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Sample records for integrating conjugative element

  1. Actinomycete integrative and conjugative elements

    PubMed Central

    te Poele, Evelien M.; Bolhuis, Henk

    2008-01-01

    This paper reviews current knowledge on actinomycete integrative and conjugative elements (AICEs). The best characterised AICEs, pSAM2 of Streptomyces ambofaciens (10.9 kb), SLP1 (17.3 kb) of Streptomyces coelicolor and pMEA300 of Amycolatopsis methanolica (13.3 kb), are present as integrative elements in specific tRNA genes, and are capable of conjugative transfer. These AICEs have a highly conserved structural organisation, with functional modules for excision/integration, replication, conjugative transfer, and regulation. Recently, it has been shown that pMEA300 and the related elements pMEA100 of Amycolatopsis mediterranei and pSE211 of Saccharopolyspora erythraea form a novel group of AICEs, the pMEA-elements, based on the unique characteristics of their replication initiator protein RepAM. Evaluation of a large collection of Amycolatopsis isolates has allowed identification of multiple pMEA-like elements. Our data show that, as AICEs, they mainly coevolved with their natural host in an integrated form, rather than being dispersed via horizontal gene transfer. The pMEA-like elements could be separated into two distinct populations from different geographical origins. One group was most closely related to pMEA300 and was found in isolates from Australia and Asia and pMEA100-related sequences were present in European isolates. Genome sequence data have enormously contributed to the recent insight that AICEs are present in many actinomycete genera. The sequence data also provide more insight into their evolutionary relationships, revealing their modular composition and their likely combined descent from bacterial plasmids and bacteriophages. Evidence is accumulating that AICEs act as modulators of host genome diversity and are also involved in the acquisition of secondary metabolite clusters and foreign DNA via horizontal gene transfer. Although still speculative, these AICEs may play a role in the spread of antibiotic resistance factors into pathogenic bacteria

  2. Diversity of integrating conjugative elements in actinobacteria

    PubMed Central

    Bordeleau, Eric; Ghinet, Mariana Gabriela; Burrus, Vincent

    2012-01-01

    Conjugation is certainly the most widespread and promiscuous mechanism of horizontal gene transfer in bacteria. During conjugation, DNA translocation across membranes of two cells forming a mating pair is mediated by two types of mobile genetic elements: conjugative plasmids and integrating conjugative elements (ICEs). The vast majority of conjugative plasmids and ICEs employ a sophisticated protein secretion apparatus called type IV secretion system to transfer to a recipient cell. Yet another type of conjugative DNA translocation machinery exists and to date appears to be unique to conjugative plasmids and ICEs of the Actinomycetales order, a sub-group of high G + C Gram-positive bacteria. This conjugative system is reminiscent of the machinery that allows segregation of chromosomal DNA during bacterial cell division and sporulation, and relies on a single FtsK-homolog protein to translocate double-stranded DNA molecules to the recipient cell. Recent thorough sequence analyses reveal that while this latter strategy appears to be used by the majority of ICEs in Actinomycetales, the former is also predicted to be important in exchange of genetic material in actinobacteria. PMID:22934248

  3. Regulation of conjugative transfer of plasmids and integrative conjugative elements.

    PubMed

    Bañuelos-Vazquez, Luis Alfredo; Torres Tejerizo, Gonzalo; Brom, Susana

    2017-05-01

    Horizontal gene transfer has been recognized as one of the principal contributors to bacterial evolution and diversification. One of the mechanisms involved in this process is conjugative transfer of plasmids and Integrative Conjugative Elements (ICEs). Plasmids and ICEs often encode traits beneficial for bacterial survival in specific environments, or for the establishment of symbiosis or pathogenesis, in addition to genes allowing conjugative transfer. In this review, we analyze the mechanisms that regulate the expression of conjugative transfer genes. For traits such as antibiotic or metal resistance, the compounds involved may induce conjugative transfer directly, while symbiosis and pathogenesis are modulated by quorum-sensing and/or signal molecules released by the host. However, multiple layers of regulation are usually involved in modulating transfer. In addition to the plasmid-encoded regulatory elements, conjugation seems to be regulated by what we have labeled as the "internal environment", defined by the interaction between the host chromosome and the plasmids or ICEs. Another regulatory level depends on the "external environment", which affects conjugative transfer due to the composition and conditions of the community. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Assembly and transfer of tripartite integrative and conjugative genetic elements

    PubMed Central

    Haskett, Timothy L.; Terpolilli, Jason J.; Bekuma, Amanuel; O’Hara, Graham W.; Sullivan, John T.; Wang, Penghao; Ronson, Clive W.

    2016-01-01

    Integrative and conjugative elements (ICEs) are ubiquitous mobile genetic elements present as “genomic islands” within bacterial chromosomes. Symbiosis islands are ICEs that convert nonsymbiotic mesorhizobia into symbionts of legumes. Here we report the discovery of symbiosis ICEs that exist as three separate chromosomal regions when integrated in their hosts, but through recombination assemble as a single circular ICE for conjugative transfer. Whole-genome comparisons revealed exconjugants derived from nonsymbiotic mesorhizobia received three separate chromosomal regions from the donor Mesorhizobium ciceri WSM1271. The three regions were each bordered by two nonhomologous integrase attachment (att) sites, which together comprised three homologous pairs of attL and attR sites. Sequential recombination between each attL and attR pair produced corresponding attP and attB sites and joined the three fragments to produce a single circular ICE, ICEMcSym1271. A plasmid carrying the three attP sites was used to recreate the process of tripartite ICE integration and to confirm the role of integrase genes intS, intM, and intG in this process. Nine additional tripartite ICEs were identified in diverse mesorhizobia and transfer was demonstrated for three of them. The transfer of tripartite ICEs to nonsymbiotic mesorhizobia explains the evolution of competitive but suboptimal N2-fixing strains found in Western Australian soils. The unheralded existence of tripartite ICEs raises the possibility that multipartite elements reside in other organisms, but have been overlooked because of their unusual biology. These discoveries reveal mechanisms by which integrases dramatically manipulate bacterial genomes to allow cotransfer of disparate chromosomal regions. PMID:27733511

  5. Conjugative Transfer and cis-Mobilization of a Genomic Island by an Integrative and Conjugative Element of Streptococcus agalactiae

    PubMed Central

    Puymège, Aurore; Bertin, Stéphane; Chuzeville, Sarah; Guédon, Gérard

    2013-01-01

    Putative integrative and conjugative elements (ICEs), i.e., genomic islands which could excise, self-transfer by conjugation, and integrate into the chromosome of the bacterial host strain, were previously identified by in silico analysis in the sequenced genomes of Streptococcus agalactiae (M. Brochet et al., J. Bacteriol. 190:6913–6917, 2008). We investigated here the mobility of the elements integrated into the 3′ end of a tRNALys gene. Three of the four putative ICEs tested were found to excise but only one (ICE_515_tRNALys) was found to transfer by conjugation not only to S. agalactiae strains but also to a Streptococcus pyogenes strain. Transfer was observed even if recipient cell already carries a related resident ICE or a genomic island flanked by attL and attR recombination sites but devoid of conjugation or recombination genes (CIs-Mobilizable Element [CIME]). The incoming ICE preferentially integrates into the 3′ end of the tRNALys gene (i.e., the attR site of the resident element), leading to a CIME-ICE structure. Transfer of the whole composite element CIME-ICE was obtained, showing that the CIME is mobilizable in cis by the ICE. Therefore, genomic islands carrying putative virulence genes but lacking the mobility gene can be mobilized by a related ICE after site-specific accretion. PMID:23275243

  6. Conjugative transfer and cis-mobilization of a genomic island by an integrative and conjugative element of Streptococcus agalactiae.

    PubMed

    Puymège, Aurore; Bertin, Stéphane; Chuzeville, Sarah; Guédon, Gérard; Payot, Sophie

    2013-03-01

    Putative integrative and conjugative elements (ICEs), i.e., genomic islands which could excise, self-transfer by conjugation, and integrate into the chromosome of the bacterial host strain, were previously identified by in silico analysis in the sequenced genomes of Streptococcus agalactiae (M. Brochet et al., J. Bacteriol. 190:6913-6917, 2008). We investigated here the mobility of the elements integrated into the 3' end of a tRNA(Lys) gene. Three of the four putative ICEs tested were found to excise but only one (ICE_515_tRNA(Lys)) was found to transfer by conjugation not only to S. agalactiae strains but also to a Streptococcus pyogenes strain. Transfer was observed even if recipient cell already carries a related resident ICE or a genomic island flanked by attL and attR recombination sites but devoid of conjugation or recombination genes (CIs-Mobilizable Element [CIME]). The incoming ICE preferentially integrates into the 3' end of the tRNA(Lys) gene (i.e., the attR site of the resident element), leading to a CIME-ICE structure. Transfer of the whole composite element CIME-ICE was obtained, showing that the CIME is mobilizable in cis by the ICE. Therefore, genomic islands carrying putative virulence genes but lacking the mobility gene can be mobilized by a related ICE after site-specific accretion.

  7. Integrative Conjugative Elements and Related Elements Are Major Contributors to the Genome Diversity of Streptococcus agalactiae▿ §

    PubMed Central

    Brochet, Mathieu; Couvé, Elisabeth; Glaser, Philippe; Guédon, Gérard; Payot, Sophie

    2008-01-01

    Thirty-five putative integrative conjugative elements and related elements were identified at 15 locations in the eight sequenced genomes of Streptococcus agalactiae. Twelve are composite, likely resulting from site-specific accretions. Circular forms were detected for five elements. Macroarray analysis confirmed their high plasticity and wide distribution in S. agalactiae. PMID:18708498

  8. SXT/R391 Integrative and Conjugative Elements (ICEs) Encode a Novel 'Trap-Door' Strategy for Mobile Element Escape.

    PubMed

    Ryan, Michael P; Armshaw, Patricia; Pembroke, J Tony

    2016-01-01

    Integrative conjugative elements (ICEs) are a class of bacterial mobile elements that have the ability to mediate their own integration, excision, and transfer from one host genome to another by a mechanism of site-specific recombination, self-circularisation, and conjugative transfer. Members of the SXT/R391 ICE family of enterobacterial mobile genetic elements display an unusual UV-inducible sensitization function which results in stress induced killing of bacterial cells harboring the ICE. This sensitization has been shown to be associated with a stress induced overexpression of a mobile element encoded conjugative transfer gene, orf43, a traV homolog. This results in cell lysis and release of a circular form of the ICE. Induction of this novel system may allow transfer of an ICE, enhancing its survival potential under conditions not conducive to conjugative transfer.

  9. The extended regulatory networks of SXT/R391 integrative and conjugative elements and IncA/C conjugative plasmids.

    PubMed

    Poulin-Laprade, Dominic; Carraro, Nicolas; Burrus, Vincent

    2015-01-01

    Nowadays, healthcare systems are challenged by a major worldwide drug resistance crisis caused by the massive and rapid dissemination of antibiotic resistance genes and associated emergence of multidrug resistant pathogenic bacteria, in both clinical and environmental settings. Conjugation is the main driving force of gene transfer among microorganisms. This mechanism of horizontal gene transfer mediates the translocation of large DNA fragments between two bacterial cells in direct contact. Integrative and conjugative elements (ICEs) of the SXT/R391 family (SRIs) and IncA/C conjugative plasmids (ACPs) are responsible for the dissemination of a broad spectrum of antibiotic resistance genes among diverse species of Enterobacteriaceae and Vibrionaceae. The biology, diversity, prevalence and distribution of these two families of conjugative elements have been the subject of extensive studies for the past 15 years. Recently, the transcriptional regulators that govern their dissemination through the expression of ICE- or plasmid-encoded transfer genes have been described. Unrelated repressors control the activation of conjugation by preventing the expression of two related master activator complexes in both types of elements, i.e., SetCD in SXT/R391 ICEs and AcaCD in IncA/C plasmids. Finally, in addition to activating ICE- or plasmid-borne genes, these master activators have been shown to specifically activate phylogenetically unrelated mobilizable genomic islands (MGIs) that also disseminate antibiotic resistance genes and other adaptive traits among a plethora of pathogens such as Vibrio cholerae and Salmonella enterica.

  10. The extended regulatory networks of SXT/R391 integrative and conjugative elements and IncA/C conjugative plasmids

    PubMed Central

    Poulin-Laprade, Dominic; Carraro, Nicolas; Burrus, Vincent

    2015-01-01

    Nowadays, healthcare systems are challenged by a major worldwide drug resistance crisis caused by the massive and rapid dissemination of antibiotic resistance genes and associated emergence of multidrug resistant pathogenic bacteria, in both clinical and environmental settings. Conjugation is the main driving force of gene transfer among microorganisms. This mechanism of horizontal gene transfer mediates the translocation of large DNA fragments between two bacterial cells in direct contact. Integrative and conjugative elements (ICEs) of the SXT/R391 family (SRIs) and IncA/C conjugative plasmids (ACPs) are responsible for the dissemination of a broad spectrum of antibiotic resistance genes among diverse species of Enterobacteriaceae and Vibrionaceae. The biology, diversity, prevalence and distribution of these two families of conjugative elements have been the subject of extensive studies for the past 15 years. Recently, the transcriptional regulators that govern their dissemination through the expression of ICE- or plasmid-encoded transfer genes have been described. Unrelated repressors control the activation of conjugation by preventing the expression of two related master activator complexes in both types of elements, i.e., SetCD in SXT/R391 ICEs and AcaCD in IncA/C plasmids. Finally, in addition to activating ICE- or plasmid-borne genes, these master activators have been shown to specifically activate phylogenetically unrelated mobilizable genomic islands (MGIs) that also disseminate antibiotic resistance genes and other adaptive traits among a plethora of pathogens such as Vibrio cholerae and Salmonella enterica. PMID:26347724

  11. Integrative and Conjugative Elements (ICEs): What They Do and How They Work

    PubMed Central

    Johnson, Christopher M.

    2016-01-01

    Horizontal gene transfer plays a major role in microbial evolution, allowing microbes to acquire new genes and phenotypes. Integrative and conjugative elements (ICEs, a.k.a. conjugative transposons) are modular mobile genetic elements integrated into a host genome and are passively propagated during chromosomal replication and cell division. Induction of ICE gene expression leads to excision, production of the conserved conjugation machinery (a type IV secretion system), and the potential to transfer DNA to appropriate recipients. ICEs typically contain cargo genes that are not usually related to the ICE life cycle and that confer phenotypes to host cells. We summarize the life cycle and discovery of ICEs, some of the regulatory mechanisms, and how the types of cargo have influenced our view of ICEs. We discuss how ICEs can acquire new cargo genes and describe challenges to the field and various perspectives on ICE biology. PMID:26473380

  12. Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer.

    PubMed

    Dahmane, Narimane; Libante, Virginie; Charron-Bourgoin, Florence; Guédon, Eric; Guédon, Gérard; Leblond-Bourget, Nathalie; Payot, Sophie

    2017-07-01

    Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole-genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3' end of the fda, rpsI, or rpmG gene) with the conjugation module of the ICESt3 subfamily. Sequence analyses also pointed out a recombination occurring at oriT (likely mediated by the relaxase) as a mechanism of ICE evolution. Despite a similar organization in two operons including three conserved genes, the regulation modules show a high diversity (about 50% amino acid sequence divergence for the encoded regulators and presence of unrelated additional genes) with a probable impact on the regulation of ICE activity. Concerning the accessory genes, ICEs of the ICESt3 subfamily appear particularly rich in restriction-modification systems and orphan methyltransferase genes. Other cargo genes that could confer a selective advantage to the cell hosting the ICE were identified, in particular, genes for bacteriocin synthesis and cadmium resistance. The functionality of 2 ICEs of S. salivarius was investigated. Autonomous conjugative transfer to other S. salivarius strains, to S. thermophilus, and to Enterococcus faecalis was observed. The analysis of the ICE-fda border sequence in these transconjugants allowed the localization of the DNA cutting site of the ICE integrase.IMPORTANCE The ICESt3 subfamily of ICEs appears to be widespread in streptococci and targets diverse chromosomal integration sites. These ICEs carry diverse cargo genes that can confer a selective advantage to the host strain. The maintenance of these mobile genetic elements likely relies in part on self-encoded restriction-modification systems. In

  13. Uncovering the Prevalence and Diversity of Integrating Conjugative Elements in Actinobacteria

    PubMed Central

    Beaudin, Julie; Brzezinski, Ryszard; Roy, Sébastien; Burrus, Vincent

    2011-01-01

    Horizontal gene transfer greatly facilitates rapid genetic adaptation of bacteria to shifts in environmental conditions and colonization of new niches by allowing one-step acquisition of novel functions. Conjugation is a major mechanism of horizontal gene transfer mediated by conjugative plasmids and integrating conjugative elements (ICEs). While in most bacterial conjugative systems DNA translocation requires the assembly of a complex type IV secretion system (T4SS), in Actinobacteria a single DNA FtsK/SpoIIIE-like translocation protein is required. To date, the role and diversity of ICEs in Actinobacteria have received little attention. Putative ICEs were searched for in 275 genomes of Actinobacteria using HMM-profiles of proteins involved in ICE maintenance and transfer. These exhaustive analyses revealed 144 putative FtsK/SpoIIIE-type ICEs and 17 putative T4SS-type ICEs. Grouping of the ICEs based on the phylogenetic analyses of maintenance and transfer proteins revealed extensive exchanges between different sub-families of ICEs. 17 ICEs were found in Actinobacteria from the genus Frankia, globally important nitrogen-fixing microorganisms that establish root nodule symbioses with actinorhizal plants. Structural analysis of ICEs from Frankia revealed their unexpected diversity and a vast array of predicted adaptive functions. Frankia ICEs were found to excise by site-specific recombination from their host's chromosome in vitro and in planta suggesting that they are functional mobile elements whether Frankiae live as soil saprophytes or plant endosymbionts. Phylogenetic analyses of proteins involved in ICEs maintenance and transfer suggests that active exchange between ICEs cargo-borne and chromosomal genes took place within the Actinomycetales order. Functionality of Frankia ICEs in vitro as well as in planta lets us anticipate that conjugation and ICEs could allow the development of genetic manipulation tools for this challenging microorganism and for many

  14. The integrative element pSAM2 from Streptomyces: kinetics and mode of conjugal transfer.

    PubMed

    Possoz, C; Ribard, C; Gagnat, J; Pernodet, J L; Guérineau, M

    2001-10-01

    pSAM2 is an 11 kb integrative element from Streptomyces ambofaciens that is capable of conjugal transfer. A system based on differential DNA modification by SalI methyltransferase was used to localize pSAM2 in the donor or recipient strain, and thus to determine the various steps associated with transfer. Initiation (i.e. excision and replication of pSAM2 in the donor) occurs a few hours after mating with a recipient strain. pSAM2 replicates in the recipient strain, spreads within the mycelium and then integrates into the chromosome. Transfer generally involves single-stranded DNA. In Streptomyces, only a few genes, such as traSA for pSAM2, are required for conjugal transfer. Using the differential sensitivity to the SalI restriction-modification system of transfers involving single- and double-stranded DNA, we found that pSAM2 was probably transferred to the recipient as double-stranded DNA. This provides the first experimental evidence for the transfer of double-stranded DNA during bacterial conjugation. Thus, TraSA, involved in pSAM2 transfer, and SpoIIIE, which is involved in chromosome partitioning in Bacillus subtilis, display similarities in both sequence and function: both seem to transport double-stranded DNA actively, either from donor to recipient or from mother cell to prespore.

  15. [Bacterial SXT/R391 family from integrating conjugative elements--a review].

    PubMed

    Luo, Peng; Hu, Chaoqun

    2014-05-04

    SXT/R391 family has the most abundant types and members in integrating conjugative elements (ICE). SXT/ R391 elements are comprised of conservative core genes and genes in variable regions. The functions of conservative core genes of SXT/R391 include integration and excision, self-transfer through conjugation, and regulation of its expression. The genes in the variable regions often encode for drug and heavy metal resistances, forming of biofilm, adjustment of bacterial motility, and toxin-antitoxin systems that prevent SXT/R391 deletion from hosts. Some genes in variable region of SXT/R391 also encode for restriction-modification system, helicase, and endonuclease. The activity of SXT/R391 is positively regulated by activator SetCD, and negatively regulated by repressor SetR. SXT/R391 cannot be easily deleted from the primary donors in the process of transfer. SXT/R391 prevent the acquirement of closely related and homogeneous elements but cannot prevent the acquirement of heterogenetic ICE, which leads to the generation of hybrid ICE under the action of recombination system encoded by SXT/R391 themselves. SXT/R391 have high transferable frequency and wide host range, and until now more than 40 different SXT/R391 elements have been discovered in various bacteria, especially in Vibrio species, which mainly distribute in coastal areas in Asia and Africa. It suggests that marine environments are likely the main reservoir for SXT/R391 and these elements probably spread from marine environmental strains to clinical strains, under increasing selective pressure. Due to the hazard caused by the prevalence and the transfer of SXT/R391, medical microbiologist and health departments should be fully alert to the spread of the elements.

  16. Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded.

    PubMed

    te Poele, Evelien M; Samborskyy, Markiyan; Oliynyk, Markiyan; Leadlay, Peter F; Bolhuis, Henk; Dijkhuizen, Lubbert

    2008-05-01

    Actinomycete integrative and conjugative elements (AICEs) are present in diverse genera of the actinomycetes, the most important bacterial producers of bioactive secondary metabolites. Comparison of pMEA100 of Amycolatopsis mediterranei, pMEA300 of Amycolatopsis methanolica and pSE211 of Saccharopolyspora erythraea, and other AICEs, revealed a highly conserved structural organisation, consisting of four functional modules (replication, excision/integration, regulation, and conjugative transfer). Features conserved in all elements, or specific for a single element, are discussed and analysed. This study also revealed two novel putative AICEs (named pSE222 and pSE102) in the Sac. erythraea genome, related to the previously described pSE211 and pSE101 elements. Interestingly, pSE102 encodes a putative aminoglycoside phosphotransferase which may confer antibiotic resistance to the host. Furthermore, two of the six pSAM2-like insertions in the Streptomyces coelicolor genome described by Bentley et al. [Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., et al., 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141-147] could be functional AICEs. Homologues of various AICE proteins were found in other actinomycetes, in Frankia species and in the obligate marine genus Salinispora and may be part of novel AICEs as well. The data presented provide a better understanding of the origin and evolution of these elements, and their functional properties. Several AICEs are able to mobilise chromosomal markers, suggesting that they play an important role in horizontal gene transfer and spread of antibiotic resistance, but also in evolution of genome plasticity.

  17. SXT/R391 Integrative and Conjugative Elements (ICEs) Encode a Novel ‘Trap-Door’ Strategy for Mobile Element Escape

    PubMed Central

    Ryan, Michael P.; Armshaw, Patricia; Pembroke, J. Tony

    2016-01-01

    Integrative conjugative elements (ICEs) are a class of bacterial mobile elements that have the ability to mediate their own integration, excision, and transfer from one host genome to another by a mechanism of site-specific recombination, self-circularisation, and conjugative transfer. Members of the SXT/R391 ICE family of enterobacterial mobile genetic elements display an unusual UV-inducible sensitization function which results in stress induced killing of bacterial cells harboring the ICE. This sensitization has been shown to be associated with a stress induced overexpression of a mobile element encoded conjugative transfer gene, orf43, a traV homolog. This results in cell lysis and release of a circular form of the ICE. Induction of this novel system may allow transfer of an ICE, enhancing its survival potential under conditions not conducive to conjugative transfer. PMID:27303400

  18. New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration.

    PubMed

    Ambroset, Chloé; Coluzzi, Charles; Guédon, Gérard; Devignes, Marie-Dominique; Loux, Valentin; Lacroix, Thomas; Payot, Sophie; Leblond-Bourget, Nathalie

    2015-01-01

    Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent.

  19. Pathogens of Bovine Respiratory Disease in North American Feedlots Conferring Multidrug Resistance via Integrative Conjugative Elements

    PubMed Central

    Klima, Cassidy L.; Zaheer, Rahat; Cook, Shaun R.; Booker, Calvin W.; Hendrick, Steve

    2014-01-01

    In this study, we determined the prevalence of bovine respiratory disease (BRD)-associated viral and bacterial pathogens in cattle and characterized the genetic profiles, antimicrobial susceptibilities, and nature of antimicrobial resistance determinants in collected bacteria. Nasopharyngeal swab and lung tissue samples from 68 BRD mortalities in Alberta, Canada (n = 42), Texas (n = 6), and Nebraska (n = 20) were screened using PCR for bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus, bovine herpesvirus 1, parainfluenza type 3 virus, Mycoplasma bovis, Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni. Excepting bovine herpesvirus 1, all agents were detected. M. haemolytica (91%) and BVDV (69%) were the most prevalent, with cooccurrence in 63% of the cattle. Isolates of M. haemolytica (n = 55), P. multocida (n = 8), and H. somni (n = 10) from lungs were also collected. Among M. haemolytica isolates, a clonal subpopulation (n = 8) was obtained from a Nebraskan feedlot. All three bacterial pathogens exhibited a high rate of antimicrobial resistance, with 45% exhibiting resistance to three or more antimicrobials. M. haemolytica (n = 18), P. multocida (n = 3), and H. somni (n = 3) from Texas and Nebraska possessed integrative conjugative elements (ICE) that conferred resistance for up to seven different antimicrobial classes. ICE were shown to be transferred via conjugation from P. multocida to Escherichia coli and from M. haemolytica and H. somni to P. multocida. ICE-mediated multidrug-resistant profiles of bacterial BRD pathogens could be a major detriment to many of the therapeutic antimicrobial strategies currently used to control BRD. PMID:24478472

  20. Pathogens of bovine respiratory disease in North American feedlots conferring multidrug resistance via integrative conjugative elements.

    PubMed

    Klima, Cassidy L; Zaheer, Rahat; Cook, Shaun R; Booker, Calvin W; Hendrick, Steve; Alexander, Trevor W; McAllister, Tim A

    2014-02-01

    In this study, we determined the prevalence of bovine respiratory disease (BRD)-associated viral and bacterial pathogens in cattle and characterized the genetic profiles, antimicrobial susceptibilities, and nature of antimicrobial resistance determinants in collected bacteria. Nasopharyngeal swab and lung tissue samples from 68 BRD mortalities in Alberta, Canada (n = 42), Texas (n = 6), and Nebraska (n = 20) were screened using PCR for bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus, bovine herpesvirus 1, parainfluenza type 3 virus, Mycoplasma bovis, Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni. Excepting bovine herpesvirus 1, all agents were detected. M. haemolytica (91%) and BVDV (69%) were the most prevalent, with cooccurrence in 63% of the cattle. Isolates of M. haemolytica (n = 55), P. multocida (n = 8), and H. somni (n = 10) from lungs were also collected. Among M. haemolytica isolates, a clonal subpopulation (n = 8) was obtained from a Nebraskan feedlot. All three bacterial pathogens exhibited a high rate of antimicrobial resistance, with 45% exhibiting resistance to three or more antimicrobials. M. haemolytica (n = 18), P. multocida (n = 3), and H. somni (n = 3) from Texas and Nebraska possessed integrative conjugative elements (ICE) that conferred resistance for up to seven different antimicrobial classes. ICE were shown to be transferred via conjugation from P. multocida to Escherichia coli and from M. haemolytica and H. somni to P. multocida. ICE-mediated multidrug-resistant profiles of bacterial BRD pathogens could be a major detriment to many of the therapeutic antimicrobial strategies currently used to control BRD.

  1. Integrative Conjugative Elements Are Widespread in Field Isolates of Mycoplasma Species Pathogenic for Ruminants

    PubMed Central

    Mick, Virginie; Dordet-Frisoni, Emilie; Marenda, Marc Serge; Sirand-Pugnet, Pascal; Blanchard, Alain

    2014-01-01

    Comparative genomics have revealed massive horizontal gene transfer (HGT) between Mycoplasma species sharing common ruminant hosts. Further results pointed toward an integrative conjugative element (ICE) as an important contributor of HGT in the small-ruminant-pathogen Mycoplasma agalactiae. To estimate the prevalence of ICEs in ruminant mycoplasmas, we surveyed their occurrence in a collection of 166 field strains representing 4 (sub)species that are recognized as major pathogens. Based on available sequenced genomes, we first defined the conserved, minimal ICE backbone as composed of 4 coding sequences (CDSs) that are evenly distributed and predicted to be essential for ICE chromosomal integration-excision and horizontal transfer. Screening of the strain collection revealed that these 4 CDSs are well represented in ruminant Mycoplasma species, suggesting widespread occurrence of ICEs. Yet their prevalence varies within and among species, with no correlation found with the individual strain history. Extrachromosomal ICE forms were also often detected, suggesting that ICEs are able to circularize in all species, a first and essential step in ICE horizontal transfer. Examination of the junction of the circular forms and comparative sequence analysis of conserved CDSs clearly pointed toward two types of ICE, the hominis and spiroplasma types, most likely differing in their mechanism of excision-integration. Overall, our data indicate the occurrence and maintenance of functional ICEs in a large number of field isolates of ruminant mycoplasmas. These may contribute to genome plasticity and gene exchanges and, presumably, to the emergence of diverse genotypes within pathogenic mycoplasmas of veterinary importance. PMID:25527550

  2. Integrative conjugative elements are widespread in field isolates of Mycoplasma species pathogenic for ruminants.

    PubMed

    Tardy, Florence; Mick, Virginie; Dordet-Frisoni, Emilie; Marenda, Marc Serge; Sirand-Pugnet, Pascal; Blanchard, Alain; Citti, Christine

    2015-03-01

    Comparative genomics have revealed massive horizontal gene transfer (HGT) between Mycoplasma species sharing common ruminant hosts. Further results pointed toward an integrative conjugative element (ICE) as an important contributor of HGT in the small-ruminant-pathogen Mycoplasma agalactiae. To estimate the prevalence of ICEs in ruminant mycoplasmas, we surveyed their occurrence in a collection of 166 field strains representing 4 (sub)species that are recognized as major pathogens. Based on available sequenced genomes, we first defined the conserved, minimal ICE backbone as composed of 4 coding sequences (CDSs) that are evenly distributed and predicted to be essential for ICE chromosomal integration-excision and horizontal transfer. Screening of the strain collection revealed that these 4 CDSs are well represented in ruminant Mycoplasma species, suggesting widespread occurrence of ICEs. Yet their prevalence varies within and among species, with no correlation found with the individual strain history. Extrachromosomal ICE forms were also often detected, suggesting that ICEs are able to circularize in all species, a first and essential step in ICE horizontal transfer. Examination of the junction of the circular forms and comparative sequence analysis of conserved CDSs clearly pointed toward two types of ICE, the hominis and spiroplasma types, most likely differing in their mechanism of excision-integration. Overall, our data indicate the occurrence and maintenance of functional ICEs in a large number of field isolates of ruminant mycoplasmas. These may contribute to genome plasticity and gene exchanges and, presumably, to the emergence of diverse genotypes within pathogenic mycoplasmas of veterinary importance.

  3. Worldwide Occurrence of Integrative Conjugative Element Encoding Multidrug Resistance Determinants in Epidemic Vibrio cholerae O1

    PubMed Central

    Marin, Michel A.; Fonseca, Erica L.; Andrade, Bruno N.; Cabral, Adriana C.; Vicente, Ana Carolina P.

