical analytical methods are often forgotten, which can be very useful especially in the early phases of the aircraft design where concept generation and evaluation demands physical visibility of design parameters to make decisions [39, 2004]. Structural analysis methods have been used by human beings since the very early civilization. Centuries before computers were invented; the pyramids were designed and constructed by Egyptians around 2000 B.C, the Parthenon was built by the Greeks, around 240 B.C, Dujiangyan was built by the Chinese. Persepolis, Hagia Sophia, Taj Mahal, Eiffel tower are only few more examples of historical buildings, bridges and monuments that were constructed before we had any advancement made in computer aided engineering. Aircraft industry is no exception either. In the first half of the 20th century, engineers used classical method and designed civil transport aircraft such as Ford Tri Motor (1926), Lockheed Vega (1927), Lockheed 9 Orion (1931), Douglas DC-3 (1935), Douglas DC-4/C-54 Skymaster (1938), Boeing 307 (1938) and Boeing 314 Clipper (1939) and managed to become airborne without difficulty. Evidencing, while advanced numerical methods such as the finite element analysis is one of the most effective structural analysis methods; classical structural analysis methods can also be as useful especially during the early phase of a fixed wing aircraft design where major decisions are made and concept generation and evaluation demands physical visibility of design parameters to make decisions

  3. Probabilistic seismic demand analysis of nonlinear structures

    NASA Astrophysics Data System (ADS)

    Shome, Nilesh

    Recent earthquakes in California have initiated improvement in current design philosophy and at present the civil engineering community is working towards development of performance-based earthquake engineering of structures. The objective of this study is to develop efficient, but accurate procedures for probabilistic analysis of nonlinear seismic behavior of structures. The proposed procedures help the near-term development of seismic-building assessments which require an estimation of seismic demand at a given intensity level. We also develop procedures to estimate the probability of exceedance of any specified nonlinear response level due to future ground motions at a specific site. This is referred as Probabilistic Seismic Demand Analysis (PSDA). The latter procedure prepares the way for the next stage development of seismic assessment that consider the uncertainties in nonlinear response and capacity. The proposed procedures require structure-specific nonlinear analyses for a relatively small set of recorded accelerograms and (site-specific or USGS-map-like) seismic hazard analyses. We have addressed some of the important issues of nonlinear seismic demand analysis, which are selection of records for structural analysis, the number of records to be used, scaling of records, etc. Initially these issues are studied through nonlinear analysis of structures for a number of magnitude-distance bins of records. Subsequently we introduce regression analysis of response results against spectral acceleration, magnitude, duration, etc., which helps to resolve these issues more systematically. We illustrate the demand-hazard calculations through two major example problems: a 5story and a 20-story SMRF building. Several simple, but quite accurate closed-form solutions have also been proposed to expedite the demand-hazard calculations. We find that vector-valued (e.g., 2-D) PSDA estimates demand hazard more accurately. This procedure, however, requires information about 2

  4. Probabilistic structural analysis methods and applications

    NASA Technical Reports Server (NTRS)

    Cruse, T. A.; Wu, Y.-T.; Dias, B.; Rajagopal, K. R.

    1988-01-01

    An advanced algorithm for simulating the probabilistic distribution of structural responses due to statistical uncertainties in loads, geometry, material properties, and boundary conditions is reported. The method effectively combines an advanced algorithm for calculating probability levels for multivariate problems (fast probability integration) together with a general-purpose finite-element code for stress, vibration, and buckling analysis. Application is made to a space propulsion system turbine blade for which the geometry and material properties are treated as random variables.

  5. Analysis of nonlinear structures via mode synthesis

    NASA Technical Reports Server (NTRS)

    Gieseke, R. K.

    1975-01-01

    An effective procedure for NASTRAN was developed that permits any number of substructures of any size to be synthesized for the purpose of developing normal modes of vibration of the complete structural system. The technique is extended to permit modal transient analysis of the subdivided system. This latter procedure permits the use of NASTRAN's ability to include nonlinear forces in the problem. The five-phase process is accomplished using standard NASTRAN rigid formats with problem-independent alter packages and DMAP sequences.

  6. Evaluation, analysis and prediction of geologic structures

    NASA Astrophysics Data System (ADS)

    Woodward, Nicholas B.

    2012-08-01

    Balanced cross-sections claim to be better because they apply a rigorous set of rules to develop the conceptual model of the structures present in an area. Balanced cross-sections can be further improved and become more useful to understanding real physical problems by collection of additional data such as seismic reflection surveys, collection of additional stratigraphic data, or collection of rock fabric information. The additional information validates the initial model and provides details on deformation conditions and on local rock responses to the deformation. Although individual cross-sections are two dimensional, the objective of evaluation and analysis of deformed regions should be three dimensional whenever possible to recognize the challenges of the real world. Subsurface system analysis derived from the hydrologic community emphasizes conceptual model development through model verification, validation, uncertainty quantification, benchmarking and meta-analysis. Their approach includes many steps informally used by the structural geology community but in a much more explicit way. Newer geological applications of structural geology would benefit from this more rigorous approach for designing and doing performance predictions as technological needs become more socially sensitive such as for carbon storage sites, new areas of energy exploration in higher population density areas, or for nuclear waste storage facilities.

  7. Remote geologic structural analysis of Yucca Flat

    NASA Astrophysics Data System (ADS)

    Foley, M. G.; Heasler, P. G.; Hoover, K. A.; Rynes, N. J.; Thiessen, R. L.; Alfaro, J. L.

    1991-12-01

    The Remote Geologic Analysis (RGA) system was developed by Pacific Northwest Laboratory (PNL) to identify crustal structures that may affect seismic wave propagation from nuclear tests. Using automated methods, the RGA system identifies all valleys in a digital elevation model (DEM), fits three-dimensional vectors to valley bottoms, and catalogs all potential fracture or fault planes defined by coplanar pairs of valley vectors. The system generates a cluster hierarchy of planar features having greater-than-random density that may represent areas of anomalous topography manifesting structural control of erosional drainage development. Because RGA uses computer methods to identify zones of hypothesized control of topography, ground truth using a well-characterized test site was critical in our evaluation of RGA's characterization of inaccessible test sites for seismic verification studies. Therefore, we applied RGA to a study area centered on Yucca Flat at the Nevada Test Site (NTS) and compared our results with both mapped geology and geologic structures and with seismic yield-magnitude models. This is the final report of PNL's RGA development project for peer review within the U.S. Department of Energy Office of Arms Control (OAC) seismic-verification community. In this report, we discuss the Yucca Flat study area, the analytical basis of the RGA system and its application to Yucca Flat, the results of the analysis, and the relation of the analytical results to known topography, geology, and geologic structures.

  8. Remote geologic structural analysis of Yucca Flat

    SciTech Connect

    Foley, M.G.; Heasler, P.G.; Hoover, K.A.; Rynes, N.J.; Thiessen, R.L.; Alfaro, J.L.

    1991-12-01

    The Remote Geologic Analysis (RGA) system was developed by Pacific Northwest Laboratory (PNL) to identify crustal structures that may affect seismic wave propagation from nuclear tests. Using automated methods, the RGA system identifies all valleys in a digital elevation model (DEM), fits three-dimensional vectors to valley bottoms, and catalogs all potential fracture or fault planes defined by coplanar pairs of valley vectors. The system generates a cluster hierarchy of planar features having greater-than-random density that may represent areas of anomalous topography manifesting structural control of erosional drainage development. Because RGA uses computer methods to identify zones of hypothesized control of topography, ground truth using a well-characterized test site was critical in our evaluation of RGA`s characterization of inaccessible test sites for seismic verification studies. Therefore, we applied RGA to a study area centered on Yucca Flat at the Nevada Test Site (NTS) and compared our results with both mapped geology and geologic structures and with seismic yield-magnitude models. This is the final report of PNL`s RGA development project for peer review within the US Department of Energy Office of Arms Control (OAC) seismic-verification community. In this report, we discuss the Yucca Flat study area, the analytical basis of the RGA system and its application to Yucca Flat, the results of the analysis, and the relation of the analytical results to known topography, geology, and geologic structures. 41 refs., 39 figs., 2 tabs.

  9. Remote geologic structural analysis of Yucca Flat

    SciTech Connect

    Foley, M.G.; Heasler, P.G.; Hoover, K.A. ); Rynes, N.J. ); Thiessen, R.L.; Alfaro, J.L. )

    1991-12-01

    The Remote Geologic Analysis (RGA) system was developed by Pacific Northwest Laboratory (PNL) to identify crustal structures that may affect seismic wave propagation from nuclear tests. Using automated methods, the RGA system identifies all valleys in a digital elevation model (DEM), fits three-dimensional vectors to valley bottoms, and catalogs all potential fracture or fault planes defined by coplanar pairs of valley vectors. The system generates a cluster hierarchy of planar features having greater-than-random density that may represent areas of anomalous topography manifesting structural control of erosional drainage development. Because RGA uses computer methods to identify zones of hypothesized control of topography, ground truth using a well-characterized test site was critical in our evaluation of RGA's characterization of inaccessible test sites for seismic verification studies. Therefore, we applied RGA to a study area centered on Yucca Flat at the Nevada Test Site (NTS) and compared our results with both mapped geology and geologic structures and with seismic yield-magnitude models. This is the final report of PNL's RGA development project for peer review within the US Department of Energy Office of Arms Control (OAC) seismic-verification community. In this report, we discuss the Yucca Flat study area, the analytical basis of the RGA system and its application to Yucca Flat, the results of the analysis, and the relation of the analytical results to known topography, geology, and geologic structures. 41 refs., 39 figs., 2 tabs.

  10. Copy number variation in the ATP-binding cassette transporter ABCC6 gene and ABCC6 pseudogenes in patients with pseudoxanthoma elasticum

    PubMed Central

    Kringen, Marianne K; Stormo, Camilla; Berg, Jens Petter; Terry, Sharon F; Vocke, Christine M; Rizvi, Samar; Hendig, Doris; Piehler, Armin P

    2015-01-01

    Single mutations in the ATP-binding cassette transporter (ABCC6) gene (OMIM 603234) are known to cause the rare autosomal recessive disease pseudoxanthoma elasticum (PXE). Recently, we have found that copy number variations (CNVs) in pseudogenes of the ABCC6 gene are quite common. The aim of this study was to investigate the frequency and possible contribution of CNV in ABCC6 and its pseudogenes in PXE. Genomic DNA from 212 PXE individuals were examined for copy number by pyrosequencing and quantitative polymerase chain reaction (PCR) and compared with healthy individuals. The frequency of PXE individuals with any CNV was higher than in healthy individuals. The majority of variation comprised known and possibly new deletions in the ABCC6 gene and duplications of the ABCC6P1 and ABCC6P2 genes. ABCC6 deletions and ABCC6P2 duplications were not observed in 142 healthy individuals. In conclusion, by pyrosequencing and quantitative PCR, we were able to detect known and possibly new deletions in the ABCC6 gene that may have caused the PXE phenotype. Pyrosequencing may be used in PXE patients who have obtained incomplete genotype from conventional techniques. The frequency of ABCC6P2 pseudogene duplication was more common in PXE patients than healthy individuals and may affect the PXE phenotype. PMID:26029710

  11. Analysis of waveguiding properties of VCSEL structures

    SciTech Connect

    Erteza, I.A.

    1996-09-01

    In this paper, the authors explore the feasibility of using the distributed Bragg reflector, grown on the substrate for a VCSEL (Vertical Cavity Surface Emitting Laser), to provide waveguiding within the substrate. This waveguiding could serve as an interconnection among VCSELs in an array. Before determining the feasibility of waveguide interconnected VCSELs, two analysis methods are presented and evaluated for their applicability to this problem. The implementations in Mathematica of both these methods are included. Results of the analysis show that waveguiding in VCSEL structures is feasible. Some of the many possible uses of waveguide interconnected VCSELs are also briefly discussed. The tools and analysis presented in this report can be used to evaluate such system concepts and to do detailed design calculations.

  12. Structural Analysis Using Computer Based Methods

    NASA Technical Reports Server (NTRS)

    Dietz, Matthew R.

    2013-01-01

    The stiffness of a flex hose that will be used in the umbilical arms of the Space Launch Systems mobile launcher needed to be determined in order to properly qualify ground umbilical plate behavior during vehicle separation post T-0. This data is also necessary to properly size and design the motors used to retract the umbilical arms. Therefore an experiment was created to determine the stiffness of the hose. Before the test apparatus for the experiment could be built, the structure had to be analyzed to ensure it would not fail under given loading conditions. The design model was imported into the analysis software and optimized to decrease runtime while still providing accurate restlts and allow for seamless meshing. Areas exceeding the allowable stresses in the structure were located and modified before submitting the design for fabrication. In addition, a mock up of a deep space habitat and the support frame was designed and needed to be analyzed for structural integrity under different loading conditions. The load cases were provided by the customer and were applied to the structure after optimizing the geometry. Once again, weak points in the structure were located and recommended design changes were made to the customer and the process was repeated until the load conditions were met without exceeding the allowable stresses. After the stresses met the required factors of safety the designs were released for fabrication.

  13. Probabilistic analysis of a materially nonlinear structure

    NASA Technical Reports Server (NTRS)

    Millwater, H. R.; Wu, Y.-T.; Fossum, A. F.

    1990-01-01

    A probabilistic finite element program is used to perform probabilistic analysis of a materially nonlinear structure. The program used in this study is NESSUS (Numerical Evaluation of Stochastic Structure Under Stress), under development at Southwest Research Institute. The cumulative distribution function (CDF) of the radial stress of a thick-walled cylinder under internal pressure is computed and compared with the analytical solution. In addition, sensitivity factors showing the relative importance of the input random variables are calculated. Significant plasticity is present in this problem and has a pronounced effect on the probabilistic results. The random input variables are the material yield stress and internal pressure with Weibull and normal distributions, respectively. The results verify the ability of NESSUS to compute the CDF and sensitivity factors of a materially nonlinear structure. In addition, the ability of the Advanced Mean Value (AMV) procedure to assess the probabilistic behavior of structures which exhibit a highly nonlinear response is shown. Thus, the AMV procedure can be applied with confidence to other structures which exhibit nonlinear behavior.

  14. Structural Analysis of Sandwich Foam Panels

    SciTech Connect

    Kosny, Jan; Huo, X. Sharon

    2010-04-01

    The Sandwich Panel Technologies including Structural Insulated Panels (SIPs) can be used to replace the conventional wooden-frame construction method. The main purpose of this Cooperative Research and Development Agreement (CRADA) between UT-Battelle, LLC and SGI Venture, Inc. was to design a novel high R-value type of metal sandwich panelized technology. This CRADA project report presents design concept discussion and numerical analysis results from thermal performance study of this new building envelope system. The main objective of this work was to develop a basic concept of a new generation of wall panel technologies which will have R-value over R-20 will use thermal mass to improve energy performance in cooling dominated climates and will be 100% termite resistant. The main advantages of using sandwich panels are as follows: (1) better energy saving structural panels with high and uniform overall wall R-value across the elevation that could not be achieved in traditional walls; and (2) reducing the use of raw materials or need for virgin lumber. For better utilization of these Sandwich panels, engineers need to have a thorough understanding of the actual performance of the panels and system. Detailed analysis and study on the capacities and deformation of individual panels and its assembly have to be performed to achieve that goal. The major project activity was to conduct structural analysis of the stresses, strains, load capacities, and deformations of individual sandwich components under various load cases. The analysis simulated the actual loading conditions of the regular residential building and used actual material properties of the steel facings and foam.

  15. Network-based modular latent structure analysis

    PubMed Central

    2014-01-01

    Background High-throughput expression data, such as gene expression and metabolomics data, exhibit modular structures. Groups of features in each module follow a latent factor model, while between modules, the latent factors are quasi-independent. Recovering the latent factors can shed light on the hidden regulation patterns of the expression. The difficulty in detecting such modules and recovering the latent factors lies in the high dimensionality of the data, and the lack of knowledge in module membership. Methods Here we describe a method based on community detection in the co-expression network. It consists of inference-based network construction, module detection, and interacting latent factor detection from modules. Results In simulations, the method outperformed projection-based modular latent factor discovery when the input signals were not Gaussian. We also demonstrate the method's value in real data analysis. Conclusions The new method nMLSA (network-based modular latent structure analysis) is effective in detecting latent structures, and is easy to extend to non-linear cases. The method is available as R code at http://web1.sph.emory.edu/users/tyu8/nMLSA/. PMID:25435002

  16. Molecular Eigensolution Symmetry Analysis and Fine Structure

    PubMed Central

    Harter, William G.; Mitchell, Justin C.

    2013-01-01

    Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES). Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES) used in Born–Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v), then applied to families of Oh clusters in SF6 spectra and to extreme clusters. PMID:23344041

  17. Structural analysis of artificial skin equivalents

    NASA Astrophysics Data System (ADS)

    Schmitt, Robert; Marx, Ulrich; Walles, Heike; Schober, Lena

    2011-06-01

    Artificial skin equivalents ASEs based on primary fibroblasts and keratinocytes show a high batch variance in their structural and morphological characteristics. Due to biological fluctuations and variable donor age, the growth processes of 3D tissue structure show a non constant quality. Since theses ASEs are used as testing system for chemicals, pharmaceuticals or cosmetics it is of major interest to know detailed and significant characteristics about each individual ASE. Until now, the microscopic analysis process is based on the destructive preparation of histologies allowing only the characterization on a random basis. In this study we present analytical methods to characterise each individual ASE by Optical Coherence Tomography OCT in combination with image processing tools. Therefore, we developed a fully automated OCT device, that performs automatic measurements of microtiter plates MTPs holing the ASEs in a sterile environment. We developed image processing algorithms to characterize the surface structure which may function as an indicator for defects in the epidermal stratum corneum. Further, we analysed the tomographic morphological structure of the ASEs. The results show, that variances in the growth state as well different collagen formation is detectable. In combination with dynamic threshold levels, we found, that OCT is a well suited technology for automatically characterizing artificial skin equivalents and may partly substitute the preparation of histologies.

  18. Probabilistic Computational Methods in Structural Failure Analysis

    NASA Astrophysics Data System (ADS)

    Krejsa, Martin; Kralik, Juraj

    2015-12-01

    Probabilistic methods are used in engineering where a computational model contains random variables. Each random variable in the probabilistic calculations contains uncertainties. Typical sources of uncertainties are properties of the material and production and/or assembly inaccuracies in the geometry or the environment where the structure should be located. The paper is focused on methods for the calculations of failure probabilities in structural failure and reliability analysis with special attention on newly developed probabilistic method: Direct Optimized Probabilistic Calculation (DOProC), which is highly efficient in terms of calculation time and the accuracy of the solution. The novelty of the proposed method lies in an optimized numerical integration that does not require any simulation technique. The algorithm has been implemented in mentioned software applications, and has been used several times in probabilistic tasks and probabilistic reliability assessments.

  19. Associated neural network independent component analysis structure

    NASA Astrophysics Data System (ADS)

    Kim, Keehoon; Kostrzweski, Andrew

    2006-05-01

    Detection, classification, and localization of potential security breaches in extremely high-noise environments are important for perimeter protection and threat detection both for homeland security and for military force protection. Physical Optics Corporation has developed a threat detection system to separate acoustic signatures from unknown, mixed sources embedded in extremely high-noise environments where signal-to-noise ratios (SNRs) are very low. Associated neural network structures based on independent component analysis are designed to detect/separate new acoustic sources and to provide reliability information. The structures are tested through computer simulations for each critical component, including a spontaneous detection algorithm for potential threat detection without a predefined knowledge base, a fast target separation algorithm, and nonparametric methodology for quantified confidence measure. The results show that the method discussed can separate hidden acoustic sources of SNR in 5 dB noisy environments with an accuracy of 80%.

  20. Geometrically nonlinear analysis of laminated elastic structures

    NASA Technical Reports Server (NTRS)

    Reddy, J. N.

    1984-01-01

    Laminated composite plates and shells that can be used to model automobile bodies, aircraft wings and fuselages, and pressure vessels among many other were analyzed. The finite element method, a numerical technique for engineering analysis of structures, is used to model the geometry and approximate the solution. Various alternative formulations for analyzing laminated plates and shells are developed and their finite element models are tested for accuracy and economy in computation. These include the shear deformation laminate theory and degenerated 3-D elasticity theory for laminates.

  1. Forum discussion on probabilistic structural analysis methods

    SciTech Connect

    Rodriguez, E.A.; Girrens, S.P.

    2000-10-01

    The use of Probabilistic Structural Analysis Methods (PSAM) has received much attention over the past several decades due in part to enhanced reliability theories, computational capabilities, and efficient algorithms. The need for this development was already present and waiting at the door step. Automotive design and manufacturing has been greatly enhanced because of PSAM and reliability methods, including reliability-based optimization. This demand was also present in the US Department of Energy (DOE) weapons laboratories in support of the overarching national security responsibility of maintaining the nations nuclear stockpile in a safe and reliable state.

  2. Fatigue-Crack-Growth Structural Analysis

    NASA Technical Reports Server (NTRS)

    Newman, J. C., Jr.

    1986-01-01

    Elastic and plastic deformations calculated under variety of loading conditions. Prediction of fatigue-crack-growth lives made with FatigueCrack-Growth Structural Analysis (FASTRAN) computer program. As cyclic loads are applied to initial crack configuration, FASTRAN predicts crack length and other parameters until complete break occurs. Loads are tensile or compressive and of variable or constant amplitude. FASTRAN incorporates linear-elastic fracture mechanics with modifications of load-interaction effects caused by crack closure. FASTRAN considered research tool, because of lengthy calculation times. FASTRAN written in FORTRAN IV for batch execution.

  3. Structural reliability analysis of laminated CMC components

    NASA Technical Reports Server (NTRS)

    Duffy, Stephen F.; Palko, Joseph L.; Gyekenyesi, John P.

    1991-01-01

    For laminated ceramic matrix composite (CMC) materials to realize their full potential in aerospace applications, design methods and protocols are a necessity. The time independent failure response of these materials is focussed on and a reliability analysis is presented associated with the initiation of matrix cracking. A public domain computer algorithm is highlighted that was coupled with the laminate analysis of a finite element code and which serves as a design aid to analyze structural components made from laminated CMC materials. Issues relevant to the effect of the size of the component are discussed, and a parameter estimation procedure is presented. The estimation procedure allows three parameters to be calculated from a failure population that has an underlying Weibull distribution.

  4. The matrix exponential in transient structural analysis

    NASA Technical Reports Server (NTRS)

    Minnetyan, Levon

    1987-01-01

    The primary usefulness of the presented theory is in the ability to represent the effects of high frequency linear response with accuracy, without requiring very small time steps in the analysis of dynamic response. The matrix exponential contains a series approximation to the dynamic model. However, unlike the usual analysis procedure which truncates the high frequency response, the approximation in the exponential matrix solution is in the time domain. By truncating the series solution to the matrix exponential short, the solution is made inaccurate after a certain time. Yet, up to that time the solution is extremely accurate, including all high frequency effects. By taking finite time increments, the exponential matrix solution can compute the response very accurately. Use of the exponential matrix in structural dynamics is demonstrated by simulating the free vibration response of multi degree of freedom models of cantilever beams.

  5. Rhetorical structure theory and text analysis

    NASA Astrophysics Data System (ADS)

    Mann, William C.; Matthiessen, Christian M. I. M.; Thompson, Sandra A.

    1989-11-01

    Recent research on text generation has shown that there is a need for stronger linguistic theories that tell in detail how texts communicate. The prevailing theories are very difficult to compare, and it is also very difficult to see how they might be combined into stronger theories. To make comparison and combination a bit more approachable, we have created a book which is designed to encourage comparison. A dozen different authors or teams, all experienced in discourse research, are given exactly the same text to analyze. The text is an appeal for money by a lobbying organization in Washington, DC. It informs, stimulates and manipulates the reader in a fascinating way. The joint analysis is far more insightful than any one team's analysis alone. This paper is our contribution to the book. Rhetorical Structure Theory (RST), the focus of this paper, is a way to account for the functional potential of text, its capacity to achieve the purposes of speakers and produce effects in hearers. It also shows a way to distinguish coherent texts from incoherent ones, and identifies consequences of text structure.

  6. Molecular anatomy of human chromosome 9: comparative mapping of the immunoglobulin processed pseudogene C epsilon 3 (IGHEP2) in primates.

    PubMed

    Tanabe, H; Ishida, T; Ueda, S; Sofuni, T; Mizusawa, H

    1996-01-01

    Karyotypic homology in relation to human chromosome 9 (HSA 9) was studied through comparative mapping of the immunoglobulin-processed pseudogene C epsilon 3 (IGHEP2) in primates. IGHEP2, which has been mapped to 9p24.2 --> p24.1 in the human genome, was assigned to PTR 11q34 (common chimpanzee), PPA 11q34 (pygmy chimpanzee), PPY 13q16 (orangutan), HLA 8qter (white-handed gibbon), HAG 8qter (agile gibbon), and MFU 14q22 (Japanese macaque) by fluorescence in situ hybridization. To verify the breakpoints of presumed pericentric inversions on the ancestral great ape chromosomes, three DNA markers on HSA 9, cCI9-37 (9q22.1 --> q22.2), cCI9-135 (9q22.32 --> q22.33), and cCI9-208 (9p13.3 --> p13.2), were also assigned to PTR/PPA 11p11 (cCI9-37 and 135), PTR/PPA 11q22 (cCI9-208), PPY 13q22 (cCI9-37 and 135), and PPY 13q12 (cCI9-208). These data more clearly define the position of the breakpoints of pericentric inversions that occurred in the human-chimp ancestral and chimpanzee ancestral chromosomes and support the hypothesis of HSA 9 genesis previously derived from banding analyses of HSA 9 and its homologs. PMID:8646893

  7. Registered report: A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

    PubMed Central

    Khan, Israr; Kerwin, John; Owen, Kate; Griner, Erin; Iorns, Elizabeth

    2015-01-01

    The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (Errington et al., 2014). This Registered report describes the proposed replication plan of key experiments from ‘A coding-independent function of gene and pseudogene mRNAs regulates tumour biology’ by Poliseno et al. (2010), published in Nature in 2010. The key experiments to be replicated are reported in Figures 1D, 2F-H, and 4A. In these experiments, Poliseno and colleagues report microRNAs miR-19b and miR-20a transcriptionally suppress both PTEN and PTENP1 in prostate cancer cells (Figure 1D; Poliseno et al., 2010). Decreased expression of PTEN and/or PTENP1 resulted in downregulated PTEN protein levels (Figure 2H), downregulation of both mRNAs (Figure 2G), and increased tumor cell proliferation (Figure 2F; Poliseno et al., 2010). Furthermore, overexpression of the PTEN 3′ UTR enhanced PTENP1 mRNA abundance limiting tumor cell proliferation, providing additional evidence for the co-regulation of PTEN and PTENP1 (Figure 4A; Poliseno et al., 2010). The Reproducibility Project: Cancer Biology is collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published in eLife. DOI: http://dx.doi.org/10.7554/eLife.08245.001 PMID:26335297

  8. Pseudogenes as Weaknesses of ACTB (Actb) and GAPDH (Gapdh) Used as Reference Genes in Reverse Transcription and Polymerase Chain Reactions

    PubMed Central

    Sun, Yuan; Li, Yan; Luo, Dianzhong; Liao, D. Joshua

    2012-01-01

    The genes encoding β-actin (ACTB in human or Actb in mouse) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH in human or Gapdh in mouse) are the two most commonly used references for sample normalization in determination of the mRNA level of interested genes by reverse transcription (RT) and ensuing polymerase chain reactions (PCR). In this study, bioinformatic analyses revealed that the ACTB, Actb, GAPDH and Gapdh had 64, 69, 67 and 197 pseudogenes (PGs), respectively, in the corresponding genome. Most of these PGs are intronless and similar in size to the authentic mRNA. Alignment of several PGs of these genes with the corresponding mRNA reveals that they are highly homologous. In contrast, the hypoxanthine phosphoribosyltransferase-1 gene (HPRT1 in human or Hprt in mouse) only had 3 or 1 PG, respectively, and the mRNA has unique regions for primer design. PCR with cDNA or genomic DNA (gDNA) as templates revealed that our HPRT1, Hprt and GAPDH primers were specific, whereas our ACTB and Actb primers were not specific enough both vertically (within the cDNA) and horizontally (compared cDNA with gDNA). No primers could be designed for the Gapdh that would not mis-prime PGs. Since most of the genome is transcribed, we suggest to peers to forgo ACTB (Actb) and GAPDH (Dapdh) as references in RT-PCR and, if there is no surrogate, to use our primers with extra caution. We also propose a standard operation procedure in which design of primers for RT-PCR starts from avoiding mis-priming PGs and all primers need be tested for specificity with both cDNA and gDNA. PMID:22927912

  9. Advanced composites structural concepts and materials technologies for primary aircraft structures: Structural response and failure analysis

    NASA Technical Reports Server (NTRS)

    Dorris, William J.; Hairr, John W.; Huang, Jui-Tien; Ingram, J. Edward; Shah, Bharat M.

    1992-01-01

    Non-linear analysis methods were adapted and incorporated in a finite element based DIAL code. These methods are necessary to evaluate the global response of a stiffened structure under combined in-plane and out-of-plane loading. These methods include the Arc Length method and target point analysis procedure. A new interface material model was implemented that can model elastic-plastic behavior of the bond adhesive. Direct application of this method is in skin/stiffener interface failure assessment. Addition of the AML (angle minus longitudinal or load) failure procedure and Hasin's failure criteria provides added capability in the failure predictions. Interactive Stiffened Panel Analysis modules were developed as interactive pre-and post-processors. Each module provides the means of performing self-initiated finite elements based analysis of primary structures such as a flat or curved stiffened panel; a corrugated flat sandwich panel; and a curved geodesic fuselage panel. This module brings finite element analysis into the design of composite structures without the requirement for the user to know much about the techniques and procedures needed to actually perform a finite element analysis from scratch. An interactive finite element code was developed to predict bolted joint strength considering material and geometrical non-linearity. The developed method conducts an ultimate strength failure analysis using a set of material degradation models.

  10. Probabilistic structural analysis methods for space propulsion system components

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.

    1986-01-01

    The development of a three-dimensional inelastic analysis methodology for the Space Shuttle main engine (SSME) structural components is described. The methodology is composed of: (1) composite load spectra, (2) probabilistic structural analysis methods, (3) the probabilistic finite element theory, and (4) probabilistic structural analysis. The methodology has led to significant technical progress in several important aspects of probabilistic structural analysis. The program and accomplishments to date are summarized.

  11. Probabilistic structural analysis methods for space propulsion system components

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.

    1987-01-01

    The development of a three-dimensional inelastic analysis methodology for the Space Shuttle main engine (SSME) structural components is described. The methodology is composed of: (1) composite load spectra, (2) probabilistic structural analysis methods, (3) the probabilistic finite element theory, and (4) probabilistic structural analysis. The methodology has led to significant technical progress in several important aspects of probabilistic structural analysis. The program and accomplishments to date are summarized.

  12. Atomic-level analysis of membrane-protein structure.

    PubMed

    Hendrickson, Wayne A

    2016-06-01

    Membrane proteins are substantially more challenging than natively soluble proteins as subjects for structural analysis. Thus, membrane proteins are greatly underrepresented in structural databases. Recently, focused consortium efforts and advances in methodology for protein production, crystallographic analysis and cryo-EM analysis have accelerated the pace of atomic-level structure determination of membrane proteins. PMID:27273628

  13. A comprehensive analysis of the chorion locus in silkmoth

    PubMed Central

    Chen, Zhiwei; Nohata, Junko; Guo, Huizhen; Li, Shenglong; Liu, Jianqiu; Guo, Youbing; Yamamoto, Kimiko; Kadono-Okuda, Keiko; Liu, Chun; Arunkumar, Kallare P.; Nagaraju, Javaregowda; Zhang, Yan; Liu, Shiping; Labropoulou, Vassiliki; Swevers, Luc; Tsitoura, Panagiota; Iatrou, Kostas; Gopinathan, Karumathil P.; Goldsmith, Marian R.; Xia, Qingyou; Mita, Kazuei

    2015-01-01

    Despite more than 40 years of intense study, essential features of the silkmoth chorion (eggshell) are still not fully understood. To determine the precise structure of the chorion locus, we performed extensive EST analysis, constructed a bacterial artificial chromosome (BAC) contig, and obtained a continuous genomic sequence of 871,711 base pairs. We annotated 127 chorion genes in two segments interrupted by a 164 kb region with 5 non-chorion genes, orthologs of which were on chorion bearing scaffolds in 4 ditrysian families. Detailed transcriptome analysis revealed expression throughout choriogenesis of most chorion genes originally categorized as “middle”, and evidence for diverse regulatory mechanisms including cis-elements, alternative splicing and promoter utilization, and antisense RNA. Phylogenetic analysis revealed multigene family associations and faster evolution of early chorion genes and transcriptionally active pseudogenes. Proteomics analysis identified 99 chorion proteins in the eggshell and micropyle localization of 1 early and 6 Hc chorion proteins. PMID:26553298

  14. A comprehensive analysis of the chorion locus in silkmoth.

    PubMed

    Chen, Zhiwei; Nohata, Junko; Guo, Huizhen; Li, Shenglong; Liu, Jianqiu; Guo, Youbing; Yamamoto, Kimiko; Kadono-Okuda, Keiko; Liu, Chun; Arunkumar, Kallare P; Nagaraju, Javaregowda; Zhang, Yan; Liu, Shiping; Labropoulou, Vassiliki; Swevers, Luc; Tsitoura, Panagiota; Iatrou, Kostas; Gopinathan, Karumathil P; Goldsmith, Marian R; Xia, Qingyou; Mita, Kazuei

    2015-01-01

    Despite more than 40 years of intense study, essential features of the silkmoth chorion (eggshell) are still not fully understood. To determine the precise structure of the chorion locus, we performed extensive EST analysis, constructed a bacterial artificial chromosome (BAC) contig, and obtained a continuous genomic sequence of 871,711 base pairs. We annotated 127 chorion genes in two segments interrupted by a 164 kb region with 5 non-chorion genes, orthologs of which were on chorion bearing scaffolds in 4 ditrysian families. Detailed transcriptome analysis revealed expression throughout choriogenesis of most chorion genes originally categorized as "middle", and evidence for diverse regulatory mechanisms including cis-elements, alternative splicing and promoter utilization, and antisense RNA. Phylogenetic analysis revealed multigene family associations and faster evolution of early chorion genes and transcriptionally active pseudogenes. Proteomics analysis identified 99 chorion proteins in the eggshell and micropyle localization of 1 early and 6 Hc chorion proteins. PMID:26553298

  15. Recent developments in structural sensitivity analysis

    NASA Technical Reports Server (NTRS)

    Haftka, Raphael T.; Adelman, Howard M.