    2014-01-01

    In the last decades, there has been an increase of cholera epidemics caused by multidrug resistant strains. Particularly, the integrative and conjugative element (ICE) seems to play a major role in the emergence of multidrug resistant Vibrio cholerae. This study fully characterized, by whole genome sequencing, new ICEs carried by multidrug resistant V. cholerae O1 strains from Nigeria (2010) (ICEVchNig1) and Nepal (1994) (ICEVchNep1). The gene content and gene order of these two ICEs are the same, and identical to ICEVchInd5, ICEVchBan5 and ICEVchHai1 previously identified in multidrug resistant V. cholerae O1. This ICE is characterized by dfrA1, sul2, strAB and floR antimicrobial resistance genes, and by unique gene content in HS4 and HS5 ICE regions. Screening for ICEs, in publicly available V. cholerae genomes, revealed the occurrence and widespread distribution of this ICE among V. cholerae O1. Metagenomic analysis found segments of this ICE in marine environments far from the direct influence of the cholera epidemic. Therefore, this study revealed the epidemiology of a spatio-temporal prevalent ICE in V. cholerae O1. Its occurrence and dispersion in V. cholerae O1 strains from different continents throughout more than two decades can be indicative of its role in the fitness of the current pandemic lineage. PMID:25265418

  4. Modular Evolution of TnGBSs, a New Family of Integrative and Conjugative Elements Associating Insertion Sequence Transposition, Plasmid Replication, and Conjugation for Their Spreading

    PubMed Central

    Guérillot, Romain; Da Cunha, Violette; Sauvage, Elisabeth; Bouchier, Christiane

    2013-01-01

    Integrative and conjugative elements (ICEs) have a major impact on gene flow and genome dynamics in bacteria. The ICEs TnGBS1 and TnGBS2, first identified in Streptococcus agalactiae, use a DDE transposase, unlike most characterized ICEs, which depend on a phage-like integrase for their mobility. Here we identified 56 additional TnGBS-related ICEs by systematic genome analysis. Interestingly, all except one are inserted in streptococcal genomes. Sequence comparison of the proteins conserved among these ICEs defined two subtypes related to TnGBS1 or TnGBS2. We showed that both types encode different conjugation modules: a type IV secretion system, a VirD4 coupling protein, and a relaxase and its cognate oriT site, shared with distinct lineages of conjugative elements of Firmicutes. Phylogenetic analysis suggested that TnGBSs evolved from two conjugative elements of different origins by the successive recruitment of a transposition module derived from insertion sequences (ISs). Furthermore, TnGBSs share replication modules with different plasmids. Mutational analyses and conjugation experiments showed that TnGBS1 and TnGBS2 combine replication and transposition upstream promoters for their transfer and stabilization. Despite an evolutionarily successful horizontal dissemination within the genus Streptococcus, these ICEs have a restricted host range. However, we reveal that for TnGBS1 and TnGBS2, this host restriction is not due to a transfer incompatibility linked to the conjugation machineries but most likely to their ability for transient maintenance through replication after their transfer. PMID:23435978

  5. Modular evolution of TnGBSs, a new family of integrative and conjugative elements associating insertion sequence transposition, plasmid replication, and conjugation for their spreading.

    PubMed

    Guérillot, Romain; Da Cunha, Violette; Sauvage, Elisabeth; Bouchier, Christiane; Glaser, Philippe

    2013-05-01

    Integrative and conjugative elements (ICEs) have a major impact on gene flow and genome dynamics in bacteria. The ICEs TnGBS1 and TnGBS2, first identified in Streptococcus agalactiae, use a DDE transposase, unlike most characterized ICEs, which depend on a phage-like integrase for their mobility. Here we identified 56 additional TnGBS-related ICEs by systematic genome analysis. Interestingly, all except one are inserted in streptococcal genomes. Sequence comparison of the proteins conserved among these ICEs defined two subtypes related to TnGBS1 or TnGBS2. We showed that both types encode different conjugation modules: a type IV secretion system, a VirD4 coupling protein, and a relaxase and its cognate oriT site, shared with distinct lineages of conjugative elements of Firmicutes. Phylogenetic analysis suggested that TnGBSs evolved from two conjugative elements of different origins by the successive recruitment of a transposition module derived from insertion sequences (ISs). Furthermore, TnGBSs share replication modules with different plasmids. Mutational analyses and conjugation experiments showed that TnGBS1 and TnGBS2 combine replication and transposition upstream promoters for their transfer and stabilization. Despite an evolutionarily successful horizontal dissemination within the genus Streptococcus, these ICEs have a restricted host range. However, we reveal that for TnGBS1 and TnGBS2, this host restriction is not due to a transfer incompatibility linked to the conjugation machineries but most likely to their ability for transient maintenance through replication after their transfer.

  6. Comparative genomic analysis of six new-found integrative conjugative elements (ICEs) in Vibrio alginolyticus.

    PubMed

    Luo, Peng; He, Xiangyan; Wang, Yanhong; Liu, Qiuting; Hu, Chaoqun

    2016-05-04

    Vibrio alginolyticus is ubiquitous in marine and estuarine environments. In 2012-2013, SXT/R391-like integrative conjugative elements (ICEs) in environmental V. alginolyticus strains were discovered and found to occur in 8.9 % of 192 V. alginolyticus strains, which suggests that V. alginolyticus may be a natural pool possessing resourceful ICEs. However, complete ICE sequences originating from this bacterium have not been reported, which represents a significant barrier to characterizing the ICEs of this bacterium and exploring their relationships with other ICEs. In the present study, we acquired six ICE sequences from five V. alginolyticus strains and performed a comparative analysis of these ICE genomes. A sequence analysis showed that there were only 14 variable bases dispersed between ICEValE0601 and ICEValHN492. ICEValE0601 and ICEValHN492 were treated as the same ICE. ICEValA056-1, ICEValE0601 and ICEValHN492 integrate into the 5' end of the host's prfC gene, and their Int and Xis share at least 97 % identity with their counterparts from SXT. ICEValE0601 or ICEValHN492 contain 50 of 52 conserved core genes in the SXT/R391 ICEs (not s025 or s026). ICEValA056-2, ICEValHN396 and ICEValHN437 have a different tRNA-ser integration site and a distinct int/xis module; however, the remaining backbone genes are highly similar to their counterparts in SXT/R391 ICEs. DNA sequences inserted into hotspot and variable regions of the ICEs are of various sizes. The variable genes of six ICEs encode a large array of functions to bestow various adaptive abilities upon their hosts, and only ICEValA056-1 contains drug-resistant genes. Many variable genes have orthologous and functionally related genes to those found in SXT/R391 ICEs, such as genes coding for a toxin-antitoxin system, a restriction-modification system, helicases and endonucleases. Six ICEs also contain a large number of unique genes or gene clusters that were not found in other ICEs. Six ICEs harbor more abundant

  7. Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis.

    PubMed

    De Maayer, Pieter; Chan, Wai-Yin; Martin, Douglas A J; Blom, Jochen; Venter, Stephanus N; Duffy, Brion; Cowan, Don A; Smits, Theo H M; Coutinho, Teresa A

    2015-01-01

    Pantoea ananatis is a highly versatile enterobacterium isolated from diverse environmental sources. The ecological diversity of this species may be attributed, in part, to the acquisition of mobile genetic elements. One such element is an Integrative and Conjugative Element (ICE). By means of in silico analyses the ICE elements belonging to a novel family, ICEPan, were identified in the genome sequences of five P. ananatis strains and characterized. PCR screening showed that ICEPan is prevalent among P. ananatis strains isolated from different environmental sources and geographic locations. Members of the ICEPan family share a common origin with ICEs of other enterobacteria, as well as conjugative plasmids of Erwinia spp. Aside from core modules for ICEPan integration, maintenance and dissemination, the ICEPan contain extensive non-conserved islands coding for proteins that may contribute toward various phenotypes such as stress response and antibiosis, and the highly diverse ICEPan thus plays a major role in the diversification of P. ananatis. An island is furthermore integrated within an ICEPan DNA repair-encoding locus umuDC and we postulate its role in stress-induced dissemination and/or expression of the genes on this island.

  8. The Bacteroides thetaiotaomicron Protein Bacteroides Host Factor A Participates in Integration of the Integrative Conjugative Element CTnDOT into the Chromosome

    PubMed Central

    Ringwald, Kenneth

    2015-01-01

    ABSTRACT CTnDOT is a conjugative transposon found in Bacteroides species. It encodes multiple antibiotic resistances and is stimulated to transfer by exposure to tetracycline. CTnDOT integration into the host chromosome requires IntDOT and a previously unknown host factor. We have identified a protein, designated BHFa (Bacteroides host factor A), that participates in integrative recombination. BHFa is the first host factor identified for a site-specific recombination reaction in the CTnDOT family of integrative and conjugative elements. Based on the amino acid sequence of BHFa, the ability to bind specifically to 4 sites in the attDOT DNA, and its activity in the integration reaction, BHFa is a member of the IHF/HU family of nucleoid-associated proteins. Other DNA bending proteins that bind DNA nonspecifically can substitute for BHFa in the integration reaction. IMPORTANCE Bacteroides species are normal members of the human colonic microbiota. These species can harbor and spread self-transmissible genetic elements (integrative conjugative elements [ICEs]) that contain antibiotic resistance genes. This work describes the role of a protein, BHFa, and its importance in the integration reaction required for the element CTnDOT to persist in Bacteroides host cells. PMID:25645562

  9. The Bacteroides thetaiotaomicron protein Bacteroides host factor A participates in integration of the integrative conjugative element CTnDOT into the chromosome.

    PubMed

    Ringwald, Kenneth; Gardner, Jeffrey

    2015-04-01

    CTnDOT is a conjugative transposon found in Bacteroides species. It encodes multiple antibiotic resistances and is stimulated to transfer by exposure to tetracycline. CTnDOT integration into the host chromosome requires IntDOT and a previously unknown host factor. We have identified a protein, designated BHFa (Bacteroides host factor A), that participates in integrative recombination. BHFa is the first host factor identified for a site-specific recombination reaction in the CTnDOT family of integrative and conjugative elements. Based on the amino acid sequence of BHFa, the ability to bind specifically to 4 sites in the attDOT DNA, and its activity in the integration reaction, BHFa is a member of the IHF/HU family of nucleoid-associated proteins. Other DNA bending proteins that bind DNA nonspecifically can substitute for BHFa in the integration reaction. Bacteroides species are normal members of the human colonic microbiota. These species can harbor and spread self-transmissible genetic elements (integrative conjugative elements [ICEs]) that contain antibiotic resistance genes. This work describes the role of a protein, BHFa, and its importance in the integration reaction required for the element CTnDOT to persist in Bacteroides host cells. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  10. ICEApl1, an Integrative Conjugative Element Related to ICEHin1056, Identified in the Pig Pathogen Actinobacillus pleuropneumoniae.

    PubMed

    Bossé, Janine T; Li, Yanwen; Fernandez Crespo, Roberto; Chaudhuri, Roy R; Rogers, Jon; Holden, Matthew T G; Maskell, Duncan J; Tucker, Alexander W; Wren, Brendan W; Rycroft, Andrew N; Langford, Paul R

    2016-01-01

    ICEApl1 was identified in the whole genome sequence of MIDG2331, a tetracycline-resistant (MIC = 8 mg/L) serovar 8 clinical isolate of Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia. PCR amplification of virB4, one of the core genes involved in conjugation, was used to identify other A. pleuropneumoniae isolates potentially carrying ICEApl1. MICs for tetracycline were determined for virB4 positive isolates, and shotgun whole genome sequence analysis was used to confirm presence of the complete ICEApl1. The sequence of ICEApl1 is 56083 bp long and contains 67 genes including a Tn10 element encoding tetracycline resistance. Comparative sequence analysis was performed with similar integrative conjugative elements (ICEs) found in other members of the Pasteurellaceae. ICEApl1 is most similar to the 59393 bp ICEHin1056, from Haemophilus influenzae strain 1056. Although initially identified only in serovar 8 isolates of A. pleuropneumoniae (31 from the UK and 1 from Cyprus), conjugal transfer of ICEApl1 to representative isolates of other serovars was confirmed. All isolates carrying ICEApl1 had a MIC for tetracycline of 8 mg/L. This is, to our knowledge, the first description of an ICE in A. pleuropneumoniae, and the first report of a member of the ICEHin1056 subfamily in a non-human pathogen. ICEApl1 confers resistance to tetracycline, currently one of the more commonly used antibiotics for treatment and control of porcine pleuropneumonia.

  11. ICEApl1, an Integrative Conjugative Element Related to ICEHin1056, Identified in the Pig Pathogen Actinobacillus pleuropneumoniae

    PubMed Central

    Bossé, Janine T.; Li, Yanwen; Fernandez Crespo, Roberto; Chaudhuri, Roy R.; Rogers, Jon; Holden, Matthew T. G.; Maskell, Duncan J.; Tucker, Alexander W.; Wren, Brendan W.; Rycroft, Andrew N.; Langford, Paul R.

    2016-01-01

    ICEApl1 was identified in the whole genome sequence of MIDG2331, a tetracycline-resistant (MIC = 8 mg/L) serovar 8 clinical isolate of Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia. PCR amplification of virB4, one of the core genes involved in conjugation, was used to identify other A. pleuropneumoniae isolates potentially carrying ICEApl1. MICs for tetracycline were determined for virB4 positive isolates, and shotgun whole genome sequence analysis was used to confirm presence of the complete ICEApl1. The sequence of ICEApl1 is 56083 bp long and contains 67 genes including a Tn10 element encoding tetracycline resistance. Comparative sequence analysis was performed with similar integrative conjugative elements (ICEs) found in other members of the Pasteurellaceae. ICEApl1 is most similar to the 59393 bp ICEHin1056, from Haemophilus influenzae strain 1056. Although initially identified only in serovar 8 isolates of A. pleuropneumoniae (31 from the UK and 1 from Cyprus), conjugal transfer of ICEApl1 to representative isolates of other serovars was confirmed. All isolates carrying ICEApl1 had a MIC for tetracycline of 8 mg/L. This is, to our knowledge, the first description of an ICE in A. pleuropneumoniae, and the first report of a member of the ICEHin1056 subfamily in a non-human pathogen. ICEApl1 confers resistance to tetracycline, currently one of the more commonly used antibiotics for treatment and control of porcine pleuropneumonia. PMID:27379024

  12. Structure, Diversity, and Mobility of the Salmonella Pathogenicity Island 7 Family of Integrative and Conjugative Elements within Enterobacteriaceae

    PubMed Central

    Seth-Smith, Helena M. B.; Fookes, Maria C.; Okoro, Chinyere K.; Baker, Stephen; Harris, Simon R.; Scott, Paul; Pickard, Derek; Quail, Michael A.; Churcher, Carol; Sanders, Mandy; Harmse, Johan; Dougan, Gordon; Parkhill, Julian

    2012-01-01

    Integrative and conjugative elements (ICEs) are self-mobile genetic elements found in the genomes of some bacteria. These elements may confer a fitness advantage upon their host bacteria through the cargo genes that they carry. Salmonella pathogenicity island 7 (SPI-7), found within some pathogenic strains of Salmonella enterica, possesses features indicative of an ICE and carries genes implicated in virulence. We aimed to identify and fully analyze ICEs related to SPI-7 within the genus Salmonella and other Enterobacteriaceae. We report the sequence of two novel SPI-7-like elements, found within strains of Salmonella bongori, which share 97% nucleotide identity over conserved regions with SPI-7 and with each other. Although SPI-7 within Salmonella enterica serovar Typhi appears to be fixed within the chromosome, we present evidence that these novel elements are capable of excision and self-mobility. Phylogenetic analyses show that these Salmonella mobile elements share an ancestor which existed approximately 3.6 to 15.8 million years ago. Additionally, we identified more distantly related ICEs, with distinct cargo regions, within other strains of Salmonella as well as within Citrobacter, Erwinia, Escherichia, Photorhabdus, and Yersinia species. In total, we report on a collection of 17 SPI-7 related ICEs within enterobacterial species, of which six are novel. Using comparative and mutational studies, we have defined a core of 27 genes essential for conjugation. We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae. PMID:22247511

  13. SXT-related integrating conjugative element and IncC plasmids in Vibrio cholerae O1 strains in Eastern Africa.

    PubMed

    Pugliese, N; Maimone, F; Scrascia, M; Materu, S F; Pazzani, Carlo

    2009-03-01

    The objective of this study was to investigate the extent of resistance patterns and associated mobile genetic elements in epidemic V. cholerae O1 El Tor strains isolated from Eastern Africa in the late 1990s. Self-transmissible genetic elements and associated clusters of genes encoding resistance were detected by conjugation experiments. Detection of SXT-related integrating conjugative elements (ICEs) and associated antibiotic resistance genes was performed by PCR to amplify the SXT element-integrase gene (int), right SXT element-chromosome junction (attP-prfC) and genes conferring resistance to chloramphenicol (floR), sulfamethoxazole (sulII), streptomycin (strA) and trimethoprim (dfrA1). Genomic relatedness was established by random amplified polymorphic DNA patterns. Of 224 strains analysed, 200 isolates exhibited resistance to four or more antimicrobials. An IncC plasmid, encoding resistance to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole and trimethoprim, conferred multidrug resistance to 113 strains isolated from Somalia and Ethiopia, whereas an SXT-related ICE, encoding resistance to chloramphenicol, streptomycin, sulfamethoxazole and trimethoprim, conferred multidrug resistance to 74 strains isolated from Sudan, Kenya and Tanzania. This study has shown the spread of SXT-related ICEs among V. cholerae O1 African isolates. It has also highlighted the role of two distinct genetic elements in conferring multiple resistance to the two distinct groups of V. cholerae O1 strains that, in the late 1990s, spread through Eastern Africa, a critical geographic region for the persistence and transmission of cholera to the entire continent.

  14. The ICEXTD of Azoarcus sp. CIB, an integrative and conjugative element with aerobic and anaerobic catabolic properties.

    PubMed

    Zamarro, María Teresa; Martín-Moldes, Zaira; Díaz, Eduardo

    2016-12-01

    Integrative and conjugative elements (ICE) play a major role in aerobic degradation of aromatic compounds, but they have not yet been shown to be involved in anaerobic degradation. We have characterized here the ICEXTD element which endows to the beta-proteobacterium Azoarcus sp. CIB with the ability to utilize aromatic hydrocarbons. The core region of ICEXTD , which shows a remarkable synteny with that of ICEclc-like elements, allows its own intracellular and intercellular mobility. ICEXTD integrates at the tRNAGly of the host chromosome, but it can also excise to produce a ready to transfer circular form. The adaptation modules of ICEXTD represent a unique combination of gene clusters for aerobic (tod genes) and anaerobic (bss-bbs and mbd genes) degradation of certain aromatic hydrocarbons, e.g., toluene, m-xylene and cumene. Transfer of ICEXTD to other Azoarcus strains, e.g., A. evansii, confers them the ability to degrade aromatic hydrocarbons both aerobically and anaerobically. Interestingly, ICEXTD allows Cupriavidus pinatubonensis, a bacterium unable to degrade anaerobically aromatic compounds, to grow with m-xylene under anoxic conditions. Thus, ICEXTD constitutes the first mobile genetic element able to expand the catabolic abilities of certain bacteria for the removal of aromatic hydrocarbons either in the presence or absence of oxygen. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  15. Characterization of a new CAMP factor carried by an integrative and conjugative element in Streptococcus agalactiae and spreading in Streptococci.

    PubMed

    Chuzeville, Sarah; Puymège, Aurore; Madec, Jean-Yves; Haenni, Marisa; Payot, Sophie

    2012-01-01

    Genetic exchanges between Streptococci occur frequently and contribute to their genome diversification. Most of sequenced streptococcal genomes carry multiple mobile genetic elements including Integrative and Conjugative Elements (ICEs) that play a major role in these horizontal gene transfers. In addition to genes involved in their mobility and regulation, ICEs also carry genes that can confer selective advantages to bacteria. Numerous elements have been described in S. agalactiae especially those integrated at the 3' end of a tRNA(Lys) encoding gene. In strain 515 of S. agalactiae, an invasive neonate human pathogen, the ICE (called 515_tRNA(Lys)) is functional and carries different putative virulence genes including one encoding a putative new CAMP factor in addition to the one previously described. This work demonstrated the functionality of this CAMP factor (CAMP factor II) in Lactococcus lactis but also in pathogenic strains of veterinary origin. The search for co-hemolytic factors in a collection of field strains revealed their presence in S. uberis, S. dysgalactiae, but also for the first time in S. equisimilis and S. bovis. Sequencing of these genes revealed the prevalence of a species-specific factor in S. uberis strains (Uberis factor) and the presence of a CAMP factor II encoding gene in S. bovis and S. equisimilis. Furthermore, most of the CAMP factor II positive strains also carried an element integrated in the tRNA(Lys) gene. This work thus describes a CAMP factor that is carried by a mobile genetic element and has spread to different streptococcal species.

  16. SXT/R391 integrative and conjugative elements in Proteus species reveal abundant genetic diversity and multidrug resistance

    PubMed Central

    Li, Xinyue; Du, Yu; Du, Pengcheng; Dai, Hang; Fang, Yujie; Li, Zhenpeng; Lv, Na; Zhu, Baoli; Kan, Biao; Wang, Duochun

    2016-01-01

    SXT/R391 integrative and conjugative elements (ICEs) are self-transmissible mobile genetic elements that are found in most members of Enterobacteriaceae. Here, we determined fifteen SXT/R391 ICEs carried by Proteus isolates from food (4.2%) and diarrhoea patients (17.3%). BLASTn searches against GenBank showed that the fifteen SXT/R391 ICEs were closely related to that from different Enterobacteriaceae species, including Proteus mirabilis. Using core gene phylogenetic analysis, the fifteen SXT/R391 ICEs were grouped into six distinct clusters, including a dominant cluster and three clusters that have not been previously reported in Proteus isolates. The SXT/R391 ICEs shared a common structure with a set of conserved genes, five hotspots and two variable regions, which contained more foreign genes, including drug-resistance genes. Notably, a class A β-lactamase gene was identified in nine SXT/R391 ICEs. Collectively, the ICE-carrying isolates carried resistance genes for 20 tested drugs. Six isolates were resistant to chloramphenicol, kanamycin, streptomycin, trimethoprim-sulfamethoxazole, sulfisoxazole and tetracycline, which are drug resistances commonly encoded by ICEs. Our results demonstrate abundant genetic diversity and multidrug resistance of the SXT/R391 ICEs carried by Proteus isolates, which may have significance for public health. It is therefore necessary to continuously monitor the antimicrobial resistance and related mobile elements among Proteus isolates. PMID:27892525

  17. Integrating conjugative elements as vectors of antibiotic, mercury, and quaternary ammonium compound resistance in marine aquaculture environments.

    PubMed

    Rodríguez-Blanco, Arturo; Lemos, Manuel L; Osorio, Carlos R

    2012-05-01

    The presence of SXT/R391-related integrating conjugative elements (ICEs) in bacterial strains isolated from fish obtained from marine aquaculture environments in 2001 to 2010 in the northwestern Iberian Peninsula was studied. ICEs were detected in 12 strains taxonomically related to Vibrio scophthalmi (3 strains), Vibrio splendidus (5 strains), Vibrio alginolyticus (1 strain), Shewanella haliotis (1 strain), and Enterovibrio nigricans (2 strains), broadening the known host range able to harbor SXT/R391-like ICEs. Variable DNA regions, which confer element-specific properties to ICEs of this family, were characterized. One of the ICEs encoded antibiotic resistance functions in variable region III, consisting of a tetracycline resistance locus. Interestingly, hot spot 4 included genes providing resistance to rifampin (ICEVspPor2 and ICEValPor1) and quaternary ammonium compounds (QACs) (ICEEniSpa1), and variable region IV included a mercury resistance operon (ICEVspSpa1 and ICEEniSpa1). The S exclusion group was more represented than the R exclusion group, accounting for two-thirds of the total ICEs. Mating experiments allowed ICE mobilization to Escherichia coli strains, showing the corresponding transconjugants' rifampin, mercury, and QAC resistance. These results show the first evidence of ICEs providing rifampin and QAC resistances, suggesting that these mobile genetic elements contribute to the dissemination of antimicrobial, heavy metal, and QAC resistance determinants in aquaculture environments.

  18. Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons.

    PubMed

    Taviani, Elisa; Ceccarelli, Daniela; Lazaro, Nivalda; Bani, Stefania; Cappuccinelli, Piero; Colwell, Rita R; Colombo, Mauro M

    2008-04-01

    Circulation of mobile genetic elements linked to drug resistance spread was studied in Vibrio strains isolated from surface urban water (river and sea) and shellfish samples in 2002-2003 in Maputo, Mozambique. Class 1 integrons and integrating conjugative elements (ICE) were investigated by PCR and mating experiments in strains of major health interest: 10 Vibrio cholerae, six Vibrio parahaemolyticus, two Vibrio alginolyticus and one Vibrio fluvialis. Resistance to at least two antibiotics (predominantly beta-lactams) was detected in all the strains, with additional resistances to sulfamethoxazole, spectinomycin, streptomycin and/or trimethoprim. Class 1 integrons contributed partially to the expression of drug resistance and were found in five isolates: four V. cholerae (blaP1 cassette, one strain also contained the dfrA15 cassette) and one V. alginolyticus (aadA2 cassette). ICEs, apparently devoid of resistance genes, were found in eight V. cholerae, three V. parahaemolyticus and one V. fluvialis isolates. A wide variability was observed by molecular characterization of ICEs. Five ICEs were included in the SXT/R391 family and seven ICEs were not classified. Our results indicate that the SXT/R391 family and related ICEs comprise a large class of polymorphic genetic elements widely circulating in environmental Vibrio strains in Africa, beside those evidently linked to drug resistance in clinical isolates.

  19. Integrating Conjugative Elements as Vectors of Antibiotic, Mercury, and Quaternary Ammonium Compound Resistance in Marine Aquaculture Environments

    PubMed Central

    Rodríguez-Blanco, Arturo; Lemos, Manuel L.

    2012-01-01

    The presence of SXT/R391-related integrating conjugative elements (ICEs) in bacterial strains isolated from fish obtained from marine aquaculture environments in 2001 to 2010 in the northwestern Iberian Peninsula was studied. ICEs were detected in 12 strains taxonomically related to Vibrio scophthalmi (3 strains), Vibrio splendidus (5 strains), Vibrio alginolyticus (1 strain), Shewanella haliotis (1 strain), and Enterovibrio nigricans (2 strains), broadening the known host range able to harbor SXT/R391-like ICEs. Variable DNA regions, which confer element-specific properties to ICEs of this family, were characterized. One of the ICEs encoded antibiotic resistance functions in variable region III, consisting of a tetracycline resistance locus. Interestingly, hot spot 4 included genes providing resistance to rifampin (ICEVspPor2 and ICEValPor1) and quaternary ammonium compounds (QACs) (ICEEniSpa1), and variable region IV included a mercury resistance operon (ICEVspSpa1 and ICEEniSpa1). The S exclusion group was more represented than the R exclusion group, accounting for two-thirds of the total ICEs. Mating experiments allowed ICE mobilization to Escherichia coli strains, showing the corresponding transconjugants' rifampin, mercury, and QAC resistance. These results show the first evidence of ICEs providing rifampin and QAC resistances, suggesting that these mobile genetic elements contribute to the dissemination of antimicrobial, heavy metal, and QAC resistance determinants in aquaculture environments. PMID:22314526

  20. Conjugal immunity of Streptomyces strains carrying the integrative element pSAM2 is due to the pif gene (pSAM2 immunity factor).

    PubMed

    Possoz, Christophe; Gagnat, Josette; Sezonov, Guennadi; Guérineau, Michel; Pernodet, Jean-Luc

    2003-03-01

    Mechanisms of conjugal immunity preventing redundant exchange between two cells harbouring the same conjugative element have been reported in diverse bacteria. Such a system does exist for pSAM2, a conjugative and integrative element of Streptomyces. The apparition of the conjugative free form of pSAM2 in the donor strain during mating can be considered as the initial step of transfer. We analysed the genes involved in transfer inhibition by mating donors harbouring pSAM2 with recipient strains containing different regions of pSAM2. The conjugal immunity was previously thought to be mediated by the transcriptional repressor KorSA. Although the transfer efficiency is reduced by its presence in the recipient, the initiation of the transfer process is not affected. In contrast, the presence in the recipient strain of a single pSAM2 gene, pif (pSAM2 immunity factor), was sufficient to abolish both transfer and initiation of transfer. Thus, the clustered genes korSA and pif act complementarily to maintain pSAM2 in a 'prophage' state under non-conjugal conditions. KorSA is involved in intracellular signalling, whereas Pif participates in intercellular signalling. The Pif nudix motif is essential for its activity. This is the first protein of the nudix family shown to be involved in bacterial conjugation.

  1. Diversity and Evolution of the Tn5801-tet(M)-Like Integrative and Conjugative Elements among Enterococcus, Streptococcus, and Staphylococcus

    PubMed Central

    León-Sampedro, Ricardo; Novais, Carla; Peixe, Luísa; Baquero, Fernando

    2016-01-01

    This work describes the diversity and evolution of Tn5801 among enterococci, staphylococci, and streptococci based on analysis of the 5,073 genomes of these bacterial groups available in gene databases. We also examined 610 isolates of Enterococcus (from 10 countries, 1987 to 2010) for the presence of this and other known CTn-tet(M) elements due to the scarcity of data about Tn5801 among enterococci. Genome location (by ICeu-I–pulsed-field gel electrophoresis [PFGE] hybridization/integration site identification), conjugation and fitness (by standard methods), Tn5801 characterization (by long-PCR mapping/sequencing), and clonality (by PFGE/multilocus sequence typing [MLST]) were studied. Twenty-three Tn5801 variants (17 unpublished) clustered in two groups, designated “A” (25 kb; n = 14; predominant in Staphylococcus aureus) and “B” (20 kb; n = 9; predominant in Streptococcus agalactiae). The percent GC content of the common backbone suggests a streptococcal origin of Tn5801 group B, with further acquisition of a 5-kb fragment that resulted in group A. Deep sequence analysis allowed identification of variants associated with clonal lineages of S. aureus (clonal complex 8 [CC8], sequence type 239 [ST239]), S. agalactiae (CC17), Enterococcus faecium (ST17/ST18), or Enterococcus faecalis (ST8), local variants, or variants located in different species and geographical areas. All Tn5801 elements were chromosomally located upstream of the guaA gene, which serves as an integration hot spot. Transferability was demonstrated only for Tn5801 type B among E. faecalis clonal backgrounds, which eventually harbored another Tn5801 copy. The study documents early acquisition of Tn5801 by Enterococcus, Staphylococcus, and Streptococcus. Clonal waves of these pathogens seem to have contributed to the geographical spread and local evolution of the transposon. Horizontal transfer, also demonstrated, could explain the variability observed, with the isolates often containing

  2. Diversity and Evolution of the Tn5801-tet(M)-Like Integrative and Conjugative Elements among Enterococcus, Streptococcus, and Staphylococcus.

    PubMed

    León-Sampedro, Ricardo; Novais, Carla; Peixe, Luísa; Baquero, Fernando; Coque, Teresa M

    2016-01-04

    This work describes the diversity and evolution of Tn5801 among enterococci, staphylococci, and streptococci based on analysis of the 5,073 genomes of these bacterial groups available in gene databases. We also examined 610 isolates of Enterococcus (from 10 countries, 1987 to 2010) for the presence of this and other known CTn-tet(M) elements due to the scarcity of data about Tn5801 among enterococci. Genome location (by ICeu-I-pulsed-field gel electrophoresis [PFGE] hybridization/integration site identification), conjugation and fitness (by standard methods), Tn5801 characterization (by long-PCR mapping/sequencing), and clonality (by PFGE/multilocus sequence typing [MLST]) were studied. Twenty-three Tn5801 variants (17 unpublished) clustered in two groups, designated "A" (25 kb; n = 14; predominant in Staphylococcus aureus) and "B" (20 kb; n = 9; predominant in Streptococcus agalactiae). The percent GC content of the common backbone suggests a streptococcal origin of Tn5801 group B, with further acquisition of a 5-kb fragment that resulted in group A. Deep sequence analysis allowed identification of variants associated with clonal lineages of S. aureus (clonal complex 8 [CC8], sequence type 239 [ST239]), S. agalactiae (CC17), Enterococcus faecium (ST17/ST18), or Enterococcus faecalis (ST8), local variants, or variants located in different species and geographical areas. All Tn5801 elements were chromosomally located upstream of the guaA gene, which serves as an integration hot spot. Transferability was demonstrated only for Tn5801 type B among E. faecalis clonal backgrounds, which eventually harbored another Tn5801 copy. The study documents early acquisition of Tn5801 by Enterococcus, Staphylococcus, and Streptococcus. Clonal waves of these pathogens seem to have contributed to the geographical spread and local evolution of the transposon. Horizontal transfer, also demonstrated, could explain the variability observed, with the isolates often containing sequences of

  3. High Prevalence of SXT/R391-Related Integrative and Conjugative Elements Carrying blaCMY-2 in Proteus mirabilis Isolates from Gulls in the South of France.

    PubMed

    Aberkane, Salim; Compain, Fabrice; Decré, Dominique; Dupont, Chloé; Laurens, Chrislène; Vittecoq, Marion; Pantel, Alix; Solassol, Jérôme; Carrière, Christian; Renaud, François; Brieu, Nathalie; Lavigne, Jean-Philippe; Bouzinbi, Nicolas; Ouédraogo, Abdoul-Salam; Jean-Pierre, Hélène; Godreuil, Sylvain

    2016-02-01

    The genetic structures involved in the dissemination of blaCMY-2 carried by Proteus mirabilis isolates recovered from different gull species in the South of France were characterized and compared to clinical isolates. blaCMY-2 was identified in P. mirabilis isolates from 27/93 yellow-legged gulls and from 37/65 slender-billed gulls. It was carried by a conjugative SXT/R391-like integrative and conjugative element (ICE) in all avian strains and in 3/7 human strains. Two clinical isolates had the same genetic background as six avian isolates.

  4. High Prevalence of SXT/R391-Related Integrative and Conjugative Elements Carrying blaCMY-2 in Proteus mirabilis Isolates from Gulls in the South of France

    PubMed Central

    Compain, Fabrice; Decré, Dominique; Dupont, Chloé; Laurens, Chrislène; Vittecoq, Marion; Pantel, Alix; Solassol, Jérôme; Carrière, Christian; Renaud, François; Brieu, Nathalie; Bouzinbi, Nicolas; Ouédraogo, Abdoul-Salam; Jean-Pierre, Hélène; Godreuil, Sylvain

    2015-01-01

    The genetic structures involved in the dissemination of blaCMY-2 carried by Proteus mirabilis isolates recovered from different gull species in the South of France were characterized and compared to clinical isolates. blaCMY-2 was identified in P. mirabilis isolates from 27/93 yellow-legged gulls and from 37/65 slender-billed gulls. It was carried by a conjugative SXT/R391-like integrative and conjugative element (ICE) in all avian strains and in 3/7 human strains. Two clinical isolates had the same genetic background as six avian isolates. PMID:26643344

  5. Mode and origin of replication of pSAM2, a conjugative integrating element of Streptomyces ambofaciens.

    PubMed

    Hagège, J; Pernodet, J L; Friedmann, A; Guérineau, M

    1993-11-01

    pSAM2 is an 11 kb integrating element from Streptomyces ambofaciens that is capable of replication. It generates single-stranded DNA during replication, and is therefore the first Streptomyces integrating element to be described that may belong to the family of elements, called the ssDNA elements, that replicate by a rolling-circle mechanism. The direction of replication has been identified. The plus origin (ori) of replication and minus origin (M-O) have been located. Streptomyces lividans harbouring replicating pSAM2 also contain numerous small covalently closed circular DNA molecules (scm) derived from pSAM2. These scm contain ori and extend on both sides of the putative nick site. Sequences at the junction points of these scm are heterogeneous but short direct repeats were always found in the vicinity of these junctions.

  6. Detection and characterization of integrative and conjugative elements (ICEs)-positive Vibrio cholerae isolates from aquacultured shrimp and the environment in Shanghai, China.

    PubMed

    He, Yu; Tang, Yuyi; Sun, Fengjiao; Chen, Lanming

    2015-12-30

    Increasing industrialization and use of antimicrobial agents in aquaculture production, have led to heavy metals and multidrug resistant (MDR) pathogens becoming serious problems. These resistances are conferred in two ways: intrinsic and transfer via conjugation, or transformation by the major transmission mediators. Integrative and conjugative elements (ICEs) are one of the major mediators; however, few studies on ICEs of environmental origin have been reported in Asia. Herein, we determined the prevalence, antimicrobial susceptibility, heavy metal resistance and genotypes of 126 strains of Vibrio cholerae isolated from aquatic products and the environment in Shanghai, China. 92.3% of isolates were ICEs-positive from aquaculture water and 89.3% of isolates from shrimp showed MDR. Tracing the V. cholerae genotypes, showed no significant relevance of genotype among the antimicrobial resistance strains bearing the ICEs or not. Thus, in aquaculture, ICEs are not the major transmission mediators of resistance to antibiotics or heavy metals. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. DNA-Damaging Agents Induce the RecA-Independent Homologous Recombination Functions of Integrating Conjugative Elements of the SXT/R391 Family

    PubMed Central

    Garriss, Geneviève; Poulin-Laprade, Dominic

    2013-01-01

    Integrating conjugative elements (ICEs) of the SXT/R391 family are major contributors to the spread of antibiotic resistance genes. These elements also catalyze their own diversity by promoting inter-ICE recombination through the action of the RecA-independent homologous recombination system that they encode. Here, we report that expression of this recombination system, which consists of the single-stranded DNA annealing protein Bet and the exonuclease Exo, is induced by DNA-damaging agents via ICE-encoded transcriptional regulators. We show that the bet and exo genes are part of a large polycistronic transcript that contains many conserved ICE genes that are not involved in the main integration/excision and conjugative transfer processes. We show that although the recombination genes are highly transcribed, their translation is subject to additional strong regulatory mechanisms. We also show that an ICE-encoded putative single-stranded DNA binding protein (Ssb) limits hybrid ICE formation. Finally, a thorough in silico analysis reveals that orthologues of Bet and Exo are widely distributed in bacterial strains belonging to very distantly related bacterial species and are carried by various mobile genetic elements. Phylogenetic analyses suggest that the annealing proteins and exonucleases that compose these systems sometimes have different evolutionary origins, underscoring the strong selective pressure to maintain the functionality of these unrelated cooperating proteins. PMID:23435980

  8. Tn5253 family integrative and conjugative elements carrying mef(I) and catQ determinants in Streptococcus pneumoniae and Streptococcus pyogenes.

    PubMed

    Mingoia, Marina; Morici, Eleonora; Morroni, Gianluca; Giovanetti, Eleonora; Del Grosso, Maria; Pantosti, Annalisa; Varaldo, Pietro E

    2014-10-01

    The linkage between the macrolide efflux gene mef(I) and the chloramphenicol inactivation gene catQ was first described in Streptococcus pneumoniae (strain Spn529), where the two genes are located in a module designated IQ element. Subsequently, two different defective IQ elements were detected in Streptococcus pyogenes (strains Spy029 and Spy005). The genetic elements carrying the three IQ elements were characterized, and all were found to be Tn5253 family integrative and conjugative elements (ICEs). The ICE from S. pneumoniae (ICESpn529IQ) was sequenced, whereas the ICEs from S. pyogenes (ICESpy029IQ and ICESpy005IQ, the first Tn5253-like ICEs reported in this species) were characterized by PCR mapping, partial sequencing, and restriction analysis. ICESpn529IQ and ICESpy029IQ were found to share the intSp 23FST81 integrase gene and an identical Tn916 fragment, whereas ICESpy005IQ has int5252 and lacks Tn916. All three ICEs were found to lack the linearized pC194 plasmid that is usually associated with Tn5253-like ICEs, and all displayed a single copy of a toxin-antitoxin operon that is typically contained in the direct repeats flanking the excisable pC194 region when this region is present. Two different insertion sites of the IQ elements were detected, one in ICESpn529IQ and ICESpy029IQ, and another in ICESpy005IQ. The chromosomal integration of the three ICEs was site specific, depending on the integrase (intSp 23FST81 or int5252). Only ICESpy005IQ was excised in circular form and transferred by conjugation. By transformation, mef(I) and catQ were cotransferred at a high frequency from S. pyogenes Spy005 and at very low frequencies from S. pneumoniae Spn529 and S. pyogenes Spy029.

  9. Diversity and Mobility of Integrative and Conjugative Elements in Bovine Isolates of Streptococcus agalactiae, S. dysgalactiae subsp. dysgalactiae, and S. uberis▿ †

    PubMed Central

    Haenni, Marisa; Saras, Estelle; Bertin, Stéphane; Leblond, Pierre; Madec, Jean-Yves; Payot, Sophie

    2010-01-01

    Bovine isolates of Streptococcus agalactiae (n = 76), Streptococcus dysgalactiae subsp. dysgalactiae (n = 32), and Streptococcus uberis (n = 101) were analyzed for the presence of different integrative and conjugative elements (ICEs) and their association with macrolide, lincosamide, and tetracycline resistance. The diversity of the isolates included in this study was demonstrated by multilocus sequence typing for S. agalactiae and pulsed-field gel electrophoresis for S. dysgalactiae and S. uberis. Most of the erythromycin-resistant strains carry an ermB gene. Five strains of S. uberis that are resistant to lincomycin but susceptible to erythromycin carry the lin(B) gene, and one has both linB and lnuD genes. In contrast to S. uberis, most of the S. agalactiae and S. dysgalactiae tetracycline-resistant isolates carry a tet(M) gene. A tet(S) gene was also detected in the three species. A Tn916-related element was detected in 30 to 50% of the tetracycline-resistant strains in the three species. Tetracycline resistance was successfully transferred by conjugation to an S. agalactiae strain. Most of the isolates carry an ICE integrated in the rplL gene. In addition, half of the S. agalactiae isolates have an ICE integrated in a tRNA lysine (tRNALys) gene. Such an element is also present in 20% of the isolates of S. dysgalactiae and S. uberis. A circular form of these ICEs was detected in all of the isolates tested, indicating that these genetic elements are mobile. These ICEs could thus also be a vehicle for horizontal gene transfer between streptococci of animal and/or human origin. PMID:20952646

  10. Mechanism of integration and excision in conjugative transposons.

    PubMed

    Mullany, P; Roberts, A P; Wang, H

    2002-12-01

    Translocation of conjugative transposons proceeds via excision of the element to generate a circular molecule that can then integrate into a new site, which can be in the same or a different cell. This review summarises some of the different mechanisms used for excision and integration of conjugative transposons.

  11. Integrating conjugative elements of the SXT/R391 family from fish-isolated Vibrios encode restriction-modification systems that confer resistance to bacteriophages.

    PubMed

    Balado, Miguel; Lemos, Manuel L; Osorio, Carlos R

    2013-02-01

    Integrating conjugative elements (ICEs) of the SXT/R391 family have been described in Vibrios, mainly Vibrio cholerae, and other bacteria as carriers of variable gene content conferring adaptive advantages upon their hosts, including antimicrobial resistance and motility regulation. However, our knowledge on their host range and ecological significance is still limited. Here, we report the identification and characterization of ICEVspPor3 and ICEValSpa1, two novel ICEs of the SXT/R391 family from fish-isolated Vibrio splendidus and Vibrio alginolyticus, respectively. We found that ICEVspPor3 carries tetracycline and HgCl(2) resistance determinants and can be transferred by conjugation to Escherichia coli and to several species of marine bacteria including some of the major bacterial fish pathogens in marine aquaculture, whereas ICEValSpa1 lacks resistance genes. Interestingly, both ICEs harbor genes encoding distinct restriction-modification (RM) systems. We demonstrate here that these RM systems, when expressed in E. coli, confer protection to infection by T1 bacteriophage and by environmental water bacteriophages. Our results provide evidences that the variable gene content of ICEs of the SXT/R391 family encodes fitness functions beyond those related to antimicrobial resistance and motility regulation and suggest that the host range of these elements in the marine environment might be broader than expected.

  12. A finite element conjugate gradient FFT method for scattering

    NASA Technical Reports Server (NTRS)

    Collins, Jeffery D.; Ross, Dan; Jin, J.-M.; Chatterjee, A.; Volakis, John L.

    1991-01-01

    Validated results are presented for the new 3D body of revolution finite element boundary integral code. A Fourier series expansion of the vector electric and mangnetic fields is employed to reduce the dimensionality of the system, and the exact boundary condition is employed to terminate the finite element mesh. The mesh termination boundary is chosen such that is leads to convolutional boundary operatores of low O(n) memory demand. Improvements of this code are discussed along with the proposed formulation for a full 3D implementation of the finite element boundary integral method in conjunction with a conjugate gradiant fast Fourier transformation (CGFFT) solution.

  13. The TetR-Type MfsR Protein of the Integrative and Conjugative Element (ICE) ICEclc Controls both a Putative Efflux System and Initiation of ICE Transfer

    PubMed Central

    Pradervand, Nicolas; Delavat, François; Sulser, Sandra; Miyazaki, Ryo

    2014-01-01

    Integrative and conjugating elements (ICE) are self-transferable DNAs widely present in bacterial genomes, which often carry a variety of auxiliary genes of potential adaptive benefit. One of the model ICE is ICEclc, an element originally found in Pseudomonas knackmussii B13 and known for its propensity to provide its host with the capacity to metabolize chlorocatechols and 2-aminophenol. In this work, we studied the mechanism and target of regulation of MfsR, a TetR-type repressor previously found to exert global control on ICEclc horizontal transfer. By using a combination of ICEclc mutant and transcriptome analysis, gene reporter fusions, and DNA binding assays, we found that MfsR is a repressor of both its own expression and that of a gene cluster putatively coding for a major facilitator superfamily efflux system on ICEclc (named mfsABC). Phylogenetic analysis suggests that mfsR was originally located immediately adjacent to the efflux pump genes but became displaced from its original cis target DNA by a gene insertion. This resulted in divergence of the original bidirectional promoters into two separated individual regulatory units. Deletion of mfsABC did not result in a strong phenotype, and despite screening a large number of compounds and conditions, we were unable to define the precise current function or target of the putative efflux pump. Our data reconstruct how the separation of an ancestor mfsR-mfsABC system led to global control of ICEclc transfer by MfsR. PMID:25182498

  14. Presence of SXT integrating conjugative element in marine bacteria isolated from the mucus of the coral Fungia echinata from Andaman Sea.

    PubMed

    Badhai, Jhasketan; Kumari, Prabla; Krishnan, Pandian; Ramamurthy, Thandavarayan; Das, Subrata K

    2013-01-01

    In this study, we characterize 18 cultivable bacteria associated within the mucus of the coral Fungia echinata from Andaman Sea, India. 16S rRNA gene sequence analysis showed that all the 18 strains isolated in this study from the coral mucus belong to the group Gammaproteobacteria and majority of them were identified as Vibrio core group. Our objective was to investigate the presence of the SXT/R391 integrating conjugative elements (ICEs) targeting integrase int(SXT) and SXT Hotspot IV genetic elements in these isolates. SXT/ICE initially reported in Vibrio cholerae contains many antibiotic and heavy metal resistance genes and acts as an effective tool for the horizontal transfer of resistance genes in other bacterial populations. Two of our strains, AN44 and AN60, were resistant to sulfamethoxazole, trimethoprim, chloramphenicol, and streptomycin, in addition to other antibiotics such as neomycin, ampicillin, rifampicin, and tetracycline. Using PCR followed by sequencing, we detected the SXT/ICE in these strains. The SXT integrase genes of AN44 and AN60 had a 99% and 100% identity with V. cholerae serogroup O139 strain SG24. This study provides the first evidence of the presence of SXT/R391 ICEs in Marinomonas sp. strain AN44 (JCM 18476(T) ) and Vibrio fortis strain AN60 (DSM 26067(T) ) isolated from the mucus of the coral F. echinata. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  15. Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes.

    PubMed

    Clawson, Michael L; Murray, Robert W; Sweeney, Michael T; Apley, Michael D; DeDonder, Keith D; Capik, Sarah F; Larson, Robert L; Lubbers, Brian V; White, Brad J; Kalbfleisch, Theodore S; Schuller, Gennie; Dickey, Aaron M; Harhay, Gregory P; Heaton, Michael P; Chitko-McKown, Carol G; Brichta-Harhay, Dayna M; Bono, James L; Smith, Timothy P L

    2016-11-29

    Mannheimia haemolytica typically resides in cattle as a commensal member of the upper respiratory tract microbiome. However, some strains can invade their lungs and cause respiratory disease and death, including those with multi-drug resistance. A nucleotide polymorphism typing system was developed for M. haemolytica from the genome sequences of 1133 North American isolates, and used to identify genetic differences between isolates from the lungs and upper respiratory tract of cattle with and without clinical signs of respiratory disease. A total of 26,081 nucleotide polymorphisms were characterized after quality control filtering of 48,403 putative polymorphisms. Phylogenetic analyses of nucleotide polymorphism genotypes split M. haemolytica into two major genotypes (1 and 2) that each were further divided into multiple subtypes. Multiple polymorphisms were identified with alleles that tagged genotypes 1 or 2, and their respective subtypes. Only genotype 2 M. haemolytica associated with the lungs of diseased cattle and the sequence of a particular integrative and conjugative element (ICE). Additionally, isolates belonging to one subtype of genotype 2 (2b), had the majority of antibiotic resistance genes detected in this study, which were assorted into seven combinations that ranged from 1 to 12 resistance genes. Typing of diverse M. haemolytica by nucleotide polymorphism genotypes successfully identified associations with diseased cattle lungs, ICE sequence, and antibiotic resistance genes. Management of cattle by their carriage of M. haemolytica could be an effective intervention strategy to reduce the prevalence of respiratory disease and supplemental needs for antibiotic treatments in North American herds.

  16. Comparative analysis of the Hrp pathogenicity island of Rubus- and Spiraeoideae-infecting Erwinia amylovora strains identifies the IT region as a remnant of an integrative conjugative element.

    PubMed

    Mann, Rachel A; Blom, Jochen; Bühlmann, Andreas; Plummer, Kim M; Beer, Steven V; Luck, Joanne E; Goesmann, Alexander; Frey, Jürg E; Rodoni, Brendan C; Duffy, Brion; Smits, Theo H M

    2012-08-01

    The Hrp pathogenicity island (hrpPAI) of Erwinia amylovora not only encodes a type III secretion system (T3SS) and other genes required for pathogenesis on host plants, but also includes the so-called island transfer (IT) region, a region that originates from an integrative conjugative element (ICE). Comparative genomic analysis of the IT regions of two Spiraeoideae- and three Rubus-infecting strains revealed that the regions in Spiraeoideae-infecting strains were syntenic and highly conserved in length and genetic information, but that the IT regions of the Rubus-infecting strains varied in gene content and length, showing a mosaic structure. None of the ICEs in E. amylovora strains were complete, as conserved ICE genes and the left border were missing, probably due to reductive genome evolution. Comparison of the hrpPAI region of E. amylovora strains to syntenic regions from other Erwinia spp. indicates that the hrpPAI and the IT regions are the result of several insertion and deletion events that have occurred within the ICE. It also suggests that the T3SS was present in a common ancestor of the pathoadapted Erwinia spp. and that insertion and deletion events in the IT region occurred during speciation.

  17. csrT Represents a New Class of csrA-Like Regulatory Genes Associated with Integrative Conjugative Elements of Legionella pneumophila

    PubMed Central

    Abbott, Zachary D.; Flynn, Kaitlin J.; Byrne, Brenda G.; Mukherjee, Sampriti; Kearns, Daniel B.

    2015-01-01

    ABSTRACT Bacterial evolution is accelerated by mobile genetic elements. To spread horizontally and to benefit the recipient bacteria, genes encoded on these elements must be properly regulated. Among the legionellae are multiple integrative conjugative elements (ICEs) that each encode a paralog of the broadly conserved regulator csrA. Using bioinformatic analyses, we deduced that specific csrA paralogs are coinherited with particular lineages of the type IV secretion system that mediates horizontal spread of its ICE, suggesting a conserved regulatory interaction. As a first step to investigate the contribution of csrA regulators to this class of mobile genetic elements, we analyzed here the activity of the csrA paralog encoded on Legionella pneumophila ICE-βox. Deletion of this gene, which we name csrT, had no observed effect under laboratory conditions. However, ectopic expression of csrT abrogated the protection to hydrogen peroxide and macrophage degradation that ICE-βox confers to L. pneumophila. When ectopically expressed, csrT also repressed L. pneumophila flagellin production and motility, a function similar to the core genome's canonical csrA. Moreover, csrT restored the repression of motility to csrA mutants of Bacillus subtilis, a finding consistent with the predicted function of CsrT as an mRNA binding protein. Since all known ICEs of legionellae encode coinherited csrA-type IV secretion system pairs, we postulate that CsrA superfamily proteins regulate ICE activity to increase their horizontal spread, thereby expanding L. pneumophila versatility. IMPORTANCE ICEs are mobile DNA elements whose type IV secretion machineries mediate spread among bacterial populations. All surveyed ICEs within the Legionella genus also carry paralogs of the essential life cycle regulator csrA. It is striking that the csrA loci could be classified into distinct families based on either their sequence or the subtype of the adjacent type IV secretion system locus. To

  18. csrT Represents a New Class of csrA-Like Regulatory Genes Associated with Integrative Conjugative Elements of Legionella pneumophila.

    PubMed

    Abbott, Zachary D; Flynn, Kaitlin J; Byrne, Brenda G; Mukherjee, Sampriti; Kearns, Daniel B; Swanson, Michele S

    2015-11-23

    Bacterial evolution is accelerated by mobile genetic elements. To spread horizontally and to benefit the recipient bacteria, genes encoded on these elements must be properly regulated. Among the legionellae are multiple integrative conjugative elements (ICEs) that each encode a paralog of the broadly conserved regulator csrA. Using bioinformatic analyses, we deduced that specific csrA paralogs are coinherited with particular lineages of the type IV secretion system that mediates horizontal spread of its ICE, suggesting a conserved regulatory interaction. As a first step to investigate the contribution of csrA regulators to this class of mobile genetic elements, we analyzed here the activity of the csrA paralog encoded on Legionella pneumophila ICE-βox. Deletion of this gene, which we name csrT, had no observed effect under laboratory conditions. However, ectopic expression of csrT abrogated the protection to hydrogen peroxide and macrophage degradation that ICE-βox confers to L. pneumophila. When ectopically expressed, csrT also repressed L. pneumophila flagellin production and motility, a function similar to the core genome's canonical csrA. Moreover, csrT restored the repression of motility to csrA mutants of Bacillus subtilis, a finding consistent with the predicted function of CsrT as an mRNA binding protein. Since all known ICEs of legionellae encode coinherited csrA-type IV secretion system pairs, we postulate that CsrA superfamily proteins regulate ICE activity to increase their horizontal spread, thereby expanding L. pneumophila versatility. ICEs are mobile DNA elements whose type IV secretion machineries mediate spread among bacterial populations. All surveyed ICEs within the Legionella genus also carry paralogs of the essential life cycle regulator csrA. It is striking that the csrA loci could be classified into distinct families based on either their sequence or the subtype of the adjacent type IV secretion system locus. To investigate whether ICE

  19. Characterisation of a novel integrative and conjugative element ICESsD9 carrying erm(B) and tet(O) resistance determinants in Streptococcus suis, and the distribution of ICESsD9-like elements in clinical isolates.

    PubMed

    Huang, Kaisong; Song, Yajing; Zhang, Qiang; Zhang, Anding; Jin, Meilin

    2016-12-01

    This study identified a novel integrative and conjugative element (ICESsD9) carrying erm(B) and tet(O) resistance determinants in Streptococcus suis D9 and determined its prevalence in clinical isolates. Comparative genome analysis was performed using Mauve and Artemis Comparison Tool visualisation programs. Inverse PCR was utilised to detect its circular intermediate. The transfer capacity of ICESsD9 was evaluated by mating assays using S. suis A7 and Enterococcus faecalis JH2-2 as recipients. A genome walking approach was employed to analyse the characteristics of integration sites in transconjugants. A total of 118 clinical S. suis isolates were tested by PCR mapping assays to detect ICESsD9-like elements. MLST was performed on isolates containing ICESsD9 variants to determine their clonal relatedness. This 55 683-bp element can actively excise from the chromosome. Additionally, it was capable of transferring both into S. suis and E. faecalis with frequencies of 1.2×10(-4) and 5.8×10(-6) per donor, respectively. When investigating integration site features, it was found that ICESsD9 can enter S. suis and E. faecalis chromosomes by different sites, generating 15-bp and 3-bp direct repeat sequences, respectively. Twelve isolates mainly belonging to sequence types ST1, ST7 and ST28 were confirmed to harbour ICESsD9-like elements. In conclusion, this study provides the first description of an ICE in S. suis that is capable of transferring both into S. suis and E. faecalis. The presence of different ICESsD9 variants in clinical isolates suggests already wide dissemination of this family element in S. suis in China. Copyright © 2016 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

  20. Genome analysis of a clinical isolate of Shewanella sp. uncovered an active hybrid integrative and conjugative element carrying an integron platform inserted in a novel genomic locus.

    PubMed

    Parmeciano Di Noto, Gisela; Jara, Eugenio; Iriarte, Andrés; Centrón, Daniela; Quiroga, Cecilia

    2016-08-01

    Shewanella spp. are currently considered to be emerging pathogens that can code for a blaOXA carbapenemase in their chromosome. Complete genome analysis of the clinical isolate Shewanella sp. Sh95 revealed that this strain is a novel species, which shares a lineage with marine isolates. Characterization of its resistome showed that it codes for genes drfA15, qacH and blaOXA-48. We propose that Shewanella sp. Sh95 acts as reservoir of blaOXA-48. Moreover, analysis of mobilome showed that it contains a novel integrative and conjugative element (ICE), named ICESh95. Comparative analysis between the close relatives ICESpuPO1 from Shewanella sp. W3-18-1 and ICE SXTMO10 from Vibrio cholerae showed that ICESh95 encompassed two new regions, a type III restriction modification system and a multidrug resistance integron. The integron platform contained a novel arrangement formed by gene cassettes drfA15 and qacH, and a class C-attC group II intron. Furthermore, insertion of ICESh95 occurred at a unique target site, which correlated with the presence of a different xis/int module. Mobility of ICESh95 was assessed and demonstrated its ability to self-transfer with high efficiency to different species of bacteria. Our results show that ICESh95 is a self-transmissible, mobile element, which can contribute to the dissemination of antimicrobial resistance; this is clearly a threat when natural bacteria from water ecosystems, such as Shewanella, act as vectors in its propagation.

  1. Pectobacterium atrosepticum and Pectobacterium carotovorum Harbor Distinct, Independently Acquired Integrative and Conjugative Elements Encoding Coronafacic Acid that Enhance Virulence on Potato Stems.

    PubMed

    Panda, Preetinanda; Vanga, Bhanupratap R; Lu, Ashley; Fiers, Mark; Fineran, Peter C; Butler, Ruth; Armstrong, Karen; Ronson, Clive W; Pitman, Andrew R

    2016-01-01

    Integrative and conjugative elements (ICEs) play a central role in the evolution of bacterial virulence, their transmission between bacteria often leading to the acquisition of virulence factors that alter host range or aggressiveness. Much is known about the functions of the virulence determinants that ICEs harbor, but little is understood about the cryptic effects of ICEs on their host cell. In this study, the importance of horizontally acquired island 2 (HAI2), an ICE in the genome of Pectobacterium atrosepticum SCRI1043, was studied using a strain in which the entire ICE had been removed by CRISPR-Cas-mediated genome editing. HAI2 encodes coronafacic acid, a virulence factor that enhances blackleg disease of potato stems caused by P. atrosepticum SCRI1043. As expected, deletion of HAI2 resulted in reduced blackleg symptoms in potato stems. A subsequent screen for HAI2-related ICEs in other strains of the Pectobacterium genus revealed their ubiquitous nature in P. atrosepticum. Yet, HAI2-related ICEs were only detected in the genomes of a few P. carotovorum strains. These strains were notable as blackleg causing strains belonging to two different subspecies of P. carotovorum. Sequence analysis of the ICEs in different strains of both P. atrosepticum and P. carotovorum confirmed that they were diverse and were present in different locations on the genomes of their bacterial host, suggesting that the cfa cluster was probably acquired independently on a number of occasions via chromosomal insertion of related ICEs. Excision assays also demonstrated that the ICEs in both P. atrosepticum and P. carotovorum are mobilized from the host chromosome. Thus, the future spread of these ICEs via lateral gene transfer might contribute to an increase in the prevalence of blackleg-causing strains of P. carotovorum.

  2. Pectobacterium atrosepticum and Pectobacterium carotovorum Harbor Distinct, Independently Acquired Integrative and Conjugative Elements Encoding Coronafacic Acid that Enhance Virulence on Potato Stems

    PubMed Central

    Panda, Preetinanda; Vanga, Bhanupratap R.; Lu, Ashley; Fiers, Mark; Fineran, Peter C.; Butler, Ruth; Armstrong, Karen; Ronson, Clive W.; Pitman, Andrew R.

    2016-01-01

    Integrative and conjugative elements (ICEs) play a central role in the evolution of bacterial virulence, their transmission between bacteria often leading to the acquisition of virulence factors that alter host range or aggressiveness. Much is known about the functions of the virulence determinants that ICEs harbor, but little is understood about the cryptic effects of ICEs on their host cell. In this study, the importance of horizontally acquired island 2 (HAI2), an ICE in the genome of Pectobacterium atrosepticum SCRI1043, was studied using a strain in which the entire ICE had been removed by CRISPR-Cas-mediated genome editing. HAI2 encodes coronafacic acid, a virulence factor that enhances blackleg disease of potato stems caused by P. atrosepticum SCRI1043. As expected, deletion of HAI2 resulted in reduced blackleg symptoms in potato stems. A subsequent screen for HAI2-related ICEs in other strains of the Pectobacterium genus revealed their ubiquitous nature in P. atrosepticum. Yet, HAI2-related ICEs were only detected in the genomes of a few P. carotovorum strains. These strains were notable as blackleg causing strains belonging to two different subspecies of P. carotovorum. Sequence analysis of the ICEs in different strains of both P. atrosepticum and P. carotovorum confirmed that they were diverse and were present in different locations on the genomes of their bacterial host, suggesting that the cfa cluster was probably acquired independently on a number of occasions via chromosomal insertion of related ICEs. Excision assays also demonstrated that the ICEs in both P. atrosepticum and P. carotovorum are mobilized from the host chromosome. Thus, the future spread of these ICEs via lateral gene transfer might contribute to an increase in the prevalence of blackleg-causing strains of P. carotovorum. PMID:27065965

  3. Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE6013 Elements in Staphylococcus aureus.