    1988-01-01

    Recent developments are reviewed in two major areas of structural sensitivity analysis: sensitivity of static and transient response; and sensitivity of vibration and buckling eigenproblems. Recent developments from the standpoint of computational cost, accuracy, and ease of implementation are presented. In the area of static response, current interest is focused on sensitivity to shape variation and sensitivity of nonlinear response. Two general approaches are used for computing sensitivities: differentiation of the continuum equations followed by discretization, and the reverse approach of discretization followed by differentiation. It is shown that the choice of methods has important accuracy and implementation implications. In the area of eigenproblem sensitivity, there is a great deal of interest and significant progress in sensitivity of problems with repeated eigenvalues. In addition to reviewing recent contributions in this area, the paper raises the issue of differentiability and continuity associated with the occurrence of repeated eigenvalues.

  16. Structured analysis and modeling of complex systems

    NASA Technical Reports Server (NTRS)

    Strome, David R.; Dalrymple, Mathieu A.

    1992-01-01

    The Aircrew Evaluation Sustained Operations Performance (AESOP) facility at Brooks AFB, Texas, combines the realism of an operational environment with the control of a research laboratory. In recent studies we collected extensive data from the Airborne Warning and Control Systems (AWACS) Weapons Directors subjected to high and low workload Defensive Counter Air Scenarios. A critical and complex task in this environment involves committing a friendly fighter against a hostile fighter. Structured Analysis and Design techniques and computer modeling systems were applied to this task as tools for analyzing subject performance and workload. This technology is being transferred to the Man-Systems Division of NASA Johnson Space Center for application to complex mission related tasks, such as manipulating the Shuttle grappler arm.

  17. Random motion analysis of flexible satellite structures

    NASA Technical Reports Server (NTRS)

    Huang, T. C.; Das, A.

    1978-01-01

    A singular perturbation formulation is used to study the responses of a flexible satellite when random measurement errors can occur. The random variables, at different instants of time, are assumed to be uncorrelated. Procedures for obtaining maxima and minima are described, and a variation of the linear method is developed for the formal solution of the two-point boundary-value problems represented by the variational equations. Random and deterministic solutions for the structural position coordinates are studied, and an analytic algorithm for treating the force equation of motion is developed. Since the random system indicated by the variational equation will always be asymptotically unstable, any analysis of stability must be based on the deterministic system.

  18. Purification and Structural Analysis of Desmoplakin.

    PubMed

    Choi, Hee-Jung; Weis, William I

    2016-01-01

    Desmoplakin (DP) is an obligate component of desmosomes, where it links the desmosomal cadherin/plakoglobin/plakophilin assembly to intermediate filaments. DP contains a large amino-terminal domain (DPNT) that binds to the cadherin/plakoglobin/plakophilin complex, a central coiled-coil domain that dimerizes the molecule, and a C-terminal domain (DPCT) that binds to intermediate filaments. DPNT contains a plakin domain, comprising a set of spectrin-like repeats. DPCT contains three plakin repeat domains, each formed by 4.5 repeats of a sequence motif known as a plakin repeat that bind to intermediate filaments. Here, we review purification, biochemical characterization, and structural analysis of the DPNT plakin domain and the DPCT plakin repeat domains. PMID:26778560

  19. Structural analysis of nucleosomal barrier to transcription

    PubMed Central

    Gaykalova, Daria A.; Kulaeva, Olga I.; Volokh, Olesya; Shaytan, Alexey K.; Hsieh, Fu-Kai; Kirpichnikov, Mikhail P.; Sokolova, Olga S.; Studitsky, Vasily M.

    2015-01-01

    Thousands of human and Drosophila genes are regulated at the level of transcript elongation and nucleosomes are likely targets for this regulation. However, the molecular mechanisms of formation of the nucleosomal barrier to transcribing RNA polymerase II (Pol II) and nucleosome survival during/after transcription remain unknown. Here we show that both DNA–histone interactions and Pol II backtracking contribute to formation of the barrier and that nucleosome survival during transcription likely occurs through allosterically stabilized histone–histone interactions. Structural analysis indicates that after Pol II encounters the barrier, the enzyme backtracks and nucleosomal DNA recoils on the octamer, locking Pol II in the arrested state. DNA is displaced from one of the H2A/H2B dimers that remains associated with the octamer. The data reveal the importance of intranucleosomal DNA–protein and protein–protein interactions during conformational changes in the nucleosome structure on transcription. Mechanisms of nucleosomal barrier formation and nucleosome survival during transcription are proposed. PMID:26460019

  20. Structures and Analysis of Carotenoid Molecules.

    PubMed

    Rodriguez-Amaya, Delia B

    2016-01-01

    Modifications of the usual C40 linear and symmetrical carotenoid skeleton give rise to a wide array of structures of carotenes and xanthophylls in plant tissues. These include acyclic, monocyclic and dicyclic carotenoids, along with hydroxy and epoxy xanthophylls and apocarotenoids. Carotenols can be unesterified or esterified (monoester) in one or two (diester) hydroxyl groups with fatty acids. E-Z isomerization increases the array of possible plant carotenoids even further. Screening and especially quantitative analysis are being carried out worldwide. Visible absorption spectrometry and near infrared reflectance spectroscopy have been used for the initial estimation of the total carotenoid content or the principal carotenoid content when large numbers of samples needed to be analyzed within a short time, as would be the case in breeding programs. Although inherently difficult, quantitative analysis of the individual carotenoids is essential. Knowledge of the sources of errors and means to avoid them has led to a large body of reliable quantitative compositional data on carotenoids. Reverse-phase HPLC with a photodiode array detector has been the preferred analytical technique, but UHPLC is increasingly employed. HPLC-MS has been used mainly for identification and NMR has been useful in unequivocally identifying geometric isomers. PMID:27485219

  1. A computer analysis program for interfacing thermal and structural codes

    NASA Technical Reports Server (NTRS)

    Thompson, R. L.; Maffeo, R. J.

    1985-01-01

    A software package has been developed to transfer three-dimensional transient thermal information accurately, efficiently, and automatically from a heat transfer analysis code to a structural analysis code. The code is called three-dimensional TRansfer ANalysis Code to Interface Thermal and Structural codes, or 3D TRANCITS. TRANCITS has the capability to couple finite difference and finite element heat transfer analysis codes to linear and nonlinear finite element structural analysis codes. TRANCITS currently supports the output of SINDA and MARC heat transfer codes directly. It will also format the thermal data output directly so that it is compatible with the input requirements of the NASTRAN and MARC structural analysis codes. Other thermal and structural codes can be interfaced using the transfer module with the neutral heat transfer input file and the neutral temperature output file. The transfer module can handle different elemental mesh densities for the heat transfer analysis and the structural analysis.

  2. Structure/load dependent vectors for linear structural dynamic analysis

    NASA Technical Reports Server (NTRS)

    Qin, Jiangning; Nguyen, Duc T.

    1992-01-01

    The dynamic solution vectors yielded by the present structure/load dependent-vectors method for large-scale linear structural dynamic analyses involving complex loadings can be used as starting vectors, so that both structure and load characteristics are encompassed by the basis vectors. The method is shown to entail fewer vectors than current alternatives for a given level of accuracy, especially in the cases of structures that have external concentrated masses. Numerical results are presented which illustrate the advantages of this dependent-vectors method relative to other reduction methods.

  3. Global-local finite element analysis of composite structures

    SciTech Connect

    Deibler, J.E.

    1992-06-01

    The development of layered finite elements has facilitated analysis of laminated composite structures. However, the analysis of a structure containing both isotropic and composite materials remains a difficult problem. A methodology has been developed to conduct a ``global-local`` finite element analysis. A ``global`` analysis of the entire structure is conducted at the appropriate loads with the composite portions replaced with an orthotropic material of equivalent materials properties. A ``local`` layered composite analysis is then conducted on the region of interest. The displacement results from the ``global`` analysis are used as loads to the ``local`` analysis. the laminate stresses and strains can then be examined and failure criteria evaluated.

  4. Global-local finite element analysis of composite structures

    SciTech Connect

    Deibler, J.E.

    1992-06-01

    The development of layered finite elements has facilitated analysis of laminated composite structures. However, the analysis of a structure containing both isotropic and composite materials remains a difficult problem. A methodology has been developed to conduct a global-local'' finite element analysis. A global'' analysis of the entire structure is conducted at the appropriate loads with the composite portions replaced with an orthotropic material of equivalent materials properties. A local'' layered composite analysis is then conducted on the region of interest. The displacement results from the global'' analysis are used as loads to the local'' analysis. the laminate stresses and strains can then be examined and failure criteria evaluated.

  5. Structural analysis of galactoarabinan from duckweed.

    PubMed

    Yu, Li; Yu, Changjiang; Zhu, Ming; Cao, Yingping; Yang, Haiyan; Zhang, Xu; Ma, Yubin; Zhou, Gongke

    2015-03-01

    A highly branched galactoarabinan named DAG1 (Mw∼4.0×10(4) Da) was purified from Lemna aequinoctialis 6000 via 70% (v/v) ethanol extraction, followed by size-exclusion chromatography on Bio-Gel P2 and Superdex 75. Methylation analysis showed that DAG1 consisted of t-Araf, (1→5)-Araf, (1→2,5)-Araf, (1→3)-Galp, and (1→3,6)-Galp in a relative proportion of approximately 6:4:3:3:3, suggesting an arabinogalactan/galactoarabinan polysacchairde. With the aid of arabinan degrading enzymes, the structure of DAG1 repeating unit was further characterized by ELISA with specific monoclonal antibodies and Yariv reagent assay. Analyses indicated that the proposed repeating unit of DAG1 had a backbone composed of seven α-(1→5)-L-arabinofuranose residues where branching occurred at O-2 with either terminal arabinoses or arabinogalactan side chain. The arabinogalactan side chain was composed of six β-(1→3)-D-galactopyranose residues, half of which were ramified at O-6 with terminal arabinoses and the last galactose was terminated with arabinose. PMID:25498703

  6. Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

    SciTech Connect

    Haibo Cao

    2003-12-12

    In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

  7. Foxo3 activity promoted by non-coding effects of circular RNA and Foxo3 pseudogene in the inhibition of tumor growth and angiogenesis.

    PubMed

    Yang, W; Du, W W; Li, X; Yee, A J; Yang, B B

    2016-07-28

    It has recently been shown that the upregulation of a pseudogene specific to a protein-coding gene could function as a sponge to bind multiple potential targeting microRNAs (miRNAs), resulting in increased gene expression. Similarly, it was recently demonstrated that circular RNAs can function as sponges for miRNAs, and could upregulate expression of mRNAs containing an identical sequence. Furthermore, some mRNAs are now known to not only translate protein, but also function to sponge miRNA binding, facilitating gene expression. Collectively, these appear to be effective mechanisms to ensure gene expression and protein activity. Here we show that expression of a member of the forkhead family of transcription factors, Foxo3, is regulated by the Foxo3 pseudogene (Foxo3P), and Foxo3 circular RNA, both of which bind to eight miRNAs. We found that the ectopic expression of the Foxo3P, Foxo3 circular RNA and Foxo3 mRNA could all suppress tumor growth and cancer cell proliferation and survival. Our results showed that at least three mechanisms are used to ensure protein translation of Foxo3, which reflects an essential role of Foxo3 and its corresponding non-coding RNAs. PMID:26657152

  8. Pseudogene of dihydrolipoyl succinyltransferase (E2k) found by PCR amplification and direct sequencing of rodent-human cell hybrid DNAs

    SciTech Connect

    Cai, X.; Ali, G.; Blass, J.P.; Szabo, P.; Tanzi, R.E.

    1994-07-01

    Previous studies have indicated that the cDNA for the E2k component of the human {alpha}-ketoglutarate dehydrogenase complex (KGDHC) hybridized not only to a major locus on chromosome 14q24.3 in a region associated with familial Alzheimer`s disease and with Joseph-Machado disease, but also to another locus on chromosome 1p31. The authors now report that PCR of genomic DNA and direct sequencing indicated that the chromosome 1 locus is an intronless pseudogene. PCR of genomic DNA amplified E2k fragments from mouse-human cell hybrids containing human chromosome 1 DNA but not from hybrids containing human chromosome 14 DNA. The resulting amplicons were of comparable sizes to those when the cDNA was used to template. The direct sequencing of these amplicons confirmed the lack of introns and indicated a frame shift, which led to the presence of four termination codons early in the coding region. PCR followed by direct sequencing of the amplicons appears to be a convenient method for identifying intronless pseudogenes.

  9. Coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures

    NASA Technical Reports Server (NTRS)

    Mcknight, R. L.; Chen, P. C.; Dame, L. T.; Huang, H.

    1992-01-01

    Accomplishments are described for the first year effort of a 5-year program to develop a methodology for coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures. These accomplishments include: (1) the results of the selective literature survey; (2) 8-, 16-, and 20-noded isoparametric plate and shell elements; (3) large deformation structural analysis; (4) eigenanalysis; (5) anisotropic heat transfer analysis; and (6) anisotropic electromagnetic analysis.

  10. Probabilistic structural analysis methods for critical SSME propulsion components

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.

    1986-01-01

    The development of a three-dimensional inelastic analysis methodology for the Space Shuttle main engine (SSME) structural components is described. The methodology is composed of: (1) composite load spectra, (2) probabilistic structural analysis methods, (3) the probabilistic finite element theory, and (4) probabilistic structural analysis. The progress in the development of generic probabilistic models for various individual loads which consist of a steady state load, a periodic load, a random load, and a spike, is discussed. The capabilities of the Numerical Evaluation of Stochastic Structures Under Stress finite element code designed for probabilistic structural analysis of the SSME are examined. Variation principles for formulation probabilistic finite elements and a structural analysis for evaluating the geometric and material properties tolerances on the structural response of turbopump blades are being designed.

  11. Analysis and design technology for high-speed aircraft structures

    NASA Technical Reports Server (NTRS)

    Starnes, James H., Jr.; Camarda, Charles J.

    1992-01-01

    Recent high-speed aircraft structures research activities at NASA Langley Research Center are described. The following topics are covered: the development of analytical and numerical solutions to global and local thermal and structural problems, experimental verification of analysis methods, identification of failure mechanisms, and the incorporation of analysis methods into design and optimization strategies. The paper describes recent NASA Langley advances in analysis and design methods, structural and thermal concepts, and test methods.

  12. Structural weight analysis of hypersonic aircraft

    NASA Technical Reports Server (NTRS)

    Ardema, M. D.

    1972-01-01

    The weights of major structural components of hypersonic, liquid hydrogen fueled aircraft are estimated and discussed. The major components are the body structure, body thermal protection system tankage and wing structure. The method of estimating body structure weight is presented in detail while the weights of the other components are estimated by methods given in referenced papers. Two nominal vehicle concepts are considered. The advanced concept employs a wing-body configuration and hot structure with a nonintegral tank, while the potential concept employs an all body configuration and cold, integral pillow tankage structure. Characteristics of these two concepts are discussed and parametric data relating their weight fractions to variations in vehicle shape and size design criteria and mission requirements, and structural arrangement are presented. Although the potential concept is shown to have a weight advantage over the advanced, it involves more design uncertainties since it is farther removed in design from existing aircraft.

  13. Advances in Computational Stability Analysis of Composite Aerospace Structures

    SciTech Connect

    Degenhardt, R.; Araujo, F. C. de

    2010-09-30

    European aircraft industry demands for reduced development and operating costs. Structural weight reduction by exploitation of structural reserves in composite aerospace structures contributes to this aim, however, it requires accurate and experimentally validated stability analysis of real structures under realistic loading conditions. This paper presents different advances from the area of computational stability analysis of composite aerospace structures which contribute to that field. For stringer stiffened panels main results of the finished EU project COCOMAT are given. It investigated the exploitation of reserves in primary fibre composite fuselage structures through an accurate and reliable simulation of postbuckling and collapse. For unstiffened cylindrical composite shells a proposal for a new design method is presented.

  14. ESF GROUND SUPPORT - STRUCTURAL STEEL ANALYSIS

    SciTech Connect

    T. Misiak

    1996-06-26

    The purpose and objective of this analysis are to expand the level of detail and confirm member sizes for steel sets included in the Ground Support Design Analysis, Reference 5.20. This analysis also provides bounding values and details and defines critical design attributes for alternative configurations of the steel set. One possible configuration for the steel set is presented. This analysis covers the steel set design for the Exploratory Studies Facility (ESF) entire Main Loop 25-foot diameter tunnel.

  15. Recent developments of the NESSUS probabilistic structural analysis computer program

    NASA Technical Reports Server (NTRS)

    Millwater, H.; Wu, Y.-T.; Torng, T.; Thacker, B.; Riha, D.; Leung, C. P.

    1992-01-01

    The NESSUS probabilistic structural analysis computer program combines state-of-the-art probabilistic algorithms with general purpose structural analysis methods to compute the probabilistic response and the reliability of engineering structures. Uncertainty in loading, material properties, geometry, boundary conditions and initial conditions can be simulated. The structural analysis methods include nonlinear finite element and boundary element methods. Several probabilistic algorithms are available such as the advanced mean value method and the adaptive importance sampling method. The scope of the code has recently been expanded to include probabilistic life and fatigue prediction of structures in terms of component and system reliability and risk analysis of structures considering cost of failure. The code is currently being extended to structural reliability considering progressive crack propagation. Several examples are presented to demonstrate the new capabilities.

  16. Probabilistic structural analysis of adaptive/smart/intelligent space structures

    NASA Technical Reports Server (NTRS)

    Pai, Shantaram S.; Chamis, Christos C.

    1992-01-01

    A three-bay, space, cantilever truss is probabilistically evaluated for adaptive/smart/intelligent behavior. For each behavior, the scatter (ranges) in buckling loads, vibration frequencies, and member axial forces are probabilistically determined. Sensitivities associated with uncertainties in the structure, material and load variables that describe the truss are determined for different probabilities. The relative magnitude for these sensitivities are used to identify significant truss variables that control/classify its behavior to respond as an adaptive/smart/intelligent structure. Results show that the probabilistic buckling loads and vibration frequencies increase for each truss classification, with a substantial increase for intelligent trusses. Similarly, the probabilistic member axial forces reduce for adaptive and intelligent trusses and increase for smart trusses.

  17. Probabilistic structural analysis of adaptive/smart/intelligent space structures

    NASA Technical Reports Server (NTRS)

    Pai, Shantaram S.; Chamis, Christos C.

    1991-01-01

    A three-bay, space, cantilever truss is probabilistically evaluated for adaptive/smart/intelligent behavior. For each behavior, the scatter (ranges) in buckling loads, vibration frequencies, and member axial forces are probabilistically determined. Sensitivities associated with uncertainties in the structure, material and load variables that describe the truss are determined for different probabilities. The relative magnitude for these sensitivities are used to identify significant truss variables that control/classify its behavior to respond as an adaptive/smart/intelligent structure. Results show that the probabilistic buckling loads and vibration frequencies increase for each truss classification, with a substantial increase for intelligent trusses. Similarly, the probabilistic member axial forces reduce for adaptive and intelligent trusses and increase for smart trusses.

  18. APT/LEDA RFQ and support frame structural analysis

    SciTech Connect

    Ellis, S.

    1997-04-01

    This report documents structural analysis of the Accelerator Production of Tritium Low Energy Demonstration Accelerator (APT/LEDA) Radio Frequency Quadrupole (RFQ) accelerator structure and its associated support frame. This work was conducted for the Department of Energy in support of the APT/LEDA. Structural analysis of the RFQ was performed to quantify stress levels and deflections due to both vacuum loading and gravity loading. This analysis also verified the proposed support scheme geometry and quantified interface loads. This analysis also determined the necessary stiffness and strength requirements of the RFQ support frame verifying the conceptual design geometry and allowing specification of individual frame elements. Complete structural analysis of the frame was completed subsequently. This report details structural analysis of the RFQ assembly with regard to gravity and vacuum loads only. Thermally induced stresses from the Radio Frequency (RF) surface resistance heating were not considered.

  19. The Specific Analysis of Structural Equation Models

    ERIC Educational Resources Information Center

    McDonald, Roderick P.

    2004-01-01

    Conventional structural equation modeling fits a covariance structure implied by the equations of the model. This treatment of the model often gives misleading results because overall goodness of fit tests do not focus on the specific constraints implied by the model. An alternative treatment arising from Pearl's directed acyclic graph theory…

  20. Computer program performs stiffness matrix structural analysis

    NASA Technical Reports Server (NTRS)

    Bamford, R.; Batchelder, R.; Schmele, L.; Wada, B. K.

    1968-01-01

    Computer program generates the stiffness matrix for a particular type of structure from geometrical data, and performs static and normal mode analyses. It requires the structure to be modeled as a stable framework of uniform, weightless members, and joints at which loads are applied and weights are lumped.

  1. Advertising Agencies: An Analysis of Industry Structure.

    ERIC Educational Resources Information Center

    Smith, Sandra J.

    Noting that advertising agencies have not been examined as a collective industry, this paper looks at the development and structure of the advertising agency industry. The first portion of the paper discusses the development of the agency. The remaining two sections deal with trends in and the structure of the industry including: (1) the growth of…

  2. Structural dynamics: Probabilistic structural analysis methods. Program overview

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.; Hopkins, Dale A.

    1991-01-01

    A brief description is provided of the fundamental aspects of a quantification process. Progress since the last structural durability conference in 1989 is summarized. The methodology to date and that to be developed during the life of the program is presented. The uncertain factors are presented. The approach is outlined that is required to achieve component and/or system certification in the shortest possible time for affordable reliability risk. Two new elements appear in a block diagram: (1) uncertainties in human factor, and (2) uncertainties in the computer code. Research to quantify the uncertainties in the human factor was initiated and is discussed.

  3. Reevaluating Human Gene Annotation: A Second-Generation Analysis of Chromosome 22

    PubMed Central

    Collins, John E.; Goward, Melanie E.; Cole, Charlotte G.; Smink, Luc J.; Huckle, Elizabeth J.; Knowles, Sarah; Bye, Jacqueline M.; Beare, David M.; Dunham, Ian

    2003-01-01

    We report a second-generation gene annotation of human chromosome 22. Using expressed sequence databases, comparative sequence analysis, and experimental verification, we have extended genes, fused previously fragmented structures, and identified new genes. The total length in exons of annotation was increased by 74% over our previously published annotation and includes 546 protein-coding genes and 234 pseudogenes. Thirty-two potential protein-coding annotations are partial copies of other genes, and may represent duplications on an evolutionary path to change or loss of function. We also identified 31 non-protein-coding transcripts, including 16 possible antisense RNAs. By extrapolation, we estimate the human genome contains 29,000–36,000 protein-coding genes, 21,300 pseudogenes, and 1500 antisense RNAs. We suggest that our revised annotation criteria provide a paradigm for future annotation of the human genome. [Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos. , -3, , , -2, , , , , -8, -6, , -81, -81, , , , , -3, -2, -2, , , , , , , -5, , , , , -7, , -8, –. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: J. Seilhamer, L. Stuve, H. Roest-Crollius, A. Levine, G. Slater, and J. Kent.] PMID:12529303

  4. Reliability analysis applied to structural tests

    NASA Technical Reports Server (NTRS)

    Diamond, P.; Payne, A. O.

    1972-01-01

    The application of reliability theory to predict, from structural fatigue test data, the risk of failure of a structure under service conditions because its load-carrying capability is progressively reduced by the extension of a fatigue crack, is considered. The procedure is applicable to both safe-life and fail-safe structures and, for a prescribed safety level, it will enable an inspection procedure to be planned or, if inspection is not feasible, it will evaluate the life to replacement. The theory has been further developed to cope with the case of structures with initial cracks, such as can occur in modern high-strength materials which are susceptible to the formation of small flaws during the production process. The method has been applied to a structure of high-strength steel and the results are compared with those obtained by the current life estimation procedures. This has shown that the conventional methods can be unconservative in certain cases, depending on the characteristics of the structure and the design operating conditions. The suitability of the probabilistic approach to the interpretation of the results from full-scale fatigue testing of aircraft structures is discussed and the assumptions involved are examined.

  5. Probabilistic structural analysis methods for space transportation propulsion systems

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Moore, N.; Anis, C.; Newell, J.; Nagpal, V.; Singhal, S.

    1991-01-01

    Information on probabilistic structural analysis methods for space propulsion systems is given in viewgraph form. Information is given on deterministic certification methods, probability of failure, component response analysis, stress responses for 2nd stage turbine blades, Space Shuttle Main Engine (SSME) structural durability, and program plans. .

  6. Digital flux-gate magnetometer structural analysis

    NASA Astrophysics Data System (ADS)

    Korepanov, Valery; Berkman, Rikhard

    1999-08-01

    Analogue and digital structures of the flux-gate magnetometer are compared. The main disturbing factors in digital circuit were singled out and the additional errors associated with the digital structure are estimated. The reader's attention is drawn to some specific problems associated with digital circuits - the special influence of the unbalanced voltage amplitude at the flux-gate-sensor output and ADC-DAC switching-time instabilities. The given analytical results could be useful for the designer when it is necessary to make a choice of the structural type of magnetometer.

  7. An analysis of doping modulated superlattice structures

    NASA Technical Reports Server (NTRS)

    Buoncristiani, A. M.

    1985-01-01

    A new method of growing doping modulated superlattice structures is discussed. This method uses organo-metallic chemical vapor deposition (MO-CVD) with the added feature of controlled plasma in the growth regions. The main objective was to study how the growth environment affected the electronic and optical properties of the superlattice structures. Because a serious safety hazard was discovered in the growth process, no superlattice structures were fabricated and the research on this material had to be terminated. The hazard had to do with the lack of adequate means for the disposal of toxic elemental beryllium.

  8. Structural Configuration Systems Analysis for Advanced Aircraft Fuselage Concepts

    NASA Technical Reports Server (NTRS)

    Mukhopadhyay, Vivek; Welstead, Jason R.; Quinlan, Jesse R.; Guynn, Mark D.

    2016-01-01

    Structural configuration analysis of an advanced aircraft fuselage concept is investigated. This concept is characterized by a double-bubble section fuselage with rear mounted engines. Based on lessons learned from structural systems analysis of unconventional aircraft, high-fidelity finite-element models (FEM) are developed for evaluating structural performance of three double-bubble section configurations. Structural sizing and stress analysis are applied for design improvement and weight reduction. Among the three double-bubble configurations, the double-D cross-section fuselage design was found to have a relatively lower structural weight. The structural FEM weights of these three double-bubble fuselage section concepts are also compared with several cylindrical fuselage models. Since these fuselage concepts are different in size, shape and material, the fuselage structural FEM weights are normalized by the corresponding passenger floor area for a relative comparison. This structural systems analysis indicates that an advanced composite double-D section fuselage may have a relative structural weight ratio advantage over a conventional aluminum fuselage. Ten commercial and conceptual aircraft fuselage structural weight estimates, which are empirically derived from the corresponding maximum takeoff gross weight, are also presented and compared with the FEM- based estimates for possible correlation. A conceptual full vehicle FEM model with a double-D fuselage is also developed for preliminary structural analysis and weight estimation.

  9. Enabling Rapid and Robust Structural Analysis During Conceptual Design

    NASA Technical Reports Server (NTRS)

    Eldred, Lloyd B.; Padula, Sharon L.; Li, Wu

    2015-01-01

    This paper describes a multi-year effort to add a structural analysis subprocess to a supersonic aircraft conceptual design process. The desired capabilities include parametric geometry, automatic finite element mesh generation, static and aeroelastic analysis, and structural sizing. The paper discusses implementation details of the new subprocess, captures lessons learned, and suggests future improvements. The subprocess quickly compares concepts and robustly handles large changes in wing or fuselage geometry. The subprocess can rank concepts with regard to their structural feasibility and can identify promising regions of the design space. The automated structural analysis subprocess is deemed robust and rapid enough to be included in multidisciplinary conceptual design and optimization studies.

  10. A novel CFD/structural analysis of a cross parachute

    SciTech Connect

    LaFarge, R.A.; Nelsen, J.M.; Gwinn, K.W.

    1993-12-31

    A novel CFD/structural analysis was performed to predict functionality of a cross parachute under loadings near the structural limits of the parachute. The determination of parachute functionality was based on the computed structural integrity of the canopy and suspension lines. In addition to the standard aerodynamic pressure loading on the canopy, the structural analysis considered the reduction in fabric strength due to the computed aerodynamic heating. The intent was to illustrate the feasibility of such an analysis with the commercially available software PATRAN.

  11. Structures for common-cause failure analysis

    SciTech Connect

    Vaurio, J.K.

    1981-01-01

    Common-cause failure methodology and terminology have been reviewed and structured to provide a systematical basis for addressing and developing models and methods for quantification. The structure is based on (1) a specific set of definitions, (2) categories based on the way faults are attributable to a common cause, and (3) classes based on the time of entry and the time of elimination of the faults. The failure events are then characterized by their likelihood or frequency and the average residence time. The structure provides a basis for selecting computational models, collecting and evaluating data and assessing the importance of various failure types, and for developing effective defences against common-cause failure. The relationships of this and several other structures are described.

  12. Structural analysis of kasugamycin inhibition of translation

    PubMed Central

    Schuwirth, Barbara S; Day, J Michael; Hau, Cathy W; Janssen, Gary R; Dahlberg, Albert E; Cate, Jamie H Doudna; Vila-Sanjurjo, Antón

    2008-01-01

    The prokaryotic ribosome is an important target of antibiotic action. We determined the X-ray structure of the aminoglycoside kasugamycin (Ksg) in complex with the Escherichia coli 70S ribosome at 3.5-Å resolution. The structure reveals that the drug binds within the messenger RNA channel of the 30S subunit between the universally conserved G926 and A794 nucleotides in 16S ribosomal RNA, which are sites of Ksg resistance. To our surprise, Ksg resistance mutations do not inhibit binding of the drug to the ribosome. The present structural and biochemical results indicate that inhibition by Ksg and Ksg resistance are closely linked to the structure of the mRNA at the junction of the peptidyl-tRNA and exit-tRNA sites (P and E sites). PMID:16998486

  13. Solid Propellant Grain Structural Integrity Analysis

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The structural properties of solid propellant rocket grains were studied to determine the propellant resistance to stresses. Grain geometry, thermal properties, mechanical properties, and failure modes are discussed along with design criteria and recommended practices.

  14. Computer applications for engineering/structural analysis. Revision 1

    SciTech Connect

    Zaslawsky, M.; Samaddar, S.K.

    1991-12-31

    Analysts and organizations have a tendency to lock themselves into specific codes with the obvious consequences of not addressing the real problem and thus reaching the wrong conclusion. This paper discusses the role of the analyst in selecting computer codes. The participation and support of a computation division in modifying the source program, configuration management, and pre- and post-processing of codes are among the subjects discussed. Specific examples illustrating the computer code selection process are described in the following problem areas: soil structure interaction, structural analysis of nuclear reactors, analysis of waste tanks where fluid structure interaction is important, analysis of equipment, structure-structure interaction, analysis of the operation of the superconductor supercollider which includes friction and transient temperature, and 3D analysis of the 10-meter telescope being built in Hawaii. Validation and verification of computer codes and their impact on the selection process are also discussed.

  15. Finite element-finite difference thermal/structural analysis of large space truss structures

    NASA Technical Reports Server (NTRS)

    Warren, Andrew H.; Arelt, Joseph E.; Eskew, William F.; Rogers, Karen M.

    1992-01-01

    A technique of automated and efficient thermal-structural processing of truss structures that interfaces the finite element and finite difference method was developed. The thermal-structural analysis tasks include development of the thermal and structural math models, thermal analysis, development of an interface and data transfer between the models, and finally an evaluation of the thermal stresses and displacements in the structure. Consequently, the objective of the developed technique was to minimize the model development time, in order to assure an automatic transfer of data between the thermal and structural models as well as to minimize the computer resources needed for the analysis itself. The method and techniques described are illustrated on the thermal/structural analysis of the Space Station Freedom main truss.

  16. Condensed Antenna Structural Models for Dynamics Analysis

    NASA Technical Reports Server (NTRS)

    Levy, R.

    1985-01-01

    Condensed degree-of-freedom models are compared with large degree-of-freedom finite-element models of a representative antenna-tipping and alidade structure, for both locked and free-rotor configurations. It is shown that: (1) the effective-mass models accurately reproduce the lower-mode natural frequencies of the finite element model; (2) frequency responses for the two types of models are in agreement up to at least 16 rad/s for specific points; and (3) transient responses computed for the same points are in good agreement. It is concluded that the effective-mass model, which best represents the five lower modes of the finite-element model, is a sufficient representation of the structure for future incorporation with a total servo control structure dynamic simulation.

  17. Targeted and robust amplification of mitochondrial DNA in the presence of nuclear-encoded mitochondrial pseudogenes using Φ29 DNA polymerases.

    PubMed

    Wolff, Jonci N

    2014-01-01

    Accidental co-amplification of nuclear-encoded mitochondrial pseudogenes (numts) in mitochondrial DNA (mtDNA) analyses is a common problem in biological and medical research alike [Yao et al., J Med Genet 45:769-772, 2008; Song et al., Proc Natl Acad Sci U S A 105:13486-13491, 2008]. A wealth of strategies have been developed to evade the contamination of mtDNA data sets with numts, but time- and cost-effective protocols of general applicability are scarce [Wolff et al., PLoS One 7:e37142, 2012]. The protocol presented here closes this gap by combining serial dilution with standard and rolling circle DNA amplification. This strategy leads to selective enrichment of mtDNA and removal of nuclear DNA (nuDNA) from template solutions, enabling mtDNA analyses in a virtually numt-free environment. PMID:24823783

  18. Structural Analysis Using NX Nastran 9.0

    NASA Technical Reports Server (NTRS)

    Rolewicz, Benjamin M.

    2014-01-01

    NX Nastran is a powerful Finite Element Analysis (FEA) software package used to solve linear and non-linear models for structural and thermal systems. The software, which consists of both a solver and user interface, breaks down analysis into four files, each of which are important to the end results of the analysis. The software offers capabilities for a variety of types of analysis, and also contains a respectable modeling program. Over the course of ten weeks, I was trained to effectively implement NX Nastran into structural analysis and refinement for parts of two missions at NASA's Kennedy Space Center, the Restore mission and the Orion mission.

  19. Total-System Approach To Design And Analysis Of Structures

    NASA Technical Reports Server (NTRS)

    Verderaime, V.

    1995-01-01

    Paper presents overview and study of, and comprehensive approach to, multidisciplinary engineering design and analysis of structures. Emphasizes issues related to design of semistatic structures in environments in which spacecraft launched, underlying concepts applicable to other structures within unique terrestrial, marine, or flight environments. Purpose of study to understand interactions among traditionally separate engineering design disciplines with view toward optimizing not only structure but also overall design process.

  20. Competing endogenous RNA networks of CYP4Z1 and pseudogene CYP4Z2P confer tamoxifen resistance in breast cancer.

    PubMed

    Zheng, Lufeng; Li, Xiaoman; Meng, Xia; Chou, Jinjiang; Hu, Jinhang; Zhang, Feng; Zhang, Zhiting; Xing, Yingying; Liu, Yu; Xi, Tao

    2016-05-15

    Patients with estrogen receptor α (ERα)-positive breast cancer can be treated with endocrine therapy using anti-estrogens such as tamoxifen; nonetheless, patients often develop resistance limiting the success of breast cancer treatment. The potential mechanisms remain elusive. In detail, many miRNAs have been associated with breast cancer tamoxifen resistance, but no studies have addressed the role of miRNA-mediated competitive endogenous RNAs network (ceRNET) in tamoxifen resistance. The ceRNET between CYP4Z1 and pseudogene CYP4Z2P has been revealed to promote breast cancer angiogenesis. However, its function in tamoxifen resistance remains unclear. Here we report CYP4Z1 and CYP4Z2P were downregulated in MCF-7 cells compared with tamoxifen-resistant MCF-7-TamR cells. Enforced upregulation of CYP4Z1- or CYP4Z2P-3'UTR level renders MCF-7 Cells resistant to tamoxifen. We find that overexpression of CYP4Z1- or CYP4Z2P-3'UTR enhances the transcriptional activity of ERα through the activation of ERα phosphorylation. Furthermore, we find that CYP4Z1- and CYP4Z2P-3'UTRs increase ERα activity dependent on cyclin-dependent kinase 3 (CDK3). Reporter gene and western blot assays revealed that CYP4Z1- and CYP4Z2P-3'UTRs act as CDK3 ceRNAs. More importantly, the blocking of CYP4Z1- and CYP4Z2P-3'UTRs reversed tamoxifen resistance in MCF-7-TamR cells. Our data demonstrates that the ceRNET between CYP4Z1 and pseudogene CYP4Z2P acts as a sub-ceRNET to promote CDK3 expression in ER-positive breast cancer and is a potential therapeutic target for treatment of tamoxifen-resistant breast cancer. PMID:26980484

  1. Cognitive Diagnostic Analysis Using Hierarchically Structured Skills

    ERIC Educational Resources Information Center

    Su, Yu-Lan

    2013-01-01

    This dissertation proposes two modified cognitive diagnostic models (CDMs), the deterministic, inputs, noisy, "and" gate with hierarchy (DINA-H) model and the deterministic, inputs, noisy, "or" gate with hierarchy (DINO-H) model. Both models incorporate the hierarchical structures of the cognitive skills in the model estimation…

  2. Theses "Discussion" Sections: A Structural Move Analysis

    ERIC Educational Resources Information Center

    Nodoushan, Mohammad Ali Salmani; Khakbaz, Nafiseh

    2011-01-01

    The current study aimed at finding the probable differences between the move structure of Iranian MA graduates' thesis discussion subgenres and those of their non-Iranian counterparts, on the one hand, and those of journal paper authors, on the other. It also aimed at identifying the moves that are considered obligatory, conventional, or optional…

  3. An Efficient Analysis Methodology for Fluted-Core Composite Structures

    NASA Technical Reports Server (NTRS)

    Oremont, Leonard; Schultz, Marc R.

    2012-01-01

    The primary loading condition in launch-vehicle barrel sections is axial compression, and it is therefore important to understand the compression behavior of any structures, structural concepts, and materials considered in launch-vehicle designs. This understanding will necessarily come from a combination of test and analysis. However, certain potentially beneficial structures and structural concepts do not lend themselves to commonly used simplified analysis methods, and therefore innovative analysis methodologies must be developed if these structures and structural concepts are to be considered. This paper discusses such an analysis technique for the fluted-core sandwich composite structural concept. The presented technique is based on commercially available finite-element codes, and uses shell elements to capture behavior that would normally require solid elements to capture the detailed mechanical response of the structure. The shell thicknesses and offsets using this analysis technique are parameterized, and the parameters are adjusted through a heuristic procedure until this model matches the mechanical behavior of a more detailed shell-and-solid model. Additionally, the detailed shell-and-solid model can be strategically placed in a larger, global shell-only model to capture important local behavior. Comparisons between shell-only models, experiments, and more detailed shell-and-solid models show excellent agreement. The discussed analysis methodology, though only discussed in the context of fluted-core composites, is widely applicable to other concepts.

  4. Structure network analysis to gain insights into GPCR function.

    PubMed

    Fanelli, Francesca; Felline, Angelo; Raimondi, Francesco; Seeber, Michele

    2016-04-15

    G protein coupled receptors (GPCRs) are allosteric proteins whose functioning fundamentals are the communication between the two poles of the helix bundle. Protein structure network (PSN) analysis is one of the graph theory-based approaches currently used to investigate the structural communication in biomolecular systems. Information on system's dynamics can be provided by atomistic molecular dynamics (MD) simulations or coarse grained elastic network models paired with normal mode analysis (ENM-NMA). The present review article describes the application of PSN analysis to uncover the structural communication in G protein coupled receptors (GPCRs). Strategies to highlight changes in structural communication upon misfolding, dimerization and activation are described. Focus is put on the ENM-NMA-based strategy applied to the crystallographic structures of rhodopsin in its inactive (dark) and signalling active (meta II (MII)) states, highlighting changes in structure network and centrality of the retinal chromophore in differentiating the inactive and active states of the receptor. PMID:27068978

  5. Application of structured analysis to a telerobotic system

    NASA Technical Reports Server (NTRS)

    Dashman, Eric; Mclin, David; Harrison, F. W.; Soloway, Donald; Young, Steven

    1990-01-01

    The analysis and evaluation of a multiple arm telerobotic research and demonstration system developed by the NASA Intelligent Systems Research Laboratory (ISRL) is described. Structured analysis techniques were used to develop a detailed requirements model of an existing telerobotic testbed. Performance models generated during this process were used to further evaluate the total system. A commercial CASE tool called Teamwork was used to carry out the structured analysis and development of the functional requirements model. A structured analysis and design process using the ISRL telerobotic system as a model is described. Evaluation of this system focused on the identification of bottlenecks in this implementation. The results demonstrate that the use of structured methods and analysis tools can give useful performance information early in a design cycle. This information can be used to ensure that the proposed system meets its design requirements before it is built.

  6. Large-scale structural analysis: The structural analyst, the CSM Testbed and the NAS System

    NASA Technical Reports Server (NTRS)

    Knight, Norman F., Jr.; Mccleary, Susan L.; Macy, Steven C.; Aminpour, Mohammad A.

    1989-01-01

    The Computational Structural Mechanics (CSM) activity is developing advanced structural analysis and computational methods that exploit high-performance computers. Methods are developed in the framework of the CSM testbed software system and applied to representative complex structural analysis problems from the aerospace industry. An overview of the CSM testbed methods development environment is presented and some numerical methods developed on a CRAY-2 are described. Selected application studies performed on the NAS CRAY-2 are also summarized.

  7. Structure coefficients for use in stellar analysis

    NASA Astrophysics Data System (ADS)

    İnlek, Gülay; Budding, Edwin

    2012-12-01

    We present new values of the structural coefficients η j , and related quantities, for realistic models of distorted stars in close binary systems. Our procedure involves numerical integration of Radau's equation for detailed structural data and we verified our technique by referring to the 8-digit results of Brooker & Olle (Mon. Not. R. Astron. Soc. 115:101, 1955) for purely mathematical models. We provide tables of representative values of η j , and related quantities, for j=2,3,…,7 for a selection of Zero Age Stellar Main Sequence (ZAMS) stellar models taken from the EZWeb compilation of the Dept. of Astronomy, University of Wisconsin-Madison. We include also some preliminary comparisons of our findings with the results of Claret and Gimenez (Astron. Astrophys. 519:A57 2010) for some observed stars.

  8. Finite-Element Modeling For Structural Analysis

    NASA Technical Reports Server (NTRS)

    Min, J. B.; Androlake, S. G.

    1995-01-01

    Report presents study of finite-element mathematical modeling as used in analyzing stresses and strains at joints between thin, shell-like components (e.g., ducts) and thicker components (e.g., flanges or engine blocks). First approach uses global/local model to evaluate system. Provides correct total response and correct representation of stresses away from any discontinuities. Second approach involves development of special transition finite elements to model transitions between shells and thicker structural components.

  9. Truncated Moment Analysis of Nucleon Structure Functions

    SciTech Connect

    A. Psaker; W. Melnitchouk; M. E. Christy; C. E. Keppel

    2007-11-16

    We employ a novel new approach using "truncated" moments, or integrals of structure functions over restricted regions of x, to study local quark-hadron duality, and the degree to which individual resonance regions are dominated by leading twists. Because truncated moments obey the same Q^2 evolution equations as the leading twist parton distributions, this approach makes possible for the first time a description of resonance region data and the phenomenon of quark-hadron duality directly from QCD.

  10. Probabilistic Computer Analysis for Rapid Evaluation of Structures.

    Energy Science and Technology Software Center (ESTSC)

    2007-03-29

    P-CARES 2.0.0, Probabilistic Computer Analysis for Rapid Evaluation of Structures, was developed for NRC staff use to determine the validity and accuracy of the analysis methods used by various utilities for structural safety evaluations of nuclear power plants. P-CARES provides the capability to effectively evaluate the probabilistic seismic response using simplified soil and structural models and to quickly check the validity and/or accuracy of the SSI data received from applicants and licensees. The code ismore » organized in a modular format with the basic modules of the system performing static, seismic, and nonlinear analysis.« less

  11. Probabilistic Computer Analysis for Rapid Evaluation of Structures.

    SciTech Connect

    XU, JIM

    2007-03-29

    P-CARES 2.0.0, Probabilistic Computer Analysis for Rapid Evaluation of Structures, was developed for NRC staff use to determine the validity and accuracy of the analysis methods used by various utilities for structural safety evaluations of nuclear power plants. P-CARES provides the capability to effectively evaluate the probabilistic seismic response using simplified soil and structural models and to quickly check the validity and/or accuracy of the SSI data received from applicants and licensees. The code is organized in a modular format with the basic modules of the system performing static, seismic, and nonlinear analysis.

  12. Novel Synthesis and Structural Analysis of Ferrihydrite

    SciTech Connect

    Smith, Stacey J.; Page, Katharine; Kim, Hyunjeong; Campbell, Branton J.; Boerio-Goates, Juliana; Woodfield, Brian F.

    2012-07-25

    Naturally occurring ferrihydrite is both impure and difficult to isolate, so the numerous applications and interesting properties of ferrihydrite have spurred the development of various synthetic techniques. Nearly all techniques are based on the hydrolysis of an iron salt and require careful control of temperature, pH, and concentration. In this Article, we report a new synthetic method which does not require such control and is perhaps the fastest and simplest route to synthesizing ferrhydrite. XRD, TEM, BET, and chemical purity characterizations show that the chemically pure, 2-line ferrihydrite product consists of crystallites 2-6 nm in diameter which aggregate to form mesoporous, high surface area agglomerates that are attractive candidates for the many adsorption applications of ferrihydrite. X-ray PDF data were also collected for the ferrihydrite product and refined against the hexagonal structural model recently proposed by Michel et al. These analyses suggest that ferrihydrite has a consistent, repeatable structure independent of variation in the synthetic method, water content of the sample, or particle size of the crystallites, and this structure can be adequately described by the proposed hexagonal model.

  13. Nonlinear dynamic analysis of quasi-symmetric anisotropic structures

    NASA Technical Reports Server (NTRS)

    Noor, Ahmed K.; Peters, Jeanne M.

    1987-01-01

    An efficient computational method for the nonlinear dynamic analysis of quasi-symmetric anisotropic structures is proposed. The application of mixed models simplifies the analytical development and improves the accuracy of the response predictions, and operator splitting allows the reduction of the analysis model of the quasi-symmetric structure to that of the corresponding symmetric structure. The preconditoned conjugate gradient provides a stable and effective technique for generating the unsymmetric response of the structure as the sum of a symmetrized response plus correction modes. The effectiveness of the strategy is demonstrated with the example of a laminated anisotropic shallow shell of quadrilateral planform subjected to uniform normal loading.

  14. Characterization of alpha-gliadin genes from diploid wheats and the comparative analysis with those from polyploid wheats.

    PubMed

    Ma, Z C; Wei, Y M; Yan, Z H; Zheng, Y L

    2007-11-01

    To carry out the comparative analysis of alpha-gliadin genes on A genomes of diploid and polyploid wheats, 8 full-length alpha-gliadin genes, including 3 functional genes and 5 pseudogenes, were obtained from diploid wheats, among which 2, 2 and 4 alpha-gliadin genes were isolated from T. urartu, T. monococcum and T. boeoticum, respectively. The results indicated that higher number of alpha-gliadin pseudogenes have been present in diploid wheats before the formation of polyploid wheats. Amino acid sequence comparative analysis among 26 alpha-gliadin genes, including 16 functional genes and 10 pseudogenes, from diploid and polyploid wheats was conducted. The results indicated that all alpha-gliadins contained four coeliac toxic peptide sequences (i.e., PSQQ, QQQP, QQPY and QPYP). The polyglutamine domains are highly variable, and the second polyglutamine stretch is usually disrupted by the lysine or arginine residue at the fourth position. The unique domain I is the most conserved domain. There are 4 and 2 conserved cysteine residues in the unique domains I and II, respectively. Comparative analysis indicated that the functional alpha-gliadin genes from A genome are highly conserved, whereas the identity of pseudogenes in diploid wheats are higher than those in hexaploid wheats. Phylogenetic analysis indicated that all the analyzed functional alpha-gliadin genes could be clustered into two major groups, among which one group could be further divided into 5 subgroups. The origin of alpha-gliadin pseudogene and functional genes were also discussed. PMID:18186192

  15. ASSESSMENT OF SEISMIC ANALYSIS METHODOLOGIES FOR DEEPLY EMBEDDED NPP STRUCTURES.

    SciTech Connect

    XU, J.; MILLER, C.; COSTANTINO, C.; HOFMAYER, C.; GRAVES, H. .

    2005-07-01

    Several of the new generation nuclear power plant designs have structural configurations which are proposed to be deeply embedded. Since current seismic analysis methodologies have been applied to shallow embedded structures (e.g., ASCE 4 suggest that simple formulations may be used to model embedment effect when the depth of embedment is less than 30% of its foundation radius), the US Nuclear Regulatory Commission is sponsoring a program at the Brookhaven National Laboratory with the objective of investigating the extent to which procedures acceptable for shallow embedment depths are adequate for larger embedment depths. This paper presents the results of a study comparing the response spectra obtained from two of the more popular analysis methods for structural configurations varying from shallow embedment to complete embedment. A typical safety related structure embedded in a soil profile representative of a typical nuclear power plant site was utilized in the study and the depths of burial (DOB) considered range from 25-100% the height of the structure. Included in the paper are: (1) the description of a simplified analysis and a detailed approach for the SSI analyses of a structure with various DOB, (2) the comparison of the analysis results for the different DOBs between the two methods, and (3) the performance assessment of the analysis methodologies for SSI analyses of deeply embedded structures. The resulting assessment from this study has indicated that simplified methods may be capable of capturing the seismic response for much deeper embedded structures than would be normally allowed by the standard practice.

  16. Structural dynamic analysis of a ball joint

    NASA Astrophysics Data System (ADS)

    Hwang, Seok-Cheol; Lee, Kwon-Hee

    2012-11-01

    Ball joint is a rotating and swiveling element that is typically installed at the interface between two parts. In an automobile, the ball joint is the component that connects the control arms to the steering knuckle. The ball joint can also be installed in linkage systems for motion control applications. This paper describes the simulation strategy for a ball joint analysis, considering manufacturing process. Its manufacturing process can be divided into plugging and spinning. Then, the interested responses is selected as the stress distribution generated between its ball and bearing. In this paper, a commercial code of NX DAFUL using an implicit integration method is introduced to calculate the response. In addition, the gap analysis is performed to investigate the fitness, focusing on the response of the displacement of a ball stud. Also, the optimum design is suggested through case studies.

  17. Structural analysis of hierarchically organized zeolites

    NASA Astrophysics Data System (ADS)

    Mitchell, Sharon; Pinar, Ana B.; Kenvin, Jeffrey; Crivelli, Paolo; Kärger, Jörg; Pérez-Ramírez, Javier

    2015-10-01

    Advances in materials synthesis bring about many opportunities for technological applications, but are often accompanied by unprecedented complexity. This is clearly illustrated by the case of hierarchically organized zeolite catalysts, a class of crystalline microporous solids that has been revolutionized by the engineering of multilevel pore architectures, which combine unique chemical functionality with efficient molecular transport. Three key attributes, the crystal, the pore and the active site structure, can be expected to dominate the design process. This review examines the adequacy of the palette of techniques applied to characterize these distinguishing features and their catalytic impact.

  18. Structural analysis of hierarchically organized zeolites.

    PubMed

    Mitchell, Sharon; Pinar, Ana B; Kenvin, Jeffrey; Crivelli, Paolo; Kärger, Jörg; Pérez-Ramírez, Javier

    2015-01-01

    Advances in materials synthesis bring about many opportunities for technological applications, but are often accompanied by unprecedented complexity. This is clearly illustrated by the case of hierarchically organized zeolite catalysts, a class of crystalline microporous solids that has been revolutionized by the engineering of multilevel pore architectures, which combine unique chemical functionality with efficient molecular transport. Three key attributes, the crystal, the pore and the active site structure, can be expected to dominate the design process. This review examines the adequacy of the palette of techniques applied to characterize these distinguishing features and their catalytic impact. PMID:26482337

  19. Structural analysis of hierarchically organized zeolites

    PubMed Central

    Mitchell, Sharon; Pinar, Ana B.; Kenvin, Jeffrey; Crivelli, Paolo; Kärger, Jörg; Pérez-Ramírez, Javier

    2015-01-01

    Advances in materials synthesis bring about many opportunities for technological applications, but are often accompanied by unprecedented complexity. This is clearly illustrated by the case of hierarchically organized zeolite catalysts, a class of crystalline microporous solids that has been revolutionized by the engineering of multilevel pore architectures, which combine unique chemical functionality with efficient molecular transport. Three key attributes, the crystal, the pore and the active site structure, can be expected to dominate the design process. This review examines the adequacy of the palette of techniques applied to characterize these distinguishing features and their catalytic impact. PMID:26482337

  20. Turbine blade structural dynamic analysis. [for space shuttle main engine

    NASA Technical Reports Server (NTRS)

    Dickerson, E. O.

    1980-01-01

    The paper presents structural dynamic analysis and test results for the Space Shuttle Main Engine turbine blades. Athough these blades are designed to avoid coincidence of natural frequencies with harmonic excitation forces, the complexity of the turbine hardware, its nonlinearities and lack of information regarding the forcing function have led to fatigue failures. A comparison of single-blade analysis and test modal frequencies, shapes, and stresses is given; analysis techniques to describe the forcing function, compute dynamic responses, and incorporate the nonlinearities of Coulomb-friction dampers are presented. Recommendations are made for new research to improve forcing function computations and structural damping estimates used in the analysis.

  1. DNA sequence and analysis of human chromosome 9.

    PubMed

    Humphray, S J; Oliver, K; Hunt, A R; Plumb, R W; Loveland, J E; Howe, K L; Andrews, T D; Searle, S; Hunt, S E; Scott, C E; Jones, M C; Ainscough, R; Almeida, J P; Ambrose, K D; Ashwell, R I S; Babbage, A K; Babbage, S; Bagguley, C L; Bailey, J; Banerjee, R; Barker, D J; Barlow, K F; Bates, K; Beasley, H; Beasley, O; Bird, C P; Bray-Allen, S; Brown, A J; Brown, J Y; Burford, D; Burrill, W; Burton, J; Carder, C; Carter, N P; Chapman, J C; Chen, Y; Clarke, G; Clark, S Y; Clee, C M; Clegg, S; Collier, R E; Corby, N; Crosier, M; Cummings, A T; Davies, J; Dhami, P; Dunn, M; Dutta, I; Dyer, L W; Earthrowl, M E; Faulkner, L; Fleming, C J; Frankish, A; Frankland, J A; French, L; Fricker, D G; Garner, P; Garnett, J; Ghori, J; Gilbert, J G R; Glison, C; Grafham, D V; Gribble, S; Griffiths, C; Griffiths-Jones, S; Grocock, R; Guy, J; Hall, R E; Hammond, S; Harley, J L; Harrison, E S I; Hart, E A; Heath, P D; Henderson, C D; Hopkins, B L; Howard, P J; Howden, P J; Huckle, E; Johnson, C; Johnson, D; Joy, A A; Kay, M; Keenan, S; Kershaw, J K; Kimberley, A M; King, A; Knights, A; Laird, G K; Langford, C; Lawlor, S; Leongamornlert, D A; Leversha, M; Lloyd, C; Lloyd, D M; Lovell, J; Martin, S; Mashreghi-Mohammadi, M; Matthews, L; McLaren, S; McLay, K E; McMurray, A; Milne, S; Nickerson, T; Nisbett, J; Nordsiek, G; Pearce, A V; Peck, A I; Porter, K M; Pandian, R; Pelan, S; Phillimore, B; Povey, S; Ramsey, Y; Rand, V; Scharfe, M; Sehra, H K; Shownkeen, R; Sims, S K; Skuce, C D; Smith, M; Steward, C A; Swarbreck, D; Sycamore, N; Tester, J; Thorpe, A; Tracey, A; Tromans, A; Thomas, D W; Wall, M; Wallis, J M; West, A P; Whitehead, S L; Willey, D L; Williams, S A; Wilming, L; Wray, P W; Young, L; Ashurst, J L; Coulson, A; Blöcker, H; Durbin, R; Sulston, J E; Hubbard, T; Jackson, M J; Bentley, D R; Beck, S; Rogers, J; Dunham, I

    2004-05-27

    Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection. PMID:15164053

  2. DNA sequence and analysis of human chromosome 9

    PubMed Central

    Humphray, S. J.; Oliver, K.; Hunt, A. R.; Plumb, R. W.; Loveland, J. E.; Howe, K. L.; Andrews, T. D.; Searle, S.; Hunt, S. E.; Scott, C. E.; Jones, M. C.; Ainscough, R.; Almeida, J. P.; Ambrose, K. D.; Ashwell, R. I. S.; Babbage, A. K.; Babbage, S.; Bagguley, C. L.; Bailey, J.; Banerjee, R.; Barker, D. J.; Barlow, K. F.; Bates, K.; Beasley, H.; Beasley, O.; Bird, C. P.; Bray-Allen, S.; Brown, A. J.; Brown, J. Y.; Burford, D.; Burrill, W.; Burton, J.; Carder, C.; Carter, N. P.; Chapman, J. C.; Chen, Y.; Clarke, G.; Clark, S. Y.; Clee, C. M.; Clegg, S.; Collier, R. E.; Corby, N.; Crosier, M.; Cummings, A. T.; Davies, J.; Dhami, P.; Dunn, M.; Dutta, I.; Dyer, L. W.; Earthrowl, M. E.; Faulkner, L.; Fleming, C. J.; Frankish, A.; Frankland, J. A.; French, L.; Fricker, D. G.; Garner, P.; Garnett, J.; Ghori, J.; Gilbert, J. G. R.; Glison, C.; Grafham, D. V.; Gribble, S.; Griffiths, C.; Griffiths-Jones, S.; Grocock, R.; Guy, J.; Hall, R. E.; Hammond, S.; Harley, J. L.; Harrison, E. S. I.; Hart, E. A.; Heath, P. D.; Henderson, C. D.; Hopkins, B. L.; Howard, P. J.; Howden, P. J.; Huckle, E.; Johnson, C.; Johnson, D.; Joy, A. A.; Kay, M.; Keenan, S.; Kershaw, J. K.; Kimberley, A. M.; King, A.; Knights, A.; Laird, G. K.; Langford, C.; Lawlor, S.; Leongamornlert, D. A.; Leversha, M.; Lloyd, C.; Lloyd, D. M.; Lovell, J.; Martin, S.; Mashreghi-Mohammadi, M.; Matthews, L.; McLaren, S.; McLay, K. E.; McMurray, A.; Milne, S.; Nickerson, T.; Nisbett, J.; Nordsiek, G.; Pearce, A. V.; Peck, A. I.; Porter, K. M.; Pandian, R.; Pelan, S.; Phillimore, B.; Povey, S.; Ramsey, Y.; Rand, V.; Scharfe, M.; Sehra, H. K.; Shownkeen, R.; Sims, S. K.; Skuce, C. D.; Smith, M.; Steward, C. A.; Swarbreck, D.; Sycamore, N.; Tester, J.; Thorpe, A.; Tracey, A.; Tromans, A.; Thomas, D. W.; Wall, M.; Wallis, J. M.; West, A. P.; Whitehead, S. L.; Willey, D. L.; Williams, S. A.; Wilming, L.; Wray, P. W.; Young, L.; Ashurst, J. L.; Coulson, A.; Blöcker, H.; Durbin, R.; Sulston, J. E.; Hubbard, T.; Jackson, M. J.; Bentley, D. R.; Beck, S.; Rogers, J.; Dunham, I.

    2009-01-01

    Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6–8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection. PMID:15164053

  3. Evaluation of structural integrity using integrated testing and analysis

    NASA Technical Reports Server (NTRS)

    Coppolino, Robert N.

    1988-01-01

    An integrated approach to dynamic testing and mathematical model analysis is described. The overall approach addresses four key tasks, namely, pretest planning and analysis, test data acquisition, data reduction and analysis, and test/analysis correlation and mathematical model updates. Several key software programs are employed to accomplish this task. They are a leading finite element code, a sophisticated data analysis processor and a graphical pre- and post-processor along with an advanced interface utility. Several practical structures are used to illustrate tools and concepts employed in the integrated test analysis process.

  4. Structural and quantitative analysis of Equisetum alkaloids.

    PubMed

    Cramer, Luise; Ernst, Ludger; Lubienski, Marcus; Papke, Uli; Schiebel, Hans-Martin; Jerz, Gerold; Beuerle, Till

    2015-08-01

    Equisetum palustre L. is known for its toxicity for livestock. Several studies in the past addressed the isolation and identification of the responsible alkaloids. So far, palustrine (1) and N(5)-formylpalustrine (2) are known alkaloids of E. palustre. A HPLC-ESI-MS/MS method in combination with simple sample work-up was developed to identify and quantitate Equisetum alkaloids. Besides the two known alkaloids six related alkaloids were detected in different Equisetum samples. The structure of the alkaloid palustridiene (3) was derived by comprehensive 1D and 2D NMR experiments. N(5)-Acetylpalustrine (4) was also thoroughly characterized by NMR for the first time. The structure of N(5)-formylpalustridiene (5) is proposed based on mass spectrometry results. Twenty-two E. palustre samples were screened by a HPLC-ESI-MS/MS method after development of a simple sample work-up and in most cases the set of all eight alkaloids were detected in all parts of the plant. A high variability of the alkaloid content and distribution was found depending on plant organ, plant origin and season ranging from 88 to 597mg/kg dried weight. However, palustrine (1) and the alkaloid palustridiene (3) always represented the main alkaloids. For the first time, a comprehensive identification, quantitation and distribution of Equisetum alkaloids was achieved. PMID:25823584

  5. Structure analysis on synthetic emerald crystals

    NASA Astrophysics Data System (ADS)

    Lee, Pei-Lun; Lee, Jiann-Shing; Huang, Eugene; Liao, Ju-Hsiou

    2013-05-01

    Single crystals of emerald synthesized by means of the flux method were adopted for crystallographic analyses. Emerald crystals with a wide range of Cr3+-doping content up to 3.16 wt% Cr2O3 were examined by X-ray single crystal diffraction refinement method. The crystal structures of the emerald crystals were refined to R 1 (all data) of 0.019-0.024 and w R 2 (all data) of 0.061-0.073. When Cr3+ substitutes for Al3+, the main adjustment takes place in the Al-octahedron and Be-tetrahedron. The effect of substitution of Cr3+ for Al3+ in the beryl structure results in progressively lengthening of the Al-O distance, while the length of the other bonds remains nearly unchanged. The substitution of Cr3+ for Al3+ may have caused the expansion of a axis, while keeping the c axis unchanged in the emerald lattice. As a consequence, the Al-O-Si and Al-O-Be bonding angles are found to decrease, while the angle of Si-O-Be increases as the Al-O distance increases during the Cr replacement.

  6. FOXFET structure — device modelling and analysis

    NASA Astrophysics Data System (ADS)

    Križaj, Dejan; Bonvicini, Walter; Amon, Slavko

    1997-02-01

    A FOXFET structure for biasing AC coupled detector structures has been analyzed by a two-dimensional device simulation. For this purpose, a floating strip junction with zero current boundary condition has been applied. The floating strip voltage increase is analyzed from depletion layer spreading through three charge regions: electron accumulation surface region, hole current flow region and depleted bulk region. As a result, the floating strip potential increases approximately as the square root of the drain/backside reverse voltage. Strip potential saturation is observed for oxide charge densities larger than 5 × 10 11 cm -2 and results in a weaker gate control and oxide thickness influence. Current conduction mechanisms are critically discussed and drift-diffusion injection from the floating strip junction is proposed instead of the thermionic emission model. Strip potential increase by an additionally injected strip current is due to the effect of space-charge-limited-current (SCLC) for an injected strip current larger than approximately 10 -9 A/μm. The dynamic resistance calculated from numerically obtained strip current/voltage curves has a slope of 0.85 for a lower injected strip current ( Is<10 -10 A/ μm) and decreases to 0.6 for a larger one.

  7. Analysis of hyperfine structure in photoassociation spectra

    NASA Astrophysics Data System (ADS)

    Bergeman, T.

    2008-05-01

    The low Doppler width in photoassociation spectra from cold atoms makes hyperfine structure clearly visible, especially with heavier alkali atoms. Recently the focus has been on photoassociation to weakly bound dimers [1,2]. However there are also useful data on somewhat more deeply bound levels [2] for which a different coupling scheme is appropriate. Following [3], we use a F = J + I representation, and develop a transformation between this and the usual case e representation which applies at asymptotically large internuclear distance. We hope to model and assign hyperfine structure in φ = 1 states, using appropriate ground and excited state wavefunctions. To obtain eigenvalues from very large DVR matrices, we use a ``stepwise diagonalization'' procedure, which appears to be more efficient than standard sparse matrix methods. [1] E. Tiesinga et al. PRA 71, 052703 (2005); K. M. Jones et al, RMP 78, 483 (2006). [2] Data on Rb2 from J. Qi, D. Wang, Y. Huang, H. Pechkis, E. Eyler, P. Gould, W. C. Stwalley, C. C. Tsai and D.J. Heinzen; Data on RbCs from A. J. Kerman, J. M. Sage, S. Sainis and D. DeMille. [3] B. Gao, PRA 54, 2022 (1996).

  8. Structural and functional analysis of chicken U4 small nuclear RNA genes.

    PubMed Central

    Hoffman, M L; Korf, G M; McNamara, K J; Stumph, W E

    1986-01-01

    Two distinct chicken U4 RNA genes have been cloned and characterized. They are closely linked within 465 base pairs of each other and have the same transcriptional orientation. The downstream U4 homology is a true gene, based on the criteria that it is colinear with chicken U4B RNA and is expressed when injected into Xenopus laevis oocytes. The upstream U4 homology, however, contains seven base substitutions relative to U4B RNA. This sequence may be a nonexpressed pseudogene, but the pattern of base substitutions suggests that it more probably encodes a variant yet functional U4 RNA product not yet characterized at the RNA level. In support of this, the two U4 genes have regions of homology with each other in their 5'-flanking DNA at two positions known to be essential for the efficient expression of vertebrate U1 and U2 small nuclear RNA genes. In the case of U1 and U2 RNA genes, the more distal region (located near position-200 with respect to the RNA cap site) is known to function as a transcriptional enhancer. Although this region is highly conserved in overall structure and sequence among U1 and U2 RNA genes, it is much less conserved in the chicken U4 RNA genes reported here. Interestingly, short sequence elements present in the -200 region of the U4 RNA genes are inverted (i.e., on the complementary strand) relative to their usual orientation upstream of U1 and U2 RNA genes. Thus, the -200 region of the U4 RNA genes may represent a natural evolutionary occurrence of an enhancer sequence inversion. Images PMID:3025618

  9. Failure Analysis and Mechanisms of Failure of Fibrous Composite Structures

    NASA Technical Reports Server (NTRS)

    Noor, A. K. (Compiler); Shuart, M. J. (Compiler); Starnes, J. H., Jr. (Compiler); Williams, J. G. (Compiler)

    1983-01-01

    The state of the art of failure analysis and current design practices, especially as applied to the use of fibrous composite materials in aircraft structures is discussed. Deficiencies in these technologies are identified, as are directions for future research.

  10. Progressive Failure Analysis Methodology for Laminated Composite Structures

    NASA Technical Reports Server (NTRS)

    Sleight, David W.

    1999-01-01

    A progressive failure analysis method has been developed for predicting the failure of laminated composite structures under geometrically nonlinear deformations. The progressive failure analysis uses C(exp 1) shell elements based on classical lamination theory to calculate the in-plane stresses. Several failure criteria, including the maximum strain criterion, Hashin's criterion, and Christensen's criterion, are used to predict the failure mechanisms and several options are available to degrade the material properties after failures. The progressive failure analysis method is implemented in the COMET finite element analysis code and can predict the damage and response of laminated composite structures from initial loading to final failure. The different failure criteria and material degradation methods are compared and assessed by performing analyses of several laminated composite structures. Results from the progressive failure method indicate good correlation with the existing test data except in structural applications where interlaminar stresses are important which may cause failure mechanisms such as debonding or delaminations.

  11. Sensitivity analysis of discrete structural systems: A survey

    NASA Technical Reports Server (NTRS)

    Adelman, H. M.; Haftka, R. T.

    1984-01-01

    Methods for calculating sensitivity derivatives for discrete structural systems are surveyed, primarily covering literature published during the past two decades. Methods are described for calculating derivatives of static displacements and stresses, eigenvalues and eigenvectors, transient structural response, and derivatives of optimum structural designs with respect to problem parameters. The survey is focused on publications addressed to structural analysis, but also includes a number of methods developed in nonstructural fields such as electronics, controls, and physical chemistry which are directly applicable to structural problems. Most notable among the nonstructural-based methods are the adjoint variable technique from control theory, and the Green's function and FAST methods from physical chemistry.

  12. Statistical energy analysis of complex structures, phase 2

    NASA Technical Reports Server (NTRS)

    Trudell, R. W.; Yano, L. I.

    1980-01-01

    A method for estimating the structural vibration properties of complex systems in high frequency environments was investigated. The structure analyzed was the Materials Experiment Assembly, (MEA), which is a portion of the OST-2A payload for the space transportation system. Statistical energy analysis (SEA) techniques were used to model the structure and predict the structural element response to acoustic excitation. A comparison of the intial response predictions and measured acoustic test data is presented. The conclusions indicate that: the SEA predicted the response of primary structure to acoustic excitation over a wide range of frequencies; and the contribution of mechanically induced random vibration to the total MEA is not significant.