    PubMed

    Sansevere, Emily A; Luo, Xiao; Park, Joo Youn; Yoon, Sunghyun; Seo, Keun Seok; Robinson, D Ashley

    2017-04-15

    ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013 Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci.IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one

  4. ICESluvan, a 94-Kilobase Mosaic Integrative Conjugative Element Conferring Interspecies Transfer of VanB-Type Glycopeptide Resistance, a Novel Bacitracin Resistance Locus, and a Toxin-Antitoxin Stabilization System

    PubMed Central

    Bjørkeng, Eva K.; Hjerde, Erik; Pedersen, Torunn; Sundsfjord, Arnfinn

    2013-01-01

    A 94-kb integrative conjugative element (ICESluvan) transferable to Enterococcus faecium and Enterococcus faecalis from an animal isolate of Streptococcus lutetiensis consists of a mosaic of genetic fragments from different Gram-positive bacteria. A variant of ICESluvan was confirmed in S. lutetiensis from a patient. A complete Tn5382/Tn1549 with a vanB2 operon is integrated into a streptococcal ICESde3396-like region harboring a putative bacteriophage exclusion system, a putative agglutinin receptor precursor, and key components of a type IV secretion system. Moreover, ICESluvan encodes a putative MobC family mobilization protein and a relaxase and, thus, in total has all genetic components essential for conjugative transfer. A 9-kb element within Tn5382/Tn1549 encodes, among others, putative proteins similar to the TnpX site-specific recombinase in Faecalibacterium and VanZ in Paenibacillus, which may contribute to the detected low-level teicoplanin resistance. Furthermore, ICESluvan encodes a novel bacitracin resistance locus that is associated with reduced susceptibility to bacitracin when transferred to E. faecium. The expression of a streptococcal pezAT toxin-antitoxin-encoding operon of ICESluvan in S. lutetiensis, E. faecium, and E. faecalis was confirmed by reverse transcription (RT)-PCR, indicating an active toxin-antitoxin system which may contribute to stabilizing ICESluvan within new hosts. Junction PCR and DNA sequencing confirmed that ICESluvan excised to form a circular intermediate in S. lutetiensis, E. faecalis, and E. faecium. Transfer between E. faecalis cells was observed in the presence of helper plasmid pIP964. Sequence analysis of the original S. lutetiensis donor and enterococcal transconjugants showed that ICESluvan integrates in a site-specific manner into the C-terminal end of the chromosomal tRNA methyltransferase gene rumA. PMID:24078615

  5. Transfer functions of the conjugative integrating element pSAM2 from Streptomyces ambofaciens: characterization of a kil-kor system associated with transfer.

    PubMed

    Hagège, J; Pernodet, J L; Sezonov, G; Gerbaud, C; Friedmann, A; Guérineau, M

    1993-09-01

    pSAM2 is an 11-kb integrating element from Streptomyces ambofaciens. During matings, pSAM2 can be transferred at high frequency, forming pocks, which are zones of growth inhibition of the recipient strain. The nucleotide sequences of the regions involved in pSAM2 transfer, pock formation, and maintenance have been determined. Seven putative open reading frames with the codon usage typical of Streptomyces genes have been identified: traSA (306 amino acids [aa]), orf84 (84 aa), spdA (224 aa), spdB (58 aa), spdC (51 aa), spdD (104 aa), and korSA (259 aa). traSA is essential for pSAM2 intermycelial transfer and pock formation. It could encode a protein with similarities to the major transfer protein, Tra, of pIJ101. TraSA protein contains a possible nucleotide-binding sequence and a transmembrane segment. spdA, spdB, spdC, and spdD influence pock size and transfer efficiency and may be required for intramycelial transfer. A kil-kor system similar to that of pIJ101 is associated with pSAM2 transfer: the korSA (kil-override) gene product could control the expression of the traSA gene, which has lethal effects when unregulated (Kil phenotype). The KorSA protein resembles KorA of pIJ101 and repressor proteins belonging to the GntR family. Thus, the integrating element pSAM2 possesses for transfer general features of nonintegrating Streptomyces plasmids: different genes are involved in the different steps of the intermycelial and intramycelial transfer, and a kil-kor system is associated with transfer. However, some differences in the functional properties, organization, and sizes of the transfer genes compared with those of other Streptomyces plasmids have been found.

  6. Semiclassical integrable matrix elements

    SciTech Connect

    Morehead, J.J.

    1996-03-01

    A semiclassical expression for matrix elements of an arbitrary operator with respect to the eigenstates of an integrable Hamiltonian is derived. This is essentially the Heisenberg correspondence principle, and it is shown via the Weyl correspondence that the approximation is valid through the lowest two orders in {h_bar}. The result is used to prove that an asymptotic form of the Clebsch-Gordan coefficients for two large and one small angular momenta is valid through two orders. {copyright} {ital 1996 The American Physical Society.}

  7. Homology among tet determinants in conjugative elements of streptococci

    SciTech Connect

    Smith, M.D.; Hazum, S.; Guild, W.R.

    1981-10-01

    A mutation to tetracycline sensitivity in a resistant strain of Streptococcus pneumoniae was shown by several criteria to be due to a point mutation in the conjugative o(cat-tet) element found in the chromosomes of strains derived from BM6001, a clinical strain resistant to tetracycline and chloramphenicol. Strains carrying the mutation were transformed back to tetracycline resistance with the high efficiency of a point marker by donor deoxyribonucleic acids from its ancestral strain and from nine other clinical isolates of pneumococcus and by deoxyribonucleic acids from Group D Streptococcus faecalis and Group B Streptococcus agalactiae strains that also carry conjugative tet elements in their chromosomes. It was not transformed to resistance by tet plasmid deoxyribonucleic acids from either gram-negative or gram-positive species, except for one that carried transposon TN916, the conjugative tet element present in the chromosomes of some S. faecalis strains. The results showed that the tet determinants in conjugative elements of several streptococcal species share a high degree of deoxyribonucleic acid sequence homology and suggested that they differ from other tet genes.

  8. Marriage of heavy main group elements with π-conjugated materials for optoelectronic applications.

    PubMed

    Parke, Sarah M; Boone, Michael P; Rivard, Eric

    2016-08-07

    This review article summarizes recent progress in the synthesis and optoelectronic properties of conjugated materials containing heavy main group elements from Group 13-16 as integral components. As will be discussed, the introduction of these elements can promote novel phosphorescent behavior and support desirable molecular and polymeric properties such as low optical band gaps and high charge mobilities for photovoltaic and thin film transistor applications.

  9. The mosaic accessory gene structures of the SXT/R391-like integrative and conjugative elements derived from Vibrio spp. isolated from aquatic products and environment in the Yangtze River estuary, China

    PubMed Central

    2013-01-01

    Background The emergence, resurgence and spread of human food-borne pathogenic Vibrios are one of the major contributors to disease burden and mortality particularly in developing countries with disputable sanitary conditions. Previous research on pathogenic Vibrio cholerae and Vibrio parahaemolitycus derived from clinical samples has proposed links between acquisition of virulence and multiple drug resistance traits and intercellular transmissibility of mobile genetic elements in the environment. To date, very few information is available on environmental Vibrio isolates. In this study, we characterized eleven Vibrio strains bearing the SXT/R391-like integrative and conjugative elements (ICEs) derived from aquatic products and environment in the Yangtze River Estuary, China. Results The eleven Vibrio strains were isolated in 2010 to 2011, and taxonomically identified, which included six Vibrio cholerae, three Vibrio parahaemolyticus, one Vibrio alginolyticus and one Vibrio natriegens. Most of the strains displayed strong resistance phenotypes to ampicillin, mercury and chromium. The majority of their ICEs, which belong to S and R exclusion system groups, contain ICEs-chromosome junction sequences and highly conserved core-genes required for ICE transfer. However, comparative sequence analysis uncovered interesting diversity in their mosaic accessory gene structures, which carry many novel genes that have not been described in any known ICEs to date. In addition, antibiotic resistance was transmitted by ICEVchChn6 and ICEVpaChn1 from V. cholerae, V. parahaemolyticus to E. coli MG1655 via conjugation, respectively. Our data also revealed that the ICEs characterized in this study are phylogenetically distant from most of the SXT/R391 ICEs reported previously, which may represent a novel cluster likely shaped by the ecological environment in the Yangtze River Estuary, China. Conclusions This study constitutes the first investigation of ICEs-positive Vibrio spp. in the

  10. Interaction between conjugative and retrotransposable elements in horizontal gene transfer.

    PubMed

    Novikova, Olga; Smith, Dorie; Hahn, Ingrid; Beauregard, Arthur; Belfort, Marlene

    2014-12-01

    Mobile genetic elements either encode their own mobilization machineries or hijack them from other mobile elements. Multiple classes of mobile elements often coexist within genomes and it is unclear whether they have the capacity to functionally interact and even collaborate. We investigate the possibility that molecular machineries of disparate mobile elements may functionally interact, using the example of a retrotransposon, in the form of a mobile group II intron, found on a conjugative plasmid pRS01 in Lactococcus lactis. This intron resides within the pRS01 ltrB gene encoding relaxase, the enzyme required for nicking the transfer origin (oriT) for conjugal transmission of the plasmid into a recipient cell. Here, we show that relaxase stimulates both the frequency and diversity of retrotransposition events using a retromobility indicator gene (RIG), and by developing a high-throughput genomic retrotransposition detection system called RIG-Seq. We demonstrate that LtrB relaxase not only nicks ssDNA of its cognate oriT in a sequence- and strand-specific manner, but also possesses weak off-target activity. Together, the data support a model in which the two different mobile elements, one using an RNA-based mechanism, the other using DNA-based transfer, do functionally interact. Intron splicing facilitates relaxase expression required for conjugation, whereas relaxase introduces spurious nicks in recipient DNA that stimulate both the frequency of intron mobility and the density of events. We hypothesize that this functional interaction between the mobile elements would promote horizontal conjugal gene transfer while stimulating intron dissemination in the donor and recipient cells.

  11. Structure of a conjugative element in Streptococcus pneumoniae

    SciTech Connect

    Vijayakumar, M.N.; Priebe, S.D.; Guild, W.R.

    1986-06-01

    The authors have cloned and mapped a 69-kilobase (kb) region of the chromosome of Streptococcus pneumoniae DP1322, which carries the conjugative Omega(cat-tet) insertion from S. pneumoniae BM6001. This element proved to be 65.5 kb in size. Location of the junctions was facilitated by cloning a preferred target region from the wild-type strain Rx1 recipient genome. This target site was preferred by both the BM6001 element and the cat-erm-tet element from Streptococcus agalactiae B109. Within the BM6001 element cat and tet were separated by 30 kb, and cat was flanked by two copies of a sequence that was also present in the recipient strain Rx1 DNA. Another sequence at least 2.4 kb in size was found inside the BM6001 element and at two places in the Rx1 genome. Its role is unknown. The ends of the BM6001 element appear to be the same as those of the B109 element, both as seen after transfer to S. pneumoniae and as mapped by others in pDP5 after transposition in Streptococcus faecalis. No homology is seen between the ends of the BM6001 element and no evidence found suggesting that it ever circularizes.

  12. Comparative analyses of a putative Francisella conjugative element.

    PubMed

    Siddaramappa, Shivakumara; Challacombe, Jean F; Petersen, Jeannine M; Pillai, Segaran; Kuske, Cheryl R

    2014-03-01

    A large circular plasmid detected in Francisella novicida-like strain PA10-7858, designated pFNPA10, was sequenced completely and analyzed. This 41,013-bp plasmid showed no homology to any of the previously sequenced Francisella plasmids and was 8-10 times larger in size than them. A total of 57 ORFs were identified within pFNPA10 and at least 9 of them encoded putative proteins with homology to different conjugal transfer proteins. The presence of iteron-like direct repeats and an ORF encoding a putative replication protein within pFNPA10 suggested that it replicated by the theta mode. Phylogenetic analyses indicated that pFNPA10 had no near neighbors in the databases and that it may have originated within an environmental Francisella lineage. Based on its features, pFNPA10 appears to be a novel extra-chromosomal genetic element within the genus Francisella. The suitability of pFNPA10 as a vector for transformation of species of Francisella by conjugation remains to be explored.

  13. ICESpy009, a Conjugative Genetic Element Carrying mef(E) in Streptococcus pyogenes.

    PubMed

    Del Grosso, Maria; Camilli, Romina; Rizzi, Ermanno; Pietrelli, Alessandro; De Bellis, Gianluca; Pantosti, Annalisa

    2016-07-01

    Efflux-mediated macrolide resistance due to mef(E) and mel, carried by the mega element, is common in Streptococcus pneumoniae, for which it was originally characterized, but it is rare in Streptococcus pyogenes In S. pyogenes, mega was previously found to be enclosed in Tn2009, a composite genetic element of the Tn916 family containing tet(M) and conferring erythromycin and tetracycline resistance. In this study, S. pyogenes isolates containing mef(E), apparently not associated with other resistance determinants, were examined to characterize the genetic context of mega. By whole-genome sequencing of one isolate, MB56Spyo009, we identified a novel composite integrative and conjugative element (ICE) carrying mega, designated ICESpy009, belonging to the ICESa2603 family. ICESpy009 was 55 kb long, contained 61 putative open reading frames (ORFs), and was found to be integrated into hylA, a novel integration site for the ICESa2603 family. The modular organization of the ICE was similar to that of members of the ICESa2603 family carried by different streptococcal species. In addition, a novel cluster of accessory resistance genes was found inside a region that encloses mega. PCR mapping targeting ICESpy009 revealed the presence of a similar ICE in five other isolates under study. While in three isolates the integration site was the same as that of ICESpy009, in two isolates the ICE was integrated into rplL, the typical integration site of the ICESa2603 family. ICESpy009 was able to transfer macrolide resistance by conjugation to both S. pyogenes and S. pneumoniae, showing the first evidence of the transferability of mega from S. pyogenes.

  14. ICESpy009, a Conjugative Genetic Element Carrying mef(E) in Streptococcus pyogenes

    PubMed Central

    Camilli, Romina; Rizzi, Ermanno; Pietrelli, Alessandro; De Bellis, Gianluca; Pantosti, Annalisa

    2016-01-01

    Efflux-mediated macrolide resistance due to mef(E) and mel, carried by the mega element, is common in Streptococcus pneumoniae, for which it was originally characterized, but it is rare in Streptococcus pyogenes. In S. pyogenes, mega was previously found to be enclosed in Tn2009, a composite genetic element of the Tn916 family containing tet(M) and conferring erythromycin and tetracycline resistance. In this study, S. pyogenes isolates containing mef(E), apparently not associated with other resistance determinants, were examined to characterize the genetic context of mega. By whole-genome sequencing of one isolate, MB56Spyo009, we identified a novel composite integrative and conjugative element (ICE) carrying mega, designated ICESpy009, belonging to the ICESa2603 family. ICESpy009 was 55 kb long, contained 61 putative open reading frames (ORFs), and was found to be integrated into hylA, a novel integration site for the ICESa2603 family. The modular organization of the ICE was similar to that of members of the ICESa2603 family carried by different streptococcal species. In addition, a novel cluster of accessory resistance genes was found inside a region that encloses mega. PCR mapping targeting ICESpy009 revealed the presence of a similar ICE in five other isolates under study. While in three isolates the integration site was the same as that of ICESpy009, in two isolates the ICE was integrated into rplL, the typical integration site of the ICESa2603 family. ICESpy009 was able to transfer macrolide resistance by conjugation to both S. pyogenes and S. pneumoniae, showing the first evidence of the transferability of mega from S. pyogenes. PMID:27067338

  15. On a concurrent element-by-element preconditioned conjugate gradient algorithm for multiple load cases

    NASA Technical Reports Server (NTRS)

    Watson, Brian; Kamat, M. P.

    1990-01-01

    Element-by-element preconditioned conjugate gradient (EBE-PCG) algorithms have been advocated for use in parallel/vector processing environments as being superior to the conventional LDL(exp T) decomposition algorithm for single load cases. Although there may be some advantages in using such algorithms for a single load case, when it comes to situations involving multiple load cases, the LDL(exp T) decomposition algorithm would appear to be decidedly more cost-effective. The authors have outlined an EBE-PCG algorithm suitable for multiple load cases and compared its effectiveness to the highly efficient LDL(exp T) decomposition scheme. The proposed algorithm offers almost no advantages over the LDL(exp T) algorithm for the linear problems investigated on the Alliant FX/8. However, there may be some merit in the algorithm in solving nonlinear problems with load incrementation, but that remains to be investigated.

  16. Microgyroscope with integrated vibratory element

    NASA Technical Reports Server (NTRS)

    Tang, Tony K. (Inventor); Rodger, Damien C. (Inventor); Gutierrez, Roman C. (Inventor)

    2002-01-01

    A microgyroscope having a suspended vertical post uses the Coriolis force to detect the rotation rate. The microgyroscope consists of a single vertical post which is the rotation rate sensing element. The vertical post is formed from the same silicon wafers as the rest of the microgyroscope. A first portion of the vertical post and the clover-leaf structure are made from a first silicon wafer. A second portion of the vertical post and the baseplate are made from a second silicon wafer. The two portions are then bonded together to from the clover-leaf gyroscope with an integrated post structure.

  17. A finite element conjugate gradient FFT method for scattering

    NASA Technical Reports Server (NTRS)

    Collins, Jeffery D.; Zapp, John; Hsa, Chang-Yu; Volakis, John L.

    1990-01-01

    An extension of a two dimensional formulation is presented for a three dimensional body of revolution. With the introduction of a Fourier expansion of the vector electric and magnetic fields, a coupled two dimensional system is generated and solved via the finite element method. An exact boundary condition is employed to terminate the mesh and the fast fourier transformation (FFT) is used to evaluate the boundary integrals for low O(n) memory demand when an iterative solution algorithm is used. By virtue of the finite element method, the algorithm is applicable to structures of arbitrary material composition. Several improvements to the two dimensional algorithm are also described. These include: (1) modifications for terminating the mesh at circular boundaries without distorting the convolutionality of the boundary integrals; (2) the development of nonproprietary mesh generation routines for two dimensional applications; (3) the development of preprocessors for interfacing SDRC IDEAS with the main algorithm; and (4) the development of post-processing algorithms based on the public domain package GRAFIC to generate two and three dimensional gray level and color field maps.

  18. Conjugated carbon monolayer membranes: methods for synthesis and integration.

    PubMed

    Unarunotai, Sakulsuk; Murata, Yuya; Chialvo, Cesar E; Mason, Nadya; Petrov, Ivan; Nuzzo, Ralph G; Moore, Jeffrey S; Rogers, John A

    2010-03-12

    Monolayer membranes of conjugated carbon represent a class of nanomaterial with demonstrated uses in various areas of electronics, ranging from transparent, flexible, and stretchable thin film conductors, to semiconducting materials in moderate and high-performance field-effect transistors. Although graphene represents the most prominent example, many other more structurally and chemically diverse systems are also of interest. This article provides a review of demonstrated synthetic and integration strategies, and speculates on future directions for the field.

  19. An Integrated Solution for Performing Thermo-fluid Conjugate Analysis

    NASA Technical Reports Server (NTRS)

    Kornberg, Oren

    2009-01-01

    A method has been developed which integrates a fluid flow analyzer and a thermal analyzer to produce both steady state and transient results of 1-D, 2-D, and 3-D analysis models. The Generalized Fluid System Simulation Program (GFSSP) is a one dimensional, general purpose fluid analysis code which computes pressures and flow distributions in complex fluid networks. The MSC Systems Improved Numerical Differencing Analyzer (MSC.SINDA) is a one dimensional general purpose thermal analyzer that solves network representations of thermal systems. Both GFSSP and MSC.SINDA have graphical user interfaces which are used to build the respective model and prepare it for analysis. The SINDA/GFSSP Conjugate Integrator (SGCI) is a formbase graphical integration program used to set input parameters for the conjugate analyses and run the models. The contents of this paper describes SGCI and its thermo-fluids conjugate analysis techniques and capabilities by presenting results from some example models including the cryogenic chill down of a copper pipe, a bar between two walls in a fluid stream, and a solid plate creating a phase change in a flowing fluid.

  20. An Integrated Solution for Performing Thermo-fluid Conjugate Analysis

    NASA Technical Reports Server (NTRS)

    Kornberg, Oren

    2009-01-01

    A method has been developed which integrates a fluid flow analyzer and a thermal analyzer to produce both steady state and transient results of 1-D, 2-D, and 3-D analysis models. The Generalized Fluid System Simulation Program (GFSSP) is a one dimensional, general purpose fluid analysis code which computes pressures and flow distributions in complex fluid networks. The MSC Systems Improved Numerical Differencing Analyzer (MSC.SINDA) is a one dimensional general purpose thermal analyzer that solves network representations of thermal systems. Both GFSSP and MSC.SINDA have graphical user interfaces which are used to build the respective model and prepare it for analysis. The SINDA/GFSSP Conjugate Integrator (SGCI) is a formbase graphical integration program used to set input parameters for the conjugate analyses and run the models. The contents of this paper describes SGCI and its thermo-fluids conjugate analysis techniques and capabilities by presenting results from some example models including the cryogenic chill down of a copper pipe, a bar between two walls in a fluid stream, and a solid plate creating a phase change in a flowing fluid.

  1. Conjugation and the periodic system of the elements

    NASA Astrophysics Data System (ADS)

    Shorygin, P. P.; Burshtein, Konstantin Ya

    1991-01-01

    The knowledge of the characteristics and mechanisms of the interaction of the active centres of complex molecules is of primary importance for the development of theoretical and applied organic chemistry, promotes a more productive utilisation of the enormous amount of experimental data available, facilitates predictions and the search for new routes to and new varieties of the synthesis, industrial technology, and applications of organic compounds, and leads to more complete ideas about their functions in chemical, physical, and physiological processes. The studies in this field have been subjected to a critical survey and attention has been paid to the possibility of distinguishing different forms of the mutual influence of atomic groups, the establishment of correlations between different parameters of conjugation and of the role of relativistic effects, the characteristics of conjugation systems incorporating heteroatoms from different groups in the Periodic System, and the study of the evolution of excited molecules. The bibliography includes 188 references.

  2. The integrated conjugative plasmid pSAM2 of Streptomyces ambofaciens is related to temperate bacteriophages.

    PubMed

    Boccard, F; Smokvina, T; Pernodet, J L; Friedmann, A; Guérineau, M

    1989-03-01

    Streptomyces ambofaciens ATCC23877 and derivatives contain the 11-kb element pSAM2 present in an integrated state or as a free and integrated plasmid. This element, able to integrate site-specifically in the genome of different Streptomyces species, is conjugative and mobilizes chromosomal markers. Besides these plasmid functions, we have shown that the site-specific recombination system of pSAM2 presents strong similarities with that of several temperate phages. The integration event is promoted by a site-specific recombinase of the integrase family. The int gene encoding this integrase is closely linked to the plasmid attachment site (attP). A small open reading frame (ORF) overlaps the int gene and the predicted protein exhibits similarities with Xis proteins involved in phages excision. The integrated copy of pSAM2 in strain ATCC23877 is flanked by att sequences (attL and attR). Another att sequence (attX) is present in this strain and attX and attL are the boundaries of a 42-kb fragment (xSAM1) absent, as well as pSAM2, from S.ambofaciens DSM40697. Sequences partially similar to pSAM2 int gene are found near the chromosomal integration zone in both S.ambofaciens strains. The possible origin of pSAM2, an element carrying plasmid as well as phage features, is discussed.

  3. 2D resistivity inversion using conjugate gradients for a finite element discretization

    NASA Astrophysics Data System (ADS)

    Bortolozo, C. A.; Santos, F. M.; Porsani, J. L.

    2014-12-01

    In this work we present a DC 2D inversion algorithm using conjugate gradients relaxation to solve the maximum likelihood inverse equations. We apply, according to Zhang (1995), the maximum likelihood inverse theory developed by Tarantola and Valette (1982) to our 2D resistivity inversion. This algorithm was chosen to this research because it doesn't need to calculate the field's derivatives. Since conjugate gradient techniques only need the results of the sensitivity matrix à or its transpose ÃT multiplying a vector, the actual computation of the sensitivity matrix are not performed, according to the methodology described in Zhang (1995). In Zhang (1995), the terms Ãx and ÃTy, are dependent of the stiffness matrix K and its partial derivative ∂K⁄∂ρ. The inversion methodology described in Zhang (1995) is for the case of 3D electrical resistivity by finite differences discretization. So it was necessary to make a series of adjustments to obtain a satisfactory result for 2D electrical inversion using finite element method. The difference between the modeling of 3D resistivity with finite difference and the 2D finite element method are in the integration variable, used in the 2D case. In the 2D case the electrical potential are initially calculated in the transformed domain, including the stiffness matrix, and only in the end is transformed in Cartesian domain. In the case of 3D, described by Zhang (1995) this is done differently, the calculation is done directly in the Cartesian domain. In the literature was not found any work describing how to deal with this problem. Because the calculations of Ãx and ÃTy must be done without having the real stiffness matrix, the adaptation consist in calculate the stiffness matrix and its partial derivative using a set of integration variables. We transform those matrix in the same form has in the potential case, but with different sets of variables. The results will be presented and are very promising.

  4. Bacteroides mobilizable and conjugative genetic elements: antibiotic resistance among clinical isolates.

    PubMed

    Quesada-Gómez, Carlos

    2011-12-01

    The conjugation is one of the most important mechanisms of horizontal gene transfer in prokaryotes, leading to genetic variation within a species and the acquisition of new traits, such as antibiotic resistance. Bacteroides is an obligate anaerobe of the colon and a significant opportunistic pathogen. Antibiotic resistance among Bacteroides spp. is rapidly increasing, largely due to the dissemination of DNA transfer factors (plasmids and transposons) harbored by members of this genus. Transfer factors can be divided into two classes, conjugative and mobilizable. Species of the intestinal Bacteroides have yielded different resistance plasmids, all of which have been intensely studied, the plasmids encode high-level MLS resistance conferred by a conserved erm gene. It has been reported an interesting observation associated with the transfer of several of these types of elements, all of which conferred Tcr and displayed greatly increased transfer efficiency following exposure to tetracycline. Many of the conjugative transposons (CTns) in Bacteroides are related to various genetic elements (such as CTnDOT, CTnERL, NBU and others). CTnDOT carries a tetracycline resistance gene, tetQ, and an erythromycin resistance gene, ermF. Resistance to drugs used to treat Bacteroides infections, such as clindamycin, has also been increasing. These conjugal elements have been found in Bacteroides clinical isolates. Thus, horizontal gene transfer could conceivably have played a role in the rising incidence of resistance in this bacterial group.

  5. Networking in microbes: conjugative elements and plasmids in the genus Alteromonas.

    PubMed

    López-Pérez, Mario; Ramon-Marco, Nieves; Rodriguez-Valera, Francisco

    2017-01-05

    To develop evolutionary models for the free living bacterium Alteromonas the genome sequences of isolates of the genus have been extensively analyzed. However, the main genetic exchange drivers in these microbes, conjugative elements (CEs), have not been considered in detail thus far. In this work, CEs have been searched in several complete Alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. Six genomes are reported here for the first time. We have found nine different plasmids of sizes ranging from 85 to 600 Kb, most of them were found in a single strain. Networks of gene similarity could be established among six of the plasmids that were also connected with another cluster of plasmids found in Shewanella strains. The cargo genes found in these plasmids included cassettes found before in chromosome flexible genomic islands of Alteromonas strains. We describe also the plasmids pAMCP48-600 and pAMCP49-600, the largest found in Alteromonas thus far (ca. 600 Kb) and containing all the hallmarks to be classified as chromids. We found in them some housekeeping genes and a cluster that code for an exocellular polysaccharide. They could represent the transport vectors for the previously described replacement flexible genomic islands. Integrative and conjugative elements (ICEs) were more common than plasmids and showed similar patterns of variation with cargo genes coding for components of additive flexible genomic islands. A nearly identical ICE was found in A. mediterranea MED64 and Vibrio cholera AHV1003 isolated from a human pathogen, indicating the potential exchange of these genes across phylogenetic distances exceeding the family threshold. We have seen evidence of how CEs can be vectors to transfer gene cassettes acquired in the chromosomal flexible genomic islands, both of the additive and replacement kind. These CEs showed evidence of how genetic material is exchanged among members of the same species but also

  6. Conjugal mobilization of the mega element carrying mef(E) from Streptococcus salivarius to Streptococcus pneumoniae.

    PubMed

    Santagati, Maria; Lupo, Agnese; Scillato, Marina; Di Martino, Andrea; Stefani, Stefania

    2009-01-01

    We report the isolation and characterization of an unusual strain of Streptococcus salivarius, 3C30, displaying both the macrolide-lincosamide-streptogramin B and the tetracycline resistance phenotypes. It harbours the mef(E), erm(B), and tet(M) genes carried by different genetic elements. The genetic element carrying mef(E), named mega, was investigated by long PCR and sequencing, while the presence of the Tn3872-like element, carrying tet(M) and erm(B), was demonstrated by sequencing of both the int-xis-Tn and the fragment between the two resistance genes. In strain 3C30 the mega element is 5388 bp in size and its nucleotide sequence is identical to that of the element described previously in S. salivarius, with the exception of a 912 bp deletion at the left end. The composite Tn3872-like element appeared to be nonconjugative while the mega element was transferred by conjugation to Streptococcus pneumoniae. It was, however, impossible to transfer it again from these transconjugants to other strains. In addition, only in the 3C30 strain did mega form circular structures, as identified by real-time PCR. In conclusion, we found a clinical strain of S. salivarius carrying both mega and Tn3872-like genetic elements. Mega is transferable by conjugation to S. pneumoniae but it is not transferable again from the transconjugants, suggesting a possible mobilization by recombinases of the coresident Tn3872-like transposon.

  7. Integral volumetric imaging using decentered elemental lenses.

    PubMed

    Sawada, Shimpei; Kakeya, Hideki

    2012-11-05

    This paper proposes a high resolution integral imaging system using a lens array composed of non-uniform decentered elemental lenses. One of the problems of integral imaging is the trade-off relationship between the resolution and the number of views. When the number of views is small, motion parallax becomes strongly discrete to maintain the viewing angle. In order to overcome this trade-off, the proposed method uses the elemental lenses whose size is smaller than that of the elemental images. To keep the images generated by the elemental lenses at constant depth, the lens array is designed so that the optical centers of elemental lenses may be located in the centers of elemental images, not in the centers of elemental lenses. To compensate optical distortion, new image rendering algorithm is developed so that undistorted 3D image may be presented with a non-uniform lens array. The proposed design of lens array can be applied to integral volumetric imaging, where display panels are layered to show volumetric images in the scheme of integral imaging.

  8. Characterization of Three Novel SXT/R391 Integrating Conjugative Elements ICEMfuInd1a and ICEMfuInd1b, and ICEMprChn1 Identified in the Genomes of Marinomonas fungiae JCM 18476T and Marinomonas profundimaris Strain D104

    PubMed Central

    Badhai, Jhasketan; Das, Subrata K.

    2016-01-01

    The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476T (ICEMfuInd1a and ICEMfuInd1b) and in Marinomonas profundimaris strain D104 (ICEMprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICEMfuInd1b and ICEMprChn1 were inserted into the genome at 5′-end of an typical host prfC gene, while ICEMfuInd1a was inserted at 5′-end of an atypical hipA-like gene. Despite their coexistence, the ICEMfuInd1a and ICEMfuInd1b were not present in a tandem fashion in the genome of M. fungiae. Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their evolution from a common SXT ancestor. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE into the M. fungiae genome due to mutations. Our analysis showed the presence of 16, 25, and 27 variable genes in the hotspots of ICEMfuInd1a, ICEMfuInd1b, and ICEMprChn1, respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hotspot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in either of the two ICEs from M. fungiae but were present within a transposon cassette in the HS-1 of the ICEMprChn1 from M

  9. Characterization of Three Novel SXT/R391 Integrating Conjugative Elements ICEMfuInd1a and ICEMfuInd1b, and ICEMprChn1 Identified in the Genomes of Marinomonas fungiae JCM 18476T and Marinomonas profundimaris Strain D104

    DOE PAGES

    Badhai, Jhasketan; Das, Subrata K.

    2016-11-25

    The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476T (ICEMfuInd1a and ICEMfuInd1b) and in Marinomonas profundimaris strain D104 (ICEMprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICEMfuInd1b and ICEMprChn1 were inserted into themore » genome at 5'-end of an typical host prfC gene, while ICEMfuInd1a was inserted at 5'-end of an atypical hipA-like gene. Despite their coexistence, the ICEMfuInd1a and ICEMfuInd1b were not present in a tandem fashion in the genome of M. fungiae. Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their evolution from a common SXT ancestor. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE into the M. fungiae genome due to mutations. Our analysis showed the presence of 16, 25, and 27 variable genes in the hotspots of ICEMfuInd1a, ICEMfuInd1b, and ICEMprChn1, respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hot spot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in either of the two ICEs from M. fungiae but were present within a transposon cassette in the HS-1 of the ICEMprChn1 from M

  10. Finite elements and the method of conjugate gradients on a concurrent processor

    NASA Technical Reports Server (NTRS)

    Lyzenga, G. A.; Raefsky, A.; Hager, B. H.