  13. Reliability analysis of structures under periodic proof tests in service

    NASA Technical Reports Server (NTRS)

    Yang, J.-N.

    1976-01-01

    A reliability analysis of structures subjected to random service loads and periodic proof tests treats gust loads and maneuver loads as random processes. Crack initiation, crack propagation, and strength degradation are treated as the fatigue process. The time to fatigue crack initiation and ultimate strength are random variables. Residual strength decreases during crack propagation, so that failure rate increases with time. When a structure fails under periodic proof testing, a new structure is built and proof-tested. The probability of structural failure in service is derived from treatment of all the random variables, strength degradations, service loads, proof tests, and the renewal of failed structures. Some numerical examples are worked out.

  14. Seismic Response Analysis and Design of Structure with Base Isolation

    SciTech Connect

    Rosko, Peter

    2010-05-21

    The paper reports the study on seismic response and energy distribution of a multi-story civil structure. The nonlinear analysis used the 2003 Bam earthquake acceleration record as the excitation input to the structural model. The displacement response was analyzed in time domain and in frequency domain. The displacement and its derivatives result energy components. The energy distribution in each story provides useful information for the structural upgrade with help of added devices. The objective is the structural displacement response minimization. The application of the structural seismic response research is presented in base-isolation example.

  15. Analysis of Smart Composite Structures Including Debonding

    NASA Technical Reports Server (NTRS)

    Chattopadhyay, Aditi; Seeley, Charles E.

    1997-01-01

    Smart composite structures with distributed sensors and actuators have the capability to actively respond to a changing environment while offering significant weight savings and additional passive controllability through ply tailoring. Piezoelectric sensing and actuation of composite laminates is the most promising concept due to the static and dynamic control capabilities. Essential to the implementation of these smart composites are the development of accurate and efficient modeling techniques and experimental validation. This research addresses each of these important topics. A refined higher order theory is developed to model composite structures with surface bonded or embedded piezoelectric transducers. These transducers are used as both sensors and actuators for closed loop control. The theory accurately captures the transverse shear deformation through the thickness of the smart composite laminate while satisfying stress free boundary conditions on the free surfaces. The theory is extended to include the effect of debonding at the actuator-laminate interface. The developed analytical model is implemented using the finite element method utilizing an induced strain approach for computational efficiency. This allows general laminate geometries and boundary conditions to be analyzed. The state space control equations are developed to allow flexibility in the design of the control system. Circuit concepts are also discussed. Static and dynamic results of smart composite structures, obtained using the higher order theory, are correlated with available analytical data. Comparisons, including debonded laminates, are also made with a general purpose finite element code and available experimental data. Overall, very good agreement is observed. Convergence of the finite element implementation of the higher order theory is shown with exact solutions. Additional results demonstrate the utility of the developed theory to study piezoelectric actuation of composite

  16. 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.

  17. RBS analysis of heteroepitaxial layered structures

    NASA Astrophysics Data System (ADS)

    Flagmeyer, R.

    1992-05-01

    Rutherford backscattering and channeling of energetic ions is applied to III-V semiconductor epitaxial systems. Grazing incidence RBS is employed to observed in-depth profiles of chemical composition, especially the well width Lz, of AlGaAs/GaAs and InGaAs/InP single quantum well (SQW) structures. In case of highly lattice-mismatched materials, RBS/channeling analyses reveal the pseudomorphic or relaxed state of the corresponding crystal lattices. Some new aspects in determining the elastic strain and in locating the misfit dislocation array in InGaAs/GaAs single heterostructures and superlattices are discussed. Finally, attention is drawn to the "internal" lattice distortion in epilayers of pseudobinary alloys, and the high sensibility of dechanneling to the intrinsic atomic displacements is demonstrated.

  18. Pore structure analysis of American coals

    SciTech Connect

    Gallegos, D.P.; Smith, D.M.; Stermer, D.L.

    1987-01-01

    The pore structure of 19 American coals, representing a wide range of rank and geographic origin, has been studied via gas adsorption, mercury porosimetry, helium displacement and NMR spin-lattice relaxation measurements. Nitrogen adsorption at 77 K was used to determine surface area in the pore range of r/sub p/ > approx. = 1nm and carbon dioxide adsorption at 273 K was used to obtain the total surface area. Porosimetry results were complicated by inter-particle void filling, surface roughness/porosity and sample compression. By employing a range of particle sizes, information concerning the relative magnitude of these mechanisms was ascertained as a function of pressure. Spin-lattice relaxation measurements of water contained in saturated coal were used to find pore size distributions over a broad range of T/sub 1/, the spin-lattice relaxation time. Good qualitative agreement was obtained between these measurements and gas adsorption/condensation results. 13 refs., 3 figs., 1 tab.

  19. Microfabricated structures for integrated DNA analysis.

    PubMed Central

    Burns, M A; Mastrangelo, C H; Sammarco, T S; Man, F P; Webster, J R; Johnsons, B N; Foerster, B; Jones, D; Fields, Y; Kaiser, A R; Burke, D T

    1996-01-01

    Photolithographic micromachining of silicon is a candidate technology for the construction of high-throughput DNA analysis devices. However, the development of complex silicon microfabricated systems has been hindered in part by the lack of a simple, versatile pumping method for integrating individual components. Here we describe a surface-tension-based pump able to move discrete nanoliter drops through enclosed channels using only local heating. This thermocapillary pump can accurately mix, measure, and divide drops by simple electronic control. In addition, we have constructed thermal-cycling chambers, gel electrophoresis channels, and radiolabeled DNA detectors that are compatible with the fabrication of thermocapillary pump channels. Since all of the components are made by conventional photolithographic techniques, they can be assembled into more complex integrated systems. The combination of pump and components into self-contained miniaturized devices may provide significant improvements in DNA analysis speed, portability, and cost. The potential of microfabricated systems lies in the low unit cost of silicon-based construction and in the efficient sample handling afforded by component integration. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:8643614

  20. Sensitivity Analysis for Coupled Aero-structural Systems

    NASA Technical Reports Server (NTRS)

    Giunta, Anthony A.

    1999-01-01

    A novel method has been developed for calculating gradients of aerodynamic force and moment coefficients for an aeroelastic aircraft model. This method uses the Global Sensitivity Equations (GSE) to account for the aero-structural coupling, and a reduced-order modal analysis approach to condense the coupling bandwidth between the aerodynamic and structural models. Parallel computing is applied to reduce the computational expense of the numerous high fidelity aerodynamic analyses needed for the coupled aero-structural system. Good agreement is obtained between aerodynamic force and moment gradients computed with the GSE/modal analysis approach and the same quantities computed using brute-force, computationally expensive, finite difference approximations. A comparison between the computational expense of the GSE/modal analysis method and a pure finite difference approach is presented. These results show that the GSE/modal analysis approach is the more computationally efficient technique if sensitivity analysis is to be performed for two or more aircraft design parameters.

  1. 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.

  2. 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.

  3. A Family Structure Approach to the Analysis of Poverty.

    ERIC Educational Resources Information Center

    Stuby, Richard G.

    A typological approach to the analysis of poverty, based on selected characteristics of family structure, is suggested since the family unit is a concrete or actual structure in society, and much of the research and many of the action programs of the war on poverty have implicitly invoked some concept of the family. The typology of family…

  4. An expert system for integrated structural analysis and design optimization for aerospace structures

    NASA Astrophysics Data System (ADS)

    1992-04-01

    The results of a research study on the development of an expert system for integrated structural analysis and design optimization is presented. An Object Representation Language (ORL) was developed first in conjunction with a rule-based system. This ORL/AI shell was then used to develop expert systems to provide assistance with a variety of structural analysis and design optimization tasks, in conjunction with procedural modules for finite element structural analysis and design optimization. The main goal of the research study was to provide expertise, judgment, and reasoning capabilities in the aerospace structural design process. This will allow engineers performing structural analysis and design, even without extensive experience in the field, to develop error-free, efficient and reliable structural designs very rapidly and cost-effectively. This would not only improve the productivity of design engineers and analysts, but also significantly reduce time to completion of structural design. An extensive literature survey in the field of structural analysis, design optimization, artificial intelligence, and database management systems and their application to the structural design process was first performed. A feasibility study was then performed, and the architecture and the conceptual design for the integrated 'intelligent' structural analysis and design optimization software was then developed. An Object Representation Language (ORL), in conjunction with a rule-based system, was then developed using C++. Such an approach would improve the expressiveness for knowledge representation (especially for structural analysis and design applications), provide ability to build very large and practical expert systems, and provide an efficient way for storing knowledge. Functional specifications for the expert systems were then developed. The ORL/AI shell was then used to develop a variety of modules of expert systems for a variety of modeling, finite element analysis, and

  5. An expert system for integrated structural analysis and design optimization for aerospace structures

    NASA Technical Reports Server (NTRS)

    1992-01-01

    The results of a research study on the development of an expert system for integrated structural analysis and design optimization is presented. An Object Representation Language (ORL) was developed first in conjunction with a rule-based system. This ORL/AI shell was then used to develop expert systems to provide assistance with a variety of structural analysis and design optimization tasks, in conjunction with procedural modules for finite element structural analysis and design optimization. The main goal of the research study was to provide expertise, judgment, and reasoning capabilities in the aerospace structural design process. This will allow engineers performing structural analysis and design, even without extensive experience in the field, to develop error-free, efficient and reliable structural designs very rapidly and cost-effectively. This would not only improve the productivity of design engineers and analysts, but also significantly reduce time to completion of structural design. An extensive literature survey in the field of structural analysis, design optimization, artificial intelligence, and database management systems and their application to the structural design process was first performed. A feasibility study was then performed, and the architecture and the conceptual design for the integrated 'intelligent' structural analysis and design optimization software was then developed. An Object Representation Language (ORL), in conjunction with a rule-based system, was then developed using C++. Such an approach would improve the expressiveness for knowledge representation (especially for structural analysis and design applications), provide ability to build very large and practical expert systems, and provide an efficient way for storing knowledge. Functional specifications for the expert systems were then developed. The ORL/AI shell was then used to develop a variety of modules of expert systems for a variety of modeling, finite element analysis, and

  6. Analysis of starch structure using fluorophore-assisted carbohydrate electrophoresis.

    PubMed

    Morell, M K; Samuel, M S; O'Shea, M G

    1998-11-01

    The analysis of the fine structure of starches is important to the investigation of linkages between starch structure and function and to the investigation of the properties and roles of starch biosynthetic, modifying and degradation enzymes. Fluorophore-assisted carbohydrate electrophoresis has recently been introduced as a method for the analysis of the oligosaccharide populations released by the enzymatic digestion of starches, which has advantages in resolution and sensitivity over previously used methods, and provides the capacity for the facile analysis of oligosaccharide populations on either a molar or mass basis. The use of fluorophore-assisted carbohydrate electrophoresis for the analysis of oligosaccharides is reviewed with particular reference to the choice of label, efficiency of labeling and separation techniques. Examples of separations using slab gel electrophoresis, DNA sequencer analysis and capillary electrophoresis are presented and we conclude that on the basis of resolution and reproducibility, capillary electrophoresis is the method of choice for the separation of oligosaccharides of degree of polymerization from 1 to 100. Examples of isoamylase-debranched starches and glycogens analyzed by capillary electrophoresis are presented. The capillary electrophoresis analysis of starch structure through the analysis of oligosaccharides released by the debranching of limit dextrins derived from starches and glycogens is introduced as a useful diagnostic of starch structure. The potential for future development of novel diagnostics for starch structure using fluorophore-assisted carbohydrate electrophoresis is discussed. PMID:9848667

  7. Reliability Analysis of Brittle, Thin Walled Structures

    SciTech Connect

    Jonathan A Salem and Lynn Powers

    2007-02-09

    One emerging application for ceramics is diesel particulate filters being used order to meet EPA regulations going into effect in 2008. Diesel particulates are known to be carcinogenic and thus need to be minimized. Current systems use filters made from ceramics such as mullite and corderite. The filters are brittle and must operate at very high temperatures during a burn out cycle used to remove the soot buildup. Thus the filters are subjected to thermal shock stresses and life time reliability analysis is required. NASA GRC has developed reliability based design methods and test methods for such applications, such as CARES/Life and American Society for Testing and Materials (ASTM) C1499 “Standard Test Method for Equibiaxial Strength of Ceramics.”

  8. Stress analysis for structures with surface cracks

    NASA Technical Reports Server (NTRS)

    Bell, J. C.

    1978-01-01

    Two basic forms of analysis, one treating stresses around arbitrarily loaded circular cracks, the other treating stresses due to loads arbitrarily distributed on the surface of a half space, are united by a boundary-point least squares method to obtain analyses for stresses from surface cracks in places or bars. Calculations were for enough cases to show how effects from the crack vary with the depth-to-length ratio, the fractional penetration ratio, the obliquity of the load, and to some extent the fractional span ratio. The results include plots showing stress intensity factors, stress component distributions near the crack, and crack opening displacement patterns. Favorable comparisons are shown with two kinds of independent experiments, but the main method for confirming the results is by wide checking of overall satisfaction of boundary conditions, so that external confirmation is not essential. Principles involved in designing analyses which promote dependability of the results are proposed and illustrated.

  9. Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet.

    PubMed

    Tyagi, M; Sharma, P; Swamy, C S; Cadet, F; Srinivasan, N; de Brevern, A G; Offmann, B

    2006-07-01

    Encoding protein 3D structures into 1D string using short structural prototypes or structural alphabets opens a new front for structure comparison and analysis. Using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet, we have developed a methodology to compare protein structures that are encoded as sequences of PBs by aligning them using dynamic programming which uses a substitution matrix for PBs. This methodology is implemented in the applications available in Protein Block Expert (PBE) server. PBE addresses common issues in the field of protein structure analysis such as comparison of proteins structures and identification of protein structures in structural databanks that resemble a given structure. PBE-T provides facility to transform any PDB file into sequences of PBs. PBE-ALIGNc performs comparison of two protein structures based on the alignment of their corresponding PB sequences. PBE-ALIGNm is a facility for mining SCOP database for similar structures based on the alignment of PBs. Besides, PBE provides an interface to a database (PBE-SAdb) of preprocessed PB sequences from SCOP culled at 95% and of all-against-all pairwise PB alignments at family and superfamily levels. PBE server is freely available at http://bioinformatics.univ-reunion.fr/PBE/. PMID:16844973

  10. A Analysis of Mush-Chimney Structure

    NASA Astrophysics Data System (ADS)

    Yang, Young-Kyun

    1995-01-01

    When a multi-component liquid is cooled and solidified, commonly, the solid phase advances from the cold boundary into the liquid as a branching forest of dendritic crystals. This creates a region of mixed solid and liquid phases, referred to as a mushy zone, in which the solid forms a rigidly connected framework with the liquid occurring in the intercrystalline gaps. When the fluid seeps through the dendrites, further freezing occurs which fills in pores of the matrix and reduces its permeability to the liquid flow. In particular, if a binary alloy (for example, NH_4Cl -H_2O solution) is cooled at bottom and a dense component (for example, NH_4 Cl) is solidified, buoyant material released during freezing in the pores returns to the melt only through thin, vertical, but widely separated, 'chimneys', the flow through the matrix between them being organized to supply these chimneys. We presented photos of a mush-chimney system obtained from the ammonium chloride experiment, and we studied how convection with horizontal divergence affects the structure and flow of the mush-chimney system. We use a simple ODE system in the mush derived by assuming that the temperature depends on vertical coordinate only. We find that the mass fraction of solid increases and the depth of a mush decreases when the strength of convection increases. We present an axisymmetric model containing only one chimney to analyze the structure of the mush-chimney system. We find solutions of the temperature, the solid fraction, and the pressure in the chimney wall. In particular, the pressure expression shows that the fluid flow needs a huge pressure in order to pass through the chimney wall if its permeability is very small. We assume that a ratio of composition is large, which allows us to neglect the pressure contribution of the chimney wall. We use the knowledge of the variables in the mush, evaluated on the chimney wall, to find the fluid flow in the chimney and the radius of chimney. Our

  11. Analysis of boron carbides' electronic structure

    NASA Technical Reports Server (NTRS)

    Howard, Iris A.; Beckel, Charles L.

    1986-01-01

    The electronic properties of boron-rich icosahedral clusters were studied as a means of understanding the electronic structure of the icosahedral borides such as boron carbide. A lower bound was estimated on bipolaron formation energies in B12 and B11C icosahedra, and the associated distortions. While the magnitude of the distortion associated with bipolaron formation is similar in both cases, the calculated formation energies differ greatly, formation being much more favorable on B11C icosahedra. The stable positions of a divalent atom relative to an icosahedral borane was also investigated, with the result that a stable energy minimum was found when the atom is at the center of the borane, internal to the B12 cage. If incorporation of dopant atoms into B12 cages in icosahedral boride solids is feasible, novel materials might result. In addition, the normal modes of a B12H12 cluster, of the C2B10 cage in para-carborane, and of a B12 icosahedron of reduced (D sub 3d) symmetry, such as is found in the icosahedral borides, were calculated. The nature of these vibrational modes will be important in determining, for instance, the character of the electron-lattice coupling in the borides, and in analyzing the lattice contribution to the thermal conductivity.

  12. Partial Wave Analysis of Coupled Photonic Structures

    NASA Technical Reports Server (NTRS)

    Fuller, Kirk A.; Smith, David D.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    The very high quality factors sustained by microcavity optical resonators are relevant to applications in wavelength filtering, routing, switching, modulation, and multiplexing/demultiplexing. Increases in the density of photonic elements require that attention be paid to how electromagnetic (EM) coupling modifies their optical properties. This is especially true when cavity resonances are involved, in which case, their characteristics may be fundamentally altered. Understanding the optical properties of microcavities that are near or in contact with photonic elements---such as other microcavities, nanostructures, couplers, and substrates---can be expected to advance our understanding of the roles that these structures may play in VLSI photonics, biosensors and similar device technologies. Wc present results from recent theoretical studies of the effects of inter- and intracavity coupling on optical resonances in compound spherical particles. Concentrically stratified spheres and bispheres constituted from homogeneous and stratified spheres are subjects of this investigation. A new formulation is introduced for the absorption of light in an arbitrary layer of a multilayered sphere, which is based on multiple reflections of the spherical partial waves of the Lorenz-Mie solution for scattering by a sphere. Absorption efficiencies, which can be used to profile cavity resonances and to infer fluorescence yields or the onset of nonlinear optical processes in the microcavities, are presented. Splitting of resonances in these multisphere systems is paid particular attention, and consequences for photonic device development and possible performance enhancements through carefully designed architectures that exploit EM coupling are considered.

  13. Algorithmic dimensionality reduction for molecular structure analysis

    PubMed Central

    Brown, W. Michael; Martin, Shawn; Pollock, Sara N.; Coutsias, Evangelos A.; Watson, Jean-Paul

    2008-01-01

    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation—a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation. PMID:18715062

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

    NASA Technical Reports Server (NTRS)

    Cruse, T. A.

    1987-01-01

    The objective is the development of several modular structural analysis packages capable of predicting the probabilistic response distribution for key structural variables such as maximum stress, natural frequencies, transient response, etc. The structural analysis packages are to include stochastic modeling of loads, material properties, geometry (tolerances), and boundary conditions. The solution is to be in terms of the cumulative probability of exceedance distribution (CDF) and confidence bounds. Two methods of probability modeling are to be included as well as three types of structural models - probabilistic finite-element method (PFEM); probabilistic approximate analysis methods (PAAM); and probabilistic boundary element methods (PBEM). The purpose in doing probabilistic structural analysis is to provide the designer with a more realistic ability to assess the importance of uncertainty in the response of a high performance structure. Probabilistic Structural Analysis Method (PSAM) tools will estimate structural safety and reliability, while providing the engineer with information on the confidence that should be given to the predicted behavior. Perhaps most critically, the PSAM results will directly provide information on the sensitivity of the design response to those variables which are seen to be uncertain.

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

    NASA Technical Reports Server (NTRS)

    Cruse, T. A.; Burnside, O. H.; Wu, Y.-T.; Polch, E. Z.; Dias, J. B.

    1988-01-01

    The objective is the development of several modular structural analysis packages capable of predicting the probabilistic response distribution for key structural variables such as maximum stress, natural frequencies, transient response, etc. The structural analysis packages are to include stochastic modeling of loads, material properties, geometry (tolerances), and boundary conditions. The solution is to be in terms of the cumulative probability of exceedance distribution (CDF) and confidence bounds. Two methods of probability modeling are to be included as well as three types of structural models - probabilistic finite-element method (PFEM); probabilistic approximate analysis methods (PAAM); and probabilistic boundary element methods (PBEM). The purpose in doing probabilistic structural analysis is to provide the designer with a more realistic ability to assess the importance of uncertainty in the response of a high performance structure. Probabilistic Structural Analysis Method (PSAM) tools will estimate structural safety and reliability, while providing the engineer with information on the confidence that should be given to the predicted behavior. Perhaps most critically, the PSAM results will directly provide information on the sensitivity of the design response to those variables which are seen to be uncertain.

  16. Tempered Water Lower Port Connector Structural Analysis Verification

    SciTech Connect

    CREA, B.A.

    2000-05-05

    Structural analysis of the lower port connection of the Tempered Water System of the Cold Vacuum Drying Facility was performed. Subsequent detailed design changes to enhance operability resulted in the need to re-evaluate the bases of the original analysis to verify its continued validity. This evaluation is contained in Appendix A of this report. The original evaluation is contained in Appendix B.

  17. Alternative Test Criteria in Covariance Structure Analysis: A Unified Approach.

    ERIC Educational Resources Information Center

    Satorra, Albert

    1989-01-01

    Within covariance structural analysis, a unified approach to asymptotic theory of alternative test criteria for testing parametric restrictions is provided. More general statistics for addressing the case where the discrepancy function is not asymptotically optimal, and issues concerning power analysis and the asymptotic theory of testing-related…

  18. Application of integrated fluid-thermal-structural analysis methods

    NASA Technical Reports Server (NTRS)

    Wieting, Allan R.; Dechaumphai, Pramote; Bey, Kim S.; Thornton, Earl A.; Morgan, Ken

    1988-01-01

    Hypersonic vehicles operate in a hostile aerothermal environment which has a significant impact on their aerothermostructural performance. Significant coupling occurs between the aerodynamic flow field, structural heat transfer, and structural response creating a multidisciplinary interaction. Interfacing state-of-the-art disciplinary analysis methods is not efficient, hence interdisciplinary analysis methods integrated into a single aerothermostructural analyzer are needed. The NASA Langley Research Center is developing such methods in an analyzer called LIFTS (Langley Integrated Fluid-Thermal-Structural) analyzer. The evolution and status of LIFTS is reviewed and illustrated through applications.

  19. Structural mode significance using INCA. [Interactive Controls Analysis computer program

    NASA Technical Reports Server (NTRS)

    Bauer, Frank H.; Downing, John P.; Thorpe, Christopher J.

    1990-01-01

    Structural finite element models are often too large to be used in the design and analysis of control systems. Model reduction techniques must be applied to reduce the structural model to manageable size. In the past, engineers either performed the model order reduction by hand or used distinct computer programs to retrieve the data, to perform the significance analysis and to reduce the order of the model. To expedite this process, the latest version of INCA has been expanded to include an interactive graphical structural mode significance and model order reduction capability.

  20. Coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures

    NASA Astrophysics Data System (ADS)

    Hartle, M. S.; McKnight, R. L.; Huang, H.; Holt, R.

    1992-04-01

    Described here are the accomplishments of a 5-year program to develop a methodology for coupled structural, thermal, electromagnetic analysis tailoring of graded component structures. The capabilities developed over the course of the program are the analyzer module and the tailoring module for the modeling of graded materials. Highlighted accomplishments for the past year include the addition of a buckling analysis capability, the addition of mode shape slope calculation for flutter analysis, verification of the analysis modules using simulated components, and verification of the tailoring module.

  1. Coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures

    NASA Technical Reports Server (NTRS)

    Hartle, M. S.; Mcknight, R. L.; Huang, H.; Holt, R.

    1992-01-01

    Described here are the accomplishments of a 5-year program to develop a methodology for coupled structural, thermal, electromagnetic analysis tailoring of graded component structures. The capabilities developed over the course of the program are the analyzer module and the tailoring module for the modeling of graded materials. Highlighted accomplishments for the past year include the addition of a buckling analysis capability, the addition of mode shape slope calculation for flutter analysis, verification of the analysis modules using simulated components, and verification of the tailoring module.

  2. Nonlinear and Failure Analysis of Composite Structures

    NASA Technical Reports Server (NTRS)

    Noor, Ahmed K.; Starnes, James H. (Technical Monitor)

    2002-01-01

    The overall goal of this research is to assess the effect of discontinuities and uncertainties on the nonlinear response and failure of stiffened composite panels subjected to combined mechanical and thermal loads. The key elements of the study are: (a) study of the effects of stiffener geometry and of transverse stresses on the response, damage initiation and propagation in stiffened composite panels; (b) use of hierarchical sensitivity coefficients to identify the major parameters that affect the response and damage in each of the different levels in the hierarchy (micromechanical, layer, panel, subcomponent and component levels); and, (c) application of fuzzy set techniques to identify the range and variation of possible responses. The computational models developed are used in conjunction with experiments to understand the physical phenomena associated with the nonlinear response and failure of stiffened composite panels. A toolkit is developed for use in conjunction with deterministic analysis programs to help the designer in assessing the effect of uncertainties in the different computational model parameters on the variability of the response quantities.

  3. Protein structure prediction and analysis using the Robetta server

    PubMed Central

    Kim, David E.; Chivian, Dylan; Baker, David

    2004-01-01

    The Robetta server (http://robetta.bakerlab.org) provides automated tools for protein structure prediction and analysis. For structure prediction, sequences submitted to the server are parsed into putative domains and structural models are generated using either comparative modeling or de novo structure prediction methods. If a confident match to a protein of known structure is found using BLAST, PSI-BLAST, FFAS03 or 3D-Jury, it is used as a template for comparative modeling. If no match is found, structure predictions are made using the de novo Rosetta fragment insertion method. Experimental nuclear magnetic resonance (NMR) constraints data can also be submitted with a query sequence for RosettaNMR de novo structure determination. Other current capabilities include the prediction of the effects of mutations on protein–protein interactions using computational interface alanine scanning. The Rosetta protein design and protein–protein docking methodologies will soon be available through the server as well. PMID:15215442

  4. Power flow analysis of an L-shaped plate structure

    NASA Technical Reports Server (NTRS)

    Cuschieri, J. M.

    1987-01-01

    In the analysis of the vibration response and structure-borne vibration transmission between elements of a complex structure, statistical energy analysis (SEA) or finite element analysis (FEA) are generally used. However, an alternative method is using vibrational power flow techniques which can be especially useful in the mid frequencies between the optimum frequency regimes for FEA and SEA. Power flow analysis has in general been used on one-dimensional beam-like structures or between structures with point joints. In this paper, the power flow technique is extended to two-dimensional plate like structures joined along a common edge without frequency or spatial averaging the results, such that the resonant response of the structure is determined. The power flow results are compared to results obtained using FEA at low frequencies and SEA at high frequencies. The agreement with FEA results is good but the power flow technique has an improved computational efficiency. Compared to the SEA results the power flow results show a closer representation of the actual response of the structure.

  5. Fuzzy finite-element analysis of smart structures

    NASA Astrophysics Data System (ADS)

    Akpan, U. O.; Koko, T. S.; Orisamolu, I. R.; Gallant, B. K.

    2001-04-01

    A fuzzy finite element based approach is developed for modelling smart structures with vague or imprecise uncertainties. Fuzzy sets are used to represent the uncertainties present in the piezoelectric, mechanical, thermal, and physical properties of the smart structure. In order to facilitate efficient computation, a sensitivity analysis procedure is used to streamline the number of input fuzzy variables, and the vertex fuzzy analysis technique is then used to compute the possibility distributions of the responses of the smart structural system. The methodology has been developed within the framework of the SMARTCOM computational tool for the design/analysis of smart composite structures. The methodology developed is found to be accurate and computationally efficient for the solution of practical problems.

  6. Thermal and structural coupling analysis of magnetically suspended flywheel rotor

    NASA Astrophysics Data System (ADS)

    Zhang, Shuna; Han, Bangcheng; Li, Hong; Fang, Jiancheng

    2006-11-01

    Magnetically suspended flywheel (MSFW) is used in spacecraft to control the attitude. The mechanical structure of MSFW must accommodate thermal strains due to the temperature differences. And both the thermal stresses and the thermal loads change as the size and shape of the structure changes. Therefore, coupling exists between the heat transfer and the static stress analysis problems. In this paper finite element method (FEM) is used to process the thermal and structural analysis of the MSFW rotor and motor stator. The solution is performed by ANSYS software code. The temperature distribution is determined by the steady state thermal analysis. Based on the temperature field results, the thermal stress and deformation fields are calculated as well. The results provide the theoretical basis for the thermal design and can also be a guide for the structural optimization of the MSFW.

  7. Automated analysis of fundamental features of brain structures.

    PubMed

    Lancaster, Jack L; McKay, D Reese; Cykowski, Matthew D; Martinez, Michael J; Tan, Xi; Valaparla, Sunil; Zhang, Yi; Fox, Peter T

    2011-12-01

    Automated image analysis of the brain should include measures of fundamental structural features such as size and shape. We used principal axes (P-A) measurements to measure overall size and shape of brain structures segmented from MR brain images. The rationale was that quantitative volumetric studies of brain structures would benefit from shape standardization as had been shown for whole brain studies. P-A analysis software was extended to include controls for variability in position and orientation to support individual structure spatial normalization (ISSN). The rationale was that ISSN would provide a bias-free means to remove elementary sources of a structure's spatial variability in preparation for more detailed analyses. We studied nine brain structures (whole brain, cerebral hemispheres, cerebellum, brainstem, caudate, putamen, hippocampus, inferior frontal gyrus, and precuneus) from the 40-brain LPBA40 atlas. This paper provides the first report of anatomical positions and principal axes orientations within a standard reference frame, in addition to "shape/size related" principal axes measures, for the nine brain structures from the LPBA40 atlas. Analysis showed that overall size (mean volume) for internal brain structures was preserved using shape standardization while variance was reduced by more than 50%. Shape standardization provides increased statistical power for between-group volumetric studies of brain structures compared to volumetric studies that control only for whole brain size. To test ISSN's ability to control for spatial variability of brain structures we evaluated the overlap of 40 regions of interest (ROIs) in a standard reference frame for the nine different brain structures before and after processing. Standardizations of orientation or shape were ineffective when not combined with position standardization. The greatest reduction in spatial variability was seen for combined standardizations of position, orientation and shape. These

  8. Structural Analysis Methods Development for Turbine Hot Section Components

    NASA Technical Reports Server (NTRS)

    Thompson, Robert L.

    1988-01-01

    The structural analysis technologies and activities of the NASA Lewis Research Center's gas turbine engine Hot Section Technology (HOST) program are summarized. The technologies synergistically developed and validated include: time-varying thermal/mechanical load models; component-specific automated geometric modeling and solution strategy capabilities; advanced inelastic analysis methods; inelastic constitutive models; high-temperature experimental techniques and experiments; and nonlinear structural analysis codes. Features of the program that incorporate the new technologies and their application to hot section component analysis and design are described. Improved and, in some cases, first-time 3-D nonlinear structural analyses of hot section components of isotropic and anisotropic nickel-base superalloys are presented.

  9. Probabilistic structural analysis of space propulsion system LOX post

    NASA Technical Reports Server (NTRS)

    Newell, J. F.; Rajagopal, K. R.; Ho, H. W.; Cunniff, J. M.

    1990-01-01

    The probabilistic structural analysis program NESSUS (Numerical Evaluation of Stochastic Structures Under Stress; Cruse et al., 1988) is applied to characterize the dynamic loading and response of the Space Shuttle main engine (SSME) LOX post. The design and operation of the SSME are reviewed; the LOX post structure is described; and particular attention is given to the generation of composite load spectra, the finite-element model of the LOX post, and the steps in the NESSUS structural analysis. The results are presented in extensive tables and graphs, and it is shown that NESSUS correctly predicts the structural effects of changes in the temperature loading. The probabilistic approach also facilitates (1) damage assessments for a given failure model (based on gas temperature, heat-shield gap, and material properties) and (2) correlation of the gas temperature with operational parameters such as engine thrust.

  10. Structures and geriatrics from a failure analysis experience viewpoint

    SciTech Connect

    Hopper, D.M. )

    1993-05-01

    In a failure analysis consulting engineering practice one sees a variety of structural failures from which observations may be made concerning geriatric structures. Representative experience with power plants, refineries, offshore structures, and forensic investigations is summarized and generic observations are made regarding the maintenance of fitness for purpose of structures. Although it is important to optimize the engineering design for a range of operational and environmental variables, it is essential that fabrication and inspection controls exist along with common sense based ongoing monitoring and operations procedures. 18 figs.

  11. [Covariance structure analysis of pharmacists' attitudes toward medication history].

    PubMed

    Sato, Hirotaka; Shimamori, Yoshimitu

    2011-01-01

    Keeping track of patients' medication histories is an important component of pharmacy practice. In this study, we conducted a questionnaire survey on medication histories among pharmacists and performed covariance structure analysis to investigate pharmacists' attitudes toward medication histories. The survey was conducted among pharmacists who work at pharmacies. With regard to the questions on medication histories, factor analysis and covariance structure analysis were performed to create a path diagram. The response rate to the questionnaire was 97.0%. The factor analysis revealed six factors, including: "patient assessment", "learning attitude", "practicing the recording of medication histories", "conscious effort to improve medication histories", "uniformity in medication histories" and "issues regarding medication histories". Meanwhile, covariance structure analysis revealed that the five-factor model excluding "issues regarding medication histories" was the best-fitted model. According to this model, it was clear that the pharmacists were extremely conscious about introducing improvements to the content of medication histories. In this study, covariance structure analysis enabled the effective analysis of the attitudes of pharmacists toward medication histories. We believe that creating and conducting a training program to clarify and resolve issues related to medication histories and then reviewing the outcome of such a training program will lead to quality improvement and standardization of the future management of medication histories. PMID:21532278

  12. Advances in Structural Integrity Analysis Methods for Aging Metallic Airframe Structures with Local Damage

    NASA Technical Reports Server (NTRS)

    Starnes, James H., Jr.; Newman, James C., Jr.; Harris, Charles E.; Piascik, Robert S.; Young, Richard D.; Rose, Cheryl A.

    2003-01-01

    Analysis methodologies for predicting fatigue-crack growth from rivet holes in panels subjected to cyclic loads and for predicting the residual strength of aluminum fuselage structures with cracks and subjected to combined internal pressure and mechanical loads are described. The fatigue-crack growth analysis methodology is based on small-crack theory and a plasticity induced crack-closure model, and the effect of a corrosive environment on crack-growth rate is included. The residual strength analysis methodology is based on the critical crack-tip-opening-angle fracture criterion that characterizes the fracture behavior of a material of interest, and a geometric and material nonlinear finite element shell analysis code that performs the structural analysis of the fuselage structure of interest. The methodologies have been verified experimentally for structures ranging from laboratory coupons to full-scale structural components. Analytical and experimental results based on these methodologies are described and compared for laboratory coupons and flat panels, small-scale pressurized shells, and full-scale curved stiffened panels. The residual strength analysis methodology is sufficiently general to include the effects of multiple-site damage on structural behavior.

  13. Coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures

    NASA Technical Reports Server (NTRS)

    Mcknight, R. L.; Huang, H.; Hartle, M.

    1992-01-01

    Accomplishments are described for the fourth years effort of a 5-year program to develop a methodology for coupled structural/thermal/electromagnetic analysis/tailoring of graded component structures. These accomplishments include: (1) demonstration of coupled solution capability; (2) alternate CSTEM electromagnetic technology; (3) CSTEM acoustic capability; (4) CSTEM tailoring; (5) CSTEM composite micromechanics using ICAN; and (6) multiple layer elements in CSTEM.

  14. V-Lab{trademark}: Virtual laboratories -- The analysis tool for structural analysis of composite components

    SciTech Connect

    1999-07-01

    V-Lab{trademark}, an acronym for Virtual Laboratories, is a design and analysis tool for fiber-reinforced composite components. This program allows the user to perform analysis, numerical experimentation, and design prototyping using advanced composite stress and failure analysis tools. The software was designed to be intuitive and easy to use, even by designers who are not experts in composite materials or structural analysis. V-Lab{trademark} is the software tool every specialist in design engineering, structural analysis, research and development and repair needs to perform accurate, fast and economical analysis of composite components.

  15. Local structure studies of materials using pair distribution function analysis

    NASA Astrophysics Data System (ADS)

    Peterson, Joseph W.

    A collection of pair distribution function studies on various materials is presented in this dissertation. In each case, local structure information of interest pushes the current limits of what these studies can accomplish. The goal is to provide insight into the individual material behaviors as well as to investigate ways to expand the current limits of PDF analysis. Where possible, I provide a framework for how PDF analysis might be applied to a wider set of material phenomena. Throughout the dissertation, I discuss 0 the capabilities of the PDF method to provide information pertaining to a material's structure and properties, ii) current limitations in the conventional approach to PDF analysis, iii) possible solutions to overcome certain limitations in PDF analysis, and iv) suggestions for future work to expand and improve the capabilities PDF analysis.

  16. Computational simulation for analysis and synthesis of impact resilient structure

    NASA Astrophysics Data System (ADS)

    Djojodihardjo, Harijono

    2013-10-01

    Impact resilient structures are of great interest in many engineering applications varying from civil, land vehicle, aircraft and space structures, to mention a few examples. To design such structure, one has to resort fundamental principles and take into account progress in analytical and computational approaches as well as in material science and technology. With such perspectives, this work looks at a generic beam and plate structure subject to impact loading and carry out analysis and numerical simulation. The first objective of the work is to develop a computational algorithm to analyze flat plate as a generic structure subjected to impact loading for numerical simulation and parametric study. The analysis will be based on dynamic response analysis. Consideration is given to the elastic-plastic region. The second objective is to utilize the computational algorithm for direct numerical simulation, and as a parallel scheme, commercial off-the shelf numerical code is utilized for parametric study, optimization and synthesis. Through such analysis and numerical simulation, effort is devoted to arrive at an optimum configuration in terms of loading, structural dimensions, material properties and composite lay-up, among others. Results will be discussed in view of practical applications.

  17. Aircraft Structural Mass Property Prediction Using Conceptual-Level Structural Analysis

    NASA Technical Reports Server (NTRS)

    Sexstone, Matthew G.

    1998-01-01

    This paper describes a methodology that extends the use of the Equivalent LAminated Plate Solution (ELAPS) structural analysis code from conceptual-level aircraft structural analysis to conceptual-level aircraft mass property analysis. Mass property analysis in aircraft structures has historically depended upon parametric weight equations at the conceptual design level and Finite Element Analysis (FEA) at the detailed design level. ELAPS allows for the modeling of detailed geometry, metallic and composite materials, and non-structural mass coupled with analytical structural sizing to produce high-fidelity mass property analyses representing fully configured vehicles early in the design process. This capability is especially valuable for unusual configuration and advanced concept development where existing parametric weight equations are inapplicable and FEA is too time consuming for conceptual design. This paper contrasts the use of ELAPS relative to empirical weight equations and FEA. ELAPS modeling techniques are described and the ELAPS-based mass property analysis process is detailed. Examples of mass property stochastic calculations produced during a recent systems study are provided. This study involved the analysis of three remotely piloted aircraft required to carry scientific payloads to very high altitudes at subsonic speeds. Due to the extreme nature of this high-altitude flight regime, few existing vehicle designs are available for use in performance and weight prediction. ELAPS was employed within a concurrent engineering analysis process that simultaneously produces aerodynamic, structural, and static aeroelastic results for input to aircraft performance analyses. The ELAPS models produced for each concept were also used to provide stochastic analyses of wing structural mass properties. The results of this effort indicate that ELAPS is an efficient means to conduct multidisciplinary trade studies at the conceptual design level.

  18. Aircraft Structural Mass Property Prediction Using Conceptual-Level Structural Analysis

    NASA Technical Reports Server (NTRS)

    Sexstone, Matthew G.

    1998-01-01

    This paper describes a methodology that extends the use of the Equivalent LAminated Plate Solution (ELAPS) structural analysis code from conceptual-level aircraft structural analysis to conceptual-level aircraft mass property analysis. Mass property analysis in aircraft structures has historically depended upon parametric weight equations at the conceptual design level and Finite Element Analysis (FEA) at the detailed design level ELAPS allows for the modeling of detailed geometry, metallic and composite materials, and non-structural mass coupled with analytical structural sizing to produce high-fidelity mass property analyses representing fully configured vehicles early in the design process. This capability is especially valuable for unusual configuration and advanced concept development where existing parametric weight equations are inapplicable and FEA is too time consuming for conceptual design. This paper contrasts the use of ELAPS relative to empirical weight equations and FEA. ELAPS modeling techniques are described and the ELAPS-based mass property analysis process is detailed Examples of mass property stochastic calculations produced during a recent systems study are provided This study involved the analysis of three remotely piloted aircraft required to carry scientific payloads to very high altitudes at subsonic speeds. Due to the extreme nature of this high-altitude flight regime,few existing vehicle designs are available for use in performance and weight prediction. ELAPS was employed within a concurrent engineering analysis process that simultaneously produces aerodynamic, structural, and static aeroelastic results for input to aircraft performance analyses. The ELAPS models produced for each concept were also used to provide stochastic analyses of wing structural mass properties. The results of this effort indicate that ELAPS is an efficient means to conduct multidisciplinary trade studies at the conceptual design level.

  19. Validation of Design and Analysis Techniques of Tailored Composite Structures

    NASA Technical Reports Server (NTRS)

    Jegley, Dawn C. (Technical Monitor); Wijayratne, Dulnath D.

    2004-01-01

    Aeroelasticity is the relationship between the elasticity of an aircraft structure and its aerodynamics. This relationship can cause instabilities such as flutter in a wing. Engineers have long studied aeroelasticity to ensure such instabilities do not become a problem within normal operating conditions. In recent decades structural tailoring has been used to take advantage of aeroelasticity. It is possible to tailor an aircraft structure to respond favorably to multiple different flight regimes such as takeoff, landing, cruise, 2-g pull up, etc. Structures can be designed so that these responses provide an aerodynamic advantage. This research investigates the ability to design and analyze tailored structures made from filamentary composites. Specifically the accuracy of tailored composite analysis must be verified if this design technique is to become feasible. To pursue this idea, a validation experiment has been performed on a small-scale filamentary composite wing box. The box is tailored such that its cover panels induce a global bend-twist coupling under an applied load. Two types of analysis were chosen for the experiment. The first is a closed form analysis based on a theoretical model of a single cell tailored box beam and the second is a finite element analysis. The predicted results are compared with the measured data to validate the analyses. The comparison of results show that the finite element analysis is capable of predicting displacements and strains to within 10% on the small-scale structure. The closed form code is consistently able to predict the wing box bending to 25% of the measured value. This error is expected due to simplifying assumptions in the closed form analysis. Differences between the closed form code representation and the wing box specimen caused large errors in the twist prediction. The closed form analysis prediction of twist has not been validated from this test.

  20. Analysis on the structure of the TMT's Atmospheric Dispersion Corrector

    NASA Astrophysics Data System (ADS)

    Zhang, Jianhuan; Liu, Yan; Tao, Jin

    2015-10-01

    The concepts of atmospheric refraction and atmospheric dispersion are introduced and the method of how to eliminate atmospheric dispersion. This article introduces the structure of Atmospheric Dispersion Correction , the installation position of ADC in TMT telescope and the introduction to the principle of ADC in detail. Using the finite element analysis software Ansys Workbench to analyze the rationality of the ADC structure. Static analysis The ADC structure is loaded with two tape lens, which is more 400kg in weight, as well as itself weight, will deform in x, y, z directions. Dynamic analysis The dynamic performances of ADC structure are very important for the construction of the instrument, for the environmental vibration need to be tested. That is the effect of ADC dynamic deformation on optical accuracy is crucial for imaging quality. Here three order modes of dynamic performance are presented for the references of ADC design. They are 1st order mode , 2nd order mode and 3rd order mode. Thermal deformation according to the ADC working environment temperature change, the instrument temperature would be from -5 to 9 degree. So the thermal deformation of ADC is performed in this temperature fluctuation. ADC structure FEA conclusions: The ADC tapered lens are assumed as a rigid body and the mechanical analysis results are: Static analysis, Kinetics analysis and Thermodynamic analysis. Based on the FEA results, we get the image motion information in the telescope plane. Then, we draw a conclusion that: image motions induced by current structure design are very small and meet the requirements of ADC.

  1. A Model-Based System For Force Structure Analysis

    NASA Astrophysics Data System (ADS)

    Levitt, Tod S.; Kirby, Robert L.; Muller, Hans E.

    1985-04-01

    Given a set of image-derived vehicle detections and/or recognized military vehicles, SIGINT cues and a priori analysis of terrain, the force structure analysis (FSA) problem is to utilize knowledge of tactical doctrine and spatial deployment information to infer the existence of military forces such as batteries, companies, battalions, regiments, divisions, etc. A model-based system for FSA has been developed. It performs symbolic reasoning about force structures represented as geometric models. The FSA system is a stand-alone module which has also been developed as part of a larger system, the Advanced Digital Radar Image Exploitation System (ADRIES) for automated SAR image exploitation. The models recursively encode the component military units of a force structure, their expected spatial deployment, search priorities for model components, prior match probabilities, and type hierarchies for uncertain recognition. Partial and uncertain matching of models against data is the basic tool for building up hypotheses of the existence of force structures. Hypothesis management includes the functions of matching models against data, predicting the existence and location of unobserved force components, localization of search areas and resolution of conflicts between competing hypotheses. A subjective Bayesian inference calculus is used to accrue certainty of force structure hypotheses and resolve conflicts. Reasoning from uncertain vehicle level data, the system has successfully inferred the correct locations and components of force structures up to the battalion level. Key words: Force structure analysis, SAR, model-based reasoning, hypothesis management, search, matching, conflict resolution, Bayesian inference, uncertainty.

  2. DTFM Modeling and Analysis Method for Gossamer Structures

    NASA Technical Reports Server (NTRS)

    Fang, Hou-Fei; Lou, Michael; Broduer, Steve (Technical Monitor)

    2001-01-01

    Gossamer systems are mostly composed of support structures formed by highly flexible, long tubular elements and pre-tensioned thin-film membranes. These systems offer order-of-magnitude reductions in mass and launch volume and will revolutionize the architecture and design of space flight systems that require large in-orbit configurations and apertures. A great interest has been generated in recent years to fly gossamer systems on near-term and future space missions. Modeling and analysis requirements for gossamer structures are unique. Simulation of in-space performance issues of gossamer structures, such as inflation deployment of flexible booms, formation and effects of wrinkle in tensioned membranes, synthesis of tubular and membrane elements into a complete structural system, usually cannot be accomplished by using the general-purpose finite-element structural analysis codes. This has led to the need of structural modeling and analysis capabilities specifically suitable for gossamer structures. The Distributed Transfer Function Method (DTFM) can potentially meet this urgent need. Additional information is contained in the original extended abstract.

  3. Hierarchical structure analysis of interstellar clouds using nonorthogonal wavelets

    NASA Technical Reports Server (NTRS)

    Langer, William D.; Wilson, Robert W.; Anderson, Charles H.

    1993-01-01

    We introduce the use of Laplacian pyramid transforms, a form of nonorthogonal wavelets, to analyze the structure of interstellar clouds. These transforms are generally better suited for analyzing structure than orthogonal wavelets because they provide more flexibility in the structure of the encoding functions - here circularly symmetric bandpass filters. This technique is applied to CO maps of Barnard 5. In the (C-13)O maps, for example, we identify 60 different fragments and clumps, as well as several cavities, or bubbles. Many features show evidence of hierarchical structure, with most of the power in the largest wavelengths. The clumps have a more chaotic structure at small wavelengths than expected for Kolmogorov turbulence, and a mass distribution proportional to M exp -5/3. The structure analysis is consistent with a picture where gravity, energy injection, compressible turbulence, and coalescence play an important role in the dynamics of B5.

  4. Purification and Structural Analysis of Plectin and BPAG1e.

    PubMed

    Manso, José A; García Rubio, Inés; Gómez-Hernández, María; Ortega, Esther; Buey, Rubén M; Carballido, Ana M; Carabias, Arturo; Alonso-García, Noelia; de Pereda, José M

    2016-01-01

    Plectin and BPAG1e belong to the plakin family of high-molecular-weight proteins that interconnect the cytoskeletal systems and anchor them to junctional complexes. Plectin and BPAG1e are prototypical plakins with a similar tripartite modular structure. The N- and C-terminal regions are built of multiple discrete structural domains, while the central rod domain mediates dimerization by coiled-coil interactions. Owing to the mosaic organization of plakins, the structure of their constituent individual domains or small multi-domain segments can be analyzed isolated. Yet, understanding the integrated function of large regions, oligomers, and heterocomplexes of plakins is difficult due to the large and segmented structure. Here, we describe methods for the production of plectin and BPAG1e samples suitable for structural and biophysical analysis. In addition, we discuss the combination of hybrid methods that yield information at several resolution levels to study the complex, multi-domain, and flexible structure of plakins. PMID:26778559

  5. Analysis and validation of carbohydrate three-dimensional structures

    SciTech Connect

    Lütteke, Thomas

    2009-02-01

    The article summarizes the information that is gained from and the errors that are found in carbohydrate structures in the Protein Data Bank. Validation tools that can locate these errors are described. Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein–carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein–carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures.

  6. Synchrotron IR microspectroscopy for protein structure analysis: Potential and questions

    DOE PAGESBeta

    Yu, Peiqiang

    2006-01-01

    Synchrotron radiation-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced technique to the study of pure protein inherent structure at a cellular level in biological tissues. In this review, a novel approach was introduced to show the potential of the newly developed, advancedmore » synchrotron-based analytical technology, which can be used to localize relatively “pure“ protein in the plant tissues and relatively reveal protein inherent structure and protein molecular chemical make-up within intact tissue at cellular and subcellular levels. Several complex protein IR spectra data analytical techniques (Gaussian and Lorentzian multi-component peak modeling, univariate and multivariate analysis, principal component analysis (PCA), and hierarchical cluster analysis (CLA) are employed to relatively reveal features of protein inherent structure and distinguish protein inherent structure differences between varieties/species and treatments in plant tissues. By using a multi-peak modeling procedure, RELATIVE estimates (but not EXACT determinations) for protein secondary structure analysis can be made for comparison purpose. The issues of pro- and anti-multi-peaking modeling/fitting procedure for relative estimation of protein structure were discussed. By using the PCA and CLA analyses, the plant molecular structure can be qualitatively separate one group from another, statistically, even though the spectral assignments are not known. The synchrotron-based technology provides a new approach for protein structure research in

  7. Nonlinear analysis of structures. [within framework of finite element method

    NASA Technical Reports Server (NTRS)

    Armen, H., Jr.; Levine, H.; Pifko, A.; Levy, A.

    1974-01-01

    The development of nonlinear analysis techniques within the framework of the finite-element method is reported. Although the emphasis is concerned with those nonlinearities associated with material behavior, a general treatment of geometric nonlinearity, alone or in combination with plasticity is included, and applications presented for a class of problems categorized as axisymmetric shells of revolution. The scope of the nonlinear analysis capabilities includes: (1) a membrane stress analysis, (2) bending and membrane stress analysis, (3) analysis of thick and thin axisymmetric bodies of revolution, (4) a general three dimensional analysis, and (5) analysis of laminated composites. Applications of the methods are made to a number of sample structures. Correlation with available analytic or experimental data range from good to excellent.

  8. Fuzzy sensitivity analysis for reliability assessment of building structures

    NASA Astrophysics Data System (ADS)

    Kala, Zdeněk

    2016-06-01

    The mathematical concept of fuzzy sensitivity analysis, which studies the effects of the fuzziness of input fuzzy numbers on the fuzziness of the output fuzzy number, is described in the article. The output fuzzy number is evaluated using Zadeh's general extension principle. The contribution of stochastic and fuzzy uncertainty in reliability analysis tasks of building structures is discussed. The algorithm of fuzzy sensitivity analysis is an alternative to stochastic sensitivity analysis in tasks in which input and output variables are considered as fuzzy numbers.

  9. Large-scale computations in analysis of structures

    SciTech Connect

    McCallen, D.B.; Goudreau, G.L.

    1993-09-01

    Computer hardware and numerical analysis algorithms have progressed to a point where many engineering organizations and universities can perform nonlinear analyses on a routine basis. Through much remains to be done in terms of advancement of nonlinear analysis techniques and characterization on nonlinear material constitutive behavior, the technology exists today to perform useful nonlinear analysis for many structural systems. In the current paper, a survey on nonlinear analysis technologies developed and employed for many years on programmatic defense work at the Lawrence Livermore National Laboratory is provided, and ongoing nonlinear numerical simulation projects relevant to the civil engineering field are described.

  10. Development of load-dependent Ritz vector method for structural dynamic analysis of large space structures

    NASA Technical Reports Server (NTRS)

    Ricles, James M.

    1990-01-01

    The development and preliminary assessment of a method for dynamic structural analysis based on load-dependent Ritz vectors are presented. The vector basis is orthogonalized with respect to the mass and structural stiffness in order that the equations of motion can be uncoupled and efficient analysis of large space structure performed. A series of computer programs was developed based on the algorithm for generating the orthogonal load-dependent Ritz vectors. Transient dynamic analysis performed on the Space Station Freedom using the software was found to provide solutions that require a smaller number of vectors than the modal analysis method. Error norm based on the participation of the mass distribution of the structure and spatial distribution of structural loading, respectively, were developed in order to provide an indication of vector truncation. These norms are computed before the transient analysis is performed. An assessment of these norms through a convergence study of the structural response was performed. The results from this assessment indicate that the error norms can provide a means of judging the quality of the vector basis and accuracy of the transient dynamic solution.

  11. Structural analysis of a flexible structural member protruding into an interior flow field

    NASA Astrophysics Data System (ADS)

    Weaver, M. A.; Gramoll, K. C.; Roach, R. L.

    1993-04-01

    A quasi-steady approach is introduced for the analysis of flexible structural members protruding into flow fields. Static equilibrium is enforced for the structure while dynamic equilibrium is enforced for the structure interaction solution, subject to the equilibrium assumptions, but only the structural aspects of obtaining such a solution are examined. This approach is applied to the problem of a flexible annular inhibitor protruding into the interior flow field of a segmented solid rocket motor. A finite element structural model, and a finite difference flow model form the basis of the solution method. The structure is iteratively loaded, with load profiles determined by the flow after each iteration. The results show that large deflections can be expected of inhibitors in solid rocket motors, and that the limitations of the analytical structural model are critical.

  12. Aero-Structural Interaction, Analysis, and Shape Sensitivity

    NASA Technical Reports Server (NTRS)

    Newman, James C., III

    1999-01-01

    A multidisciplinary sensitivity analysis technique that has been shown to be independent of step-size selection is examined further. The accuracy of this step-size independent technique, which uses complex variables for determining sensitivity derivatives, has been previously established. The primary focus of this work is to validate the aero-structural analysis procedure currently being used. This validation consists of comparing computed and experimental data obtained for an Aeroelastic Research Wing (ARW-2). Since the aero-structural analysis procedure has the complex variable modifications already included into the software, sensitivity derivatives can automatically be computed. Other than for design purposes, sensitivity derivatives can be used for predicting the solution at nearby conditions. The use of sensitivity derivatives for predicting the aero-structural characteristics of this configuration is demonstrated.

  13. Assessment of structural analysis technology for elastic shell collapse problems

    NASA Technical Reports Server (NTRS)

    Knight, N. F., Jr.; Macy, S. C.; Mccleary, S. L.

    1989-01-01

    The prediction of the ultimate load carrying capability for compressively loaded shell structures is a challenging nonlinear analysis problem. Selected areas of finite element technology research and nonlinear solution technology are assessed. Herein, a finite element analysis procedure is applied to four shell collapse problems which have been used by computational structural mechanics researchers in the past. This assessment will focus on a number of different shell element formulations and on different approaches used to account for geometric nonlinearities. The results presented confirm that these aspects of nonlinear shell analysis can have a significant effect on the predicted nonlinear structural response. All analyses were performed using the CSM Testbed software system which allowed a convenient assessment of different element formulations with a consistent approach to solving the discretized nonlinear equations.

  14. The dream of Irma's injection: a structural analysis.

    PubMed

    Kuper, A; Stone, A A

    1982-10-01

    Lévi-Strauss developed a radically new, structural approach to the analysis of myth that may be adapted for use in the analysis of dreams. The method provides an alternative to psychoanalytic dream interpretation, focusing particularly on the internal dialectic of the dream--the movement from the initial premise to the resolution. This emphasis on the internal coherence and structured development of the dream contrasts strongly with the Freudian piecemeal decoding of dreams. The method is exemplified by analysis of Freud's classic Irma dream; it reveals a structure and message that have hitherto remained obscure. The interpretation connects the dream to Freud's theoretical ideas rather than to his supposed psychosexual fixations. PMID:6751099

  15. Finite-element thermo-viscoplastic analysis of aerospace structures

    NASA Technical Reports Server (NTRS)

    Pandey, Ajay; Dechaumphai, Pramote; Thornton, Earl A.

    1990-01-01

    The time-dependent thermo-viscoplastic response of aerospace structures subjected to intense aerothermal loads is predicted using the finite-element method. The finite-element analysis uses the Bodner-Partom unified viscoplastic constitutive relations to determine rate-dependent nonlinear material behavior. The methodology is verified by comparison with experimental data and other numerical results for a uniaxially-loaded bar. The method is then used (1) to predict the structural response of a rectangular plate subjected to line heating along a centerline, and (2) to predict the thermal-structural response of a convectively-cooled engine cowl leading edge subjected to aerodynamic shock-shock interference heating. Compared to linear elastic analysis, the viscoplastic analysis results in lower peak stresses and regions of plastic deformations.

  16. Finite element thermo-viscoplastic analysis of aerospace structures

    NASA Technical Reports Server (NTRS)

    Pandey, Ajay K.; Dechaumphai, Pramote; Thornton, Earl A.

    1990-01-01

    The time-dependent thermo-viscoplastic response of aerospace structures subjected to intense aerothermal loads is predicted using the finite-element method. The finite-element analysis uses the Bodner-Partom unified viscoplastic constitutive relations to determine rate-dependent nonlinear material behavior. The methodology is verified by comparison with experimental data and other numerical results for a uniaxially-loaded bar. The method is then used (1) to predict the structural response of a rectangular plate subjected to line heating along a centerline, and (2) to predict the thermal-structural response of a convectively-cooled engine cowl leading edge subjected to aerodynamic shock-shock interference heating. Compared to linear elastic analysis, the viscoplastic analysis results in lower peak stresses and regions of plastic deformations.

  17. Finite element thermal analysis of convectively-cooled aircraft structures

    NASA Technical Reports Server (NTRS)

    Wieting, A. R.; Thornton, E. A.

    1981-01-01

    The design complexity and size of convectively-cooled engine and airframe structures for hypersonic transports necessitate the use of large general purpose computer programs for both thermal and structural analyses. Generally thermal analyses are based on the lumped-parameter finite difference technique, and structural analyses are based on the finite element technique. Differences in these techniques make it difficult to achieve an efficient interface. It appears, therefore, desirable to conduct an integrated analysis based on a common technique. A summary is provided of efforts by NASA concerned with the development of an integrated thermal structural analysis capability using the finite element method. Particular attention is given to the development of conduction/forced-convection finite element methodology and applications which illustrate the capabilities of the developed concepts.

  18. Process for structural geologic analysis of topography and point data

    DOEpatents

    Eliason, Jay R.; Eliason, Valerie L. C.

    1987-01-01

    A quantitative method of geologic structural analysis of digital terrain data is described for implementation on a computer. Assuming selected valley segments are controlled by the underlying geologic structure, topographic lows in the terrain data, defining valley bottoms, are detected, filtered and accumulated into a series line segments defining contiguous valleys. The line segments are then vectorized to produce vector segments, defining valley segments, which may be indicative of the underlying geologic structure. Coplanar analysis is performed on vector segment pairs to determine which vectors produce planes which represent underlying geologic structure. Point data such as fracture phenomena which can be related to fracture planes in 3-dimensional space can be analyzed to define common plane orientation and locations. The vectors, points, and planes are displayed in various formats for interpretation.

  19. A computer program for cyclic plasticity and structural fatigue analysis

    NASA Technical Reports Server (NTRS)

    Kalev, I.

    1980-01-01

    A computerized tool for the analysis of time independent cyclic plasticity structural response, life to crack initiation prediction, and crack growth rate prediction for metallic materials is described. Three analytical items are combined: the finite element method with its associated numerical techniques for idealization of the structural component, cyclic plasticity models for idealization of the material behavior, and damage accumulation criteria for the fatigue failure.

  20. Structural analysis of cylindrical thrust chambers, volume 3

    NASA Technical Reports Server (NTRS)

    Pearson, M. L.

    1981-01-01

    A system of three computer programs is described for use in conjunction with the BOPAGE finite element program. The programs are demonstrated by analyzing cumulative plastic deformation in a regeneratively cooled rocket thrust chamber. The codes provide the capability to predict geometric and material nonlinear behavior of cyclically loaded structures without performing a cycle-by-cycle analysis over the life of the structure. The program set consists of a BOPACE restart tape reader routine, and extrapolation program and a plot package.

  1. Recent literature on structural modeling, identification, and analysis

    NASA Technical Reports Server (NTRS)

    Craig, Roy R., Jr.

    1990-01-01

    The literature on the mathematical modeling of large space structures is first reviewed, with attention given to continuum models, model order reduction, substructuring, and computational techniques. System identification and mode verification are then discussed with reference to the verification of mathematical models of large space structures. In connection with analysis, the paper surveys recent research on eigensolvers and dynamic response solvers for large-order finite-element-based models.

  2. Better Finite-Element Analysis of Composite Shell Structures

    NASA Technical Reports Server (NTRS)

    Clarke, Gregory

    2007-01-01

    A computer program implements a finite-element-based method of predicting the deformations of thin aerospace structures made of isotropic materials or anisotropic fiber-reinforced composite materials. The technique and corresponding software are applicable to thin shell structures in general and are particularly useful for analysis of thin beamlike members having open cross-sections (e.g. I-beams and C-channels) in which significant warping can occur.

  3. Structural Configuration Analysis of Crew Exploration Vehicle Concepts

    NASA Technical Reports Server (NTRS)

    Mukhopadhyay, V.

    2006-01-01

    Structural configuration modeling and finite element analysis of crew exploration vehicle (CEV) concepts are presented. In the structural configuration design approach, parametric solid models of the pressurized shell and tanks are developed. The CEV internal cabin pressure is same as in the International Space Station (ISS) to enable docking with the ISS without an intermediate airlock. Effects of this internal pressure load on the stress distribution, factor of safety, mass and deflections are investigated. Uniform 7 mm thick skin shell, 5 mm thick shell with ribs and frames, and isogrid skin construction options are investigated. From this limited study, the isogrid construction appears to provide most strength/mass ratio. Initial finite element analysis results on the service module tanks are also presented. These rapid finite element analyses, stress and factor of safety distribution results are presented as a part of lessons learned and to build up a structural mass estimation and sizing database for future technology support. This rapid structural analysis process may also facilitate better definition of the vehicles and components for rapid prototyping. However, these structural analysis results are highly conceptual and exploratory in nature and do not reflect current configuration designs being conducted at the program level by NASA and industry.

  4. Fuzzy Structures Analysis of Aircraft Panels in NASTRAN

    NASA Technical Reports Server (NTRS)

    Sparrow, Victor W.; Buehrle, Ralph D.

    2001-01-01

    This paper concerns an application of the fuzzy structures analysis (FSA) procedures of Soize to prototypical aerospace panels in MSC/NASTRAN, a large commercial finite element program. A brief introduction to the FSA procedures is first provided. The implementation of the FSA methods is then disclosed, and the method is validated by comparison to published results for the forced vibrations of a fuzzy beam. The results of the new implementation show excellent agreement to the benchmark results. The ongoing effort at NASA Langley and Penn State to apply these fuzzy structures analysis procedures to real aircraft panels is then described.

  5. An approximate methods approach to probabilistic structural analysis

    NASA Technical Reports Server (NTRS)

    Mcclung, R. C.; Millwater, H. R.; Wu, Y.-T.; Thacker, B. H.; Burnside, O. H.

    1989-01-01

    A probabilistic structural analysis method (PSAM) is described which makes an approximate calculation of the structural response of a system, including the associated probabilistic distributions, with minimal computation time and cost, based on a simplified representation of the geometry, loads, and material. The method employs the fast probability integration (FPI) algorithm of Wu and Wirsching. Typical solution strategies are illustrated by formulations for a representative critical component chosen from the Space Shuttle Main Engine (SSME) as part of a major NASA-sponsored program on PSAM. Typical results are presented to demonstrate the role of the methodology in engineering design and analysis.

  6. Development and Application of Viscoplastic Models in Nonlinear Structural Analysis

    NASA Technical Reports Server (NTRS)

    Keith, Theo G., Jr.; Arya, Vinod K.

    1996-01-01

    A number of numerical solution technologies were developed for advanced analysis capabilities involving the finite element method in advanced constitutive modeling and structural analysis for improved and rational designs of aerospace propulsive systems. These technologies were incorporated into several advanced viscoplastic models and were applied to a wide spectrum of structural engineering problems involving extremes of thermal/mechanical loading. Results of the research performed under the grant were presented at a number of scientific meetings and conferences and have resulted in numerous publications.

  7. Fiber composite analysis and design. Volume 2: Structures

    SciTech Connect

    Rosen, B.W.

    1998-09-01

    Recent years have witnessed a significant increase in the understanding and utilization of fibrous composite materials. There has also been a much larger increase in the amount of published literature in this field. This book builds upon existing literature to present a review of the available capability for composite structural design and analysis. The aim is to provide guidance for one who seeks to become familiar with the tools required for designing with fibrous composites. Thus, the book identifies the key concepts associated with the use of these unique materials. This second volume addresses the design and analysis of structural configurations for the practical and efficient utilization of fiber composite materials.

  8. Ab Initio Structure Analysis Using Laboratory Powder Diffraction Data

    NASA Astrophysics Data System (ADS)

    Sasaki, Akito

    Today, laboratory X-ray diffractometers are seeing increasingly wide use in the ab initio crystal structure analysis of organic powder samples. This is because optics and optical devices have been improved, making it possible to obtain precise integrated intensities of reflections in high 2-theta ranges. Another reason is that one can use direct-space methods, which do not require “high-resolution diffraction data”, much more easily than before. Described here are some key points to remember when performig ab initio crystal structure analysis using powder diffraction data from organic compounds.

  9. Structural dynamic analysis of the Space Shuttle Main Engine

    NASA Technical Reports Server (NTRS)

    Scott, L. P.; Jamison, G. T.; Mccutcheon, W. A.; Price, J. M.

    1981-01-01

    This structural dynamic analysis supports development of the SSME by evaluating components subjected to critical dynamic loads, identifying significant parameters, and evaluating solution methods. Engine operating parameters at both rated and full power levels are considered. Detailed structural dynamic analyses of operationally critical and life limited components support the assessment of engine design modifications and environmental changes. Engine system test results are utilized to verify analytic model simulations. The SSME main chamber injector assembly is an assembly of 600 injector elements which are called LOX posts. The overall LOX post analysis procedure is shown.

  10. Structure calculation, refinement and validation using CcpNmr Analysis

    PubMed Central

    Skinner, Simon P.; Goult, Benjamin T.; Fogh, Rasmus H.; Boucher, Wayne; Stevens, Tim J.; Laue, Ernest D.; Vuister, Geerten W.

    2015-01-01

    CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological questions. This report describes how CcpNmr Analysis can seamlessly link together all of the tasks in the NMR structure-determination process. It details each of the stages from generating NMR restraints [distance, dihedral, hydrogen bonds and residual dipolar couplings (RDCs)], exporting these to and subsequently re-importing them from structure-calculation software (such as the programs CYANA or ARIA) and analysing and validating the results obtained from the structure calculation to, ultimately, the streamlined deposition of the completed assignments and the refined ensemble of structures into the PDBe repository. Until recently, such solution-structure determination by NMR has been quite a laborious task, requiring multiple stages and programs. However, with the new enhancements to CcpNmr Analysis described here, this process is now much more intuitive and efficient and less error-prone. PMID:25615869

  11. Identification and Evolution of Functional Alleles of the Previously Described Pollen Specific Myrosinase Pseudogene AtTGG6 in Arabidopsis thaliana

    PubMed Central

    Fu, Lili; Han, Bingying; Tan, Deguan; Wang, Meng; Ding, Mei; Zhang, Jiaming

    2016-01-01

    Myrosinases are β-thioglucoside glucohydrolases and serve as defense mechanisms against insect pests and pathogens by producing toxic compounds. AtTGG6 in Arabidopsis thaliana was previously reported to be a myrosinase pseudogene but specifically expressed in pollen. However, we found that AlTGG6, an ortholog to AtTGG6 in A. lyrata (an outcrossing relative of A. thaliana) was functional, suggesting that functional AtTGG6 alleles may still exist in A. thaliana. AtTGG6 alleles in 29 A. thaliana ecotypes were cloned and sequenced. Results indicate that ten alleles were functional and encoded Myr II type myrosinase of 512 amino acids, and myrosinase activity was confirmed by overexpressing AtTGG6 in Pichia pastoris. However, the 19 other ecotypes had disabled alleles with highly polymorphic frame-shift mutations and diversified sequences. Thirteen frame-shift mutation types were identified, which occurred independently many times in the evolutionary history within a few thousand years. The functional allele was expressed specifically in pollen similar to the disabled alleles but at a higher expression level, suggesting its role in defense of pollen against insect pests such as pollen beetles. However, the defense function may have become less critical after A. thaliana evolved to self-fertilization, and thus resulted in loss of function in most ecotypes. PMID:26907263

  12. The polymorphic ADP-ribosyltransferase (NAD[sup +]) pseudogene 1 in humans interrupts an endogenous pol-like element on 13q34

    SciTech Connect

    Lyn, D.; Istock, N.L.; Smulson, M. ); Deaven, L.L. )

    1993-11-01

    A recently constructed chromosome 13-enriched library was used to isolate the entire human ADP-ribosyltransferase (NAD[sup +]) pseudogene 1 gene (ADPRTP1) on 13q34. Recently, ADPRTP1 was shown to detect a restriction fragment length polymorphism that was associated with a predisposition to cancer. The complete sequence of the ADPRTP1 (3808 bases) was determined and found to resemble an intronless cDNA, including 137 bases of the 5[prime] untranslated region and a short poly(A) tail. A previously uncharacterized, endogenous pol-like element (1.53 kb) in which the DNA sequences were interrupted by the polymorphic ADPRTP1 was identified. The solitary pol-related retroviral element may represent a multimember family of viral-like DNA sequences dispersed throughout the human genome. Altogether a 9.25-kb genomic region that also encompassed two Alu elements and the long-terminal repeat-like element of the [open quotes]O[close quotes]-LTR family was characterized. 27 refs., 4 figs., 1 tab.