    1984-01-01

    An algorithm for the iterative solution of finite element problems on a concurrent processor is presented. The method of conjugate gradients is used to solve the system of matrix equations, which is distributed among the processors of a MIMD computer according to an element-based spatial decomposition. This algorithm is implemented in a two-dimensional elastostatics program on the Caltech Hypercube concurrent processor. The results of tests on up to 32 processors show nearly linear concurrent speedup, with efficiencies over 90% for sufficiently large problems.

  11. Functional analysis of a bacitracin resistance determinant located on ICECp1, a novel Tn916-like element from a conjugative plasmid in Clostridium perfringens.

    PubMed

    Han, Xiaoyan; Du, Xiang-Dang; Southey, Luke; Bulach, Dieter M; Seemann, Torsten; Yan, Xu-Xia; Bannam, Trudi L; Rood, Julian I

    2015-11-01

    Bacitracins are mixtures of structurally related cyclic polypeptides with antibiotic properties. They act by interfering with the biosynthesis of the bacterial cell wall. In this study, we analyzed an avian necrotic enteritis strain of Clostridium perfringens that was resistant to bacitracin and produced NetB toxin. We identified a bacitracin resistance locus that resembled a bacitracin resistance determinant from Enterococcus faecalis. It contained the structural genes bcrABD and a putative regulatory gene, bcrR. Mutagenesis studies provided evidence that both bcrA and bcrB are essential for bacitracin resistance, and that evidence was supported by the results of experiments in which the introduction of both the bcrA and bcrB genes into a bacitracin-susceptible C. perfringens strain was required to confer bacitracin resistance. The wild-type strain was shown to contain at least three large, putatively conjugative plasmids, and the bcrRABD locus was localized to an 89.7-kb plasmid, pJIR4150. This plasmid was experimentally shown to be conjugative and was sequenced. The sequence revealed that it also carries a tpeL toxin gene and is related to the pCW3 family of conjugative antibiotic resistance and toxin plasmids from C. perfringens. The bcr genes were located on a genetic element, ICECp1, which is related to the Tn916 family of integrative conjugative elements (ICEs). ICECp1 appears to be the first Tn916-like element shown to confer bacitracin resistance. In summary, we identified in a toxin-producing C. perfringens strain a novel mobile bacitracin resistance element which was experimentally shown to be essential for bacitracin resistance and is carried by a putative ICE located on a conjugative plasmid.

  12. Characterization of Three Novel SXT/R391 Integrating Conjugative Elements ICEMfuInd1a and ICEMfuInd1b, and ICEMprChn1 Identified in the Genomes of Marinomonas fungiae JCM 18476T and Marinomonas profundimaris Strain D104

    SciTech Connect

    Badhai, Jhasketan; Das, Subrata K.

    2016-11-25

    The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476T (ICEMfuInd1a and ICEMfuInd1b) and in Marinomonas profundimaris strain D104 (ICEMprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICEMfuInd1b and ICEMprChn1 were inserted into the genome at 5'-end of an typical host prfC gene, while ICEMfuInd1a was inserted at 5'-end of an atypical hipA-like gene. Despite their coexistence, the ICEMfuInd1a and ICEMfuInd1b were not present in a tandem fashion in the genome of M. fungiae. Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their evolution from a common SXT ancestor. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE into the M. fungiae genome due to mutations. Our analysis showed the presence of 16, 25, and 27 variable genes in the hotspots of ICEMfuInd1a, ICEMfuInd1b, and ICEMprChn1, respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hot spot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in

  13. Integrating Protein Engineering and Bioorthogonal Click Conjugation for Extracellular Vesicle Modulation and Intracellular Delivery

    PubMed Central

    Wang, Ming; Altinoglu, Sarah; Takeda, Yuji S.; Xu, Qiaobing

    2015-01-01

    Exosomes are small, cell-secreted vesicles that transfer proteins and genetic information between cells. This intercellular transmission regulates many physiological and pathological processes. Therefore, exosomes have emerged as novel biomarkers for disease diagnosis and as nanocarriers for drug delivery. Here, we report an easy-to-adapt and highly versatile methodology to modulate exosome composition and conjugate exosomes for intracellular delivery. Our strategy combines the metabolic labeling of newly synthesized proteins or glycan/glycoproteins of exosome-secreting cells with active azides and bioorthogonal click conjugation to modify and functionalize the exosomes. The azide-integrated can be conjugated to a variety of small molecules and proteins and can efficiently deliver conjugates into cells. The metabolic engineering of exosomes diversifies the chemistry of exosomes and expands the functions that can be introduced into exosomes, providing novel, powerful tools to study the roles of exosomes in biology and expand the biomedical potential of exosomes. PMID:26529317

  14. Importance of Mobile Genetic Elements and Conjugal Gene Transfer for Subsurface Microbial Community Adaptation to Biotransformation of Metals

    SciTech Connect

    Sorensen, Soren J.

    2005-06-01

    The overall goal of this project is to investigate the effect of mobile genetic elements and conjugal gene transfer on subsurface microbial community adaptation to mercury and chromium stress and biotransformation. Our studies focus on the interaction between the fate of these metals in the subsurface and the microbial community structure and activity.

  15. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements

    PubMed Central

    Iyer, Lakshminarayan M.; Burroughs, A. Maxwell; Anand, Swadha; de Souza, Robson F.

    2017-01-01

    ABSTRACT Intense biological conflicts between prokaryotic genomes and their genomic parasites have resulted in an arms race in terms of the molecular “weaponry” deployed on both sides. Using a recursive computational approach, we uncovered a remarkable class of multidomain proteins with 2 to 15 domains in the same polypeptide deployed by viruses and plasmids in such conflicts. Domain architectures and genomic contexts indicate that they are part of a widespread conflict strategy involving proteins injected into the host cell along with parasite DNA during the earliest phase of infection. Their unique feature is the combination of domains with highly disparate biochemical activities in the same polypeptide; accordingly, we term them polyvalent proteins. Of the 131 domains in polyvalent proteins, a large fraction are enzymatic domains predicted to modify proteins, target nucleic acids, alter nucleotide signaling/metabolism, and attack peptidoglycan or cytoskeletal components. They further contain nucleic acid-binding domains, virion structural domains, and 40 novel uncharacterized domains. Analysis of their architectural network reveals both pervasive common themes and specialized strategies for conjugative elements and plasmids or (pro)phages. The themes include likely processing of multidomain polypeptides by zincin-like metallopeptidases and mechanisms to counter restriction or CRISPR/Cas systems and jump-start transcription or replication. DNA-binding domains acquired by eukaryotes from such systems have been reused in XPC/RAD4-dependent DNA repair and mitochondrial genome replication in kinetoplastids. Characterization of the novel domains discovered here, such as RNases and peptidases, are likely to aid in the development of new reagents and elucidation of the spread of antibiotic resistance. IMPORTANCE This is the first report of the widespread presence of large proteins, termed polyvalent proteins, predicted to be transmitted by genomic parasites such as

  16. Elements of an integrated health monitoring framework

    NASA Astrophysics Data System (ADS)

    Fraser, Michael; Elgamal, Ahmed; Conte, Joel P.; Masri, Sami; Fountain, Tony; Gupta, Amarnath; Trivedi, Mohan; El Zarki, Magda

    2003-07-01

    Internet technologies are increasingly facilitating real-time monitoring of Bridges and Highways. The advances in wireless communications for instance, are allowing practical deployments for large extended systems. Sensor data, including video signals, can be used for long-term condition assessment, traffic-load regulation, emergency response, and seismic safety applications. Computer-based automated signal-analysis algorithms routinely process the incoming data and determine anomalies based on pre-defined response thresholds and more involved signal analysis techniques. Upon authentication, appropriate action may be authorized for maintenance, early warning, and/or emergency response. In such a strategy, data from thousands of sensors can be analyzed with near real-time and long-term assessment and decision-making implications. Addressing the above, a flexible and scalable (e.g., for an entire Highway system, or portfolio of Networked Civil Infrastructure) software architecture/framework is being developed and implemented. This framework will network and integrate real-time heterogeneous sensor data, database and archiving systems, computer vision, data analysis and interpretation, physics-based numerical simulation of complex structural systems, visualization, reliability & risk analysis, and rational statistical decision-making procedures. Thus, within this framework, data is converted into information, information into knowledge, and knowledge into decision at the end of the pipeline. Such a decision-support system contributes to the vitality of our economy, as rehabilitation, renewal, replacement, and/or maintenance of this infrastructure are estimated to require expenditures in the Trillion-dollar range nationwide, including issues of Homeland security and natural disaster mitigation. A pilot website (http://bridge.ucsd.edu/compositedeck.html) currently depicts some basic elements of the envisioned integrated health monitoring analysis framework.

  17. Construction of two selectable markers for integrative/conjugative plasmids in Flavobacterium columnare

    NASA Astrophysics Data System (ADS)

    Zhang, Jin; Zou, Hong; Wang, Liangfa; Huang, Bei; Li, Nan; Wang, Guitang; Nie, Pin

    2012-03-01

    Flavobacterium columnare, the etiological agent of columnaris disease, is one of the most important and widespread bacterial pathogens of freshwater fish. In this study, we constructed two artificial selectable markers (chloramphenicol and spectinomycin resistance) for gene transfer in F. columnare. These two new artificial selectable markers, which were created by placing the chloramphenicol or spectinomycin resistance gene under the control of the native acs regulatory region of F. columnare, were functional in both F. columnare and Escherichia coli. The integrative/conjugative plasmids constructed by using these markers were introduced into F. columnare G4 via electroporation or conjugation. The integrated plasmid DNA was confirmed by Southern blotting and PCR analysis. These two markers can be employed in future investigations into gene deletion and the pathogenicity of virulence factors in F. columnare.

  18. International Space Station Multi-Element Integrated Test

    NASA Technical Reports Server (NTRS)

    Filler, Russell E.; Stone, Brock R. (Technical Monitor)

    1999-01-01

    The International Space Station offers a unique challenge for integrated testing since the entire station is not launched as an integrated vehicle. The ISS design evolved for over 10 years from the station Freedom program that was based on a "ship and shoot" approach. Ship and shoot assumed the program would accept the hardware for launch and integrate the vehicle on orbit without any ground element-to-element integrated testing. Element-to-Element powered-on integrated testing is needed to identify operational problems on the ground rather than once the hardware is on orbit. The industry is accustomed to testing an integrated vehicle and then verifying it is ready for its operational missions. These tests require ground element emulators to represent on-orbit elements. The ISS Multi-Element Integrated Tests (MEIT) are element-to-element integrated tests bringing together hardware representing several flights. The major purpose of these tests is: 1) Element-to-Element interface compatibility, 2) Systems end-to-end operability and functionality and 3) utilize on-orbit procedures with the crew and mission control center. Execution of these tests is critical since the hardware is available for only a limited period of time. Test configurations are defined which test specific interfaces or functionality. These tests develop operational confidence in the Element-to-Element interfaces and identify major problems on the ground to avoid on-orbit anomalies that could threaten mission success, element survivability or assembly activities. This paper addresses the MEIT process, configurations and lessons-learned from these tests.

  19. Applications of DNA integrating elements: Facing the bias bully

    PubMed Central

    de Jong, Johann; Wessels, Lodewyk F A; van Lohuizen, Maarten; de Ridder, Jeroen; Akhtar, Waseem

    2014-01-01

    Retroviruses and DNA transposons are an important part of molecular biologists' toolbox. The applications of these elements range from functional genomics to oncogene discovery and gene therapy. However, these elements do not integrate uniformly across the genome, which is an important limitation to their use. A number of genetic and epigenetic factors have been shown to shape the integration preference of these elements. Insight into integration bias can significantly enhance the analysis and interpretation of results obtained using these elements. For three different applications, we outline how bias can affect results, and can potentially be addressed. PMID:26442173

  20. 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 analysis is presented. New thermal finite elements which yield exact nodal and element temperatures 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.

  1. 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.

  2. Numerical orbit integration efficiency of the Delaunay-Similar elements

    NASA Technical Reports Server (NTRS)

    Pierce, S.

    1974-01-01

    Orbit equations with a set of conservative and a set of nonconservative perturbing potentials were considered. Scheifele's DS formulation of these equations has dependent variables similar to Delaunay's orbital elements with the true anomaly as the independent variable. Efficiency curves of computing cost v.s. accuracy were constructed for Adams integrators of order of 2 through 15 with several correcting algorithms and for a Runga-Kutta integrator. Considering stability regions, choices were made for the optimally efficient integration modes for the DS elements. Integrating in these modes reduces computing costs for a specified accuracy.

  3. A finite element: Boundary integral method for electromagnetic scattering. Ph.D. Thesis Technical Report, Feb. - Sep. 1992

    NASA Technical Reports Server (NTRS)

    Collins, J. D.; Volakis, John L.

    1992-01-01

    A method that combines the finite element and boundary integral techniques for the numerical solution of electromagnetic scattering problems is presented. The finite element method is well known for requiring a low order storage and for its capability to model inhomogeneous structures. Of particular emphasis in this work is the reduction of the storage requirement by terminating the finite element mesh on a boundary in a fashion which renders the boundary integrals in convolutional form. The fast Fourier transform is then used to evaluate these integrals in a conjugate gradient solver, without a need to generate the actual matrix. This method has a marked advantage over traditional integral equation approaches with respect to the storage requirement of highly inhomogeneous structures. Rectangular, circular, and ogival mesh termination boundaries are examined for two-dimensional scattering. In the case of axially symmetric structures, the boundary integral matrix storage is reduced by exploiting matrix symmetries and solving the resulting system via the conjugate gradient method. In each case several results are presented for various scatterers aimed at validating the method and providing an assessment of its capabilities. Important in methods incorporating boundary integral equations is the issue of internal resonance. A method is implemented for their removal, and is shown to be effective in the two-dimensional and three-dimensional applications.

  4. Submillimeter Quasioptical Josephson Junction Oscillator with Integrated Tuning Elements

    DTIC Science & Technology

    1994-04-30

    demonstrate a Quasioptical Josephson Oscillator with Integratd Tuning Elements using standard Conductus niobium. technology. T~his device is based on a...Elements Contract #F49620-93-C0037 AE$.R 94 0347 Aleksandar Pance Conductus , Inc. Approved for public release; (408) 524 9820 distribution unlimited...Report Summary The goal of this program was to demonstrate a Quasioptical Josephson Oscillator with Integrated Tuning Elements using standard Conductus

  5. ESOH: The Hidden Integrated Logistics Support Element

    DTIC Science & Technology

    2010-06-01

    Air Warfare Center -Weapons Division,NAWCWD 6.7.1.4,1 Administration Circle Stop 1002 ,China Lake ,CA,93555-6100 8. PERFORMING ORGANIZATION REPORT...Reliability-Centered Maintenance (RCM) – Level of Repair Analysis (LORA) – Integrated Maintenance Concept (IMC) – Diminishing Manufacturing Sources...Replacement TT-L-20 LACQUER, CAMOUFLAGE (S/S BY A-A-3164) A-A-3164 TT-L-26 LACQUER (BRUSHING, CLEAR AND PIGMENTED FOR EXTERIOR AND INTERIOR USE) (NO S/S

  6. Photochemically Generated Elemental Selenium Forms Conjugates with Serum Proteins that Are Preferentially Cytotoxic to Leukemia and Selected Solid Tumor Cells

    PubMed Central

    Daziano, Jean-Pierre; Günther, Wolfgang H.H.; Krieg, Marianne; Tsujino, Ichiro; Miyagi, Kiyoko; Anderson, Gregory S.; Sampson, Reynée W.; Ostrowski, Martin D.; Muir, Sarah A.; Bula, Raymond J.; Sieber, Fritz

    2012-01-01

    The objective of this study was to determine if and how photoproducts contribute to the anti-tumor effect of merocyanine-mediated PDT. A panel of barbituric, thiobarbituric and selenobarbituric acid analogues of Merocyanine 540 was photobleached, and the resulting photoproducts were characterized by absorption, fluorescence emission, mass, energy dispersive X-ray, and X-ray photoelectron spectroscopy, and tested for cytotoxic activity against tumor cell lines and freshly explanted bone marrow cells. While all dyes were readily photobleached, only photoproducts of selone dyes showed cytotoxic activity. One-hour incubations with micromolar concentrations of selone-derived photoproducts were sufficient to reduce leukemia/lymphoma cells ≥10,000 fold while preserving virtually all normal CD34-positive bone marrow cells. Of 6 multi-drug resistant tumor cell lines tested, 5 were as sensitive or more sensitive to photoproducts than the corresponding wild-type lines. Physicochemical characterizations of the cytotoxic activity indicated that it consisted of conjugates of subnano particles of elemental selenium and (lipo)proteins. The discovery of cytotoxic Se-protein conjugates provides a rare example of photoproducts contributing substantially to the anti-tumor effect of PDT and challenges the long-held view that Se in oxidation state zero is biologically inert. Agents modeled after our Se-protein conjugates may prove useful for the treatment of leukemia. PMID:22211823

  7. A finite element boundary integral formulation for radiation and scattering by cavity antennas using tetrahedral elements

    NASA Technical Reports Server (NTRS)

    Gong, J.; Volakis, J. L.; Chatterjee, A.; Jin, J. M.

    1992-01-01

    A hybrid finite element boundary integral formulation is developed using tetrahedral and/or triangular elements for discretizing the cavity and/or aperture of microstrip antenna arrays. The tetrahedral elements with edge based linear expansion functions are chosen for modeling the volume region and triangular elements are used for discretizing the aperture. The edge based expansion functions are divergenceless thus removing the requirement to introduce a penalty term and the tetrahedral elements permit greater geometrical adaptability than the rectangular bricks. The underlying theory and resulting expressions are discussed in detail together with some numerical scattering examples for comparison and demonstration.

  8. Treatment of domain integrals in boundary element methods

    SciTech Connect

    Nintcheu Fata, Sylvain

    2012-01-01

    A systematic and rigorous technique to calculate domain integrals without a volume-fitted mesh has been developed and validated in the context of a boundary element approximation. In the proposed approach, a domain integral involving a continuous or weakly-singular integrand is first converted into a surface integral by means of straight-path integrals that intersect the underlying domain. Then, the resulting surface integral is carried out either via analytic integration over boundary elements or by use of standard quadrature rules. This domain-to-boundary integral transformation is derived from an extension of the fundamental theorem of calculus to higher dimension, and the divergence theorem. In establishing the method, it is shown that the higher-dimensional version of the first fundamental theorem of calculus corresponds to the well-known Poincare lemma. The proposed technique can be employed to evaluate integrals defined over simply- or multiply-connected domains with Lipschitz boundaries which are embedded in an Euclidean space of arbitrary but finite dimension. Combined with the singular treatment of surface integrals that is widely available in the literature, this approach can also be utilized to effectively deal with boundary-value problems involving non-homogeneous source terms by way of a collocation or a Galerkin boundary integral equation method using only the prescribed surface discretization. Sample problems associated with the three-dimensional Poisson equation and featuring the Newton potential are successfully solved by a constant element collocation method to validate this study.

  9. Adaptive Through-Thickness Integration Strategy for Shell Elements

    NASA Astrophysics Data System (ADS)

    Burchitz, I. A.; Meinders, T.; Huétink, J.

    2007-05-01

    Reliable numerical prediction of springback in sheet metal forming is essential for the automotive industry. There are numerous factors that influence the accuracy of springback prediction by using the finite element method. One of the reasons is the through-thickness numerical integration of shell elements. It is known that even for simple problems the traditional integration schemes may require up to 50 integration points to achieve a high accuracy of springback analysis. An adaptive through-thickness integration strategy can be a good alternative. The strategy defines abscissas and weights depending on the integrand's properties and, thus, can adapt itself to improve the accuracy of integration. A concept of the adaptive through-thickness integration strategy for shell elements is presented. It is tested using a simple problem of bending of a beam under tension. Results show that for a similar set of material and process parameters the adaptive Simpson's rule with 7 integration points performs better than the traditional trapezoidal rule with 50 points. The adaptive through-thickness integration strategy for shell elements can improve the accuracy of springback prediction at minimal costs.

  10. The Conjugative Relaxase TrwC Promotes Integration of Foreign DNA in the Human Genome.

    PubMed

    González-Prieto, Coral; Gabriel, Richard; Dehio, Christoph; Schmidt, Manfred; Llosa, Matxalen

    2017-06-15

    Bacterial conjugation is a mechanism of horizontal DNA transfer. The relaxase TrwC of the conjugative plasmid R388 cleaves one strand of the transferred DNA at the oriT gene, covalently attaches to it, and leads the single-stranded DNA (ssDNA) into the recipient cell. In addition, TrwC catalyzes site-specific integration of the transferred DNA into its target sequence present in the genome of the recipient bacterium. Here, we report the analysis of the efficiency and specificity of the integrase activity of TrwC in human cells, using the type IV secretion system of the human pathogen Bartonella henselae to introduce relaxase-DNA complexes. Compared to Mob relaxase from plasmid pBGR1, we found that TrwC mediated a 10-fold increase in the rate of plasmid DNA transfer to human cells and a 100-fold increase in the rate of chromosomal integration of the transferred DNA. We used linear amplification-mediated PCR and plasmid rescue to characterize the integration pattern in the human genome. DNA sequence analysis revealed mostly reconstituted oriT sequences, indicating that TrwC is active and recircularizes transferred DNA in human cells. One TrwC-mediated site-specific integration event was detected, proving that TrwC is capable of mediating site-specific integration in the human genome, albeit with very low efficiency compared to the rate of random integration. Our results suggest that TrwC may stabilize the plasmid DNA molecules in the nucleus of the human cell, probably by recircularization of the transferred DNA strand. This stabilization would increase the opportunities for integration of the DNA by the host machinery.IMPORTANCE Different biotechnological applications, including gene therapy strategies, require permanent modification of target cells. Long-term expression is achieved either by extrachromosomal persistence or by integration of the introduced DNA. Here, we studied the utility of conjugative relaxase TrwC, a bacterial protein with site

  11. Novel type of the elements of integrated diffractive optics

    NASA Astrophysics Data System (ADS)

    Minin, I. V.; Minin, O. V.; Shi, S.; Chen, C.; Mititu, J.; Prather, D.

    2006-05-01

    Novels diffractive element in the THz waveband offers the potential to realize novel types of devices for communications, sensing, integrated optics, networks, transmission lines, and so on. To this end, diffractive planar elements fabricated on non-flat surfaces make it possible to enrich the "pool of devices" for applications including integrated optics at different waveband, including THz, and to design elements with novel properties and potentials. This can be illustrated most clearly using as an example optical element such as that for optical polychromatic computers. For instance, the diffractive element discussed above can be used as a nonlinear device for polychromatic radiation or multiplexer or a focusing element with selectivity in the multimode regime. Frequency characteristics for such elements are determined by the extent of concavity (convexity) of the surface of the element and by the direction of incidence wave onto it. Therefore, when working on a wavelength λ is not equal to λ 0, the position of the focusing area in space (the amount of its displacement) and focusing properties should depend on the direction of incidence of the radiation. Hence, it is possible to distinguish between a signal incident on the "tip" of the element from that falling on its "base," simply by placing radiation receivers at the corresponding points in space. Thus, in this paper we will present detailed simulation results obtained using a parallel FDTD method and the application of the proposed device to focusing and frequency-selective properties of flat conical diffractive elements in THz waveband.

  12. Site-Specific Integration of Foreign DNA into Minimal Bacterial and Human Target Sequences Mediated by a Conjugative Relaxase

    PubMed Central

    Agúndez, Leticia; González-Prieto, Coral; Machón, Cristina; Llosa, Matxalen

    2012-01-01

    Background Bacterial conjugation is a mechanism for horizontal DNA transfer between bacteria which requires cell to cell contact, usually mediated by self-transmissible plasmids. A protein known as relaxase is responsible for the processing of DNA during bacterial conjugation. TrwC, the relaxase of conjugative plasmid R388, is also able to catalyze site-specific integration of the transferred DNA into a copy of its target, the origin of transfer (oriT), present in a recipient plasmid. This reaction confers TrwC a high biotechnological potential as a tool for genomic engineering. Methodology/Principal Findings We have characterized this reaction by conjugal mobilization of a suicide plasmid to a recipient cell with an oriT-containing plasmid, selecting for the cointegrates. Proteins TrwA and IHF enhanced integration frequency. TrwC could also catalyze integration when it is expressed from the recipient cell. Both Y18 and Y26 catalytic tyrosil residues were essential to perform the reaction, while TrwC DNA helicase activity was dispensable. The target DNA could be reduced to 17 bp encompassing TrwC nicking and binding sites. Two human genomic sequences resembling the 17 bp segment were accepted as targets for TrwC-mediated site-specific integration. TrwC could also integrate the incoming DNA molecule into an oriT copy present in the recipient chromosome. Conclusions/Significance The results support a model for TrwC-mediated site-specific integration. This reaction may allow R388 to integrate into the genome of non-permissive hosts upon conjugative transfer. Also, the ability to act on target sequences present in the human genome underscores the biotechnological potential of conjugative relaxase TrwC as a site-specific integrase for genomic modification of human cells. PMID:22292089

  13. A general time element using Cartesian coordinates: Eccentric orbit integration

    NASA Technical Reports Server (NTRS)

    Janin, G.

    1980-01-01

    A general time element, valid with any arbitrary independent variables, and used with Cartesian coordinates for the integration of the elliptic motion in orbits, is examined. The derivation of the time element from a set of canonical elements of the Delaunay type, developed in the extended phase space, is presented. The application of the method using an example of a transfer orbit for a geosynchronous mission is presented. The eccentric and elliptic anomaly are utilized as the independent variable. The reduction of the in track error resulting from using Cartesian coordinates with the time element is reported.

  14. Identification of a methyl-specific restriction system mediated by a conjugative element from Streptomyces bambergiensis.

    PubMed Central

    Zotchev, S B; Schrempf, H; Hutchinson, C R

    1995-01-01

    pBL2 was identified genetically but not physically in Streptomyces lividans after its mating with S. bambergiensis. During conjugation, pBL2 was transferred at high frequency to S. lividans and S. coelicolor. pBL2.1 DNA isolated from S. coelicolor exconjugants as a circular plasmid was shown to derive from the genome of S. bambergiensis. S. lividans carrying pBL2 or pBL2.1 acquired a methyl-specific restriction (MsrA+) phenotype. The corresponding enzyme was partially purified and shown to resemble a class II endonuclease which cleaves Dam-methylated DNA preferentially. PMID:7642510

  15. Integration Site Selection by the Bacteroides Conjugative Transposon CTnBST▿

    PubMed Central

    Song, Bo; Shoemaker, Nadja B.; Gardner, Jeffrey F.; Salyers, Abigail A.

    2007-01-01

    A newly discovered Bacteroides conjugative transposon (CTn), CTnBST, integrates more site specifically than two other well-studied CTns, the Bacteroides CTn CTnDOT and the enterococcal CTn Tn916. Moreover, the integrase of CTnBST, IntBST, had the C-terminal 6-amino-acid signature that is associated with the catalytic regions of members of the tyrosine recombinase family, most of which integrate site specifically. Also, in most of these integrases, all of the conserved amino acids are required for integration. In the case of IntBST, however, we found that changing three of the six conserved amino acids in the signature, one of which was the presumed catalytic tyrosine, resulted in a 1,000-fold decrease in integration frequency. Changes in the other amino acids had little or no effect. Thus, although the CTnBST integrase still seems to be a member of the tyrosine recombinase family, it clearly differs to some extent from other members of the family in its catalytic site. We also determined the sequence requirements for CTnBST integration in the 18-bp region where the crossover occurs preferentially during integration. We found that CTnBST integrates in this preferred site about one-half of the time but can also use other sites. A consensus sequence was tentatively derived by comparison of a few secondary sites: AATCTGNNAAAT. We report here that within the consensus region, no single base change affected the frequency of integration. However, 3 bp at one end of the consensus sequence (CTG) proved to be essential for integration into the preferred site. This sequence appeared to be at one end of a 7-bp crossover region, CTGNNAA. The other bases could vary without affecting either integration frequency or specificity. Thus, in contrast to well-studied site-specific recombinases which require homology throughout the crossover region, integration of CTnBST requires homology at one end of the crossover region but not at the other end. PMID:17616597

  16. A λ Cro-Like Repressor Is Essential for the Induction of Conjugative Transfer of SXT/R391 Elements in Response to DNA Damage.

    PubMed

    Poulin-Laprade, Dominic; Burrus, Vincent

    2015-12-01

    Integrative and conjugative elements (ICEs) of the SXT/R391 family are the main contributors to acquired multidrug resistance in the seventh pandemic lineage of Vibrio cholerae, the etiological agent of the diarrheal disease cholera. Conjugative transfer of SXT/R391 ICEs is triggered by antibiotics and agents promoting DNA damage through RecA-dependent autoproteolysis of SetR, an ICE-encoded λ CI-like repressor. Here, we describe the role of CroS, a distant λ Cro homolog, as a key component contributing to the regulation of expression of the activator SetCD that orchestrates the expression of the conjugative transfer genes. We show that deletion of croS abolishes the SOS response-dependent induction of SXT despite the presence of a functional setR gene. Using quantitative reverse transcription-PCR and lacZ reporter assays, we also show that CroS represses setR and setCD expression by binding to operator sites shared with SetR. Furthermore, we provide evidence of an additional operator site bound by SetR and CroS. Finally, we show that SetCD expression generates a positive feedback loop due to SXT excision and replication in a fraction of the cell population. Together, these results refine our understanding of the genetic regulation governing the propagation of major vectors of multidrug resistance. Healthcare systems worldwide are challenged by an alarming drug resistance crisis caused by the massive and rapid propagation of antibiotic resistance genes and the associated emergence of multidrug-resistant pathogenic bacteria. SXT/R391 ICEs contribute to this phenomenon not only in clinical and environmental vibrios but also in several members of the family Enterobacteriaceae. We have identified and characterized here the regulator CroS as a key factor in the stimulation of conjugative transfer of these ICEs in response to DNA-damaging agents. We have also untangled conflicting evidence regarding autoactivation of transfer by the master activator of SXT/R391 ICEs

  17. A λ Cro-Like Repressor Is Essential for the Induction of Conjugative Transfer of SXT/R391 Elements in Response to DNA Damage

    PubMed Central

    Poulin-Laprade, Dominic

    2015-01-01

    ABSTRACT Integrative and conjugative elements (ICEs) of the SXT/R391 family are the main contributors to acquired multidrug resistance in the seventh pandemic lineage of Vibrio cholerae, the etiological agent of the diarrheal disease cholera. Conjugative transfer of SXT/R391 ICEs is triggered by antibiotics and agents promoting DNA damage through RecA-dependent autoproteolysis of SetR, an ICE-encoded λ CI-like repressor. Here, we describe the role of CroS, a distant λ Cro homolog, as a key component contributing to the regulation of expression of the activator SetCD that orchestrates the expression of the conjugative transfer genes. We show that deletion of croS abolishes the SOS response-dependent induction of SXT despite the presence of a functional setR gene. Using quantitative reverse transcription-PCR and lacZ reporter assays, we also show that CroS represses setR and setCD expression by binding to operator sites shared with SetR. Furthermore, we provide evidence of an additional operator site bound by SetR and CroS. Finally, we show that SetCD expression generates a positive feedback loop due to SXT excision and replication in a fraction of the cell population. Together, these results refine our understanding of the genetic regulation governing the propagation of major vectors of multidrug resistance. IMPORTANCE Healthcare systems worldwide are challenged by an alarming drug resistance crisis caused by the massive and rapid propagation of antibiotic resistance genes and the associated emergence of multidrug-resistant pathogenic bacteria. SXT/R391 ICEs contribute to this phenomenon not only in clinical and environmental vibrios but also in several members of the family Enterobacteriaceae. We have identified and characterized here the regulator CroS as a key factor in the stimulation of conjugative transfer of these ICEs in response to DNA-damaging agents. We have also untangled conflicting evidence regarding autoactivation of transfer by the master activator

  18. Evidence of a conjugal erythromycin resistance element in the Lyme disease spirochete Borrelia burgdorferi

    PubMed Central

    Jackson, Charlene R.; Boylan, Julie; Frye, Jonathan G.; Gherardini, Frank C.