  13. Extensive duplication events account for multiple control regions and pseudo-genes in the mitochondrial genome of the velvet worm Metaperipatus inae (Onychophora, Peripatopsidae).

    PubMed

    Braband, Anke; Podsiadlowski, Lars; Cameron, Stephen L; Daniels, Savel; Mayer, Georg

    2010-10-01

    The phylogeny of Onychophora (velvet worms) is unresolved and even the monophyly of the two major onychophoran subgroups, Peripatidae and Peripatopsidae, is uncertain. Previous studies of complete mitochondrial genomes from two onychophoran species revealed two strikingly different gene arrangement patterns from highly conserved in a representative of Peripatopsidae to highly derived in a species of Peripatidae, suggesting that these data might be informative for clarifying the onychophoran phylogeny. In order to assess the diversity of mitochondrial genomes among onychophorans, we analyzed the complete mitochondrial genome of Metaperipatus inae, a second representative of Peripatopsidae from Chile. Compared to the proposed ancestral gene order in Onychophora, the mitochondrial genome of M. inae shows dramatic rearrangements, although all protein-coding and ribosomal RNA genes are encoded on the same strands as in the ancestral peripatopsid genome. The retained strand affiliation of all protein-coding and ribosomal RNA genes and the occurrence of three control regions and several pseudo-genes suggest that the derived mitochondrial gene arrangement pattern in M. inae evolved by partial genome duplications, followed by a subsequent loss of redundant genes. Our findings, thus, confirm the diversity of the mitochondrial gene arrangement patterns among onychophorans and support their utility for clarifying the phylogeography of Onychophora, in particular of the Peripatopsidae species from South Africa and Chile. PMID:20510379

  14. Pseudogene PTENP1 Functions as a Competing Endogenous RNA (ceRNA) to Regulate PTEN Expression by Sponging miR-499-5p.

    PubMed

    Wang, Lei; Zhang, Ning; Wang, Zun; Ai, Dong-Mei; Cao, Zhen-Yu; Pan, Hua-Ping

    2016-07-01

    Increasing evidence has shown that pseudogenes can widely regulate gene expression. However, little is known about the specific role of PTENP1 and miR-499-5p in insulin resistance. The relative transcription level of PTENP1 was examined in db/db mice and high fat diet (HFD)-fed mice by real-time PCR. To explore the effect of PTENP1 on insulin resistance, adenovirus overexpressing or inhibiting vectors were injected through the tail vein. Bioinformatics predictions and a luciferase reporter assay were used to explore the interaction between PTENP1 and miR-499-5p. The relative transcription level of PTENP1 was largely enhanced in db/db mice and HFD-fed mice. Furthermore, the overexpression of PTENP1 resulted in impaired Akt/GSK activation as well as glycogen synthesis, while PTENP1 inhibition led to the improved activation of Akt/GSK and enhanced glycogen contents. More importantly, PTENP1 could directly bind miR-499-5p, thereby becoming a sink for miR-499-5p. PTENP1 overexpression results in the impairment of the insulin-signaling pathway and may function as a competing endogenous RNA for miR-499-5p, thereby contributing to insulin resistance. PMID:27449620

  15. Structural Damage Prediction and Analysis for Hypervelocity Impacts: Handbook

    NASA Technical Reports Server (NTRS)

    Elfer, N. C.

    1996-01-01

    This handbook reviews the analysis of structural damage on spacecraft due to hypervelocity impacts by meteoroid and space debris. These impacts can potentially cause structural damage to a Space Station module wall. This damage ranges from craters, bulges, minor penetrations, and spall to critical damage associated with a large hole, or even rupture. The analysis of damage depends on a variety of assumptions and the area of most concern is at a velocity beyond well controlled laboratory capability. In the analysis of critical damage, one of the key questions is how much momentum can actually be transfered to the pressure vessel wall. When penetration occurs without maximum bulging at high velocity and obliquities (if less momentum is deposited in the rear wall), then large tears and rupture may be avoided. In analysis of rupture effects of cylindrical geometry, biaxial loading, bending of the crack, a central hole strain rate and R-curve effects are discussed.

  16. Factors Influencing Progressive Failure Analysis Predictions for Laminated Composite Structure

    NASA Technical Reports Server (NTRS)

    Knight, Norman F., Jr.

    2008-01-01

    Progressive failure material modeling methods used for structural analysis including failure initiation and material degradation are presented. Different failure initiation criteria and material degradation models are described that define progressive failure formulations. These progressive failure formulations are implemented in a user-defined material model for use with a nonlinear finite element analysis tool. The failure initiation criteria include the maximum stress criteria, maximum strain criteria, the Tsai-Wu failure polynomial, and the Hashin criteria. The material degradation model is based on the ply-discounting approach where the local material constitutive coefficients are degraded. Applications and extensions of the progressive failure analysis material model address two-dimensional plate and shell finite elements and three-dimensional solid finite elements. Implementation details are described in the present paper. Parametric studies for laminated composite structures are discussed to illustrate the features of the progressive failure modeling methods that have been implemented and to demonstrate their influence on progressive failure analysis predictions.

  17. Towards a document structure editor for software requirements analysis

    NASA Technical Reports Server (NTRS)

    Kowalski, Vincent J.; Lekkos, Anthony A.

    1986-01-01

    Of the six or seven phases of the software engineering life cycle, requirements analysis tends to be the least understood and the least formalized. Correspondingly, a scarcity of useful software tools exist which aid in the development of user and system requirements. It is proposed that requirements analysis should culminate in a set of documents similar to those that usually accompany a delivered Software product. The design of a software tool, the Document Structure Editor, which facilitates the development of such documentation.

  18. CONSERTING: integrating copy number analysis with structural variation detection

    PubMed Central

    Chen, Xiang; Gupta, Pankaj; Wang, Jianmin; Nakitandwe, Joy; Roberts, Kathryn; Dalton, James D.; Parker, Matthew; Patel, Samir; Holmfeldt, Linda; Payne, Debbie; Easton, John; Ma, Jing; Rusch, Michael; Wu, Gang; Patel, Aman; J. Baker, Suzanne; Dyer, Michael A.; Shurtleff, Sheila; Espy, Stephen; Pounds, Stanley; Downing, James R.; Ellison, David W.; Mullighan, Charles G.; Zhang, Jinghui

    2015-01-01

    We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), a novel algorithm for detecting somatic copy number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation by read depth change and localized structural variation detection, achieving high accuracy and sensitivity. Analysis of 43 pediatric and adult cancer genomes revealed novel oncogenic CNAs, complex re-arrangements and subclonal CNAs missed by alternative approaches. PMID:25938371

  19. Advanced stress analysis methods applicable to turbine engine structures

    NASA Technical Reports Server (NTRS)

    Pian, T. H. H.

    1985-01-01

    Advanced stress analysis methods applicable to turbine engine structures are investigated. Constructions of special elements which containing traction-free circular boundaries are investigated. New versions of mixed variational principle and version of hybrid stress elements are formulated. A method is established for suppression of kinematic deformation modes. semiLoof plate and shell elements are constructed by assumed stress hybrid method. An elastic-plastic analysis is conducted by viscoplasticity theory using the mechanical subelement model.

  20. NRT Rotor Structural / Aeroelastic Analysis for the Preliminary Design Review

    SciTech Connect

    Ennis, Brandon Lee; Paquette, Joshua A.

    2015-10-01

    This document describes the initial structural design for the National Rotor Testbed blade as presented during the preliminary design review at Sandia National Laboratories on October 28- 29, 2015. The document summarizes the structural and aeroelastic requirements placed on the NRT rotor for satisfactory deployment at the DOE/SNL SWiFT experimental facility to produce high-quality datasets for wind turbine model validation. The method and result of the NRT blade structural optimization is also presented within this report, along with analysis of its satisfaction of the design requirements.

  1. Numerical analysis of free vibrations of damped rotating structures

    NASA Technical Reports Server (NTRS)

    Gupta, K. K.

    1977-01-01

    This paper is concerned with the efficient numerical solution of damped and undamped free vibration problems of rotating structures. While structural discretization is achieved by the finite element method, the associated eigenproblem solution is effected by a combined Sturm sequence and inverse iteration technique that enables the computation of a few required roots only without having to compute any other. For structures of complex configurations, a modal synthesis technique is also presented, which is based on appropriate combinations of eigenproblem solution of various structural components. Such numerical procedures are general in nature, which fully exploit matrix sparsity inherent in finite element discretizations, and prove to be most efficient for the vibration analysis of any damped rotating structure, such as rotating machineries, helicopter and turbine blades, spinning space stations, among others.

  2. Seismic response analysis of an instrumented building structure

    USGS Publications Warehouse

    Li, H.-J.; Zhu, S.-Y.; Celebi, M.

    2003-01-01

    The Sheraton - Universal hotel, an instrumented building lying in North Hollywood, USA is selected for case study in this paper. The finite element method is used to produce a linear time - invariant structural model, and the SAP2000 program is employed for the time history analysis of the instrumented structure under the base excitation of strong motions recorded in the basement during the Northridge, California earthquake of 17 January 1994. The calculated structural responses are compared with the recorded data in both time domain and frequency domain, and the effects of structural parameters evaluation and indeterminate factors are discussed. Some features of structural response, such as the reason why the peak responses of acceleration in the ninth floor are larger than those in the sixteenth floor, are also explained.

  3. Improved finite element methodology for integrated thermal structural analysis

    NASA Technical Reports Server (NTRS)

    Dechaumphai, P.; Thornton, E. A.

    1982-01-01

    An integrated thermal-structural finite element approach for efficient coupling of thermal and structural analyses is presented. New thermal finite elements which yield exact nodal and element temperature for one dimensional linear steady state heat transfer problems are developed. A nodeless variable formulation is used to establish improved thermal finite elements for one dimensional nonlinear transient and two dimensional linear transient heat transfer problems. The thermal finite elements provide detailed temperature distributions without using additional element nodes and permit a common discretization with lower order congruent structural finite elements. The accuracy of the integrated approach is evaluated by comparisons with analytical solutions and conventional finite element thermal-structural analyses for a number of academic and more realistic problems. Results indicate that the approach provides a significant improvement in the accuracy and efficiency of thermal stress analysis for structures with complex temperature distributions.

  4. Time-dependent reliability analysis and condition assessment of structures

    SciTech Connect

    Ellingwood, B.R.

    1997-01-01

    Structures generally play a passive role in assurance of safety in nuclear plant operation, but are important if the plant is to withstand the effect of extreme environmental or abnormal events. Relative to mechanical and electrical components, structural systems and components would be difficult and costly to replace. While the performance of steel or reinforced concrete structures in service generally has been very good, their strengths may deteriorate during an extended service life as a result of changes brought on by an aggressive environment, excessive loading, or accidental loading. Quantitative tools for condition assessment of aging structures can be developed using time-dependent structural reliability analysis methods. Such methods provide a framework for addressing the uncertainties attendant to aging in the decision process.

  5. Finite Rotation Analysis of Highly Thin and Flexible Structures

    NASA Technical Reports Server (NTRS)

    Clarke, Greg V.; Lee, Keejoo; Lee, Sung W.; Broduer, Stephen J. (Technical Monitor)

    2001-01-01

    Deployable space structures such as sunshields and solar sails are extremely thin and highly flexible with limited bending rigidity. For analytical investigation of their responses during deployment and operation in space, these structures can be modeled as thin shells. The present work examines the applicability of the solid shell element formulation to modeling of deployable space structures. The solid shell element formulation that models a shell as a three-dimensional solid is convenient in that no rotational parameters are needed for the description of kinematics of deformation. However, shell elements may suffer from element locking as the thickness becomes smaller unless special care is taken. It is shown that, when combined with the assumed strain formulation, the solid shell element formulation results in finite element models that are free of locking even for extremely thin structures. Accordingly, they can be used for analysis of highly flexible space structures undergoing geometrically nonlinear finite rotations.

  6. Topological framework for local structure analysis in condensed matter

    PubMed Central

    Lazar, Emanuel A.; Han, Jian; Srolovitz, David J.

    2015-01-01

    Physical systems are frequently modeled as sets of points in space, each representing the position of an atom, molecule, or mesoscale particle. As many properties of such systems depend on the underlying ordering of their constituent particles, understanding that structure is a primary objective of condensed matter research. Although perfect crystals are fully described by a set of translation and basis vectors, real-world materials are never perfect, as thermal vibrations and defects introduce significant deviation from ideal order. Meanwhile, liquids and glasses present yet more complexity. A complete understanding of structure thus remains a central, open problem. Here we propose a unified mathematical framework, based on the topology of the Voronoi cell of a particle, for classifying local structure in ordered and disordered systems that is powerful and practical. We explain the underlying reason why this topological description of local structure is better suited for structural analysis than continuous descriptions. We demonstrate the connection of this approach to the behavior of physical systems and explore how crystalline structure is compromised at elevated temperatures. We also illustrate potential applications to identifying defects in plastically deformed polycrystals at high temperatures, automating analysis of complex structures, and characterizing general disordered systems. PMID:26460045

  7. High-Throughput Analysis of RNA Structure and Ribonucleoprotein Assembly

    PubMed Central

    McGinnis, Jennifer L.; Duncan, Caia D. S.; Weeks, Kevin M.

    2016-01-01

    RNA folds to form complex structures vital to many cellular functions. Proteins facilitate RNA folding at both the secondary and tertiary structure levels. An absolute prerequisite for understanding RNA folding and ribonucleoprotein (RNP) assembly reactions is a complete understanding of the RNA structure at each stage of the folding or assembly process. Here we provide a guide for comprehensive and high-throughput analysis of RNA secondary and tertiary structure using SHAPE and hydroxyl radical footprinting. As an example of the strong and sometimes surprising conclusions that can emerge from high-throughput analysis of RNA folding and RNP assembly, we summarize the structure of the bI3 group I intron RNA in four distinct states. Dramatic structural rearrangements occur in both secondary and tertiary structure as the RNA folds from the free state to the active, six-component, RNP complex. As high-throughput and high-resolution approaches are applied broadly to large protein-RNA complexes, other proteins previously viewed as making simple contributions to RNA folding are also likely to be found to exert multifaceted, long-range, cooperative, and non-additive effects on RNA folding. These protein-induced contributions add another level of control, and potential regulatory function, in RNP complexes. PMID:20946765

  8. Topological framework for local structure analysis in condensed matter.

    PubMed

    Lazar, Emanuel A; Han, Jian; Srolovitz, David J

    2015-10-27

    Physical systems are frequently modeled as sets of points in space, each representing the position of an atom, molecule, or mesoscale particle. As many properties of such systems depend on the underlying ordering of their constituent particles, understanding that structure is a primary objective of condensed matter research. Although perfect crystals are fully described by a set of translation and basis vectors, real-world materials are never perfect, as thermal vibrations and defects introduce significant deviation from ideal order. Meanwhile, liquids and glasses present yet more complexity. A complete understanding of structure thus remains a central, open problem. Here we propose a unified mathematical framework, based on the topology of the Voronoi cell of a particle, for classifying local structure in ordered and disordered systems that is powerful and practical. We explain the underlying reason why this topological description of local structure is better suited for structural analysis than continuous descriptions. We demonstrate the connection of this approach to the behavior of physical systems and explore how crystalline structure is compromised at elevated temperatures. We also illustrate potential applications to identifying defects in plastically deformed polycrystals at high temperatures, automating analysis of complex structures, and characterizing general disordered systems. PMID:26460045

  9. Selecting Earthquake Records for Nonlinear Dynamic Analysis of Structures

    SciTech Connect

    Rodriguez, Mario E.

    2008-07-08

    An area in earthquake risk reduction that needs an urgent examination is the selection of earthquake records for nonlinear dynamic analysis of structures. An often-mentioned shortcoming from results of nonlinear dynamic analyses of structures is that these results are limited to the type of records that these analyses use as input data. This paper proposes a procedure for selecting earthquake records for nonlinear dynamic analysis of structures. This procedure uses a seismic damage index evaluated using the hysteretic energy dissipated by a Single Degree of Freedom System (SDOF) representing a multi-degree-of freedom structure responding to an earthquake record, and the plastic work capacity of the system at collapse. The type of structural system is considered using simple parameters. The proposed method is based on the evaluation of the damage index for a suite of earthquake records and a selected type of structural system. A set of 10 strong ground motion records is analyzed to show an application of the proposed procedure for selecting earthquake records for structural design.

  10. Structural analysis of airborne flux estimates over a region

    NASA Technical Reports Server (NTRS)

    Caramori, Paulo; Schuepp, Peter; Desjardins, Raymond; Macpherson, Ian

    1994-01-01

    Aircraft-based observations of turbulence fields of velocity, moisture, and temperature are used to study coherent turbulent structures that dominate turbulent transfer of moisture and heat above three different eco-systems. Flux traces are defragmented, to reconstruct the presumed full size (along the sampled transect) of these structures, and flux traces are simplified by elimination of those that contribute negligibly to the flux estimate. Structures are analyzed in terms of size, spatial distribution, and contribution to the flux, in the four 'quadrant' modes of eddy-covariance transfer (excess up/down and deficit up/down). The effect of nonlinear detrending of moisture and temperature data on this 'structural analysis,' over surfaces with heterogeneous surface wetness, is also examined. Results over grassland, wetland, and moist and dry agricultural land, show that nonlinear detrending may provide a more physically realistic description of structures. Significant differences are observed between structure size and associated relative flux contribution, between moist and dry areas, with smaller structures playing a more important role over the moist areas. Structure size generally increases with height, as spatial reorganization from smaller structures into larger ones takes place. This coincides with a gradual loss of surface 'signature' (position and clustering of plumes above localized source areas). The data are expected to provide a basis for an eventual statistical description of boundary-layer transfer events , and help to interpret the link between boundary-layer transfer and hydrological surface conditions.

  11. Structural Health Monitoring Analysis for the Orbiter Wing Leading Edge

    NASA Technical Reports Server (NTRS)

    Yap, Keng C.

    2010-01-01

    This viewgraph presentation reviews Structural Health Monitoring Analysis for the Orbiter Wing Leading Edge. The Wing Leading Edge Impact Detection System (WLE IDS) and the Impact Analysis Process are also described to monitor WLE debris threats. The contents include: 1) Risk Management via SHM; 2) Hardware Overview; 3) Instrumentation; 4) Sensor Configuration; 5) Debris Hazard Monitoring; 6) Ascent Response Summary; 7) Response Signal; 8) Distribution of Flight Indications; 9) Probabilistic Risk Analysis (PRA); 10) Model Correlation; 11) Impact Tests; 12) Wing Leading Edge Modeling; 13) Ascent Debris PRA Results; and 14) MM/OD PRA Results.

  12. Visual Analysis of Complex Networks and Community Structure

    NASA Astrophysics Data System (ADS)

    Wu, Bin; Ye, Qi; Wang, Yi; Bi, Ran; Suo, Lijun; Hu, Deyong; Yang, Shengqi

    Many real-world domains can be represented as complex networks.A good visualization of a large and complex network is worth more than millions of words. Visual depictions of networks, which exploit human visual processing, are more prone to cognition of the structure of such complex networks than the computational representation. We star by briefly introducing some key technologies of network visualization, such as graph drawing algorithm and community discovery methods. The typical tools for network visualization are also reviewed. A newly developed software framework JSNVA for network visual analysis is introduced. Finally,the applications of JSNVA in bibliometric analysis and mobile call graph analysis are presented.

  13. Equivalent Skin Analysis of Wing Structures Using Neural Networks

    NASA Technical Reports Server (NTRS)

    Liu, Youhua; Kapania, Rakesh K.

    2000-01-01

    An efficient method of modeling trapezoidal built-up wing structures is developed by coupling. in an indirect way, an Equivalent Plate Analysis (EPA) with Neural Networks (NN). Being assumed to behave like a Mindlin-plate, the wing is solved using the Ritz method with Legendre polynomials employed as the trial functions. This analysis method can be made more efficient by avoiding most of the computational effort spent on calculating contributions to the stiffness and mass matrices from each spar and rib. This is accomplished by replacing the wing inner-structure with an "equivalent" material that combines to the skin and whose properties are simulated by neural networks. The constitutive matrix, which relates the stress vector to the strain vector, and the density of the equivalent material are obtained by enforcing mass and stiffness matrix equities with rec,ard to the EPA in a least-square sense. Neural networks for the material properties are trained in terms of the design variables of the wing structure. Examples show that the present method, which can be called an Equivalent Skin Analysis (ESA) of the wing structure, is more efficient than the EPA and still fairly good results can be obtained. The present ESA is very promising to be used at the early stages of wing structure design.

  14. Mixed time integration methods for transient thermal analysis of structures

    NASA Technical Reports Server (NTRS)

    Liu, W. K.

    1983-01-01

    The computational methods used to predict and optimize the thermal-structural behavior of aerospace vehicle structures are reviewed. In general, two classes of algorithms, implicit and explicit, are used in transient thermal analysis of structures. Each of these two methods has its own merits. Due to the different time scales of the mechanical and thermal responses, the selection of a time integration method can be a difficult yet critical factor in the efficient solution of such problems. Therefore mixed time integration methods for transient thermal analysis of structures are being developed. The computer implementation aspects and numerical evaluation of these mixed time implicit-explicit algorithms in thermal analysis of structures are presented. A computationally-useful method of estimating the critical time step for linear quadrilateral element is also given. Numerical tests confirm the stability criterion and accuracy characteristics of the methods. The superiority of these mixed time methods to the fully implicit method or the fully explicit method is also demonstrated.

  15. Composite Structure Modeling and Analysis of Advanced Aircraft Fuselage Concepts

    NASA Technical Reports Server (NTRS)

    Mukhopadhyay, Vivek; Sorokach, Michael R.

    2015-01-01

    NASA Environmentally Responsible Aviation (ERA) project and the Boeing Company are collabrating to advance the unitized damage arresting composite airframe technology with application to the Hybrid-Wing-Body (HWB) aircraft. The testing of a HWB fuselage section with Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) construction is presently being conducted at NASA Langley. Based on lessons learned from previous HWB structural design studies, improved finite-element models (FEM) of the HWB multi-bay and bulkhead assembly are developed to evaluate the performance of the PRSEUS construction. In order to assess the comparative weight reduction benefits of the PRSEUS technology, conventional cylindrical skin-stringer-frame models of a cylindrical and a double-bubble section fuselage concepts are developed. Stress analysis with design cabin-pressure load and scenario based case studies are conducted for design improvement in each case. Alternate analysis with stitched composite hat-stringers and C-frames are also presented, in addition to the foam-core sandwich frame and pultruded rod-stringer construction. The FEM structural stress, strain and weights are computed and compared for relative weight/strength benefit assessment. The structural analysis and specific weight comparison of these stitched composite advanced aircraft fuselage concepts demonstrated that the pressurized HWB fuselage section assembly can be structurally as efficient as the conventional cylindrical fuselage section with composite stringer-frame and PRSEUS construction, and significantly better than the conventional aluminum construction and the double-bubble section concept.

  16. Nonlinear damage detection in composite structures using bispectral analysis

    NASA Astrophysics Data System (ADS)

    Ciampa, Francesco; Pickering, Simon; Scarselli, Gennaro; Meo, Michele

    2014-03-01

    Literature offers a quantitative number of diagnostic methods that can continuously provide detailed information of the material defects and damages in aerospace and civil engineering applications. Indeed, low velocity impact damages can considerably degrade the integrity of structural components and, if not detected, they can result in catastrophic failure conditions. This paper presents a nonlinear Structural Health Monitoring (SHM) method, based on ultrasonic guided waves (GW), for the detection of the nonlinear signature in a damaged composite structure. The proposed technique, based on a bispectral analysis of ultrasonic input waveforms, allows for the evaluation of the nonlinear response due to the presence of cracks and delaminations. Indeed, such a methodology was used to characterize the nonlinear behaviour of the structure, by exploiting the frequency mixing of the original waveform acquired from a sparse array of sensors. The robustness of bispectral analysis was experimentally demonstrated on a damaged carbon fibre reinforce plastic (CFRP) composite panel, and the nonlinear source was retrieved with a high level of accuracy. Unlike other linear and nonlinear ultrasonic methods for damage detection, this methodology does not require any baseline with the undamaged structure for the evaluation of the nonlinear source, nor a priori knowledge of the mechanical properties of the specimen. Moreover, bispectral analysis can be considered as a nonlinear elastic wave spectroscopy (NEWS) technique for materials showing either classical or non-classical nonlinear behaviour.

  17. Finite Element Analysis of Wrinkled Membrane Structures for Sunshield Applications

    NASA Technical Reports Server (NTRS)

    Johnston, John D.; Brodeur, Stephen J. (Technical Monitor)

    2002-01-01

    The deployable sunshield is an example of a gossamer structure envisioned for use on future space telescopes. The basic structure consists of multiple layers of pretensioned, thin-film membranes supported by deployable booms. The prediction and verification of sunshield dynamics has been identified as an area in need of technology development due to the difficulties inherent in predicting nonlinear structural behavior of the membranes and because of the challenges involved. in ground testing of the full-scale structure. This paper describes a finite element analysis of a subscale sunshield that has been subjected to ground testing in support of the Next Generation Space Telescope (NGST) program. The analysis utilizes a nonlinear material model that accounts for wrinkling of the membranes. Results are presented from a nonlinear static preloading analysis and subsequent dynamics analyses to illustrate baseline sunshield structural characteristics. Studies are then described which provide further insight into the effect of membrane. preload on sunshield dynamics and the performance of different membrane modeling techniques. Lastly, a comparison of analytical predictions and ground test results is presented.

  18. Structural Damage Prediction and Analysis for Hypervelocity Impact: Consulting

    NASA Technical Reports Server (NTRS)

    1995-01-01

    A portion of the contract NAS8-38856, 'Structural Damage Prediction and Analysis for Hypervelocity Impacts,' from NASA Marshall Space Flight Center (MSFC), included consulting which was to be documented in the final report. This attachment to the final report contains memos produced as part of that consulting.

  19. Teaching Reading: Mexico's Global Method of Structural Analysis.

    ERIC Educational Resources Information Center

    Orozco, Cecilio

    In 1985, the Global Method of Structural Analysis (GMSA) for teaching reading was introduced to first and second graders in Mexico. Breaking away from the more traditional educational methods, it established a basis for more flexible education and effectively utilized critical thinking skills. The preparation stage (reading readiness) begins in…

  20. Probabilistic structural analysis methods for improving Space Shuttle engine reliability

    NASA Technical Reports Server (NTRS)

    Boyce, L.

    1989-01-01

    Probabilistic structural analysis methods are particularly useful in the design and analysis of critical structural components and systems that operate in very severe and uncertain environments. These methods have recently found application in space propulsion systems to improve the structural reliability of Space Shuttle Main Engine (SSME) components. A computer program, NESSUS, based on a deterministic finite-element program and a method of probabilistic analysis (fast probability integration) provides probabilistic structural analysis for selected SSME components. While computationally efficient, it considers both correlated and nonnormal random variables as well as an implicit functional relationship between independent and dependent variables. The program is used to determine the response of a nickel-based superalloy SSME turbopump blade. Results include blade tip displacement statistics due to the variability in blade thickness, modulus of elasticity, Poisson's ratio or density. Modulus of elasticity significantly contributed to blade tip variability while Poisson's ratio did not. Thus, a rational method for choosing parameters to be modeled as random is provided.

  1. Limitations of the Concept of Stress in Structural Analysis.

    ERIC Educational Resources Information Center

    Edelman, Steven Harold

    1989-01-01

    Provides an introduction and explanations of stress-strain relationships, measuring stress, a goal of structural analysis, and legitimate applications of the concept of stress. Diagrams include a derivation of the stress tensor, graphical representations of stress-strain relations, and related problems. (RT)

  2. The NASA NASTRAN structural analysis computer program - New content

    NASA Technical Reports Server (NTRS)

    Weidman, D. J.

    1978-01-01

    Capabilities of a NASA-developed structural analysis computer program, NASTRAN, are evaluated with reference to finite-element modelling. Applications include the automotive industry as well as aerospace. It is noted that the range of sub-programs within NASTRAN has expanded, while keeping user cost low.

  3. Finite element forced vibration analysis of rotating cyclic structures

    NASA Technical Reports Server (NTRS)

    Elchuri, V.; Smith, G. C. C.

    1981-01-01

    A capability was added to the general purpose finite element program NASTRAN Level 17.7 to conduct forced vibration analysis of tuned cyclic structures rotating about their axes of symmetry. The effects of Coriolis and centripetal accelerations together with those due to linear acceleration of the axis of rotation were included. The theoretical development of this capability is presented.

  4. Open pore structure analysis of lithium bearing ceramics

    NASA Astrophysics Data System (ADS)

    Elbel, H.

    1988-07-01

    The analysis of the open pore structure includes mercury porosimetry, helium stereopycnometry, gas permeability and specific surface area measurements. These methods were used in the analysis of different types of Li 2SiO 3 and Li 4SiO 4 specimens whose behaviour is tested under operation conditions in various irradiation experiments. Mercury porosimetry yielded density of the specimens, size distribution of the channels and amount of the open porosity. The correlation between mercury pressure and channel diameter was approximated by the Washburn equation. Density determinations by means of helium stereopycnometry demonstrated the existence of open pore volume below the mercury porosimetry detection. Additional information about the structure of open porosity was obtained by gas permeability measurements evaluated using the Carman relation, which is a generalization of the Hagen-Poiseuille law. This approach correlates structure parameters of the open porosity with permeability coefficients. The specific surface area was determined by applying the BET theory to volumetric nitrogen gas adsorption.

  5. Analysis Methods for Progressive Damage of Composite Structures

    NASA Technical Reports Server (NTRS)

    Rose, Cheryl A.; Davila, Carlos G.; Leone, Frank A.

    2013-01-01

    This document provides an overview of recent accomplishments and lessons learned in the development of general progressive damage analysis methods for predicting the residual strength and life of composite structures. These developments are described within their State-of-the-Art (SoA) context and the associated technology barriers. The emphasis of the authors is on developing these analysis tools for application at the structural level. Hence, modeling of damage progression is undertaken at the mesoscale, where the plies of a laminate are represented as a homogenous orthotropic continuum. The aim of the present effort is establish the ranges of validity of available models, to identify technology barriers, and to establish the foundations of the future investigation efforts. Such are the necessary steps towards accurate and robust simulations that can replace some of the expensive and time-consuming "building block" tests that are currently required for the design and certification of aerospace structures.

  6. Analysis of forest structure using thematic mapper simulator data

    NASA Technical Reports Server (NTRS)

    Peterson, D. L.; Westman, W. E.; Brass, J. A.; Stephenson, N. J.; Ambrosia, V. G.; Spanner, M. A.

    1986-01-01

    The potential of Thematic Mapper Simulator (TMS) data for sensing forest structure information has been explored by principal components and feature selection techniques. In a survey of forest structural properties conducted for 123 field sites of the Sequoia National Park, the canopy closure could be well estimated (r = 0.62 to 0.69) by a variety of channel bands and band ratios, without reference to the forest type. Estimation of the basal area was less successful (r = 0.51 or less) on the average, but could be improved for certain forest types when data were stratified by floristic composition. To achieve such a stratification, individual sites were ordinated by a detrended correspondence analysis based on the canopy of dominant species. The analysis of forest structure in the Sequoia data suggests that total basal area can be best predicted in stands of lower density, and in younger even-aged managed stands.

  7. Analysis of the kinesin superfamily: insights into structure and function.

    PubMed

    Miki, Harukata; Okada, Yasushi; Hirokawa, Nobutaka

    2005-09-01

    Kinesin superfamily proteins (KIFs) are key players or 'hub' proteins in the intracellular transport system, which is essential for cellular function and morphology. The KIF superfamily is also the first large protein family in mammals whose constituents have been completely identified and confirmed both in silico and in vivo. Numerous studies have revealed the structures and functions of individual family members; however, the relationships between members or a perspective of the whole superfamily structure until recently remained elusive. Here, we present a comprehensive summary based on a large, systematic phylogenetic analysis of the kinesin superfamily. All available sequences in public databases, including genomic information from all model organisms, were analyzed to yield the most complete phylogenetic kinesin tree thus far, comprising 14 families. This comprehensive classification builds on the recently proposed standardized nomenclature for kinesins and allows systematic analysis of the structural and functional relationships within the kinesin superfamily. PMID:16084724

  8. Structural Analysis of the Redesigned Ice/Frost Ramp Bracket

    NASA Technical Reports Server (NTRS)

    Phillips, D. R.; Dawicke, D. S.; Gentz, S. J.; Roberts, P. W.; Raju, I. S.

    2007-01-01

    This paper describes the interim structural analysis of a redesigned Ice/Frost Ramp bracket for the Space Shuttle External Tank (ET). The proposed redesigned bracket consists of mounts for attachment to the ET wall, supports for the electronic/instrument cables and propellant repressurization lines that run along the ET, an upper plate, a lower plate, and complex bolted connections. The eight nominal bolted connections are considered critical in the summarized structural analysis. Each bolted connection contains a bolt, a nut, four washers, and a non-metallic spacer and block that are designed for thermal insulation. A three-dimensional (3D) finite element model of the bracket is developed using solid 10-node tetrahedral elements. The loading provided by the ET Project is used in the analysis. Because of the complexities associated with accurately modeling the bolted connections in the bracket, the analysis is performed using a global/local analysis procedure. The finite element analysis of the bracket identifies one of the eight bolted connections as having high stress concentrations. A local area of the bracket surrounding this bolted connection is extracted from the global model and used as a local model. Within the local model, the various components of the bolted connection are refined, and contact is introduced along the appropriate interfaces determined by the analysts. The deformations from the global model are applied as boundary conditions to the local model. The results from the global/local analysis show that while the stresses in the bolts are well within yield, the spacers fail due to compression. The primary objective of the interim structural analysis is to show concept viability for static thermal testing. The proposed design concept would undergo continued design optimization to address the identified analytical assumptions and concept shortcomings, assuming successful thermal testing.

  9. Integrative Analysis of Metabolic Models – from Structure to Dynamics

    PubMed Central

    Hartmann, Anja; Schreiber, Falk

    2015-01-01

    The characterization of biological systems with respect to their behavior and functionality based on versatile biochemical interactions is a major challenge. To understand these complex mechanisms at systems level modeling approaches are investigated. Different modeling formalisms allow metabolic models to be analyzed depending on the question to be solved, the biochemical knowledge and the availability of experimental data. Here, we describe a method for an integrative analysis of the structure and dynamics represented by qualitative and quantitative metabolic models. Using various formalisms, the metabolic model is analyzed from different perspectives. Determined structural and dynamic properties are visualized in the context of the metabolic model. Interaction techniques allow the exploration and visual analysis thereby leading to a broader understanding of the behavior and functionality of the underlying biological system. The System Biology Metabolic Model Framework (SBM2 – Framework) implements the developed method and, as an example, is applied for the integrative analysis of the crop plant potato. PMID:25674560

  10. Thermal and Structural Analysis of MIG for Gyrotron

    NASA Astrophysics Data System (ADS)

    Singh, Udaybir; Kumar, Anil; Kumar, Nitin; Kumar, Narendra; Raju, R. S.; Purohit, L. P.; Sinha, A. K.

    2011-04-01

    The paper presents the thermal analysis of the Magnetron Injection Gun for 42 GHz, 200 kW gyrotron, which is used to provide a high quality hollow electron beam. The Finite Element Analysis code ANSYS has been used for the thermal and the structural simulation. The thermal analysis of the structure of Magnetron Injection Gun has been carried out to find out the effect of heater temperature required for maintaining more than 1,000°C at cathode emitter surface to get 10 A of beam current. These results have been experimentally verified. The experimental results closely match the ANSYS results. The effect of the radial expansion of the emitter radius on beam quality has also been analyzed.

  11. Probabilistic structural analysis using a general purpose finite element program

    NASA Astrophysics Data System (ADS)

    Riha, D. S.; Millwater, H. R.; Thacker, B. H.

    1992-07-01

    This paper presents an accurate and efficient method to predict the probabilistic response for structural response quantities, such as stress, displacement, natural frequencies, and buckling loads, by combining the capabilities of MSC/NASTRAN, including design sensitivity analysis and fast probability integration. Two probabilistic structural analysis examples have been performed and verified by comparison with Monte Carlo simulation of the analytical solution. The first example consists of a cantilevered plate with several point loads. The second example is a probabilistic buckling analysis of a simply supported composite plate under in-plane loading. The coupling of MSC/NASTRAN and fast probability integration is shown to be orders of magnitude more efficient than Monte Carlo simulation with excellent accuracy.

  12. Design and analysis of composite structures with stress concentrations

    NASA Technical Reports Server (NTRS)

    Garbo, S. P.

    1983-01-01

    An overview of an analytic procedure which can be used to provide comprehensive stress and strength analysis of composite structures with stress concentrations is given. The methodology provides designer/analysts with a user-oriented procedure which, within acceptable engineering accuracy, accounts for the effects of a wide range of application design variables. The procedure permits the strength of arbitrary laminate constructions under general bearing/bypass load conditions to be predicted with only unnotched unidirectional strength and stiffness input data required. Included is a brief discussion of the relevancy of this analysis to the design of primary aircraft structure; an overview of the analytic procedure with theory/test correlations; and an example of the use and interaction of this strength analysis relative to the design of high-load transfer bolted composite joints.

  13. ACT Payload Shroud Structural Concept Analysis and Optimization

    NASA Technical Reports Server (NTRS)

    Zalewski, Bart B.; Bednarcyk, Brett A.

    2010-01-01

    Aerospace structural applications demand a weight efficient design to perform in a cost effective manner. This is particularly true for launch vehicle structures, where weight is the dominant design driver. The design process typically requires many iterations to ensure that a satisfactory minimum weight has been obtained. Although metallic structures can be weight efficient, composite structures can provide additional weight savings due to their lower density and additional design flexibility. This work presents structural analysis and weight optimization of a composite payload shroud for NASA s Ares V heavy lift vehicle. Two concepts, which were previously determined to be efficient for such a structure are evaluated: a hat stiffened/corrugated panel and a fiber reinforced foam sandwich panel. A composite structural optimization code, HyperSizer, is used to optimize the panel geometry, composite material ply orientations, and sandwich core material. HyperSizer enables an efficient evaluation of thousands of potential designs versus multiple strength and stability-based failure criteria across multiple load cases. HyperSizer sizing process uses a global finite element model to obtain element forces, which are statistically processed to arrive at panel-level design-to loads. These loads are then used to analyze each candidate panel design. A near optimum design is selected as the one with the lowest weight that also provides all positive margins of safety. The stiffness of each newly sized panel or beam component is taken into account in the subsequent finite element analysis. Iteration of analysis/optimization is performed to ensure a converged design. Sizing results for the hat stiffened panel concept and the fiber reinforced foam sandwich concept are presented.

  14. Characterization of rainbow trout myostatin-2 genes (rtMSTN-2a & -2b): genomic organization, differential expression and pseudogenization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Myostatin is an extremely potent negative regulator of vertebrate skeletal muscle development. A phylogenetic analysis suggests that salmonids should possess four distinct genes, although only MSTN-1 orthologs have been characterized. Described herein are the rainbow trout (rt) MSTN-2a and -2b genes...

  15. Total systems design analysis of high performance structures

    NASA Technical Reports Server (NTRS)

    Verderaime, V.

    1993-01-01

    Designer-control parameters were identified at interdiscipline interfaces to optimize structural systems performance and downstream development and operations with reliability and least life-cycle cost. Interface tasks and iterations are tracked through a matrix of performance disciplines integration versus manufacturing, verification, and operations interactions for a total system design analysis. Performance integration tasks include shapes, sizes, environments, and materials. Integrity integrating tasks are reliability and recurring structural costs. Significant interface designer control parameters were noted as shapes, dimensions, probability range factors, and cost. Structural failure concept is presented, and first-order reliability and deterministic methods, benefits, and limitations are discussed. A deterministic reliability technique combining benefits of both is proposed for static structures which is also timely and economically verifiable. Though launch vehicle environments were primarily considered, the system design process is applicable to any surface system using its own unique filed environments.

  16. Structural Analysis Methods for Structural Health Management of Future Aerospace Vehicles

    NASA Technical Reports Server (NTRS)

    Tessler, Alexander

    2007-01-01

    Two finite element based computational methods, Smoothing Element Analysis (SEA) and the inverse Finite Element Method (iFEM), are reviewed, and examples of their use for structural health monitoring are discussed. Due to their versatility, robustness, and computational efficiency, the methods are well suited for real-time structural health monitoring of future space vehicles, large space structures, and habitats. The methods may be effectively employed to enable real-time processing of sensing information, specifically for identifying three-dimensional deformed structural shapes as well as the internal loads. In addition, they may be used in conjunction with evolutionary algorithms to design optimally distributed sensors. These computational tools have demonstrated substantial promise for utilization in future Structural Health Management (SHM) systems.

  17. Probabilistic Finite Element Analysis & Design Optimization for Structural Designs

    NASA Astrophysics Data System (ADS)

    Deivanayagam, Arumugam

    This study focuses on implementing probabilistic nature of material properties (Kevlar® 49) to the existing deterministic finite element analysis (FEA) of fabric based engine containment system through Monte Carlo simulations (MCS) and implementation of probabilistic analysis in engineering designs through Reliability Based Design Optimization (RBDO). First, the emphasis is on experimental data analysis focusing on probabilistic distribution models which characterize the randomness associated with the experimental data. The material properties of Kevlar® 49 are modeled using experimental data analysis and implemented along with an existing spiral modeling scheme (SMS) and user defined constitutive model (UMAT) for fabric based engine containment simulations in LS-DYNA. MCS of the model are performed to observe the failure pattern and exit velocities of the models. Then the solutions are compared with NASA experimental tests and deterministic results. MCS with probabilistic material data give a good prospective on results rather than a single deterministic simulation results. The next part of research is to implement the probabilistic material properties in engineering designs. The main aim of structural design is to obtain optimal solutions. In any case, in a deterministic optimization problem even though the structures are cost effective, it becomes highly unreliable if the uncertainty that may be associated with the system (material properties, loading etc.) is not represented or considered in the solution process. Reliable and optimal solution can be obtained by performing reliability optimization along with the deterministic optimization, which is RBDO. In RBDO problem formulation, in addition to structural performance constraints, reliability constraints are also considered. This part of research starts with introduction to reliability analysis such as first order reliability analysis, second order reliability analysis followed by simulation technique that

  18. Applications of twin analysis to studying meteorite impact structures

    NASA Astrophysics Data System (ADS)

    Schedl, Andrew

    2006-04-01

    This paper describes a technique, twin analysis of dolomite and calcite, which was used to estimate the level of erosion of an impact crater. If the age of impact is known, the level of erosion gives the amount of sediments present at that time. The estimate of the level of erosion, and the presence or absence of tectonic strains in calcite constrains the age of impact. This technique might also be useful in identifying deeply eroded impact structures. Twin analysis gives the greatest shortening direction, ɛ1. Tilt corrected ɛ1 directions converge at or above the present day surface, if a shallow gas explosion or meteorite impact explains the structure, rather than a deep gas or cryptovolcanic explosion. The energy density recorded by twinning distinguishes an impact from a shallow gas explosion for structures ≤ 100 m diameter. At Serpent Mound, a well-established impact structure, ɛ1 directions converge at 1400 ± 390 m (95% confidence interval of the mean) above the present day structure and the sample closest to the center of the structure records an energy density of 1.7 × 10 7 J/m 3. These results are consistent with previous studies showing that Serpent Mound is an impact (e.g., [R.W. Carlton, C. Koeberl, M.T. Baranoski, G.A. Schumacker, Discovery of microscopic evidence for shock metamorphism at the Serpent Mound structure, south-central Ohio: confirmation of an origin by impact, Earth and Planet. Sci. Lett. 162 (1998) 177-185]). The level of erosion and other data suggests that Serpent Mound formed between 290 and 256 Ma and was originally 8.5 to 11 km in diameter. Dolomite twinning is not observed at Serpent Mound suggesting that this technique may only be useful for studying larger, more deeply eroded structures.

  19. LAr Dewar Coil Feed Frame Pipe Analysis (Structural Analysis of General Structures, SAGS)

    SciTech Connect

    Parker, A.W.; /Fermilab

    1990-01-31

    This frame pipe analysis addresses the D0 LAr dewar Condenser tube (coil) feed pipe thermal contraction stresses and moments. The configuration is shown in PEI drawing C-32545, Rev 0, and the parameters detailed in the letter of November 20, 1989, located in appendix A. Note that all other thermal considerations for these condensing coils have been made in D0 EN 3740.512-234. The conclusion of this report is the feed lines, previously deemed appropriate without detailed analysis, have been demonstrated to be adequately designed for the intended service and require no further investigation.

  20. Recent advances in computational structural reliability analysis methods

    NASA Technical Reports Server (NTRS)

    Thacker, Ben H.; Wu, Y.-T.; Millwater, Harry R.; Torng, Tony Y.; Riha, David S.

    1993-01-01

    The goal of structural reliability analysis is to determine the probability that the structure will adequately perform its intended function when operating under the given environmental conditions. Thus, the notion of reliability admits the possibility of failure. Given the fact that many different modes of failure are usually possible, achievement of this goal is a formidable task, especially for large, complex structural systems. The traditional (deterministic) design methodology attempts to assure reliability by the application of safety factors and conservative assumptions. However, the safety factor approach lacks a quantitative basis in that the level of reliability is never known and usually results in overly conservative designs because of compounding conservatisms. Furthermore, problem parameters that control the reliability are not identified, nor their importance evaluated. A summary of recent advances in computational structural reliability assessment is presented. A significant level of activity in the research and development community was seen recently, much of which was directed towards the prediction of failure probabilities for single mode failures. The focus is to present some early results and demonstrations of advanced reliability methods applied to structural system problems. This includes structures that can fail as a result of multiple component failures (e.g., a redundant truss), or structural components that may fail due to multiple interacting failure modes (e.g., excessive deflection, resonate vibration, or creep rupture). From these results, some observations and recommendations are made with regard to future research needs.

  1. Design and Analysis of Muon Beam Stop Support Structures

    SciTech Connect

    Okafor, Udenna

    2015-01-01

    The primary objective of this thesis is to design and analyze support structures to be used in the installation, test and final positioning of the MBS throughout the life of the Mu2e experiment. There several requirements for the MBS imposed by both the scope of the experiment and, other components within the DS bore. The functions of the MBS are: 1. To limit the induced rates in the Tracker, the Calorimeter and the Cosmic Ray Veto due to backsplash-and-secondary interactions, and 2. To reduce radiation levels external to the Detector solenoid. The structures used in supporting the MBS will also adhere to requirements imposed by its functions. These requirements are critical to the support structures and affect design decisions. Other requirements critical to the design are imposed by the weight, positional tolerance and assembly procedure of the MBS, and also, the magnetic field and vacuum dose rate of the DS bore. A detailed breakdown of how each requirement affects the structural design can be found in chapter 2. Chapter 3 describes the design of each support structure and its attachment to the MBS while chapter 4 describes the results from structural analysis of the support structures. Chapter 5 describes evaluation for the design through testing and calculations while the conclusion in chapter 6 reports the current status at the time of this thesis submission with a plan for future work to be completed until final design and installation.

  2. Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily

    PubMed Central

    Lakshmi, Balasubramanian; Mishra, Madhulika; Srinivasan, Narayanaswamy; Archunan, Govindaraju

    2015-01-01

    Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity. PMID:26263546

  3. NASTRAN forced vibration analysis of rotating cyclic structures

    NASA Technical Reports Server (NTRS)

    Elchuri, V.; Smith, G. C. C.; Gallo, A. M.

    1983-01-01

    Theoretical aspects of a new capability developed and implemented in NASTRAN level 17.7 to analyze forced vibration of a cyclic structure rotating about its axis of symmetry are presented. Fans, propellers, and bladed shrouded discs of turbomachines are some examples of such structures. The capability includes the effects of Coriolis and centripetal accelerations on the rotating structure which can be loaded with: (1) directly applied loads moving with the structure and (2) inertial loas due to the translational acceleration of the axis of rotation (''base' acceleration). Steady-state sinusoidal or general periodic loads are specified to represent: (1) the physical loads on various segments of the complete structure, or (2) the circumferential harmonic components of the loads in (1). The cyclic symmetry feature of the rotating structure is used in deriving and solving the equations of forced motion. Consequently, only one of the cyclic sectors is modelled and analyzed using finite elements, yielding substantial savings in the analysis cost. Results, however, are obtained for the entire structure. A tuned twelve bladed disc example is used to demonstrate the various features of the capability.

  4. Analysis concepts for large telescope structures under earthquake load

    NASA Astrophysics Data System (ADS)

    Koch, Franz

    1997-03-01

    The very large telescope (VLT) of ESO will be placed on Cerro Paranal in the Atacama desert in northern Chile. This site provides excellent conditions for astronomical observations. However, it is likely that important seismic activities occur. The telescope structure and its components have to resist the largest earthquakes expected during their lifetime. Therefore, design specifications and structural analyses have to take into account loads caused by such earthquakes. The present contribution shows some concepts and techniques in the assessment of earthquake resistant telescope design by the finite element method (FEM). After establishing the general design criteria and the geological and geotechnical characteristics of the site location, the seismic action can be defined. A description of various representations of the seismic action and the procedure to define the commonly used response spectrum are presented in more detail. A brief description of the response spectrum analysis method and of the result evaluation procedure follows. Additionally, some calculation concepts for parts of the entire telescope structure under seismic loads are provided. Finally, a response spectrum analysis of the entire VLT structure performed at ESO is presented to show a practical application of the analysis method and evaluation procedure mentioned above.

  5. Python package for model STructure ANalysis (pySTAN)

    NASA Astrophysics Data System (ADS)

    Van Hoey, Stijn; van der Kwast, Johannes; Nopens, Ingmar; Seuntjens, Piet

    2013-04-01

    The selection and identification of a suitable hydrological model structure is more than fitting parameters of a model structure to reproduce a measured hydrograph. The procedure is highly dependent on various criteria, i.e. the modelling objective, the characteristics and the scale of the system under investigation as well as the available data. Rigorous analysis of the candidate model structures is needed to support and objectify the selection of the most appropriate structure for a specific case (or eventually justify the use of a proposed ensemble of structures). This holds both in the situation of choosing between a limited set of different structures as well as in the framework of flexible model structures with interchangeable components. Many different methods to evaluate and analyse model structures exist. This leads to a sprawl of available methods, all characterized by different assumptions, changing conditions of application and various code implementations. Methods typically focus on optimization, sensitivity analysis or uncertainty analysis, with backgrounds from optimization, machine-learning or statistics amongst others. These methods also need an evaluation metric (objective function) to compare the model outcome with some observed data. However, for current methods described in literature, implementations are not always transparent and reproducible (if available at all). No standard procedures exist to share code and the popularity (and amount of applications) of the methods is sometimes more dependent on the availability than the merits of the method. Moreover, new implementations of existing methods are difficult to verify and the different theoretical backgrounds make it difficult for environmental scientists to decide about the usefulness of a specific method. A common and open framework with a large set of methods can support users in deciding about the most appropriate method. Hence, it enables to simultaneously apply and compare different

  6. Residual Strength Analysis Methodology: Laboratory Coupons to Structural Components

    NASA Technical Reports Server (NTRS)

    Dawicke, D. S.; Newman, J. C., Jr.; Starnes, J. H., Jr.; Rose, C. A.; Young, R. D.; Seshadri, B. R.

    2000-01-01

    The NASA Aircraft Structural Integrity (NASIP) and Airframe Airworthiness Assurance/Aging Aircraft (AAA/AA) Programs have developed a residual strength prediction methodology for aircraft fuselage structures. This methodology has been experimentally verified for structures ranging from laboratory coupons up to full-scale structural components. The methodology uses the critical crack tip opening angle (CTOA) fracture criterion to characterize the fracture behavior and a material and a geometric nonlinear finite element shell analysis code to perform the structural analyses. The present paper presents the results of a study to evaluate the fracture behavior of 2024-T3 aluminum alloys with thickness of 0.04 inches to 0.09 inches. The critical CTOA and the corresponding plane strain core height necessary to simulate through-the-thickness effects at the crack tip in an otherwise plane stress analysis, were determined from small laboratory specimens. Using these parameters, the CTOA fracture criterion was used to predict the behavior of middle crack tension specimens that were up to 40 inches wide, flat panels with riveted stiffeners and multiple-site damage cracks, 18-inch diameter pressurized cylinders, and full scale curved stiffened panels subjected to internal pressure and mechanical loads.

  7. An approximate methods approach to probabilistic structural analysis

    NASA Technical Reports Server (NTRS)

    Mcclung, R. C.; Millwater, H. R.; Wu, Y.-T.; Thacker, B. H.; Burnside, O. H.

    1989-01-01

    A major research and technology program in Probabilistic Structural Analysis Methods (PSAM) is currently being sponsored by the NASA Lewis Research Center with Southwest Research Institute as the prime contractor. This program is motivated by the need to accurately predict structural response in an environment where the loadings, the material properties, and even the structure may be considered random. The heart of PSAM is a software package which combines advanced structural analysis codes with a fast probability integration (FPI) algorithm for the efficient calculation of stochastic structural response. The basic idea of PAAM is simple: make an approximate calculation of system response, including calculation of the associated probabilities, with minimal computation time and cost, based on a simplified representation of the geometry, loads, and material. The deterministic solution resulting should give a reasonable and realistic description of performance-limiting system responses, although some error will be inevitable. If the simple model has correctly captured the basic mechanics of the system, however, including the proper functional dependence of stress, frequency, etc. on design parameters, then the response sensitivities calculated may be of significantly higher accuracy.

  8. A novel node-structural map for angiogenesis analysis

    NASA Astrophysics Data System (ADS)

    Xiong, Yizhi; Zhao, Tong; Talavera, Dodanim; Honigmann, Rocio S.; Farkas, Daniel L.

    2005-04-01

    We introduce a novel node-structural map method for digital image-based analysis of angiogenesis, and apply it to quantitate the effect of pro-angiogenic (e.g. VEGF) and anti-angiogenic (e.g. anti-VEGF) treatments on blood vessel patterns in the quail chorioallantoic membrane (CAM) in vivo model. After vessel segmentation and skeletonization, a node-structural map is derived to represent the structural property of each pixel in the skeletonized image, such as end nodes (root and leaf), branch and furcation/junction nodes. By combining the node-structural map with vascular thickness map, our proposed method provides more detailed morphometric and structural measurement of vascular angiogenesis, such as average diameter, average branch length, branch thickness distribution, density of branch and furcation nodes, etc. Furthermore, the concept of vascular generations will be proposed. Accordingly, more detailed measurements related to the generations of the vascular tree can be easily evaluated. From the quantitative analysis results, it correctly shows the fact that VEGF/anti-VEGF can modify the blood vessel pattern and increase/decrease the vessel density in CAM significantly, compared to the phosphate-buffered saline treated controls.

  9. A new structural analysis/synthesis capability - ACCESS. [Approximation Concepts Code for Efficient Structural Synthesis

    NASA Technical Reports Server (NTRS)

    Schmit, L. A.; Miura, H.

    1975-01-01

    The creation of an efficient automated capability for minimum weight design of structures is reported. The ACCESS 1 computer program combines finite element analysis techniques and mathematical programming algorithms using an innovative collection of approximation concepts. Design variable linking, constraint deletion techniques and approximate analysis methods are used to generate a sequence of small explicit mathematical programming problems which retain the essential features of the design problem. Organization of the finite element analysis is carefully matched to the design optimization task. The efficiency of the ACCESS 1 program is demonstrated by giving results for several example problems.

  10. Horizontal Structure: A Neo-Piagetian Analysis of Structural Parallels across Domains.

    ERIC Educational Resources Information Center

    McKeough, Anne M.

    An analysis of children's narrative composition and art revealed concurrent development at both a general structural level and at a fine-grained detail level. A three-part study investigated whether this general cognitive pattern would be maintained across a different range of tasks: literary composition, scientific reasoning, and working memory.…

  11. Structure of RIASEC Scores in China: A Structural Meta-Analysis

    ERIC Educational Resources Information Center

    Long, Lirong; Tracey, Terence J. G.

    2006-01-01

    A structural meta-analysis was conducted to evaluate the fit of four different representations of the relations among RIASEC types, Holland's (1985, 1997) circular order model, Gati's (1991) three-group partition model, Rounds and Tracey's (1996) alternative three-group partition model, and Liu and Rounds' (2003) modified octant model, on 29…

  12. Structure and function analysis of protein–nucleic acid complexes

    NASA Astrophysics Data System (ADS)

    Kuznetsova, S. A.; Oretskaya, T. S.

    2016-05-01

    The review summarizes published data on the results and achievements in the field of structure and function analysis of protein–nucleic acid complexes by means of main physical and biochemical methods, including X-ray diffraction, nuclear magnetic resonance spectroscopy, electron and atomic force microscopy, small-angle X-ray and neutron scattering, footprinting and cross-linking. Special attention is given to combined approaches. The advantages and limitations of each method are considered, and the prospects of their application for wide-scale structural studies in vivo are discussed. The bibliography includes 145 references.

  13. Analysis of variance tables based on experimental structure.

    PubMed

    Brien, C J

    1983-03-01

    A stepwise procedure for obtaining the experimental structure for a particular experiment is presented together with rules for deriving the analysis-of-variance table from that structure. The procedure involves the division of the factors into groups and is essentially a generalization of the method of Nelder (1965, Proceedings of the Royal Society, Series A 283, 147-162; 1965, Proceedings of the Royal Society, Series A 283, 163-178), to what are termed 'multi-tiered' experiments. The proposed method is illustrated for a wine-tasting experiment. PMID:6871362

  14. Structural analysis in real time using continuous monitoring

    NASA Astrophysics Data System (ADS)

    Braunstein, Juergen; Viano, Charles; Hodac, Bernard

    2005-05-01

    OSMOS developed a completely automatic monitoring-system, which is ideal for the determination and monitoring of the structural state of civil engineering structures. Static and dynamic data are recorded as needed and are available via internet for further analysis. In case of bridges, automatic calculation of the axle load of the flowing traffic is implemented, a weigh in motion system (WIMS). When configurable thresholds are exceeded alarms are sent by SMS, e-mail, SNMP-trap for facility-management-systems or by fax.

  15. Formulation of numerical procedures for dynamic analysis of spinning structures

    NASA Technical Reports Server (NTRS)

    Gupta, K. K.

    1986-01-01

    The paper presents the descriptions of recently developed numerical algorithms that prove to be useful for the solution of the free vibration problem of spinning structures. First, a generalized procedure for the computation of nodal centrifugal forces in a finite element owing to any specified spin rate is derived in detail. This is followed by a description of an improved eigenproblem solution procedure that proves to be economical for the free vibration analysis of spinning structures. Numerical results are also presented which indicate the efficacy of the currently developed procedures.

  16. Synthesis of aircraft structures using integrated design and analysis methods

    NASA Technical Reports Server (NTRS)

    Sobieszczanski-Sobieski, J.; Goetz, R. C.

    1978-01-01

    A systematic research is reported to develop and validate methods for structural sizing of an airframe designed with the use of composite materials and active controls. This research program includes procedures for computing aeroelastic loads, static and dynamic aeroelasticity, analysis and synthesis of active controls, and optimization techniques. Development of the methods is concerned with the most effective ways of integrating and sequencing the procedures in order to generate structural sizing and the associated active control system, which is optimal with respect to a given merit function constrained by strength and aeroelasticity requirements.

  17. The Riccati transfer matrix method. [for computerized structural analysis

    NASA Technical Reports Server (NTRS)

    Horner, G. C.; Pilkey, W. D.

    1977-01-01

    The Riccati transfer matrix method is a new technique for analyzing structural members. This new technique makes use of an existing large catalog of transfer matrices for various structural members such as rotating shafts. The numerical instability encountered when calculating high resonant frequencies, static response of a flexible member on a stiff foundation, or the response of a long member by the transfer matrix method is eliminated by the Riccati transfer matrix method. The computational time and storage requirements of the Riccati transfer matrix method are about half the values for the transfer matrix method. A rotating shaft analysis demonstrates the numerical accuracy of the method.

  18. Analysis of fluid-structural instability in water

    SciTech Connect

    Piccirillo, N.

    1997-02-01

    Recent flow testing of stainless steel hardware in a high pressure/high temperature water environment produced an apparent fluid-structural instability. The source of instability was investigated by studying textbook theory and by performing NASTRAN finite element analyses. The modal analyses identified the mode that was being excited, but the flutter instability analysis showed that the design is stable if minimal structural damping is present. Therefore, it was suspected that the test hardware was the root cause of the instability. Further testing confirmed this suspicion.

  19. Structure analysis methods for crystalline solids and supercooled liquids

    NASA Astrophysics Data System (ADS)

    Yu, Da-Qi; Chen, Min; Han, Xiu-Jun

    2005-11-01

    The three most widely used methods for analyzing atomic structures are evaluated by simulating crystalline solids and supercooled liquids. The local order parameter approach due to Volkov [Phys. Rev. E 66, 061401 (2002)] fails in randomly perturbed body-centered-cubic environments, while the pair analysis method behaves as an approximate approach depending on how the neighborhood is defined. As to the Voronoi analysis method, we improve the procedure of Brostow [Phys. Rev. B 57, 13448 (1998)] to eliminate distorted Voronoi faces and edges which originate from thermal vibrations and computational rounding errors. The improved procedure works robustly in face-centered-cubic, body-centered-cubic, and hexagonal close-packed environments. When the pair analysis technique and the Voronoi analysis method are applied to detect the microstructure and its evolution in supercooled liquids, qualitatively consistent results are attained.

  20. Design and Analysis of a Stiffened Composite Structure Repair Concept

    NASA Technical Reports Server (NTRS)

    Przekop, Adam

    2011-01-01

    A design and analysis of a repair concept applicable to a stiffened thin-skin composite panel based on the Pultruded Rod Stitched Efficient Unitized Structure is presented. Since the repair concept is a bolted repair using metal components, it can easily be applied in the operational environment. Initial analyses are aimed at validating the finite element modeling approach by comparing with available test data. Once confidence in the analysis approach is established several repair configurations are explored and the most efficient one presented. Repairs involving damage to the top of the stiffener alone are considered in addition to repairs involving a damaged stiffener, flange and underlying skin. High fidelity finite element modeling techniques such as mesh-independent definition of compliant fasteners, elastic-plastic metallic material properties and geometrically nonlinear analysis are utilized in the effort. The results of the analysis are presented and factors influencing the design are assessed and discussed.

  1. The Least Squares Stochastic Finite Element Method in Structural Stability Analysis of Steel Skeletal Structures

    NASA Astrophysics Data System (ADS)

    Kamiński, M.; Szafran, J.

    2015-05-01

    The main purpose of this work is to verify the influence of the weighting procedure in the Least Squares Method on the probabilistic moments resulting from the stability analysis of steel skeletal structures. We discuss this issue also in the context of the geometrical nonlinearity appearing in the Stochastic Finite Element Method equations for the stability analysis and preservation of the Gaussian probability density function employed to model the Young modulus of a structural steel in this problem. The weighting procedure itself (with both triangular and Dirac-type) shows rather marginal influence on all probabilistic coefficients under consideration. This hybrid stochastic computational technique consisting of the FEM and computer algebra systems (ROBOT and MAPLE packages) may be used for analogous nonlinear analyses in structural reliability assessment.

  2. High expression of dual-specificity phosphatase 5 pseudogene 1 (DUSP5P1) is associated with poor prognosis in acute myeloid leukemia

    PubMed Central

    Zhou, Ling-Yu; Yin, Jia-Yu; Tang, Qin; Zhai, Ling-Ling; Zhang, Tin-Juan; Wang, Yu-Xin; Yang, Dong-Qin; Qian, Jun; Lin, Jiang; Deng, Zhao-Qun

    2015-01-01

    The purpose of this study was to investigate the expression status of Dual-Specificity Phosphatase 5 Pseudogene 1 (DUSP5P1) and its clinical relevance in patients with acute myeloid leukemia (AML). Real-time quantitative PCR (RQ-PCR) was performed to detect the status of DUSP5P1 expression in 89 patients with de novo AML and 24 normal controls. The level of DUSP5P1 expression was significantly up-regulated in AML compared to controls (P=0.031). The patients with high expression of DUSP5P1 had higher percentage of blasts in bone marrow (BM) than those without high expression (P=0.027). The occurrence rate of DUSP5P1 high expression was significantly higher in M1 (2/8, 25%) and M2 subtypes (9/33, 27%) than in M3 subtype (0/17, 0%) (P=0.034). At the same time, the frequency of DUSP5P1 high expression in patients with intermediate (13/53, 24%) and poor karyotypes (5/11, 45%) was significantly higher than that in patients with favorable karyotype (0/21, 0%) (P=0.003). Meanwhile, DUSP5P1 high-expressed patients had significantly shorter overall survival (OS) than those with low expression (median 4.5 vs. 10.5 months, respectively, P=0.038). Our findings indicated that high expression of DUSP5P1 may identify high-risk AML patients and is associated with poor prognosis in AML. PMID:26884884

  3. Mitochondrial DNA as a non-invasive biomarker: Accurate quantification using real time quantitative PCR without co-amplification of pseudogenes and dilution bias

    SciTech Connect

    Malik, Afshan N.; Shahni, Rojeen; Rodriguez-de-Ledesma, Ana; Laftah, Abas; Cunningham, Phil

    2011-08-19

    Highlights: {yields} Mitochondrial dysfunction is central to many diseases of oxidative stress. {yields} 95% of the mitochondrial genome is duplicated in the nuclear genome. {yields} Dilution of untreated genomic DNA leads to dilution bias. {yields} Unique primers and template pretreatment are needed to accurately measure mitochondrial DNA content. -- Abstract: Circulating mitochondrial DNA (MtDNA) is a potential non-invasive biomarker of cellular mitochondrial dysfunction, the latter known to be central to a wide range of human diseases. Changes in MtDNA are usually determined by quantification of MtDNA relative to nuclear DNA (Mt/N) using real time quantitative PCR. We propose that the methodology for measuring Mt/N needs to be improved and we have identified that current methods have at least one of the following three problems: (1) As much of the mitochondrial genome is duplicated in the nuclear genome, many commonly used MtDNA primers co-amplify homologous pseudogenes found in the nuclear genome; (2) use of regions from genes such as {beta}-actin and 18S rRNA which are repetitive and/or highly variable for qPCR of the nuclear genome leads to errors; and (3) the size difference of mitochondrial and nuclear genomes cause a 'dilution bias' when template DNA is diluted. We describe a PCR-based method using unique regions in the human mitochondrial genome not duplicated in the nuclear genome; unique single copy region in the nuclear genome and template treatment to remove dilution bias, to accurately quantify MtDNA from human samples.

  4. Molecular cloning and chromosomal localization of a pseudogene related to the human Acyl-CoA binding protein/diazepam binding inhibitor

    SciTech Connect

    Gersuk, V.H.; Rose, T.M.; Todaro, G.J.

    1995-01-20

    The acyl-CoA binding protein (ACBP) and the diazepam binding inhibitor (DBI) or endozepine are independent isolates of a single 86-amino-acid, 10-kDa protein. ACBP/DBI is highly conserved between species and has been identified in several diverse organisms, including human, cow, rat, frog, duck, insects, plants, and yeast. Although the genomic locus has not yet been cloned in humans, complementary DNA clones with different 5{prime} ends have been isolated and characterized. These cDNA clones appear to be encoded by a single gene. However, Southern blot analyses, in situ hybridizations, and somatic cell hybrid chromosomal mapping all suggest that there are multiple ACBP/DBI-related sequences in the genome. To identify potential members of this gene family, degenerate oligonucleotides corresponding to highly conserved regions of ACBP/DBI were used to screen a human genomic DNA library using the polymerase chain reaction. A novel gene, DBIP1, that is closely related to ACBP/DBI but is clearly distinct was identified. DBIP1 bears extensive sequence homology to ACBP/DBI but lacks the introns predicted by rat and duck genomic sequence studies. A 1-base deletion in the coding region results in a frameshift and, along with the absence of introns and the lack of a detectable transcript, suggests that DBIP1 is a pseudogene. ACBP/DBI has previously been mapped to chromosome 2, although this was recently disputed, and a chromosome 6 location was suggested. We show that ACBP/DBI is correctly placed on chromosome 2 and that the gene identified on chromosome 6 is DBIP1. 33 refs., 3 figs., 1 tab.