    2007-01-01

    We report the identification of isolates of Borrelia burgdorferi strain B31 that exhibit an unusual macrolide–lincosamide (ML) or macrolide–lincosamide–streptogramin A (MLSA) antibiotic resistance pattern. Low-passage isolates were resistant to high levels (>100 μg/mL) of erythromycin, spiramycin and the lincosamides but were sensitive to dalfopristin, an analogue of streptogramin B. Interestingly, the high-passage erythromycin-resistant strain B31 was resistant to quinupristin, an analogue of streptogramin A (25 μg/mL). Biochemical analysis revealed that resistance was not due to antibiotic inactivation or energy-dependent efflux but was instead due to modification of ribosomes in these isolates. Interestingly, we were able to demonstrate high-frequency transfer of the resistance phenotype via conjugation from B. burgdorferi to Bacillus subtilis (10−2–10−4) or Enterococcus faecalis (10−5). An intergeneric conjugal system in B. burgdorferi suggests that horizontal gene transfer may play a role in its evolution and is a potential tool for developing new genetic systems to study the pathogenesis of Lyme disease. PMID:17905571

  19. Asynchronous variational integration using continuous assumed gradient elements

    PubMed Central

    Wolff, Sebastian; Bucher, Christian

    2013-01-01

    Asynchronous variational integration (AVI) is a tool which improves the numerical efficiency of explicit time stepping schemes when applied to finite element meshes with local spatial refinement. This is achieved by associating an individual time step length to each spatial domain. Furthermore, long-term stability is ensured by its variational structure. This article presents AVI in the context of finite elements based on a weakened weak form (W2) Liu (2009) [1], exemplified by continuous assumed gradient elements Wolff and Bucher (2011) [2]. The article presents the main ideas of the modified AVI, gives implementation notes and a recipe for estimating the critical time step. PMID:23543620

  20. A general time element for orbit integration in Cartesian coordinates

    NASA Technical Reports Server (NTRS)

    Janin, G.; Bond, V. R.

    1981-01-01

    Two techniques are discussed for increasing the accuracy of the numerical integration of eccentric orbits in Cartesian coordinates. One involves the use of an independent variable different from time; this increases the efficiency of the numerical integration. The other uses a time element, which reduces the in-track error. A general expression is given of a time element valid for an arbitrary independent variable. It is pointed out that this time element makes it possible to switch the independent variable merely by applying a scaling factor; there is no need to change the differential equations of the motion. Eccentric, true, and elliptic anomalies are used as independent variables in the case of a transfer orbit for a geosynchronous orbit. The elliptic anomaly is shown to perform much better than the other classical anomalies.

  1. Elements of an advanced integrated operator control station

    SciTech Connect

    Clarke, M.M.; Kreifeldt, J.G.

    1984-01-01

    One of the critical determinants of peformance for any remotely operated maintenance system is the compatibility achieved between elements of the man/machine interface (e.g., master manipulator controller, controls, displays, etc.) and the human operator. In the Remote Control Engineering task of the Consolidated Fuel Reprocessing Program, considerable attention has been devoted to optimizing the man/machine interface of the operator control station. This system must be considered an integral element of the overall maintenance work system which includes transporters, manipulators, remote viewing, and other parts. The control station must reflect the integration of the operator team, control/display panels, manipulator master controllers, and remote viewing monitors. Human factors principles and experimentation have been used in the development of an advanced integrated operator control station designed for the advance servomanipulator. Key features of this next-generation design are summarized in this presentation. 7 references, 4 figures.

  2. Elements of an advanced integrated operator control station

    SciTech Connect

    Clarke, M.M.; Kreifeldt, J.G.

    1984-01-01

    One of the critical determinants of performance for any remotely operated maintenance system is the compatibility achieved between elements of the man/machine interface (e.g., master manipulator controller, controls, displays) and the human operator. In the remote control engineering task of the Consolidated Fuel Reprocessing Program, considerable attention has been devoted to optimizing the man/machine interface of the operator control station. This system must be considered an integral element of the overall maintenance work system which includes transporters, manipulators, remote viewing, and other parts. The control station must reflect the integration of the operator team, control/display panels, manipulator master controllers, and remote viewing monitors. Human factors principles and experimentation have been used in the development of an advanced integrated operator control station designed for the advance servomanipulator. Key features of this next-generation design are summarized in this presentation. 7 references, 4 figures.

  3. Social research design: framework for integrating philosophical and practical elements.

    PubMed

    Cunningham, Kathryn Burns

    2014-09-01

    To provide and elucidate a comprehensible framework for the design of social research. An abundance of information exists concerning the process of designing social research. The overall message that can be gleaned is that numerable elements - both philosophical (ontological and epistemological assumptions and theoretical perspective) and practical (issue to be addressed, purpose, aims and research questions) - are influential in the process of selecting a research methodology and methods, and that these elements and their inter-relationships must be considered and explicated to ensure a coherent research design that enables well-founded and meaningful conclusions. There is a lack of guidance concerning the integration of practical and philosophical elements, hindering their consideration and explication. The author's PhD research into loneliness and cancer. This is a methodology paper. A guiding framework that incorporates all of the philosophical and practical elements influential in social research design is presented. The chronological and informative relationships between the elements are discussed. The framework presented can be used by social researchers to consider and explicate the practical and philosophical elements influential in the selection of a methodology and methods. It is hoped that the framework presented will aid social researchers with the design and the explication of the design of their research, thereby enhancing the credibility of their projects and enabling their research to establish well-founded and meaningful conclusions.

  4. A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins

    PubMed Central

    Coluzzi, Charles; Guédon, Gérard; Devignes, Marie-Dominique; Ambroset, Chloé; Loux, Valentin; Lacroix, Thomas; Payot, Sophie; Leblond-Bourget, Nathalie

    2017-01-01

    Recent analyses of bacterial genomes have shown that integrated elements that transfer by conjugation play an essential role in horizontal gene transfer. Among these elements, the integrative and mobilizable elements (IMEs) are known to encode their own excision and integration machinery, and to carry all the sequences or genes necessary to hijack the mating pore of a conjugative element for their own transfer. However, knowledge of their prevalence and diversity is still severely lacking. In this work, an extensive analysis of 124 genomes from 27 species of Streptococcus reveals 144 IMEs. These IMEs encode either tyrosine or serine integrases. The identification of IME boundaries shows that 141 are specifically integrated in 17 target sites. The IME-encoded relaxases belong to nine superfamilies, among which four are previously unknown in any mobilizable or conjugative element. A total of 118 IMEs are found to encode a non-canonical relaxase related to rolling circle replication initiators (belonging to the four novel families or to MobT). Surprisingly, among these, 83 encode a TcpA protein (i.e., a non-canonical coupling protein (CP) that is more closely related to FtsK than VirD4) that was not previously known to be encoded by mobilizable elements. Phylogenetic analyses reveal not only many integration/excision module replacements but also losses, acquisitions or replacements of TcpA genes between IMEs. This glimpse into the still poorly known world of IMEs reveals that mobilizable elements have a very high prevalence. Their diversity is even greater than expected, with most encoding a CP and/or a non-canonical relaxase. PMID:28373865

  5. A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins.

    PubMed

    Coluzzi, Charles; Guédon, Gérard; Devignes, Marie-Dominique; Ambroset, Chloé; Loux, Valentin; Lacroix, Thomas; Payot, Sophie; Leblond-Bourget, Nathalie

    2017-01-01

    Recent analyses of bacterial genomes have shown that integrated elements that transfer by conjugation play an essential role in horizontal gene transfer. Among these elements, the integrative and mobilizable elements (IMEs) are known to encode their own excision and integration machinery, and to carry all the sequences or genes necessary to hijack the mating pore of a conjugative element for their own transfer. However, knowledge of their prevalence and diversity is still severely lacking. In this work, an extensive analysis of 124 genomes from 27 species of Streptococcus reveals 144 IMEs. These IMEs encode either tyrosine or serine integrases. The identification of IME boundaries shows that 141 are specifically integrated in 17 target sites. The IME-encoded relaxases belong to nine superfamilies, among which four are previously unknown in any mobilizable or conjugative element. A total of 118 IMEs are found to encode a non-canonical relaxase related to rolling circle replication initiators (belonging to the four novel families or to MobT). Surprisingly, among these, 83 encode a TcpA protein (i.e., a non-canonical coupling protein (CP) that is more closely related to FtsK than VirD4) that was not previously known to be encoded by mobilizable elements. Phylogenetic analyses reveal not only many integration/excision module replacements but also losses, acquisitions or replacements of TcpA genes between IMEs. This glimpse into the still poorly known world of IMEs reveals that mobilizable elements have a very high prevalence. Their diversity is even greater than expected, with most encoding a CP and/or a non-canonical relaxase.

  6. Integrated gravity and gravity gradient 3D inversion using the non-linear conjugate gradient

    NASA Astrophysics Data System (ADS)

    Qin, Pengbo; Huang, Danian; Yuan, Yuan; Geng, Meixia; Liu, Jie

    2016-03-01

    Gravity data, which are critical in mineral, oil, and gas exploration, are obtained from the vertical component of the gravity field, while gravity gradient data are measured from changes in the gravity field in three directions. However, few studies have sought to improve exploration techniques by integrating gravity and gravity gradient data using inversion methods. In this study, we developed a new method to integrate gravity and gravity gradient data in a 3D density inversion using the non-linear conjugate gradient (NLCG) method and the minimum gradient support (MGS) functional to regularize the 3D inverse problem and to obtain a clear and accurate image of the anomalous body. The NLCG algorithm, which is suitable for solving large-scale nonlinear optimization problems and requires no memory storage, was compared to the Broyden-Fletcher-Goldfarb-Shanno (BFGS) quasi-Newton algorithm and the results indicated that the convergence rate of NLCG is slower, but that the storage requirement and computation time is lower. To counteract the decay in kernel function, we introduced a depth weighting function for anomalous bodies at the same depth, with information about anomalous body depth obtained from well log and seismic exploration data. For anomalous bodies at different depths, we introduced a spatial gradient weighting function to incorporate additional information obtained in the inversion. We concluded that the spatial gradient weighting function enhanced the spatial resolution of the recovered model. Furthermore, our results showed that including multiple components for inversion increased the resolution of the recovered model. We validated our model by applying our inversion method to survey data from Vinton salt dome, Louisiana, USA. The results showed good agreement with known geologic information; thus confirming the accuracy of this approach.

  7. Integrated Two‐Analyte Population Pharmacokinetic Model for Antibody–Drug Conjugates in Patients: Implications for Reducing Pharmacokinetic Sampling

    PubMed Central

    Gibiansky, L; Agarwal, P; Dere, RC; Li, C; Chu, Y‐W; Hirata, J; Joshi, A; Jin, JY; Girish, S

    2016-01-01

    An integrated pharmacokinetics (PK) model that simultaneously describes concentrations of total antibody (Tab) and antibody‐conjugated monomethyl auristatin E (acMMAE) following administration of monomethyl auristatin E (MMAE)‐containing antibody–drug conjugates (ADCs) was developed based on phase I PK data with extensive sampling for two ADCs. Two linear two‐compartment models that shared all parameters were used to describe the PK of Tab and acMMAE, except that the deconjugation rate was an additional clearance pathway included in the acMMAE PK model compared to Tab. Further, the model demonstrated its ability to predict Tab concentrations and PK parameters based on observed acMMAE PK and various reduced or eliminated Tab PK sampling schemes of phase II data. Thus, this integrated model allows for the reduction of Tab PK sampling in late‐phase clinical development without compromising Tab PK characterization. PMID:27863168

  8. The Tcp conjugation system of Clostridium perfringens.

    PubMed

    Wisniewski, Jessica A; Rood, Julian I

    2017-03-07

    The Gram-positive pathogen Clostridium perfringens possesses a family of large conjugative plasmids that is typified by the tetracycline resistance plasmid pCW3. Since these plasmids may carry antibiotic resistance genes or genes encoding extracellular or sporulation-associated toxins, the conjugative transfer of these plasmids appears to be important for the epidemiology of C. perfringens-mediated diseases. Sequence analysis of members of this plasmid family identified a highly conserved 35kb region that encodes proteins with various functions, including plasmid replication and partitioning. The tcp conjugation locus also was identified in this region, initially based on low-level amino acid sequence identity to conjugation proteins from the integrative conjugative element Tn916. Genetic studies confirmed that the tcp locus is required for conjugative transfer and combined with biochemical and structural analyses have led to the development of a functional model of the Tcp conjugation apparatus. This review summarises our current understanding of the Tcp conjugation system, which is now one of the best-characterized conjugation systems in Gram-positive bacteria.

  9. Finite element methods for integrated aerodynamic heating analysis

    NASA Technical Reports Server (NTRS)

    Peraire, J.

    1990-01-01

    Over the past few years finite element based procedures for the solution of high speed viscous compressible flows were developed. The objective of this research is to build upon the finite element concepts which have already been demonstrated and to develop these ideas to produce a method which is applicable to the solution of large scale practical problems. The problems of interest range from three dimensional full vehicle Euler simulations to local analysis of three-dimensional viscous laminar flow. Transient Euler flow simulations involving moving bodies are also to be included. An important feature of the research is to be the coupling of the flow solution methods with thermal/structural modeling techniques to provide an integrated fluid/thermal/structural modeling capability. The progress made towards achieving these goals during the first twelve month period of the research is presented.

  10. The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation.

    PubMed

    Guglielmini, Julien; Quintais, Leonor; Garcillán-Barcia, Maria Pilar; de la Cruz, Fernando; Rocha, Eduardo P C

    2011-08-01

    Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. Conjugation allows the broadest range and the highest gene transfer input per transfer event. While conjugative plasmids have been studied for decades, the number and diversity of integrative conjugative elements (ICE) in prokaryotes remained unknown. We defined a large set of protein profiles of the conjugation machinery to scan over 1,000 genomes of prokaryotes. We found 682 putative conjugative systems among all major phylogenetic clades and showed that ICEs are the most abundant conjugative elements in prokaryotes. Nearly half of the genomes contain a type IV secretion system (T4SS), with larger genomes encoding more conjugative systems. Surprisingly, almost half of the chromosomal T4SS lack co-localized relaxases and, consequently, might be devoted to protein transport instead of conjugation. This class of elements is preponderant among small genomes, is less commonly associated with integrases, and is rarer in plasmids. ICEs and conjugative plasmids in proteobacteria have different preferences for each type of T4SS, but all types exist in both chromosomes and plasmids. Mobilizable elements outnumber self-conjugative elements in both ICEs and plasmids, which suggests an extensive use of T4SS in trans. Our evolutionary analysis indicates that switch of plasmids to and from ICEs were frequent and that extant elements began to differentiate only relatively recently. According to the present results, ICEs are the most abundant conjugative elements in practically all prokaryotic clades and might be far more frequently domesticated into non-conjugative protein transport systems than previously thought. While conjugative plasmids and ICEs have different means of genomic stabilization, their mechanisms of mobility by conjugation show strikingly conserved patterns, arguing for a unitary view of conjugation in shaping the genomes of prokaryotes by

  11. The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

    PubMed Central

    Guglielmini, Julien; Quintais, Leonor; Garcillán-Barcia, Maria Pilar; de la Cruz, Fernando; Rocha, Eduardo P. C.

    2011-01-01

    Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. Conjugation allows the broadest range and the highest gene transfer input per transfer event. While conjugative plasmids have been studied for decades, the number and diversity of integrative conjugative elements (ICE) in prokaryotes remained unknown. We defined a large set of protein profiles of the conjugation machinery to scan over 1,000 genomes of prokaryotes. We found 682 putative conjugative systems among all major phylogenetic clades and showed that ICEs are the most abundant conjugative elements in prokaryotes. Nearly half of the genomes contain a type IV secretion system (T4SS), with larger genomes encoding more conjugative systems. Surprisingly, almost half of the chromosomal T4SS lack co-localized relaxases and, consequently, might be devoted to protein transport instead of conjugation. This class of elements is preponderant among small genomes, is less commonly associated with integrases, and is rarer in plasmids. ICEs and conjugative plasmids in proteobacteria have different preferences for each type of T4SS, but all types exist in both chromosomes and plasmids. Mobilizable elements outnumber self-conjugative elements in both ICEs and plasmids, which suggests an extensive use of T4SS in trans. Our evolutionary analysis indicates that switch of plasmids to and from ICEs were frequent and that extant elements began to differentiate only relatively recently. According to the present results, ICEs are the most abundant conjugative elements in practically all prokaryotic clades and might be far more frequently domesticated into non-conjugative protein transport systems than previously thought. While conjugative plasmids and ICEs have different means of genomic stabilization, their mechanisms of mobility by conjugation show strikingly conserved patterns, arguing for a unitary view of conjugation in shaping the genomes of prokaryotes by

  12. CTXφ contains a hybrid genome derived from tandemly integrated elements

    PubMed Central

    Davis, Brigid M.; Waldor, Matthew K.

    2000-01-01

    CTXφ is a filamentous, temperate bacteriophage whose genome includes ctxAB, the genes that encode cholera toxin. In toxigenic isolates of Vibrio cholerae, tandem arrays of prophage DNA, usually interspersed with the related genetic element RS1, are integrated site-specifically within the chromosome. We have discovered that these arrays routinely yield hybrid virions, composed of DNA from two adjacent prophages or from a prophage and a downstream RS1. Coding sequences are always derived from the 5′ prophage whereas most of an intergenic sequence, intergenic region 1, is always derived from the 3′ element. The presence of tandem elements is required for production of virions: V. cholerae strains that contain a solitary prophage rarely yield CTX virions, and the few virions detected result from imprecise excision of prophage DNA. Thus, generation of the replicative form of CTXφ, pCTX, a step that precedes production of virions, does not depend on reversal of the process for site-specific integration of CTXφ DNA into the V. cholerae chromosome. Production of pCTX also does not depend on RecA-mediated homologous recombination between adjacent prophages. We hypothesize that the CTXφ-specific proteins required for replication of pCTX can also function on a chromosomal substrate, and that, unlike the processes used by other integrating phages, production of pCTX and CTXφ does not require excision of the prophage from the chromosome. Use of this replication strategy maximizes vertical transmission of prophage DNA while still enabling dissemination of CTXφ to new hosts. PMID:10880564

  13. Streptococcal group B integrative and mobilizable element IMESag-rpsI encodes a functional relaxase involved in its transfer

    PubMed Central

    Lorenzo-Diaz, Fabian; Fernández-Lopez, Cris; Douarre, Pierre-Emmanuel; Baez-Ortega, Adrian; Flores, Carlos; Glaser, Philippe

    2016-01-01

    Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance. Although IMEs seem to be the most prevalent class of elements transferable by conjugation, they are poorly known. Here, we have studied a GBS-IME, termed IMESag-rpsI, which is widely distributed in GBS despite not carrying any apparent virulence trait. Analyses of 240 whole genomes showed that IMESag-rpsI is present in approximately 47% of the genomes, has a roughly constant size (approx. 9 kb) and is always integrated at a single location, the 3′-end of the gene encoding the ribosomal protein S9 (rpsI). Based on their genetic variation, several IMESag-rpsI types were defined (A–J) and classified in clonal complexes (CCs). CC1 was the most populated by IMESag-rpsI (more than 95%), mostly of type-A (71%). One CC1 strain (S. agalactiae HRC) was deep-sequenced to understand the rationale underlying type-A IMESag-rpsI enrichment in GBS. Thirteen open reading frames were identified, one of them encoding a protein (MobSag) belonging to the broadly distributed family of relaxases MOBV1. Protein MobSag was purified and, by a newly developed method, shown to cleave DNA at a specific dinucleotide. The S. agalactiae HRC-IMESag-rpsI is able to excise from the chromosome, as shown by the presence of circular intermediates, and it harbours a fully functional mobilization module. Further, the mobSag gene encoded by this mobile element is able to promote plasmid transfer among pneumococcal

  14. Streptococcal group B integrative and mobilizable element IMESag-rpsI encodes a functional relaxase involved in its transfer.

    PubMed

    Lorenzo-Diaz, Fabian; Fernández-Lopez, Cris; Douarre, Pierre-Emmanuel; Baez-Ortega, Adrian; Flores, Carlos; Glaser, Philippe; Espinosa, Manuel

    2016-10-01

    Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance. Although IMEs seem to be the most prevalent class of elements transferable by conjugation, they are poorly known. Here, we have studied a GBS-IME, termed IMESag-rpsI, which is widely distributed in GBS despite not carrying any apparent virulence trait. Analyses of 240 whole genomes showed that IMESag-rpsI is present in approximately 47% of the genomes, has a roughly constant size (approx. 9 kb) and is always integrated at a single location, the 3'-end of the gene encoding the ribosomal protein S9 (rpsI). Based on their genetic variation, several IMESag-rpsI types were defined (A-J) and classified in clonal complexes (CCs). CC1 was the most populated by IMESag-rpsI (more than 95%), mostly of type-A (71%). One CC1 strain (S. agalactiae HRC) was deep-sequenced to understand the rationale underlying type-A IMESag-rpsI enrichment in GBS. Thirteen open reading frames were identified, one of them encoding a protein (MobSag) belonging to the broadly distributed family of relaxases MOBV1 Protein MobSag was purified and, by a newly developed method, shown to cleave DNA at a specific dinucleotide. The S. agalactiae HRC-IMESag-rpsI is able to excise from the chromosome, as shown by the presence of circular intermediates, and it harbours a fully functional mobilization module. Further, the mobSag gene encoded by this mobile element is able to promote plasmid transfer among pneumococcal

  15. Complete Sequence of a F33:A-:B- Conjugative Plasmid Carrying the oqxAB, fosA3, and blaCTX-M-55 Elements from a Foodborne Escherichia coli Strain

    PubMed Central

    Xie, Miaomiao; Xie, Liqi; Lin, Dachuan; Li, Ruichao; Zhou, Yuanjie; Chan, Edward W.; Chen, Sheng

    2016-01-01

    This study reports the complete sequence of pE80, a conjugative IncFII plasmid recovered from an Escherichia coli strain isolated from chicken meat. This plasmid harbors multiple resistance determinants including oqxAB, fosA3, blaCTX-M-55, and blaTEM-1, and is a close variant of the recently reported p42-2 element, which was recovered from E. coli of veterinary source. Recovery of pE80 constitutes evidence that evolution or genetic re-arrangement of IncFII type plasmids residing in animal-borne organisms is an active event, which involves acquisition and integration of foreign resistance elements into the plasmid backbone. Dissemination of these plasmids may further compromise the effectiveness of current antimicrobial strategies. PMID:27833607

  16. Solution processed integrated pixel element for an imaging device

    NASA Astrophysics Data System (ADS)

    Swathi, K.; Narayan, K. S.

    2016-09-01

    We demonstrate the implementation of a solid state circuit/structure comprising of a high performing polymer field effect transistor (PFET) utilizing an oxide layer in conjunction with a self-assembled monolayer (SAM) as the dielectric and a bulk-heterostructure based organic photodiode as a CMOS-like pixel element for an imaging sensor. Practical usage of functional organic photon detectors requires on chip components for image capture and signal transfer as in the CMOS/CCD architecture rather than simple photodiode arrays in order to increase speed and sensitivity of the sensor. The availability of high performing PFETs with low operating voltage and photodiodes with high sensitivity provides the necessary prerequisite to implement a CMOS type image sensing device structure based on organic electronic devices. Solution processing routes in organic electronics offers relatively facile procedures to integrate these components, combined with unique features of large-area, form factor and multiple optical attributes. We utilize the inherent property of a binary mixture in a blend to phase-separate vertically and create a graded junction for effective photocurrent response. The implemented design enables photocharge generation along with on chip charge to voltage conversion with performance parameters comparable to traditional counterparts. Charge integration analysis for the passive pixel element using 2D TCAD simulations is also presented to evaluate the different processes that take place in the monolithic structure.

  17. An origin of transfer (oriT) on the conjugative element pRS01 from Lactococcus lactis subsp. lactis ML3.

    PubMed

    Mills, D A; Phister, T G; Dunny, G M; McKay, L L

    1998-04-01

    Previous analysis of the Tra1 region of the conjugative element pRS01 from Lactococcus lactis subsp. lactis ML3 suggested that an origin of transfer (oriT) was present. Deletion derivatives of this cloned Tra1 region were assayed for mobilization in the presence of the wild-type pRS01 element in trans. The pRS01 oriT was localized to a 446-nucleotide segment in the intergenic region between open reading frames ltrD and ltrE. Sequence analysis of this region revealed a cluster of direct and inverted repeat structures characteristic of oriT regions associated with other conjugative systems.

  18. A linear discretization of the volume conductor boundary integral equation using analytically integrated elements.

    PubMed

    de Munck, J C

    1992-09-01

    A method is presented to compute the potential distribution on the surface of a homogeneous isolated conductor of arbitrary shape. The method is based on an approximation of a boundary integral equation as a set linear algebraic equations. The potential is described as a piecewise linear or quadratic function. The matrix elements of the discretized equation are expressed as analytical formulas.

  19. DPTEdb, an integrative database of transposable elements in dioecious plants

    PubMed Central

    Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gu, Lian-Feng; Gao, Wu-Jun

    2016-01-01

    Dioecious plants usually harbor ‘young’ sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants. Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php PMID:27173524

  20. DPTEdb, an integrative database of transposable elements in dioecious plants.

    PubMed

    Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gu, Lian-Feng; Gao, Wu-Jun

    2016-01-01

    Dioecious plants usually harbor 'young' sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants.Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php.

  1. Mobile elements and viral integrations prompt considerations for bacterial DNA integration as a novel carcinogen

    PubMed Central

    Robinson, Kelly M.; Hotopp, Julie C. Dunning

    2014-01-01

    Insertional mutagenesis has been repeatedly demonstrated in cancer genomes and has a role in oncogenesis. Mobile genetic elements can induce cancer development by random insertion into cancer related genes or by inducing translocations. L1s are typically implicated in cancers of an epithelial cell origin, while Alu elements have been implicated in leukemia as well as epithelial cell cancers. Likewise, viral infections have a significant role in cancer development predominantly through integration into the human genome and mutating or deregulating cancer related genes. Human papilloma virus is the best-known example of viral integrations contributing to carcinogenesis. However, hepatitis B virus, Epstein-Barr virus, and Merkel cell polyomavirus also integrate into the human genome and disrupt cancer related genes. Thus far, the role of microbes in cancer has primarily been attributed to mutations induced through chronic inflammation or toxins, as is the case with Helicobacter pylori and enterotoxigenic Bacteroides fragilis. We hypothesize that like mobile elements and viral DNA, bacterial and parasitic DNA may also integrate into the human somatic genome and be oncogenic. Until recently it was believed that bacterial DNA could not integrate into the human genome, but new evidence demonstrates that bacterial insertional mutagenesis may occur in cancer cells. Although this work does not show causation between bacterial insertions and cancer, it prompts more research in this area. Promising new sequencing technologies may reduce the risk of artifactual chimeric sequences, thus diminishing some of the challenges of identifying novel insertions in the somatic human genome. PMID:24956175

  2. A combined finite element and boundary integral formulation for solution via CGFFT of 2-dimensional scattering problems

    NASA Technical Reports Server (NTRS)

    Collins, Jeffery D.; Volakis, John L.

    1989-01-01

    A new technique is presented for computing the scattering by 2-D structures of arbitrary composition. The proposed solution approach combines the usual finite element method with the boundary integral equation to formulate a discrete system. This is subsequently solved via the conjugate gradient (CG) algorithm. A particular characteristic of the method is the use of rectangular boundaries to enclose the scatterer. Several of the resulting boundary integrals are therefore convolutions and may be evaluated via the fast Fourier transform (FFT) in the implementation of the CG algorithm. The solution approach offers the principle advantage of having O(N) memory demand and employs a 1-D FFT versus a 2-D FFT as required with a traditional implementation of the CGFFT algorithm. The speed of the proposed solution method is compared with that of the traditional CGFFT algorithm, and results for rectangular bodies are given and shown to be in excellent agreement with the moment method.

  3. MAR Elements and Transposons for Improved Transgene Integration and Expression

    PubMed Central

    Ley, Déborah; Harraghy, Niamh; Le Fourn, Valérie; Bire, Solenne; Girod, Pierre-Alain; Regamey, Alexandre; Rouleux-Bonnin, Florence; Bigot, Yves; Mermod, Nicolas

    2013-01-01

    Reliable and long-term expression of transgenes remain significant challenges for gene therapy and biotechnology applications, especially when antibiotic selection procedures are not applicable. In this context, transposons represent attractive gene transfer vectors because of their ability to promote efficient genomic integration in a variety of mammalian cell types. However, expression from genome-integrating vectors may be inhibited by variable gene transcription and/or silencing events. In this study, we assessed whether inclusion of two epigenetic control elements, the human Matrix Attachment Region (MAR) 1–68 and X-29, in a piggyBac transposon vector, may lead to more reliable and efficient expression in CHO cells. We found that addition of the MAR 1–68 at the center of the transposon did not interfere with transposition frequency, and transgene expressing cells could be readily detected from the total cell population without antibiotic selection. Inclusion of the MAR led to higher transgene expression per integrated copy, and reliable expression could be obtained from as few as 2–4 genomic copies of the MAR-containing transposon vector. The MAR X-29-containing transposons was found to mediate elevated expression of therapeutic proteins in polyclonal or monoclonal CHO cell populations using a transposable vector devoid of selection gene. Overall, we conclude that MAR and transposable vectors can be used to improve transgene expression from few genomic transposition events, which may be useful when expression from a low number of integrated transgene copies must be obtained and/or when antibiotic selection cannot be applied. PMID:23646143

  4. MAR elements and transposons for improved transgene integration and expression.

    PubMed

    Ley, Déborah; Harraghy, Niamh; Le Fourn, Valérie; Bire, Solenne; Girod, Pierre-Alain; Regamey, Alexandre; Rouleux-Bonnin, Florence; Bigot, Yves; Mermod, Nicolas

    2013-01-01

    Reliable and long-term expression of transgenes remain significant challenges for gene therapy and biotechnology applications, especially when antibiotic selection procedures are not applicable. In this context, transposons represent attractive gene transfer vectors because of their ability to promote efficient genomic integration in a variety of mammalian cell types. However, expression from genome-integrating vectors may be inhibited by variable gene transcription and/or silencing events. In this study, we assessed whether inclusion of two epigenetic control elements, the human Matrix Attachment Region (MAR) 1-68 and X-29, in a piggyBac transposon vector, may lead to more reliable and efficient expression in CHO cells. We found that addition of the MAR 1-68 at the center of the transposon did not interfere with transposition frequency, and transgene expressing cells could be readily detected from the total cell population without antibiotic selection. Inclusion of the MAR led to higher transgene expression per integrated copy, and reliable expression could be obtained from as few as 2-4 genomic copies of the MAR-containing transposon vector. The MAR X-29-containing transposons was found to mediate elevated expression of therapeutic proteins in polyclonal or monoclonal CHO cell populations using a transposable vector devoid of selection gene. Overall, we conclude that MAR and transposable vectors can be used to improve transgene expression from few genomic transposition events, which may be useful when expression from a low number of integrated transgene copies must be obtained and/or when antibiotic selection cannot be applied.