  5. OCT4 pseudogene 5 upregulates OCT4 expression to promote proliferation by competing with miR-145 in endometrial carcinoma.

    PubMed

    Bai, Mingzhu; Yuan, Mu; Liao, Hong; Chen, Jiazhou; Xie, Binying; Yan, Dong; Xi, Xiaowei; Xu, Xianming; Zhang, Zhenbo; Feng, Youji

    2015-04-01

    OCT4 plays a critical role in the maintenance of stem cell pluripotency and proliferation, and is overexpressed in multiple human tumors, including endometrial cancer. OCT4 expression can be modulated by miR-145 and the OCT4 pseudogene 5 (OCT4-pg5), which share similar binding sites in the OCT4 3'-untranslated region. The goal of the present study was to evaluate the interaction between miR-145 and OCT4‑pg5 on OCT4 expression in endometrial cancer. We assessed OCT4-pg5 expression in 14 benign endometrium and 29 endometrial carcinoma samples. Furthermore, miR-145 mimic transfection was performed to explore its effect on OCT4-pg5 and OCT4 expression, and small interfering RNA (siRNA)-mediated knockdown of OCT4 was conducted to determine whether the effect of OCT4-pg5 on cellular growth was OCT4-dependent. We observed that OCT4-pg5 was abnormally activated in the endometrial carcinomas, and that overexpression of OCT4-pg5 contributed to enhanced cell proliferation and OCT4-PI3K/AKT-cyclin D1 signaling. Moreover, the miR-145 mimic depleted OCT4 expression, whereas elevated OCT4-pg5 restored OCT4 expression and OCT4-PI3K/AKT-cyclin D1 signaling. In conclusion, these data indicate that OCT4-pg5 can act as an RNA sponge to protect OCT4 transcripts from being inhibited by miR-145, providing novel insight into the control of OCT4 expression. PMID:25634023

  6. Design-Oriented Analysis of Aircraft Fuselage Structures

    NASA Technical Reports Server (NTRS)

    Giles, Gary L.

    1998-01-01

    A design-oriented analysis capability for aircraft fuselage structures that utilizes equivalent plate methodology is described. This new capability is implemented as an addition to the existing wing analysis procedure in the Equivalent Laminated Plate Solution (ELAPS) computer code. The wing and fuselage analyses are combined to model entire airframes. The paper focuses on the fuselage model definition, the associated analytical formulation and the approach used to couple the wing and fuselage analyses. The modeling approach used to minimize the amount of preparation of input data by the user and to facilitate the making of design changes is described. The fuselage analysis is based on ring and shell equations but the procedure is formulated to be analogous to that used for plates in order to take advantage of the existing code in ELAPS. Connector springs are used to couple the wing and fuselage models. Typical fuselage analysis results are presented for two analytical models. Results for a ring-stiffened cylinder model are compared with results from conventional finite-element analyses to assess the accuracy of this new analysis capability. The connection of plate and ring segments is demonstrated using a second model that is representative of the wing structure for a channel-wing aircraft configuration.

  7. Multiscale analysis of structure development in expanded starch snacks

    NASA Astrophysics Data System (ADS)

    van der Sman, R. G. M.; Broeze, J.

    2014-11-01

    In this paper we perform a multiscale analysis of the food structuring process of the expansion of starchy snack foods like keropok, which obtains a solid foam structure. In particular, we want to investigate the validity of the hypothesis of Kokini and coworkers, that expansion is optimal at the moisture content, where the glass transition and the boiling line intersect. In our analysis we make use of several tools, (1) time scale analysis from the field of physical transport phenomena, (2) the scale separation map (SSM) developed within a multiscale simulation framework of complex automata, (3) the supplemented state diagram (SSD), depicting phase transition and glass transition lines, and (4) a multiscale simulation model for the bubble expansion. Results of the time scale analysis are plotted in the SSD, and give insight into the dominant physical processes involved in expansion. Furthermore, the results of the time scale analysis are used to construct the SSM, which has aided us in the construction of the multiscale simulation model. Simulation results are plotted in the SSD. This clearly shows that the hypothesis of Kokini is qualitatively true, but has to be refined. Our results show that bubble expansion is optimal for moisture content, where the boiling line for gas pressure of 4 bars intersects the isoviscosity line of the critical viscosity 106 Pa.s, which runs parallel to the glass transition line.

  8. Advanced stress analysis methods applicable to turbine engine structures

    NASA Technical Reports Server (NTRS)

    Pian, Theodore H. H.

    1991-01-01

    The following tasks on the study of advanced stress analysis methods applicable to turbine engine structures are described: (1) constructions of special elements which contain traction-free circular boundaries; (2) formulation of new version of mixed variational principles and new version of hybrid stress elements; (3) establishment of methods for suppression of kinematic deformation modes; (4) construction of semiLoof plate and shell elements by assumed stress hybrid method; and (5) elastic-plastic analysis by viscoplasticity theory using the mechanical subelement model.

  9. Stress analysis for wall structure in mobile hot cell design

    NASA Astrophysics Data System (ADS)

    Bahrin, Muhammad Hannan; Rahman, Anwar Abdul; Hamzah, Mohd Arif; Mamat, Mohd Rizal; Azman, Azraf; Hasan, Hasni

    2016-01-01

    Malaysian Nuclear Agency is developing a Mobile Hot Cell (MHC) in order to handle and manage Spent High Activity Radioactive Sources (SHARS) such as teletherapy heads and irradiators. At present, there are only two units of MHC in the world, in South Africa and China. Malaysian Mobile Hot cell is developed by Malaysian Nuclear Agency with the assistance of IAEA expert, based on the design of South Africa and China, but with improved features. Stress analysis has been performed on the design in order to fulfil the safety requirement in operation of MHC. This paper discusses the loading analysis effect from the sand to the MHC wall structure.

  10. Structure Model Analysis of the Kashima 34m Telescope

    NASA Astrophysics Data System (ADS)

    Nakajima, Junichi; Nakamura, Toshio; Saita, Takeshi; Horiguchi, Junji; Yuge, Kouhei

    2001-03-01

    Deformation analysis of the Kashima 34-m radio telescope is performed. Although the telescope has a large aperture and accurate reflector panels, the dish support structures determine the high-frequency performance. Especially in millimeter wavelength, deformations above 1-mm affect the telescope efficiency seriously. We have modeled 34-m telescopes into elements and used a finite element method FEM to simulate accurate telescope deformations. The first results we obtained agreed well with the realistic deformation. Future analysis and telescope evaluations based on computer simulations are possible with this FEM model.

  11. Structural analysis of a new type lightweight optical mirror blank

    NASA Astrophysics Data System (ADS)

    Li, Yeping; Cui, Xiangqun; Hu, Ningsheng

    2010-07-01

    To reduce the cost and increase the feasibility of the astronomical optical telescope, modern large optical telescope is normally required to be as light as possible. Therefore lightweight mirror is always pursued by large telescopes development. In this paper, a new type lightweight optical mirror blank, the evaluation of its technical feasibility and the reduction of cost are introduced. For the purpose of applying active optics with this lightweight mirror blank, the structural analysis, thermal analysis and optical performance simulation by the finite element method have been presented.

  12. Structure in gamma ray burst time profiles: Statistical Analysis 1

    NASA Technical Reports Server (NTRS)

    Lestrade, John Patrick

    1992-01-01

    Since its launch on April 5, 1991, the Burst And Transient Source Experiment (BATSE) has observed and recorded over 500 gamma-ray bursts (GRB). The analysis of the time profiles of these bursts has proven to be difficult. Attempts to find periodicities through Fourier analysis have been fruitless except one celebrated case. Our goal is to be able to qualify the observed time-profiles structure. Before applying this formation to bursts, we have tested it on profiles composed of random Poissonian noise. This paper is a report of those preliminary results.

  13. Ulysses Data Analysis: Magnetic Topology of Heliospheric Structures

    NASA Technical Reports Server (NTRS)

    Crooker, Nancy

    2001-01-01

    In this final technical report on research funded by a NASA grant, a project overview is given by way of summaries on nine published papers. Research has included: 1) Using suprathermal electron data to study heliospheric magnetic structures; 2) Analysis of magnetic clouds, coronal mass ejections (CME), and the heliospheric current sheet (HCS); 3) Analysis of the corotating interaction region (CIR) which develop from interactions between solar wind streams of different velocities; 4) Use of Ulysses data in the interpretation of heliospheric events and phenomena.

  14. Thermal/structural analysis of a transpiration cooled nozzle

    NASA Technical Reports Server (NTRS)

    Gregory, Peyton B.; Thompson, Jon E.; Babcock, Dale A.; Gray, Carl E., Jr.; Mouring, Chris A.

    1992-01-01

    The 8-foot High Temperature Tunnel (HTT) at LaRC is a combustion driven, high enthalpy blow down wind tunnel. In Mar. 1991, during check out of the transpiration cooled nozzle, pieces of platelets were found in the tunnel test section. It was determined that incorrect tolerancing between the platelets and the housing was the primary cause of the platelet failure. An analysis was performed to determine the tolerance layout between the platelets and the housing to meet the structural and performance criteria under a range of thermal, pressure, and bolt preload conditions. Three recommendations resulted as a product of this analysis.

  15. In situ structural analysis of the human nuclear pore complex.

    PubMed

    von Appen, Alexander; Kosinski, Jan; Sparks, Lenore; Ori, Alessandro; DiGuilio, Amanda L; Vollmer, Benjamin; Mackmull, Marie-Therese; Banterle, Niccolo; Parca, Luca; Kastritis, Panagiotis; Buczak, Katarzyna; Mosalaganti, Shyamal; Hagen, Wim; Andres-Pons, Amparo; Lemke, Edward A; Bork, Peer; Antonin, Wolfram; Glavy, Joseph S; Bui, Khanh Huy; Beck, Martin

    2015-10-01

    Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations. PMID:26416747

  16. In situ structural analysis of the human nuclear pore complex

    PubMed Central

    Ori, Alessandro; DiGuilio, Amanda L.; Vollmer, Benjamin; Mackmull, Marie-Therese; Banterle, Niccolo; Parca, Luca; Kastritis, Panagiotis; Buczak, Katarzyna; Mosalaganti, Shyamal; Hagen, Wim; Andres-Pons, Amparo; Lemke, Edward A.; Bork, Peer; Antonin, Wolfram; Glavy, Joseph S.; Bui, Khanh Huy; Beck, Martin

    2016-01-01

    Summary Nuclear pore complexes (NPCs) are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Elucidating their 110 MDa structure imposes a formidable challenge and requires in situ structural biology approaches. Fifteen out of about thirty nucleoporins (Nups) are structured and form the Y- and inner ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ∼60 nm in diameter 1. The scaffold is decorated with transport channel Nups that often contain phenylalanine (FG)-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y-complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here, we combined cryo electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modeling to generate the most comprehensive architectural model of the NPC to date. Our data suggest previously unknown protein interfaces across Y-complexes and to inner ring complex members. We demonstrate that the higher eukaryotic transport channel Nup358 (RanBP2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport channel Nups. We conclude that, similarly to coated vesicles, multiple copies of the same structural building block - although compositionally identical - engage in different local sets of interactions and conformations. PMID:26416747

  17. Nonlinear constitutive theory for turbine engine structural analysis

    NASA Technical Reports Server (NTRS)

    Thompson, R. L.

    1982-01-01

    A number of viscoplastic constitutive theories and a conventional constitutive theory are evaluated and compared in their ability to predict nonlinear stress-strain behavior in gas turbine engine components at elevated temperatures. Specific application of these theories is directed towards the structural analysis of combustor liners undergoing transient, cyclic, thermomechanical load histories. The combustor liner material considered in this study is Hastelloy X. The material constants for each of the theories (as a function of temperature) are obtained from existing, published experimental data. The viscoplastic theories and a conventional theory are incorporated into a general purpose, nonlinear, finite element computer program. Several numerical examples of combustor liner structural analysis using these theories are given to demonstrate their capabilities. Based on the numerical stress-strain results, the theories are evaluated and compared.

  18. Static analysis of cable networks and their supporting structures

    SciTech Connect

    Mitsugi, J.

    1994-04-01

    A nonlinear static analysis method for cable structures, particularly emphasizing cable networks, is presented. Cable strains are measured from the current geometry and compressed cables are analytically disassembled with the construction of the equilibrium equation and the stiffness matrix. Finite rotations of cable intersections, referred to as nodes, and cable elements passing through more than two nodes are included in the formulation. An integrated analysis with a linear finite element method is also presented to account for the elastic deformations of supporting structures for the cable networks. The formulation is programmed for a CRAY2 supercomputer using parallel processing to solve the linear equations. Applications of the method used for mesh antenna development are also presented. 13 refs.

  19. The ATLAS integrated structural analysis and design software system

    NASA Technical Reports Server (NTRS)

    Dreisbach, R. L.; Giles, G. L.

    1978-01-01

    The ATLAS system provides an extensive set of integrated technical computer-program modules for the analysis and design of general structural configurations, as well as capabilities that are particularly suited for the aeroelastic design of flight vehicles. The system is based on the stiffness formulation of the finite element structural analysis method and can be executed in batch and interactive computing environments on CDC 6600/CYBER computers. Problem-definition input data are written in an engineering-oriented language using a free field format. Input-data default values, generation options, and data quality checks provided by the preprocessors minimize the amount of data and flowtime for problem definition/verfication. Postprocessors allow selected input and calculated data to be extracted, manipulated, and displayed via on-line and off-line prints or plots for monitoring and verifying problem solutions. The sequence and mode of execution of selected program modules are controlled by a common user-oriented language.

  20. Analysis of fine structure in the nuclear continuum

    SciTech Connect

    Shevchenko, A.; Kalmykov, Y.; Neumann-Cosel, P. von; Ponomarev, V. Yu.; Richter, A.; Wambach, J.; Carter, J.; Usman, I.; Cooper, G. R. J.; Fearick, R. W.

    2008-02-15

    Fine structure has been shown to be a general phenomenon of nuclear giant resonances of different multipolarities over a wide mass range. In this article we assess various techniques that have been proposed to extract quantitative information from the fine structure in terms of characteristic scales. These include the so-called local scaling dimension, the entropy index method, Fourier analysis, and continuous and discrete wavelet transforms. As an example, results on the isoscalar giant quadrupole resonance in {sup 208}Pb from high-energy-resolution inelastic proton scattering and calculations with the quasiparticle-phonon model are analyzed. Wavelet analysis, both continuous and discrete, of the spectra is shown to be a powerful tool to extract the magnitude and localization of characteristic scales.

  1. Development of Probabilistic Structural Analysis Integrated with Manufacturing Processes

    NASA Technical Reports Server (NTRS)

    Pai, Shantaram S.; Nagpal, Vinod K.

    2007-01-01

    An effort has been initiated to integrate manufacturing process simulations with probabilistic structural analyses in order to capture the important impacts of manufacturing uncertainties on component stress levels and life. Two physics-based manufacturing process models (one for powdered metal forging and the other for annular deformation resistance welding) have been linked to the NESSUS structural analysis code. This paper describes the methodology developed to perform this integration including several examples. Although this effort is still underway, particularly for full integration of a probabilistic analysis, the progress to date has been encouraging and a software interface that implements the methodology has been developed. The purpose of this paper is to report this preliminary development.

  2. Recent developments in thermal analysis of large space structures

    NASA Technical Reports Server (NTRS)

    Oneill, R. F.

    1983-01-01

    A numerical procedure for analysis of shadowed space heating of sparse structures, SSQ, is discussed. The SSQ program avoids inordinate computational complexity by confining attention to a single elemental location on a structural member of interest throughout an entire orbital period, proceeding then to similar treatment of individual alternate locations. The procedure considers a spacecraft in circular orbit and assumes fixed-Earth orientation of the spacecraft. Shadow orientation and interval duration, merged shadows, and computation of solar heat flux and thermal response are addressed. The output options of the SSQ FORTRAN 5 program and its efficiency are discussed. Application of the system to the analysis of a parabolic expandable truss antenna is considered.

  3. Structural weights analysis of advanced aerospace vehicles using finite element analysis

    NASA Technical Reports Server (NTRS)

    Bush, Lance B.; Lentz, Christopher A.; Rehder, John J.; Naftel, J. Chris; Cerro, Jeffrey A.

    1989-01-01

    A conceptual/preliminary level structural design system has been developed for structural integrity analysis and weight estimation of advanced space transportation vehicles. The system includes a three-dimensional interactive geometry modeler, a finite element pre- and post-processor, a finite element analyzer, and a structural sizing program. Inputs to the system include the geometry, surface temperature, material constants, construction methods, and aerodynamic and inertial loads. The results are a sized vehicle structure capable of withstanding the static loads incurred during assembly, transportation, operations, and missions, and a corresponding structural weight. An analysis of the Space Shuttle external tank is included in this paper as a validation and benchmark case of the system.

  4. Multilevel Dynamic Generalized Structured Component Analysis for Brain Connectivity Analysis in Functional Neuroimaging Data.

    PubMed

    Jung, Kwanghee; Takane, Yoshio; Hwang, Heungsun; Woodward, Todd S

    2016-06-01

    We extend dynamic generalized structured component analysis (GSCA) to enhance its data-analytic capability in structural equation modeling of multi-subject time series data. Time series data of multiple subjects are typically hierarchically structured, where time points are nested within subjects who are in turn nested within a group. The proposed approach, named multilevel dynamic GSCA, accommodates the nested structure in time series data. Explicitly taking the nested structure into account, the proposed method allows investigating subject-wise variability of the loadings and path coefficients by looking at the variance estimates of the corresponding random effects, as well as fixed loadings between observed and latent variables and fixed path coefficients between latent variables. We demonstrate the effectiveness of the proposed approach by applying the method to the multi-subject functional neuroimaging data for brain connectivity analysis, where time series data-level measurements are nested within subjects. PMID:25697370

  5. Forced vibration analysis of rotating cyclic structures in NASTRAN

    NASA Technical Reports Server (NTRS)

    Elchuri, V.; Gallo, A. M.; Skalski, S. C.

    1981-01-01

    A new capability was added to the general purpose finite element program NASTRAN Level 17.7 to conduct forced vibration analysis of tuned cyclic structures rotating about their axis of symmetry. The effects of Coriolis and centripetal accelerations together with those due to linear acceleration of the axis of rotation were included. The theoretical, user's, programmer's and demonstration manuals for this new capability are presented.

  6. Thermal analysis of a hypersonic wing test structure

    NASA Technical Reports Server (NTRS)

    Sandlin, Doral R.; Swanson, Neil J., Jr.

    1989-01-01

    The three-dimensional finite element modeling techniques developed for the thermal analysis of a hypersonic wing test structure (HWTS) are described. The computed results are compared to measured test data. In addition, the results of a NASA two-dimensional parameter finite difference local thermal model and the results of a contractor two-dimensional lumped parameter finite difference local thermal model will be presented.

  7. A structured approach to voice range profile (phonetogram) analysis.

    PubMed

    Sulter, A M; Wit, H P; Schutte, H K; Miller, D G

    1994-10-01

    A new method to analyze voice range profiles (phonetograms) is described. The structured analysis is based on quantitatively determining the features: shape, area, and "speaking range" dynamics, without distorting the shape of phonetograms. The parameter sets describing these features are calculated independently of fundamental frequency, which makes it possible to compare phonetograms. Two phonetograms representing a normal and a pathological example are used to illustrate the proposed method. The process provides a tool for establishing normative data for specified groups. PMID:7823554

  8. Thermal and structural analysis of a filter vessel ceramic tubesheet

    SciTech Connect

    Mallett, R.H.; Swindeman, R.W.; Zievers, J.F.

    1995-08-01

    A ceramic tubesheet assembly for a hot gas filter vessel is analyzed using the finite element method to determine stresses under differential pressure loading. The stresses include local concentration effects. Selection of the stress measures for evaluation of structural integrity is discussed. Specification of stress limits based upon limited data is considered. Stress results from this ongoing design analysis technology project are shown for one design concept.

  9. Fractal analysis of the hierarchic structure of fossil coal surface

    SciTech Connect

    Alekseev, A.D.; Vasilenko, T.A.; Kirillov, A.K.

    2008-05-15

    The fractal analysis is described as method of studying images of surface of fossil coal, one of the natural sorbent, with the aim of determining its structural surface heterogeneity. The deformation effect as a reduction in the dimensions of heterogeneity boundaries is considered. It is shown that the theory of nonequilibrium dynamic systems permits to assess a formation level of heterogeneities involved into a sorbent composition by means of the Hurst factor.

  10. Structural Test and Analysis of a Hybrid Inflatable Antenna

    NASA Technical Reports Server (NTRS)

    Gaspar, James L.; Mann, Troy; Sreekantamurthy, Tham; Behun, Vaughn

    2007-01-01

    NASA is developing ultra-lightweight structures technology for communication antennas for space missions. One of the research goals is to evaluate the structural characteristics of inflatable and rigidizable antennas through test and analysis. Being able to test and analyze the structural characteristics of a full scale antenna is important to enable the simulation of various mission scenarios to determine system performance in space. Recent work completed to evaluate a Hybrid Inflatable Antenna concept will be discussed. Tests were completed on a 2-m prototype to optimize its static shape and identify its modal dynamics that are important for analytical model validation. These test results were used to evaluate a preliminary finite element model of the antenna, and this model development and correlation activity is also described in the paper.

  11. An easily implemented static condensation method for structural sensitivity analysis

    NASA Technical Reports Server (NTRS)

    Gangadharan, S. N.; Haftka, R. T.; Nikolaidis, E.

    1990-01-01

    A black-box approach to static condensation for sensitivity analysis is presented with illustrative examples of a cube and a car structure. The sensitivity of the structural response with respect to joint stiffness parameter is calculated using the direct method, forward-difference, and central-difference schemes. The efficiency of the various methods for identifying joint stiffness parameters from measured static deflections of these structures is compared. The results indicate that the use of static condensation can reduce computation times significantly and the black-box approach is only slightly less efficient than the standard implementation of static condensation. The ease of implementation of the black-box approach recommends it for use with general-purpose finite element codes that do not have a built-in facility for static condensation.

  12. Computational modeling and impact analysis of textile composite structures

    NASA Astrophysics Data System (ADS)

    Hur, Hae-Kyu

    This study is devoted to the development of an integrated numerical modeling enabling one to investigate the static and the dynamic behaviors and failures of 2-D textile composite as well as 3-D orthogonal woven composite structures weakened by cracks and subjected to static-, impact- and ballistic-type loads. As more complicated modeling about textile composite structures is introduced, some of homogenization schemes, geometrical modeling and crack propagations become more difficult problems to solve. To overcome these problems, this study presents effective mesh-generation schemes, homogenization modeling based on a repeating unit cell and sinusoidal functions, and also a cohesive element to study micro-crack shapes. This proposed research has two: (1) studying behavior of textile composites under static loads, (2) studying dynamic responses of these textile composite structures subjected to the transient/ballistic loading. In the first part, efficient homogenization schemes are suggested to show the influence of textile architectures on mechanical characteristics considering the micro modeling of repeating unit cell. Furthermore, the structures of multi-layered or multi-phase composites combined with different laminar such as a sub-laminate, are considered to find the mechanical characteristics. A simple progressive failure mechanism for the textile composites is also presented. In the second part, this study focuses on three main phenomena to solve the dynamic problems: micro-crack shapes, textile architectures and textile effective moduli. To obtain a good solutions of the dynamic problems, this research attempts to use four approaches: (I) determination of governing equations via a three-level hierarchy: micro-mechanical unit cell analysis, layer-wise analysis accounting for transverse strains and stresses, and structural analysis based on anisotropic plate layers, (II) development of an efficient computational approach enabling one to perform transient

  13. Fixed point sensitivity analysis of interacting structured populations.

    PubMed

    Barabás, György; Meszéna, Géza; Ostling, Annette

    2014-03-01

    Sensitivity analysis of structured populations is a useful tool in population ecology. Historically, methodological development of sensitivity analysis has focused on the sensitivity of eigenvalues in linear matrix models, and on single populations. More recently there have been extensions to the sensitivity of nonlinear models, and to communities of interacting populations. Here we derive a fully general mathematical expression for the sensitivity of equilibrium abundances in communities of interacting structured populations. Our method yields the response of an arbitrary function of the stage class abundances to perturbations of any model parameters. As a demonstration, we apply this sensitivity analysis to a two-species model of ontogenetic niche shift where each species has two stage classes, juveniles and adults. In the context of this model, we demonstrate that our theory is quite robust to violating two of its technical assumptions: the assumption that the community is at a point equilibrium and the assumption of infinitesimally small parameter perturbations. Our results on the sensitivity of a community are also interpreted in a niche theoretical context: we determine how the niche of a structured population is composed of the niches of the individual states, and how the sensitivity of the community depends on niche segregation. PMID:24368160

  14. Functional and Structural Analysis of the Conserved EFhd2 Protein

    PubMed Central

    Acosta, Yancy Ferrer; Rodríguez Cruz, Eva N.; Vaquer, Ana del C.; Vega, Irving E.

    2013-01-01

    EFhd2 is a novel protein conserved from C. elegans to H. sapiens. This novel protein was originally identified in cells of the immune and central nervous systems. However, it is most abundant in the central nervous system, where it has been found associated with pathological forms of the microtubule-associated protein tau. The physiological or pathological roles of EFhd2 are poorly understood. In this study, a functional and structural analysis was carried to characterize the molecular requirements for EFhd2’s calcium binding activity. The results showed that mutations of a conserved aspartate on either EF-hand motif disrupted the calcium binding activity, indicating that these motifs work in pair as a functional calcium binding domain. Furthermore, characterization of an identified single-nucleotide polymorphisms (SNP) that introduced a missense mutation indicates the importance of a conserved phenylalanine on EFhd2 calcium binding activity. Structural analysis revealed that EFhd2 is predominantly composed of alpha helix and random coil structures and that this novel protein is thermostable. EFhd2’s thermo stability depends on its N-terminus. In the absence of the N-terminus, calcium binding restored EFhd2’s thermal stability. Overall, these studies contribute to our understanding on EFhd2 functional and structural properties, and introduce it into the family of canonical EF-hand domain containing proteins. PMID:22973849

  15. Recent innovations in the structural analysis of heparin.

    PubMed

    Yates, Edwin A; Rudd, Timothy R

    2016-06-01

    Heparin, the widely used anticoagulant drug, is unusual among major pharmaceutical agents being neither single chemical entity nor a defined mixture of compounds. Its composition, while conforming to approximate average disaccharide composition or sulfation levels, exhibits heterogeneity and variability depending on the source, as well as its geographical origin. Furthermore, individual polysaccharide chains, whose physico-chemical properties are extremely similar, cannot be separated with current state-of-the-art techniques, presenting a challenge to those interested in the quality control of heparin, in ensuring its provenance and safety, and those with an interest in investigating the relationships between its structure and biological activity. The review consists of two main sections: The first is the Introduction, comprising (i) The History, Occurrence and Use of Heparin and (ii) Approaches to Structure-Activity Relationships. The second section is Improved Techniques for Structural Analysis, comprising; (i) Separation and Identification, (ii) Spectroscopic Methods, (iii) Enzymatic Approaches and (iv) Other Physico-Chemical Approaches. The ~60 references cover recent technological advances in the study of heparin structural analysis, largely since 2010. PMID:27264867

  16. Topology structure synthesis and analysis of spatial pyramid deployable truss structures for satellite SAR antenna

    NASA Astrophysics Data System (ADS)

    Wang, Yan; Deng, Zongquan; Liu, Rongqiang; Yang, Hui; Guo, Hongwei

    2014-07-01

    Many attentions for structural synthesis are paid to planar linkages and parallel mechanisms, while design novel pyramid deployable truss structure(PDTS) of satellite SAR mainly depends on experience of designer. To design novel configuration of PDTS, a two-step topology structure synthesis and analysis approach is proposed. Firstly, a conceptual configuration of PDTS is synthesized. Weighted graph and weighted adjacency matrix are established to realize topological description for PDTS. Graph properties are then summarized to distinguish differentia between PDTS and other type structures. According to graph properties, a procedure for synthesis conceptual configuration of PDTS is presented. Secondly, join relationship of components in a PDTS is analyzed. Kinematic chain and corresponding incidence/adjacency matrix are employed to analyze join relationship of PDTS. Properties and simplified rules of kinematic chain are extracted to construct kinematic chain. A procedure for construction kinematic chain of PDTS is then established. Finally, with this two-step approach all 11 rectangular pyramid deployable structures whose folded state is planar are discovered and their kinematic chains are constructed. Based on synthesis results, a novel deployable support structure for satellite SAR is designed. The proposed research can be applied to obtain some novel PDTSs, which is of great importance to design some novel deployable support structures for satellite SAR antenna.

  17. PASCO- STRUCTURAL PANEL ANALYSIS AND SIZING CODE (MACINTOSH VERSION)

    NASA Technical Reports Server (NTRS)

    Lucas, S. H.

    1994-01-01

    The Panel Analysis and Sizing Code (PASCO) was developed for the buckling and vibration analysis and sizing of prismatic structures having an arbitrary cross section. PASCO is primarily intended for analyzing and sizing stiffened panels made of laminated orthotropic materials and is of particular value in analyzing and sizing filamentary composite structures. When used in the analysis mode, PASCO calculates laminate stiffnesses, lamina stress and strains (including the effects of temperature and panel bending), buckling loads, vibration frequencies, and overall panel stiffness. When used in the sizing mode, PASCO adjusts sizing variables to provide a low-mass panel design that carries a set of specified loadings without exceeding buckling or material strength allowables and that meets other design requirements such as upper and lower bounds on sizing variables, upper and lower bounds on overall bending, extensional and shear stiffnesses, and lower bounds on vibration frequencies. Although emphasis in PASCO is placed on flat panels having several identical bays, the only restriction on configuration modeling is that the structure is assumed to be prismatic. In addition, it is assumed that loads and temperatures do not vary along the length of a panel. Because of their wide application in aerospace structures, stiffened panels are readily handled by PASCO. The panel cross section may be composed of an arbitrary assemblage of thin, flat, rectangular plate elements that are connected together along their longitudinal edges. Each plate element consists of a balanced symmetric laminate of any number of layers of orthotropic material. Any group of element widths, layer thicknesses, and layer orientation angles may be selected as sizing variables. Substructuring is available to increase the efficiency of the analysis and to simplify the modeling of complicated structures. The Macintosh version of PASCO includes an interactive, graphic preprocessor called MacPASCO. The main

  18. PASCO- STRUCTURAL PANEL ANALYSIS AND SIZING CODE (DEC VAX VERSION)

    NASA Technical Reports Server (NTRS)

    Anderson, M. S.

    1994-01-01

    The Panel Analysis and Sizing Code (PASCO) was developed for the buckling and vibration analysis and sizing of prismatic structures having an arbitrary cross section. PASCO is primarily intended for analyzing and sizing stiffened panels made of laminated orthotropic materials and is of particular value in analyzing and sizing filamentary composite structures. When used in the analysis mode, PASCO calculates laminate stiffnesses, lamina stress and strains (including the effects of temperature and panel bending), buckling loads, vibration frequencies, and overall panel stiffness. When used in the sizing mode, PASCO adjusts sizing variables to provide a low-mass panel design that carries a set of specified loadings without exceeding buckling or material strength allowables and that meets other design requirements such as upper and lower bounds on sizing variables, upper and lower bounds on overall bending, extensional and shear stiffnesses, and lower bounds on vibration frequencies. Although emphasis in PASCO is placed on flat panels having several identical bays, the only restriction on configuration modeling is that the structure is assumed to be prismatic. In addition, it is assumed that loads and temperatures do not vary along the length of a panel. Because of their wide application in aerospace structures, stiffened panels are readily handled by PASCO. The panel cross section may be composed of an arbitrary assemblage of thin, flat, rectangular plate elements that are connected together along their longitudinal edges. Each plate element consists of a balanced symmetric laminate of any number of layers of orthotropic material. Any group of element widths, layer thicknesses, and layer orientation angles may be selected as sizing variables. Substructuring is available to increase the efficiency of the analysis and to simplify the modeling of complicated structures. The Macintosh version of PASCO includes an interactive, graphic preprocessor called MacPASCO. The main

  19. The evolution and utility of ribosomal ITS sequences in Bambusinae and related species: divergence, pseudogenes, and implications for phylogeny.

    PubMed

    Song, Hui-Xing; Gao, Su-Ping; Jiang, Ming-Yan; Liu, Guang-Li; Yu, Xiao-Fang; Chen, Qi-Bing

    2012-08-01

    Ribosomal internal transcribed spacer (ITS) sequences are commonly used for phylogenetic reconstruction because they are highly reiterated as components of rDNA repeats, and hence are often subject to rapid homogenization through concerted evolution. Concerted evolution leads to intragenomic uniformity of repeats even between loci on nonhomologous chromosomes. However, a number of studies have shown that the ITS polymorphism within individuals is quite common. The molecular systematics of Bambusinae and related species were recently assessed by different teams using independently generated ITS sequences, and the results disagreed in some remarkable features. Here we compared the ITS sequences of the members of Bambusa s. l., the genera Dendrocalamus, Dinochloa, Gigantochloa, Guadua, Melocalamus, Monocladus, Oxytenanthera, Thyrsostachys, Pleioblastus, Pseudosasa and Schizostachyum.We have reanalysed the ITS sequences used by different research teams to reveal the underlying patterns of their different results. After excluding the sequences suspected to represent paralogous loci, a phylogenetic analysis of the subtribe Bambusinae species were performed using maximum parsimony and maximum-likelihood methods. The implications of the findings are discussed. The risk of incorporating ITS paralogues in plant evolutionary studies that can distort the phylogenetic signal should caution molecular systematists. PMID:22942083

  20. Interest of perceptive vision for document structure analysis

    NASA Astrophysics Data System (ADS)

    Lemaitre, Aurélie; Camillerapp, Jean; Coüasnon, Bertrand

    2010-02-01

    This work addresses the problem of document image analysis, and more particularly the topic of document structure recognition in old, damaged and handwritten document. The goal of this paper is to present the interest of the human perceptive vision for document analysis. We focus on two aspects of the model of perceptive vision: the perceptive cycle and the visual attention. We present the key elements of the perceptive vision that can be used for document analysis. Thus, we introduce the perceptive vision in an existing method for document structure recognition, which enable both to show how we used the properties of the perceptive vision and to compare the results obtained with and without perceptive vision. We apply our method for the analysis of several kinds of documents (archive registers, old newspapers, incoming mails . . . ) and show that the perceptive vision significantly improves their recognition. Moreover, the use of the perceptive vision simplifies the description of complex documents. At last, the running time is often reduced.