  5. Quasi-three dimensional modeling of functionally-integrated elements of large-scale integrated circuits

    NASA Astrophysics Data System (ADS)

    Petrosyants, K. O.; Gurov, A. I.

    1984-08-01

    Functional integration allows a substantial reduction in the number of metallized connections and contact areas to the individual regions of a semiconductor structure, and realization of the basic connections between the elements within the semiconductor volume. Planning of a functionally integrated structure (FIS), which assures device parameters optimum for circuit engineering applications, is unthinkable without consideration of sufficient precise machine models. A series of models concerned with the special features of construction of FIS of various types was developed. A quasi-three dimensional model is presented of the functionally integrated elements of a bipolar BIS, which are multilayer semiconductor structures with an arbitrarily arranged diffused region and metallized contacts, controlled by a current or voltage. The model is described by a system of differential equations in partial derivatives of the elliptical type with integral limitations. A numerical algorithm uses a Newtonian procedure of quasilinearization in conjunction with a block method of upper relaxation. The model is realized in FORTRAN IV for a unified system of computers, intended to solve a wide range of problems which originate during planning of BIS, in particular choice of the optimum versions of topology, routes, and the electrical regime of the elements.

  6. Isolation of a novel IS3 group insertion element and construction of an integration vector for Lactobacillus spp.

    PubMed Central

    Walker, D C; Klaenhammer, T R

    1994-01-01

    An insertion sequence (IS) element from Lactobacillus johnsonii was isolated, characterized, and exploited to construct an IS-based integration vector. L. johnsonii NCK61, a high-frequency conjugal donor of bacteriocin production (Laf+) and immunity (Lafr), was transformed to erythromycin resistance (Emr) with the shuttle vector pSA3. The NCK61 conjugative functions were used to mobilize pSA3 into a Laf- Lafs EMs recipient. DNA from the Emr transconjugants transformed into Escherichia coli MC1061 yielded a resolution plasmid with the same size as that of pSA3 with a 1.5-kb insertion. The gram-positive replication region of the resolution plasmid was removed to generate a pSA3-based suicide vector (pTRK327) bearing the 1.5-kb insert of Lactobacillus origin. Plasmid pTRK327 inserted randomly into the chromosomes of both Lactobacillus gasseri ATCC 33323 and VPI 11759. No homology was detected between plasmid and total host DNAs, suggesting a Rec-independent insertion. The DNA sequence of the 1.5-kb region revealed the characteristics of an IS element (designated IS1223): a length of 1,492 bp; flanking, 25-bp, imperfect inverted repeats; and two overlapping open reading frames (ORFs). Sequence comparisons revealed 71.1% similarity, including 35.7% identity, between the deduced ORFB protein of the E. coli IS element IS150 and the putative ORFB protein encoded by the Lactobacillus IS element. A putative frameshift site was detected between the overlapping ORFs of the Lactobacillus IS element. It is proposed that, similar to IS150, IS1223 produces an active transposase via translational frameshifting between two tandem, overlapping ORFs. Images PMID:8071209

  7. Finite element methods for integrated aerodynamic heating analysis

    NASA Technical Reports Server (NTRS)

    Morgan, K.; Peraire, J.

    1991-01-01

    This report gives a description of the work which has been undertaken during the second year of a three year research program. The objectives of the program are to produce finite element based procedures for the solution of the large scale practical problems which are of interest to the Aerothermal Loads Branch (ALB) at NASA Langley Research Establishment. The problems of interest range from Euler simulations of full three dimensional vehicle configurations to local analyses of three dimensional viscous laminar flow. Adaptive meshes produced for both steady state and transient problems are to be considered. An important feature of the work is the provision of specialized techniques which can be used at ALB for the development of an integrated fluid/thermal/structural modeling capability.

  8. 49 CFR 192.911 - What are the elements of an integrity management program?

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 3 2012-10-01 2012-10-01 false What are the elements of an integrity management program? 192.911 Section 192.911 Transportation Other Regulations Relating to Transportation (Continued... Transmission Pipeline Integrity Management § 192.911 What are the elements of an integrity management program...

  9. 49 CFR 192.911 - What are the elements of an integrity management program?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 3 2011-10-01 2011-10-01 false What are the elements of an integrity management program? 192.911 Section 192.911 Transportation Other Regulations Relating to Transportation (Continued... Transmission Pipeline Integrity Management § 192.911 What are the elements of an integrity management program...

  10. 49 CFR 192.911 - What are the elements of an integrity management program?

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 3 2014-10-01 2014-10-01 false What are the elements of an integrity management program? 192.911 Section 192.911 Transportation Other Regulations Relating to Transportation (Continued... Transmission Pipeline Integrity Management § 192.911 What are the elements of an integrity management program...

  11. Rapid Prototyping Integrated With Nondestructive Evaluation and Finite Element Analysis

    NASA Technical Reports Server (NTRS)

    Abdul-Aziz, Ali; Baaklini, George Y.

    2001-01-01

    Most reverse engineering approaches involve imaging or digitizing an object then creating a computerized reconstruction that can be integrated, in three dimensions, into a particular design environment. Rapid prototyping (RP) refers to the practical ability to build high-quality physical prototypes directly from computer aided design (CAD) files. Using rapid prototyping, full-scale models or patterns can be built using a variety of materials in a fraction of the time required by more traditional prototyping techniques (refs. 1 and 2). Many software packages have been developed and are being designed to tackle the reverse engineering and rapid prototyping issues just mentioned. For example, image processing and three-dimensional reconstruction visualization software such as Velocity2 (ref. 3) are being used to carry out the construction process of three-dimensional volume models and the subsequent generation of a stereolithography file that is suitable for CAD applications. Producing three-dimensional models of objects from computed tomography (CT) scans is becoming a valuable nondestructive evaluation methodology (ref. 4). Real components can be rendered and subjected to temperature and stress tests using structural engineering software codes. For this to be achieved, accurate high-resolution images have to be obtained via CT scans and then processed, converted into a traditional file format, and translated into finite element models. Prototyping a three-dimensional volume of a composite structure by reading in a series of two-dimensional images generated via CT and by using and integrating commercial software (e.g. Velocity2, MSC/PATRAN (ref. 5), and Hypermesh (ref. 6)) is being applied successfully at the NASA Glenn Research Center. The building process from structural modeling to the analysis level is outlined in reference 7. Subsequently, a stress analysis of a composite cooling panel under combined thermomechanical loading conditions was performed to validate

  12. A CAD Approach to Integrating NDE With Finite Element

    NASA Technical Reports Server (NTRS)

    Abdul-Aziz, Ali; Downey, James; Ghosn, Louis J.; Baaklini, George Y.

    2004-01-01

    Nondestructive evaluation (NDE) is one of several technologies applied at NASA Glenn Research Center to determine atypical deformities, cracks, and other anomalies experienced by structural components. NDE consists of applying high-quality imaging techniques (such as x-ray imaging and computed tomography (CT)) to discover hidden manufactured flaws in a structure. Efforts are in progress to integrate NDE with the finite element (FE) computational method to perform detailed structural analysis of a given component. This report presents the core outlines for an in-house technical procedure that incorporates this combined NDE-FE interrelation. An example is presented to demonstrate the applicability of this analytical procedure. FE analysis of a test specimen is performed, and the resulting von Mises stresses and the stress concentrations near the anomalies are observed, which indicates the fidelity of the procedure. Additional information elaborating on the steps needed to perform such an analysis is clearly presented in the form of mini step-by-step guidelines.

  13. The marriage of metallacycle transfer chemistry with Suzuki-Miyaura cross-coupling to give main group element-containing conjugated polymers.

    PubMed

    He, Gang; Kang, Le; Torres Delgado, William; Shynkaruk, Olena; Ferguson, Michael J; McDonald, Robert; Rivard, Eric

    2013-04-10

    A versatile and general synthetic route for the synthesis of conjugated main group element-based polymers, previously inaccessible by conventional means, is reported. These polymers contain five-membered chalcogenophene rings based on S, Se, and Te, and we demonstrate that optoelectronic properties can be readily tuned via controlled atom substitution chemistry. In addition, regioregular hybrid thiophene-selenophene-tellurophene and selenophene-fluorene copolymers were synthesized to provide a further illustration of the scope of the presented metallacycle transfer/cross-coupling polymerization method.

  14. Integrated thermal-structural finite element analysis. [for applications to hypersonic transport design

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

    An integrated thermal-structural finite element approach for efficient coupling of thermal and structural analysis is presented. An integrated thermal-structural rod element is developed and used in four thermal-structural applications; the accuracy of this integrated approach is illustrated by comparisons with the customary approach of finite difference thermal-finite element structural analyses. Results show that integrated thermal-structural analysis of structures modeled with rod elements is more accurate than conventional analysis, and that its further development promises significant results.

  15. Unraveling the regulatory network of IncA/C plasmid mobilization: When genomic islands hijack conjugative elements.

    PubMed

    Carraro, Nicolas; Matteau, Dominick; Burrus, Vincent; Rodrigue, Sébastien

    2015-01-01

    Conjugative plasmids of the A/C incompatibility group (IncA/C) have become substantial players in the dissemination of multidrug resistance. These large conjugative plasmids are characterized by their broad host-range, extended spectrum of antimicrobials resistance, and prevalence in enteric bacteria recovered from both environmental and clinical settings. Until recently, relatively little was known about the basic biology of IncA/C plasmids, mostly because of the hindrance of multidrug resistance for molecular biology experiments. To circumvent this issue, we previously developed pVCR94ΔX, a convenient prototype that codes for a reduced set of antibiotic resistances. Using pVCR94ΔX, we then characterized the regulatory pathway governing IncA/C plasmid dissemination. We found that the expression of roughly 2 thirds of the genes encoded by this plasmid, including large operons involved in the conjugation process, depends on an FlhCD-like master activator called AcaCD. Beyond the mobility of IncA/C plasmids, AcaCD was also shown to play a key role in the mobilization of different classes of genomic islands (GIs) identified in various pathogenic bacteria. By doing so, IncA/C plasmids can have a considerable impact on bacterial genomes plasticity and evolution.

  16. Workshop on the Integration of Finite Element Modeling with Geometric Modeling

    NASA Technical Reports Server (NTRS)

    Wozny, Michael J.

    1987-01-01

    The workshop on the Integration of Finite Element Modeling with Geometric Modeling was held on 12 May 1987. It was held to discuss the geometric modeling requirements of the finite element modeling process and to better understand the technical aspects of the integration of these two areas. The 11 papers are presented except for one for which only the abstract is given.

  17. Studies on transposable elements in yeast. I. ROAM mutations causing increased expression of yeast genes: their activation by signals directed toward conjugation functions and their formation by insertion of Tyl repetitive elements

    SciTech Connect

    Errede, B.; Cardillo, T.S.; Wever, G.; Sherman, F.

    1981-01-01

    Mechanisms available to eukaryotic organisms for the coordinate regulation of gene expression are being examined by genetic and biochemical characterization of an unusual mutation, CYC7-H2, which causes over-production of iso-2-cytochrome c in the yeast Saccharomyces cerevisiae. The CYC7-H2 mutation causes overproduction in haploid strains but only a 1- to 40-fold overproduction in MATa/MAT..cap alpha.. diploid strains. This regulation of overproduction has been characterized as a response to signals controlling conjugation in yeast. Furthermore, the abnormal controlling region has been identified as an insertion of a transposable and reiterated Ty1 element adjacent to the structural gene. Therefore, we suggest that Ty1 elements or portions of Ty1 elements occur adjacent to some of the genes required for conjugation and that they normally function to control expression of this process. The suggested role of reiterated sequences may represent a general mechanism of coordinate regulation in eukaryotes. The CYC7-H2 mutation is closely related to other regulatory mutations occurring at the cargA, cargB and DUR1,2 loci. Similar to the CYC7-H2 mutation, the mutations designated cargA/sup +/O/sup h/, cargB/sup +/O/sup h/, and durO/sup h/ cause constitutive production of their respective gene products at much lower levels of MATa/MAT..cap alpha.. diploid strains than in the corresponding haploid strains. A consistent relationship between conjugation competence and the level of overproduction in all four mutants has been established. Observations characterizing the regulation of overproduction in the CYC7-H2 mutant are presented with the additional and parallel observations for the O/sup h/ mutants. Together these results provide a demonstration of the specificity and equivalence of regulatory control exhibited by ROAM mutants.

  18. Recent advances and progress towards an integrated interdisciplinary thermal-structural finite element technology

    NASA Technical Reports Server (NTRS)

    Namburu, Raju R.; Tamma, Kumar K.

    1993-01-01

    An integrated finite element approach is presented for interdisciplinary thermal-structural problems. Of the various numerical approaches, finite element methods with direct time integration procedures are most widely used for these nonlinear problems. Traditionally, combined thermal-structural analysis is performed sequentially by transferring data between thermal and structural analysis. This approach is generally effective and routinely used. However, to solve the combined thermal-structural problems, this approach results in cumbersome data transfer, incompatible algorithmic representations, and different discretized element formulations. The integrated approach discussed in this paper effectively combines thermal and structural fields, thus overcoming the above major shortcomings. The approach follows Lax-Wendroff type finite element formulations with flux and stress based representations. As a consequence, this integrated approach uses common algorithmic representations and element formulations. Illustrative test examples show that the approach is effective for integrated thermal-structural problems.

  19. Comparison of symbolic and numerical integration methods for an assumed-stress hybrid shell element

    NASA Technical Reports Server (NTRS)

    Rengarajan, Govind; Knight, Norman F., Jr.; Aminpour, Mohammad A.

    1993-01-01

    Hybrid shell elements have long been regarded with reserve by the commercial finite element developers despite the high degree of reliability and accuracy associated with such formulations. The fundamental reason is the inherent higher computational cost of the hybrid approach as compared to the displacement-based formulations. However, a noteworthy factor in favor of hybrid elements is that numerical integration to generate element matrices can be entirely avoided by the use of symbolic integration. In this paper, the use of the symbolic computational approach is presented for an assumed-stress hybrid shell element with drilling degrees of freedom and the significant time savings achieved is demonstrated through an example.

  20. Monolithic Lumped Element Integrated Circuit (M2LEIC) Transistors.

    DTIC Science & Technology

    INTEGRATED CIRCUITS, *MONOLITHIC STRUCTURES(ELECTRONICS), *TRANSISTORS, CHIPS(ELECTRONICS), FABRICATION, EPITAXIAL GROWTH, ULTRAHIGH FREQUENCY, POLYSILICONS, PHOTOLITHOGRAPHY, RADIOFREQUENCY POWER, IMPEDANCE MATCHING .

  1. Integration of geometric modeling and advanced finite element preprocessing

    NASA Technical Reports Server (NTRS)

    Shephard, Mark S.; Finnigan, Peter M.

    1987-01-01

    The structure to a geometry based finite element preprocessing system is presented. The key features of the system are the use of geometric operators to support all geometric calculations required for analysis model generation, and the use of a hierarchic boundary based data structure for the major data sets within the system. The approach presented can support the finite element modeling procedures used today as well as the fully automated procedures under development.

  2. A new integrated slot element feed array for multibeam systems

    NASA Technical Reports Server (NTRS)

    Yngvesson, K. Sigfrid; Johansson, Joakim F.; Kollberg, Erik L.

    1986-01-01

    A feed array consisting of constant width slot antennas (CWSA), fed from a block containing fin-line transitions, has been developed. The array has a two-dimensional configuration, with five elements each on five parallel substrates. Beamwidths are compatible with use in f/D = 1.0 multibeam systems, with optimum taper. Array element spacings are close to a factor of two smaller than for other typical arrays, and spillover efficiency is about 65 percent.

  3. Application of modified integration rule to time-domain finite-element acoustic simulation of rooms.

    PubMed

    Okuzono, Takeshi; Otsuru, Toru; Tomiku, Reiji; Okamoto, Noriko

    2012-08-01

    The applicability of the modified integration rule for time-domain finite-element analysis is tested in sound field analysis of rooms involving rectangular elements, distorted elements, and finite impedance boundary conditions. Dispersion error analysis in three dimensions is conducted to evaluate the dispersion error in time-domain finite-element analysis using eight-node hexahedral elements. The results of analysis confirmed that fourth-order accuracy with respect to dispersion error is obtainable using the Fox-Goodwin method (FG) with a modified integration rule, even for rectangular elements. The stability condition in three-dimensional analysis using the modified integration rule is also presented. Numerical experiments demonstrate that FG with a modified integration rule performs much better than FG with the conventional integration rule for problems with rectangular elements, distorted elements, and with finite impedance boundary conditions. Further, as another advantage, numerical results revealed that the use of modified integration rule engenders faster convergence of the iterative solver than a conventional rule for problems with the same degrees of freedom.

  4. An Integrated Encyclopedia of DNA Elements in the Human Genome

    PubMed Central

    2012-01-01

    Summary The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure, and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall the project provides new insights into the organization and regulation of our genes and genome, and an expansive resource of functional annotations for biomedical research. PMID:22955616

  5. An integrated encyclopedia of DNA elements in the human genome.

    PubMed

    2012-09-06

    The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

  6. Integrating Health Behavior Theory and Design Elements in Serious Games.

    PubMed

    Cheek, Colleen; Fleming, Theresa; Lucassen, Mathijs Fg; Bridgman, Heather; Stasiak, Karolina; Shepherd, Matthew; Orpin, Peter

    2015-01-01

    Internet interventions for improving health and well-being have the potential to reach many people and fill gaps in service provision. Serious gaming interfaces provide opportunities to optimize user adherence and impact. Health interventions based in theory and evidence and tailored to psychological constructs have been found to be more effective to promote behavior change. Defining the design elements which engage users and help them to meet their goals can contribute to better informed serious games. To elucidate design elements important in SPARX, a serious game for adolescents with depression, from a user-centered perspective. We proposed a model based on an established theory of health behavior change and practical features of serious game design to organize ideas and rationale. We analyzed data from 5 studies comprising a total of 22 focus groups and 66 semistructured interviews conducted with youth and families in New Zealand and Australia who had viewed or used SPARX. User perceptions of the game were applied to this framework. A coherent framework was established using the three constructs of self-determination theory (SDT), autonomy, competence, and relatedness, to organize user perceptions and design elements within four areas important in design: computer game, accessibility, working alliance, and learning in immersion. User perceptions mapped well to the framework, which may assist developers in understanding the context of user needs. By mapping these elements against the constructs of SDT, we were able to propose a sound theoretical base for the model. This study's method allowed for the articulation of design elements in a serious game from a user-centered perspective within a coherent overarching framework. The framework can be used to deliberately incorporate serious game design elements that support a user's sense of autonomy, competence, and relatedness, key constructs which have been found to mediate motivation at all stages of the change

  7. Integrated particles sensor formed on single substrate using fringes formed by diffractive elements

    NASA Technical Reports Server (NTRS)

    Gharib, Morteza (Inventor); Fourguette, Dominique (Inventor); Modarress, Darius (Inventor); Taugwalder, Frederic (Inventor); Forouhar, Siamak (Inventor)

    2005-01-01

    Integrated sensors are described using lasers on substrates. In one embodiment, a first sensor forms a laser beam and uses a quartz substrate to sense particle motion by interference of the particles with a diffraction beam caused by a laser beam. A second sensor uses gradings to produce an interference. In another embodiment, an integrated sensor includes a laser element, producing a diverging beam, and a single substrate which includes a first diffractive optical element placed to receive the diverging beam and produce a fringe based thereon, a scattering element which scatters said fringe beam based on particles being detected, and a second diffractive element receiving scattered light.

  8. A computer program for anisotropic shallow-shell finite elements using symbolic integration

    NASA Technical Reports Server (NTRS)

    Andersen, C. M.; Bowen, J. T.

    1976-01-01

    A FORTRAN computer program for anisotropic shallow-shell finite elements with variable curvature is described. A listing of the program is presented together with printed output for a sample case. Computation times and central memory requirements are given for several different elements. The program is based on a stiffness (displacement) finite-element model in which the fundamental unknowns consist of both the displacement and the rotation components of the reference surface of the shell. Two triangular and four quadrilateral elements are implemented in the program. The triangular elements have 6 or 10 nodes, and the quadrilateral elements have 4 or 8 nodes. Two of the quadrilateral elements have internal degrees of freedom associated with displacement modes which vanish along the edges of the elements (bubble modes). The triangular elements and the remaining two quadrilateral elements do not have bubble modes. The output from the program consists of arrays corresponding to the stiffness, the geometric stiffness, the consistent mass, and the consistent load matrices for individual elements. The integrals required for the generation of these arrays are evaluated by using symbolic (or analytic) integration in conjunction with certain group-theoretic techniques. The analytic expressions for the integrals are exact and were developed using the symbolic and algebraic manipulation language.

  9. Integrating Health Behavior Theory and Design Elements in Serious Games

    PubMed Central

    Fleming, Theresa; Lucassen, Mathijs FG; Bridgman, Heather; Stasiak, Karolina; Shepherd, Matthew; Orpin, Peter

    2015-01-01

    Background Internet interventions for improving health and well-being have the potential to reach many people and fill gaps in service provision. Serious gaming interfaces provide opportunities to optimize user adherence and impact. Health interventions based in theory and evidence and tailored to psychological constructs have been found to be more effective to promote behavior change. Defining the design elements which engage users and help them to meet their goals can contribute to better informed serious games. Objective To elucidate design elements important in SPARX, a serious game for adolescents with depression, from a user-centered perspective. Methods We proposed a model based on an established theory of health behavior change and practical features of serious game design to organize ideas and rationale. We analyzed data from 5 studies comprising a total of 22 focus groups and 66 semistructured interviews conducted with youth and families in New Zealand and Australia who had viewed or used SPARX. User perceptions of the game were applied to this framework. Results A coherent framework was established using the three constructs of self-determination theory (SDT), autonomy, competence, and relatedness, to organize user perceptions and design elements within four areas important in design: computer game, accessibility, working alliance, and learning in immersion. User perceptions mapped well to the framework, which may assist developers in understanding the context of user needs. By mapping these elements against the constructs of SDT, we were able to propose a sound theoretical base for the model. Conclusions This study’s method allowed for the articulation of design elements in a serious game from a user-centered perspective within a coherent overarching framework. The framework can be used to deliberately incorporate serious game design elements that support a user’s sense of autonomy, competence, and relatedness, key constructs which have been found

  10. Environmental Medicine: Integrating a Missing Element into Medical Education.

    ERIC Educational Resources Information Center

    Pope, Andrew M., Ed.; Rall, David P., Ed.

    This volume articulates a general program of implementation strategies and provides practical advice for integrating environmental medicine content into medical education. Chapter 1 is an introduction to the issues and the organization of the volume. Chapter 2 lays the foundation for a curriculum centered on six competency-based learning…

  11. Numerical Estimation of the Pseudo-Jahn-Teller Effect Using Nonadiabatic Coupling Integrals in Monocyclic and Bicyclic Conjugated Molecules.

    PubMed

    Koseki, Shiro; Toyota, Azumao; Muramatsu, Takashi; Asada, Toshio; Matsunaga, Nikita

    2016-12-29

    The pseudo-Jahn-Teller (pJT) effect in monocyclic and bicyclic conjugated molecules was investigated by using the state-averaged multiconfiguration self-consistent field (MCSCF) method, together with the 6-31G(d,p) basis sets. Following the perturbation theory, the force constant along a normal mode Q is given by the sum of the classical force constant and the vibronic contribution (VC) resulting from the interaction of the ground state with excited states. The latter is given as the sum of individual contributions arising from vibronic interactions between the ground state and excited states. In the present work, each VC was calculated on the basis of nonadiabatic coupling (NAC) integrals. Furthermore, the classical force constant was estimated by taking advantage of the VC and the force constant obtained by vibrational analyses. For pentalene and heptalene, the present method seems to overestimate the VC in absolute value because of the small energy gap between the ground state and the lowest excited state. However, we are confident that the VC and the classical force constant for the other molecules are reasonable in magnitude in comparison with available literature information. Thus, it is proved that the present method is applicable and useful for numerical estimation of pJT effect.

  12. July 30, 2007, Five Elements of a Tribal Integrated Waste Management Plan Memo

    EPA Pesticide Factsheets

    The purpose of this memorandum is to identify the elements that the Office of Solid Waste (OSW) believes should generally be included in integrated waste management plans (IWMP) that are developed by tribes.

  13. Ferritin-Polymer Conjugates: Grafting Chemistry and Integration into Nanoscale Assemblies

    SciTech Connect

    Y Hu; D Samanta; S Parelkar; S Hong; Q Wang; T Russell; T Emrick

    2011-12-31

    Controlled free radical polymerization chemistry is used to graft polymer chains to the corona of horse spleen ferritin (HSF) nanocages. Specifically, poly(methacryloyloxyethyl phosphorylcholine) (polyMPC) and poly(PEG methacrylate) (polyPEGMA) chains are grafted onto the nanocages by atom transfer radical polymerization (ATRP), in which the molecular weight of the polymer grafts is controlled by the monomer-to-initiator feed ratio. PolyMPC and polyPEGMA-grafted ferritin show a generally suppressed inclusion into diblock copolymer films relative to native ferritin, and the polymer coating is seen to mask the ferritin nanocages from antibody recognition. The solubility of polyPEGMA-coated ferritin in organic solvents enables its processing with polystyrene-block-poly(ethylene oxide) copolymers, and selective integration into the PEO domains of microphase-separated copolymer structures.

  14. Carbon Nanotubes as Structural Elements in Integrated Biological Nanodevices

    NASA Astrophysics Data System (ADS)

    Prakash, Rohit; Cheney, Richard; Washburn, Sean; Superfine, Richard; Falvo, Michael

    2003-11-01

    Because of their unique mechanical, electrical, and spatial properties, Carbon Nanotubes (CNT) is an ideal candidate for nanometer scale electromechanical systems. An obstacle that arises immediately is the ability to produce substantial forces. Instead of following this course of miniaturization, it is possible integrate force-generating components that have been present for many years: biological motors. These protein complexes are responsible for muscle contractility and the intracellular transport of chromosomes and vesicles; they typically produce forces on a scale of piconewtons. We report progress toward attaching biological motor/filament complexes onto CNTs. We will also present results showing that individual carbon nanotubes (CNTs) can be visualized with fluorescence microscopy through non-covalent labeling with conventional fluorophores. These studies lend themselves not only to the integration of nano-scale objects into biological sciences, but also give us some understanding of the surface properties of CNTs.

  15. Integrated force method versus displacement method for finite element analysis

    NASA Technical Reports Server (NTRS)

    Patnaik, S. N.; Berke, L.; Gallagher, R. H.

    1991-01-01

    A novel formulation termed the integrated force method (IFM) has been developed in recent years for analyzing structures. In this method all the internal forces are taken as independent variables, and the system equilibrium equations (EEs) are integrated with the global compatibility conditions (CCs) to form the governing set of equations. In IFM the CCs are obtained from the strain formulation of St. Venant, and no choices of redundant load systems have to be made, in constrast to the standard force method (SFM). This property of IFM allows the generation of the governing equation to be automated straightforwardly, as it is in the popular stiffness method (SM). In this report IFM and SM are compared relative to the structure of their respective equations, their conditioning, required solution methods, overall computational requirements, and convergence properties as these factors influence the accuracy of the results. Overall, this new version of the force method produces more accurate results than the stiffness method for comparable computational cost.

  16. Integrated force method versus displacement method for finite element analysis

    NASA Technical Reports Server (NTRS)

    Patnaik, Surya N.; Berke, Laszlo; Gallagher, Richard H.

    1990-01-01

    A novel formulation termed the integrated force method (IFM) has been developed in recent years for analyzing structures. In this method all the internal forces are taken as independent variables, and the system equilibrium equations (EE's) are integrated with the global compatibility conditions (CC's) to form the governing set of equations. In IFM the CC's are obtained from the strain formulation of St. Venant, and no choices of redundant load systems have to be made, in constrast to the standard force method (SFM). This property of IFM allows the generation of the governing equation to be automated straightforwardly, as it is in the popular stiffness method (SM). In this report IFM and SM are compared relative to the structure of their respective equations, their conditioning, required solution methods, overall computational requirements, and convergence properties as these factors influence the accuracy of the results. Overall, this new version of the force method produces more accurate results than the stiffness method for comparable computational cost.

  17. Numerical integration of structural elements in NIKE3D and DYNA3D

    NASA Astrophysics Data System (ADS)

    Maker, B. N.; Whirley, R. G.; Engelmann, B. E.

    1992-08-01

    The beam and shell elements found in many linear elastic finite element codes accept integrated cross sectional properties as input, and produce solutions using classical beam and shell theory. These theories are built upon the equation of resultant forces and moments with integrals of assumed stress distributions over the cross section. In contrast, the structural elements in NIKE3D and DYNA3D are formulated to represent nonlinear geometric and material behavior. Thus stress distributions may not necessarily be representable by simple functions of cross section variables. In NIKE3D and DYNA3D, the Hughes-Liu beam element and all shell elements accommodate these more general stress distributions by computing stresses at various points in the cross section. The integration of stresses within each element is then performed numerically, using a variety of methods. This report describes these numerical integration procedures in detail, and highlights their application to engineering problems. Several other features of the structural elements are also described, including force and moment resultants, user-defined reference surfaces, and user-defined integration rules. Finally, the shear correction factor is described in a section which relates results from NIKE3D and DYNA3D to those obtained from classical beam theory.

  18. Safeguards-by-Design: An Element of 3S Integration

    SciTech Connect

    R. S. Bean; T. A. Bjornard; D. J. Hebdich

    2009-04-01

    In 2008, the “20/20 Vision for the Future” background report by the IAEA Director General identified the possibility of integrating certain activities related to safeguards, safety, and security. Later in the year, the independent Commission report prepared at the request of the IAEA Director General noted that the Agency’s roles in nuclear safeguards, safety, and security (3S) complement and can mutually reinforce each other. Safeguards-by-design (SBD) is a practical measure that strengthens 3S integration, especially for the stage of nuclear facility design and construction, but also with ramifications for other stages of the facility life-cycle. This paper describes the SBD concept, with examples for diverse regulatory environments, being developed in the U.S under the U.S. Department of Energy (DOE) Next Generation Safeguards Initiative and the Advanced Fuel Cycle Initiative. This is compared with related international SBD work performed in the recent IAEA workshop on “Facility Design and Plant Operation Features that Facilitate the Implementation of IAEA Safeguards”. Potential future directions for further development of SBD and its integration within 3S are identified.

  19. Recurrent procedure for constructing nonisotropic matrix elements of the collision integral of the nonlinear Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Ender, I. A.; Bakaleinikov, L. A.; Flegontova, E. Yu.; Gerasimenko, A. B.

    2017-08-01

    We have proposed an algorithm for the sequential construction of nonisotropic matrix elements of the collision integral, which are required to solve the nonlinear Boltzmann equation using the moments method. The starting elements of the matrix are isotropic and assumed to be known. The algorithm can be used for an arbitrary law of interactions for any ratio of the masses of colliding particles.

  20. Spin-photonic devices based on optical integration of Pancharatnam-Berry phase elements

    NASA Astrophysics Data System (ADS)

    Zhou, Junxiao; Liu, Yachao; Ke, Yougang; Liu, Yuanyuan; Luo, Hailu; Wen, Shuangchun

    2016-10-01

    Development of spin-photonic devices requires the integration of abundant functions and the miniaturization of the elements. Pancharatnam-Berry phase elements have fulfilled these requirements and can be attained by using dielectric metasurfaces with subwavelength nanostructures. Here, we review some of our works on Pancharatnam- Berry phase elements and make an introduction of some integrated spin-photonic devices. We propose to integrate Pancharatnam-Berry phase lens into dynamical phase lens, which can be conveniently used to modulate spin states of photons. By integrating a Pancharatnam-Berry phase lens into a conventional plano-concave lens, we can obtain spin-filtering of photons. Moreover, we demonstrate that the generation of complex wavefronts characterized with different spin states can be implemented by the Pancharatnam-Berry phase lens. Further, based on the spin-dependent property of Pancharatnam-Berry phase element, we realize the three-dimensional photonic spin Hall effect with lateral and longitudinal spin-dependent splitting simultaneously. We foresee that this optical integration concept of designing Pancharatnam-Berry phase elements, which circumvents the limitations of bulky optical components in conventional integrated optics, will significantly impact multipurpose optical elements, particularly spin-based photonics devices.

  1. Multi-Element Integrated Project Planning at Kennedy Space Center

    NASA Technical Reports Server (NTRS)

    Mullon, Robert

    2008-01-01

    This presentation demonstrates how the ASRC Scheduling team developed working practices to support multiple NASA and ASRC Project Managers using the enterprise capabilities of Primavera P6 and P6 Web Access. This work has proceeded as part of Kennedy Ground Systems' preparation for its transition from the Shuttle Program to the Constellation Program. The presenters will cover Primavera's enterprise-class capabilities for schedule development, integrated critical path analysis, and reporting, as well as advanced Primavera P6 Web Access tools and techniques for communicating project status.

  2. Mechanical integrity and piping systems -- The forgotten elements

    SciTech Connect

    Miller, S.D.; Uscocovich, J.S.

    1996-07-01

    Many codes and regulations address the issue of process piping inspections, the most recent being AP1570. OSH1910.119 paragraph (j) also contains requirements for maintaining the mechanical integrity of an operating system through inspections and tests. This paper includes details for an examination approach dealing with process piping as a system, including often neglected items such as piping supports and expansion joints. A training methodology will be discussed which incorporates site walkdowns, operating history, typical failures and other items which may be used to formulate a site specific and flexible program to ensure safe and reliable piping systems as well as compliance with OSHA 1910.119 paragraph (j).

  3. KorSA from the Streptomyces Integrative Element pSAM2 Is a Central Transcriptional Repressor: Target Genes and Binding Sites

    PubMed Central

    Sezonov, Guennadi; Possoz, Christophe; Friedmann, Annick; Pernodet, Jean-Luc; Guérineau, Michel

    2000-01-01

    pSAM2, a 10.9-kb mobile integrative genetic element from Streptomyces ambofaciens, possesses, as do a majority of Streptomyces conjugative plasmids, a kil-kor system associated with its transfer. The kor function of pSAM2 was attributed to the korSA gene, but its direct role remained unclear. The present study was focused on the determination of the KorSA targets. It was shown that KorSA acts as a transcriptional repressor by binding to a conserved 17-nucleotide sequence found upstream of only two genes: its own gene, korSA, and pra, a gene positively controlling pSAM2 replication, integration, and excision. A unique feature of KorSA, compared to Kor proteins from other Streptomyces conjugative plasmids, is that it does not directly regulate pSAM2 transfer. KorSA does not bind to the pSAM2 genes coding for transfer and intramycelial spreading. Through the repression of pra, KorSA is able to negatively regulate pSAM2 functions activated by Pra and, consequently, to maintain pSAM2 integrated in the chromosome. PMID:10671443

  4. KorSA from the Streptomyces integrative element pSAM2 is a central transcriptional repressor: target genes and binding sites.

    PubMed

    Sezonov, G; Possoz, C; Friedmann, A; Pernodet, J L; Guérineau, M

    2000-03-01

    pSAM2, a 10.9-kb mobile integrative genetic element from Streptomyces ambofaciens, possesses, as do a majority of Streptomyces conjugative plasmids, a kil-kor system associated with its transfer. The kor function of pSAM2 was attributed to the korSA gene, but its direct role remained unclear. The present study was focused on the determination of the KorSA targets. It was shown that KorSA acts as a transcriptional repressor by binding to a conserved 17-nucleotide sequence found upstream of only two genes: its own gene, korSA, and pra, a gene positively controlling pSAM2 replication, integration, and excision. A unique feature of KorSA, compared to Kor proteins from other Streptomyces conjugative plasmids, is that it does not directly regulate pSAM2 transfer. KorSA does not bind to the pSAM2 genes coding for transfer and intramycelial spreading. Through the repression of pra, KorSA is able to negatively regulate pSAM2 functions activated by Pra and, consequently, to maintain pSAM2 integrated in the chromosome.

  5. Mixed Element Formulation for the Finite Element-Boundary Integral Method

    DTIC Science & Technology

    2006-03-01

    bottom) of the prism. For conjunction with other elements. The edges the vertical edges, k1 and k2 are defined in in the extrusion direction are orthogonal...are the vertical prism expansion functions, important because they have the ability to X ki k2 model irregular surface geometries with 7 2 3...3.2 3!4 3!6 38 4 4.𔃼 4.4 4𔄀 4𔄂 5 wher p dnote thefac theeithr th tes orFrequ-n,¢[GHzI source edge are associated with a test Figure 4: Radar Cross

  6. Evaluation of the Current Biased Integrated Optical Processors Based on Bistable Dode Elements.

    DTIC Science & Technology

    1994-07-01

    to monolithically integrate gates since the diodes no longer share a common ground. (a) OR GATE DETECTORS "I I TIR IMODULATOR MIRROR (b)D NOR GATE...C.L. Tang, "Semiconductor laser logic gate suitable for monolithic integration ", Appl. Phys. Lett., Vol. 51, p. 1780, Nov. 1987 3. P.D. Swanson, M.A...RL-TR-94-97 Final Technical Report July 1994 EVALUATION OF CURRENT BIASED INTEGRATED OPTICAL PROCESSORS 3ASED ON BISTABLE DIODE ELEMENTS Cornell

  7. The tapered slot antenna - A new integrated element for millimeter-wave applications

    NASA Astrophysics Data System (ADS)

    Yngvesson, K. Sigfrid; Kim, Young-Sik; Korzeniowski, T. L.; Kollberg, Erik L.; Johansson, Joakim F.

    1989-02-01

    Tapered slot antennas (TSAs) with a number of potential applications as single elements and focal-plane arrays are discussed. TSAs are fabricated with photolithographic techniques and integrated in either hybrid or MMIC circuits with receiver or transmitter components. They offer considerably narrower beams than other integrated antenna elements and have high aperture efficiency and packing density as array elements. Both the circuit and radiation properties of TSAs are reviewed. Topics covered include: antenna beamwidth, directivity, and gain of single-element TSAs; their beam shape and the effect of different taper shapes; and the input impedance and the effects of using thick dielectrics. These characteristics are also given for TSA arrays, as are the circuit properties of the array elements. Different array structures and their applications are also described.

  8. The tapered slot antenna - A new integrated element for millimeter-wave applications

    NASA Technical Reports Server (NTRS)

    Yngvesson, K. Sigfrid; Kim, Young-Sik; Korzeniowski, T. L.; Kollberg, Erik L.; Johansson, Joakim F.

    1989-01-01

    Tapered slot antennas (TSAs) with a number of potential applications as single elements and focal-plane arrays are discussed. TSAs are fabricated with photolithographic techniques and integrated in either hybrid or MMIC circuits with receiver or transmitter components. They offer considerably narrower beams than other integrated antenna elements and have high aperture efficiency and packing density as array elements. Both the circuit and radiation properties of TSAs are reviewed. Topics covered include: antenna beamwidth, directivity, and gain of single-element TSAs; their beam shape and the effect of different taper shapes; and the input impedance and the effects of using thick dielectrics. These characteristics are also given for TSA arrays, as are the circuit properties of the array elements. Different array structures and their applications are also described.

  9. Conjugated Polymer Solar Cells

    DTIC Science & Technology

    2006-05-01

    for films was measured in a pumped vacuum cell. The quantum yield was calculated from the integrated PL spectra and measured optical density...At the same time, the known disadvantages of pristine conjugated polymers are: • the quantum yield of free charges is far below than unity under...possibility of improving the photovoltaic properties of conjugated polymers using polymer CTCs. EXPECTED RESULTS We planned to perform a well -directed

  10. Velocity-pressure integrated versus penalty finite element methods for high Reynolds number flows

    NASA Technical Reports Server (NTRS)

    Kim, Sang-Wook

    1988-01-01

    Velocity-pressure integrated and consistent penalty finite element computations of high Reynolds number, laminar flows are presented. In both of the methods, the pressure has been interpolated using linear shape functions for a triangular element. The triangular element is contained inside the bi-quadratic isoparametric element. It has been reported previously that the pressure interpolation method, when used in the velocity-pressure integrated method, yielded accurate computational results for high Reynolds number flows. It is shown that use of the same pressure interpolation method in the consistent penalty finite element method yielded accurate velocity and pressure fields which were comparable to those obtained using the velocity-pressure integrated method. Accuracy of the two finite element methods has been demonstrated by comparing the computational results with available experimental data and/or fine-grid finite difference computational results. Advantages and disadvantages of the two methods are discussed on the basis of accuracy and convergence nature. Example problems considered include a lid-driven cavity flow for Reynolds number of 10,000, a laminar backward-facing step flow, a laminar flow through a nest of cylinders, and a channel flow with an internal blockage. A finite element computer program (NSFLOW/P) for the 2-D, incompressible Navier-Stokes equations is also presented.

  11. A finite element-boundary integral method for cavities in a circular cylinder

    NASA Technical Reports Server (NTRS)

    Kempel, Leo C.; Volakis, John L.

    1992-01-01

    Conformal antenna arrays offer many cost and weight advantages over conventional antenna systems. However, due to a lack of rigorous mathematical models for conformal antenna arrays, antenna designers resort to measurement and planar antenna concepts for designing non-planar conformal antennas. Recently, we have found the finite element-boundary integral method to be very successful in modeling large planar arrays of arbitrary composition in a metallic plane. We extend this formulation to conformal arrays on large metallic cylinders. In this report, we develop the mathematical formulation. In particular, we discuss the shape functions, the resulting finite elements and the boundary integral equations, and the solution of the conformal finite element-boundary integral system. Some validation results are presented and we further show how this formulation can be applied with minimal computational and memory resources.

  12. Relaxase DNA Binding and Cleavage Are Two Distinguishable Steps in Conjugative DNA Processing That Involve Different Sequence Elements of the nic Site*

    PubMed Central

    Lucas, María; González-Pérez, Blanca; Cabezas, Matilde; Moncalian, Gabriel; Rivas, Germán; de la Cruz, Fernando

    2010-01-01

    TrwC, the relaxase of plasmid R388, catalyzes a series of concerted DNA cleavage and strand transfer reactions on a specific site (nic) of its origin of transfer (oriT). nic contains the cleavage site and an adjacent inverted repeat (IR2). Mutation analysis in the nic region indicated that recognition of the IR2 proximal arm and the nucleotides located between IR2 and the cleavage site were essential for supercoiled DNA processing, as judged either by in vitro nic cleavage or by mobilization of a plasmid containing oriT. Formation of the IR2 cruciform and recognition of the distal IR2 arm and loop were not necessary for these reactions to take place. On the other hand, IR2 was not involved in TrwC single-stranded DNA processing in vitro. For single-stranded DNA nic cleavage, TrwC recognized a sequence embracing six nucleotides upstream of the cleavage site and two nucleotides downstream. This suggests that TrwC DNA binding and cleavage are two distinguishable steps in conjugative DNA processing and that different sequence elements are recognized by TrwC in each step. IR2-proximal arm recognition was crucial for the initial supercoiled DNA binding. Subsequent recognition of the adjacent single-stranded DNA binding site was required to position the cleavage site in the active center of the protein so that the nic cleavage reaction could take place. PMID:20061574

  13. Relaxase DNA binding and cleavage are two distinguishable steps in conjugative DNA processing that involve different sequence elements of the nic site.

    PubMed

    Lucas, María; González-Pérez, Blanca; Cabezas, Matilde; Moncalian, Gabriel; Rivas, Germán; de la Cruz, Fernando

    2010-03-19

    TrwC, the relaxase of plasmid R388, catalyzes a series of concerted DNA cleavage and strand transfer reactions on a specific site (nic) of its origin of transfer (oriT). nic contains the cleavage site and an adjacent inverted repeat (IR(2)). Mutation analysis in the nic region indicated that recognition of the IR(2) proximal arm and the nucleotides located between IR(2) and the cleavage site were essential for supercoiled DNA processing, as judged either by in vitro nic cleavage or by mobilization of a plasmid containing oriT. Formation of the IR(2) cruciform and recognition of the distal IR(2) arm and loop were not necessary for these reactions to take place. On the other hand, IR(2) was not involved in TrwC single-stranded DNA processing in vitro. For single-stranded DNA nic cleavage, TrwC recognized a sequence embracing six nucleotides upstream of the cleavage site and two nucleotides downstream. This suggests that TrwC DNA binding and cleavage are two distinguishable steps in conjugative DNA processing and that different sequence elements are recognized by TrwC in each step. IR(2)-proximal arm recognition was crucial for the initial supercoiled DNA binding. Subsequent recognition of the adjacent single-stranded DNA binding site was required to position the cleavage site in the active center of the protein so that the nic cleavage reaction could take place.

  14. Steps in creating a methodology for interpreting a geodiversity element -integrating a geodiversity element in the popular knowledge

    NASA Astrophysics Data System (ADS)

    Toma, Cristina; Andrasanu, Alexandru

    2017-04-01

    Conserving geodiversity and especially geological heritage is not very well integrated in the general knowledge as biodiversity is, for example. Keeping that in mind we are trying, through this research, to find a better way of transmitting a geological process to the general public. The means to integrate a geodiversity element in the popular knowledge is through interpretation. Interpretation "translates" the scientific information into a common language with very well known facts by the general public. The purpose of this paper is creating a framework for a methodology necessary in interpreting a geodiversity element - salt - in Buzau Land Geopark. We will approach the salt subject through a scheme in order to have a general view of the process and to better understand and explain it to the general public. We will look into the subject from three scientific points of view: GEODIVERSITY, ANTHROPOLOGY, and the SOCIO-ECONOMICAL aspect. Each of these points of view or domains will be divided into themes. For GEODIVERSITY we will have the following themes: Formation, Accumulation, Diapirism process, Chemical formula, Landscape (here we will include also the specific biodiversity with the halophile plants), Landforms, Hazard. For ANTHROPOLOGY will contain themes of tangible and intangible heritage like: Salt symbolistic, Stories and ritual usage, Recipes, How the knowledge is transmitted. The SOCIO-ECONOMIC aspect will be reflected through themes like: Extractive methods, Usage, Interdictions, Taxes, Commercial exchanges. Each theme will have a set of keywords that will be described and each one will be at the base of the elements that together will form the interpretation of the geodiversity element - the salt. The next step will be to clearly set the scope of the interpretation, to which field of expertise is our interpretation process addressed: Education (Undergraduate or post-graduate Students), Science, Geotourism, Entrepreneurship. After putting together the

  15. Velocity-pressure integrated versus penalty finite element methods for high Reynolds number flows

    NASA Technical Reports Server (NTRS)

    Kim, S.-W.; Decker, Rand A.

    1989-01-01

    Velocity-pressure integrated and consistent penalty finite element computations of high Reynolds number laminar flows are presented. In both methods the pressure has been interpolated using linear shape functions for a triangular element which is contained inside the biquadratic flow element. It has been shown previously that the pressure interpolation method, when used in conjunction with the velocity-pressure integrated method, yields accurate computational results for high-Reynolds-number flows. It is shown in this paper that use of the same pressure interpolation method in the consistent penalty finite element method yields computational results which are comparable to those of the velocity-pressure integrated method for both the velocity and the pressure fields. Accuracy of the two finite element methods has been demonstrated by comparing the computational results with available experimental data and/or fine grid finite difference computational results. Advantages and disadvantages of the two finite element methods are discussed on the basis of accuracy and convergence nature. Example problems considered include a lid-driven cavity flow of Reynolds number 10000, a laminar backward-facing step flow and a laminar flow through a nest of cylinders.

  16. Integrator element as a promoter of active learning in engineering teaching

    NASA Astrophysics Data System (ADS)

    Oliveira, Paulo C.; Oliveira, Cristina G.

    2014-03-01

    In this paper, we present a teaching proposal used in an Introductory Physics course to civil engineering students from Porto's Engineering Institute/Instituto Superior de Engenharia do Porto (ISEP). The proposal was born from the need to change students' perception and motivation for learning physics. It consists in the use of an integrator element, called the physics elevator project. This integrator element allows us to use, in a single project, all the content taught in the course and uses several active learning strategies. In this paper, we analyse this project as: (i) a clarifying element of the contents covered in the course; (ii) a promoter element of motivation and active participation in class and finally and (iii) a link between the contents covered in the course and the 'real world'. The data were collected by a questionnaire and interviews to students. From the data collected, it seems that the integrator element improves students' motivation towards physics and develops several skills that they consider to be important to their professional future. It also acts as a clarifying element and makes the connection between the physics that is taught and the 'real world'.

  17. Unit of Learning Model for LMS/LCMS Integrating Psycho-pedagogical Elements

    NASA Astrophysics Data System (ADS)

    Wang, Kai-Li; Trigano, Philippe

    In order to make Learning Management System (LMS) and Learning Content Management System (LCMS) more adaptable, this paper provides a way of integrating psychological and pedagogical elements in the online course structure generation process, based on platform of netUniversité. The elements are integrated in an interactive user questionnaire, which is based on the results of quantitative research. As a part of user model and the preface of learning design, this questionnaire was presented in an ontology, to solve the problem of combinatorial explosion.

  18. Improved accuracy for finite element structural analysis via a new integrated force method

    NASA Technical Reports Server (NTRS)

    Patnaik, Surya N.; Hopkins, Dale A.; Aiello, Robert A.; Berke, Laszlo

    1992-01-01

    A comparative study was carried out to determine the accuracy of finite element analyses based on the stiffness method, a mixed method, and the new integrated force and dual integrated force methods. The numerical results were obtained with the following software: MSC/NASTRAN and ASKA for the stiffness method; an MHOST implementation method for the mixed method; and GIFT for the integrated force methods. The results indicate that on an overall basis, the stiffness and mixed methods present some limitations. The stiffness method generally requires a large number of elements in the model to achieve acceptable accuracy. The MHOST method tends to achieve a higher degree of accuracy for course models than does the stiffness method implemented by MSC/NASTRAN and ASKA. The two integrated force methods, which bestow simultaneous emphasis on stress equilibrium and strain compatibility, yield accurate solutions with fewer elements in a model. The full potential of these new integrated force methods remains largely unexploited, and they hold the promise of spawning new finite element structural analysis tools.

  19. Why farming with high tech methods should integrate elements of organic agriculture.

    PubMed

    Ammann, Klaus

    2009-09-01

    In the previous article [Ammann, K. (2008) Feature: integrated farming: why organic farmers should use transgenic crops. New Biotechnol. 25, 101-107], in a plea for the introduction of transgenic crops into organic and integrated farming, it was announced that the complementary topic, namely that high tech farmers should integrate elements of organic agriculture, will be a follow up. Some selected arguments for such a view are summarised here. Basically, they comprise a differentiated view on agro-biodiversity outside the field of production; landscape management methods to enhance biodiversity levels. Both elements are compatible with basic ideas of organic farming. First, Precision Farming is given as one example of the many ways to support agricultural production through high technology, with the aim of reducing energy input, maintaining excellent soil conditions and enhancing yield. It is clear from this analysis that modern agriculture and certain elements of organic-integrated agriculture are compatible. There are sectors of high tech farming, such as the introduction of a better recycling scheme and also a better focus on socio-economic aspects, which need to be taken up seriously from organic-integrated farming, a system which puts a lot of emphasis on those elements and for which important research data are available. In the final part a new concept of dynamic sustainability is presented.

  20. Improved accuracy for finite element structural analysis via an integrated force method

    NASA Technical Reports Server (NTRS)

    Patnaik, S. N.; Hopkins, D. A.; Aiello, R. A.; Berke, L.

    1992-01-01

    A comparative study was carried out to determine the accuracy of finite element analyses based on the stiffness method, a mixed method, and the new integrated force and dual integrated force methods. The numerical results were obtained with the following software: MSC/NASTRAN and ASKA for the stiffness method; an MHOST implementation method for the mixed method; and GIFT for the integrated force methods. The results indicate that on an overall basis, the stiffness and mixed methods present some limitations. The stiffness method generally requires a large number of elements in the model to achieve acceptable accuracy. The MHOST method tends to achieve a higher degree of accuracy for course models than does the stiffness method implemented by MSC/NASTRAN and ASKA. The two integrated force methods, which bestow simultaneous emphasis on stress equilibrium and strain compatibility, yield accurate solutions with fewer elements in a model. The full potential of these new integrated force methods remains largely unexploited, and they hold the promise of spawning new finite element structural analysis tools.

  1. Designing new institutions for implementing integrated disaster risk management: key elements and future directions.

    PubMed

    Gopalakrishnan, Chennat; Okada, Norio

    2007-12-01

    The goal of integrated disaster risk management is to promote an overall improvement in the quality of safety and security in a region, city or community at disaster risk. This paper presents the case for a thorough overhaul of the institutional component of integrated disaster risk management. A review of disaster management institutions in the United States indicates significant weaknesses in their ability to contribute effectively to the implementation of integrated disaster risk management. Our analysis and findings identify eight key elements for the design of dynamic new disaster management institutions. Six specific approaches are suggested for incorporating the identified key elements in building new institutions that would have significant potential for enhancing the effective implementation of integrated disaster risk management. We have developed a possible blueprint for effective design and construction of efficient, sustainable and functional disaster management institutions.

  2. Finite element solution for energy conservation using a highly stable explicit integration algorithm

    NASA Technical Reports Server (NTRS)

    Baker, A. J.; Manhardt, P. D.

    1972-01-01

    Theoretical derivation of a finite element solution algorithm for the transient energy conservation equation in multidimensional, stationary multi-media continua with irregular solution domain closure is considered. The complete finite element matrix forms for arbitrarily irregular discretizations are established, using natural coordinate function representations. The algorithm is embodied into a user-oriented computer program (COMOC) which obtains transient temperature distributions at the node points of the finite element discretization using a highly stable explicit integration procedure with automatic error control features. The finite element algorithm is shown to posses convergence with discretization for a transient sample problem. The condensed form for the specific heat element matrix is shown to be preferable to the consistent form. Computed results for diverse problems illustrate the versatility of COMOC, and easily prepared output subroutines are shown to allow quick engineering assessment of solution behavior.

  3. Mapping data elements to terminological resources for integrating biomedical data sources.

    PubMed

    Mougin, Fleur; Burgun, Anita; Bodenreider, Olivier

    2006-11-24

    Data integration is a crucial task in the biomedical domain and integrating data sources is one approach to integrating data. Data elements (DEs) in particular play an important role in data integration. We combine schema- and instance-based approaches to mapping DEs to terminological resources in order to facilitate data sources integration. We extracted DEs from eleven disparate biomedical sources. We compared these DEs to concepts and/or terms in biomedical controlled vocabularies and to reference DEs. We also exploited DE values to disambiguate underspecified DEs and to identify additional mappings. 82.5% of the 474 DEs studied are mapped to entries of a terminological resource and 74.7% of the whole set can be associated with reference DEs. Only 6.6% of the DEs had values that could be semantically typed. Our study suggests that the integration of biomedical sources can be achieved automatically with limited precision and largely facilitated by mapping DEs to terminological resources.

  4. Social behavior and decision making in bacterial conjugation.

    PubMed

    Koraimann, Günther; Wagner, Maria A

    2014-01-01

    Bacteria frequently acquire novel genes by horizontal gene transfer (HGT). HGT through the process of bacterial conjugation is highly efficient and depends on the presence of conjugative plasmids (CPs) or integrated conjugative elements (ICEs) that provide the necessary genes for DNA transmission. This review focuses on recent advancements in our understanding of ssDNA transfer systems and regulatory networks ensuring timely and spatially controlled DNA transfer (tra) gene expression. As will become obvious by comparing different systems, by default, tra genes are shut off in cells in which conjugative elements are present. Only when conditions are optimal, donor cells-through epigenetic alleviation of negatively acting roadblocks and direct stimulation of DNA transfer genes-become transfer competent. These transfer competent cells have developmentally transformed into specialized cells capable of secreting ssDNA via a T4S (type IV secretion) complex directly into recipient cells. Intriguingly, even under optimal conditions, only a fraction of the population undergoes this transition, a finding that indicates specialization and cooperative, social behavior. Thereby, at the population level, the metabolic burden and other negative consequences of tra gene expression are greatly reduced without compromising the ability to horizontally transfer genes to novel bacterial hosts. This undoubtedly intelligent strategy may explain why conjugative elements-CPs and ICEs-have been successfully kept in and evolved with bacteria to constitute a major driving force of bacterial evolution.

  5. Conjugate Reinforcement.

    ERIC Educational Resources Information Center

    Lewis, Richard F.

    Conjugate reinforcement is a new attention measure which has emerged from experimental psychology. It can provide accurate measurement of a subject's attention to a stimulus. In conjugate reinforcement, the duration of the stimulus varies directly and immediately with the subject's rate of response. In this process, the subject must demonstrate…

  6. A finite element-boundary integral method for conformal antenna arrays on a circular cylinder

    NASA Technical Reports Server (NTRS)

    Kempel, Leo C.; Volakis, John L.; Woo, Alex C.; Yu, C. Long

    1992-01-01

    Conformal antenna arrays offer many cost and weight advantages over conventional antenna systems. In the past, antenna designers have had to resort to expensive measurements in order to develop a conformal array design. This is due to the lack of rigorous mathematical models for conformal antenna arrays, and as a result the design of conformal arrays is primarily based on planar antenna design concepts. Recently, we have found the finite element-boundary integral method to be very successful in modeling large planar arrays of arbitrary composition in a metallic plane. Herewith we shall extend this formulation for conformal arrays on large metallic cylinders. In this we develop the mathematical formulation. In particular we discuss the finite element equations, the shape elements, and the boundary integral evaluation, and it is shown how this formulation can be applied with minimal computation and memory requirements. The implementation shall be discussed in a later report.

  7. A finite element-boundary integral method for conformal antenna arrays on a circular cylinder

    NASA Technical Reports Server (NTRS)

    Kempel, Leo C.; Volakis, John L.

    1992-01-01

    Conformal antenna arrays offer many cost and weight advantages over conventional antenna systems. In the past, antenna designers have had to resort to expensive measurements in order to develop a conformal array design. This was due to the lack of rigorous mathematical models for conformal antenna arrays. As a result, the design of conformal arrays was primarily based on planar antenna design concepts. Recently, we have found the finite element-boundary integral method to be very successful in modeling large planar arrays of arbitrary composition in a metallic plane. We are extending this formulation to conformal arrays on large metallic cylinders. In doing so, we will develop a mathematical formulation. In particular, we discuss the finite element equations, the shape elements, and the boundary integral evaluation. It is shown how this formulation can be applied with minimal computation and memory requirements.

  8. Conjugate symplectic B-series

    NASA Astrophysics Data System (ADS)

    Hairer, Ernst; Zbinden, Christophe J.

    2012-09-01

    For the long-time integration of Hamiltonian differential equations the use of symplectic methods is recommended. In practice it is often sufficient to apply a method that is conjugate (up to a sufficiently high order) to a symplectic integrator. This article gives a criterion on the conjugate symplecticity of methods that can be represented as a B-series. It allows to characterize the conjugate symplecticity of a large class of numerical integrators including Lobatto IIIA and Lobatto IIIB methods, as well as energy-preserving collocation methods.

  9. Application of the Coupled Finite Element-Combined Field Integral Equation Technique (FEICFIE) to the Radiation Problem

    NASA Technical Reports Server (NTRS)

    Jamnejad, V.; Cwik, T.; Zuffada, C.

    1994-01-01

    A coupled finite element-combined field integral equation technique was originally developed for solving scattering problems involving inhomogeneous objects of arbitrary shape and large dimensions in wavelength.

  10. Development of Finite Elements for Two-Dimensional Structural Analysis Using the Integrated Force Method

    NASA Technical Reports Server (NTRS)

    Kaljevic, Igor; Patnaik, Surya N.; Hopkins, Dale A.

    1996-01-01

    The Integrated Force Method has been developed in recent years for the analysis of structural mechanics problems. This method treats all independent internal forces as unknown variables that can be calculated by simultaneously imposing equations of equilibrium and compatibility conditions. In this paper a finite element library for analyzing two-dimensional problems by the Integrated Force Method is presented. Triangular- and quadrilateral-shaped elements capable of modeling arbitrary domain configurations are presented. The element equilibrium and flexibility matrices are derived by discretizing the expressions for potential and complementary energies, respectively. The displacement and stress fields within the finite elements are independently approximated. The displacement field is interpolated as it is in the standard displacement method, and the stress field is approximated by using complete polynomials of the correct order. A procedure that uses the definitions of stress components in terms of an Airy stress function is developed to derive the stress interpolation polynomials. Such derived stress fields identically satisfy the equations of equilibrium. Moreover, the resulting element matrices are insensitive to the orientation of local coordinate systems. A method is devised to calculate the number of rigid body modes, and the present elements are shown to be free of spurious zero-energy modes. A number of example problems are solved by using the present library, and the results are compared with corresponding analytical solutions and with results from the standard displacement finite element method. The Integrated Force Method not only gives results that agree well with analytical and displacement method results but also outperforms the displacement method in stress calculations.

  11. Esophageal and Small Intestinal Mucosal Integrity in Eosinophilic Esophagitis and Response to an Elemental Diet

    PubMed Central

    Warners, Marijn J; Vlieg-Boerstra, Berber J; Verheij, Joanne; van Hamersveld, Patricia H P; van Rhijn, Bram D; Van Ampting, Marleen T J; Harthoorn, Lucien F; de Jonge, Wouter J; Smout, Andreas J P M; Bredenoord, Albert J

    2017-01-01

    Objectives: The esophageal mucosal integrity is impaired in eosinophilic esophagitis (EoE) and it has been suggested that the duodenal permeability is increased. The absence of food allergens may restore the integrity. The aims of this study were to assess duodenal permeability in EoE and to evaluate the effect of an elemental diet on the esophageal and duodenal integrity. Methods: In this prospective study 17 adult EoE patients and 8 healthy controls (HC) were included. Esophageal biopsy specimens were sampled before and after 4 weeks of elemental diet to measure eosinophil counts and gene expression of tight junction and barrier integrity proteins. Esophageal and duodenal impedance were measured by electrical tissue impedance spectroscopy and Ussing chambers were used to measure transepithelial resistance (TER) and transepithelial molecule flux. Small intestinal permeability was measured using a test, measuring lactulose/mannitol (L/M) ratios. Results: In EoE patients, the esophageal but not the duodenal integrity was impaired, compared with HC. We observed no significant difference between L/M ratios of HC and EoE patients. After diet, eosinophil counts decreased significantly, which was paralleled by normalization of esophageal impedance and transepithelial molecule flux. The esophageal TER improved significantly, but did not reach values seen in HC. Esophageal expression of genes encoding for barrier integrity proteins filaggrin and desmoglein-1 was impaired at baseline and restored after diet. Conclusions: An elemental diet restores esophageal integrity, suggesting that it is at least partly secondary to allergen exposure. Duodenal integrity seems not to be affected in EoE, and possibly plays a minor role in its pathophysiology. PMID:28417991

  12. Esophageal and Small Intestinal Mucosal Integrity in Eosinophilic Esophagitis and Response to an Elemental Diet.

    PubMed

    Warners, Marijn J; Vlieg-Boerstra, Berber J; Verheij, Joanne; van Hamersveld, Patricia H P; van Rhijn, Bram D; Van Ampting, Marleen T J; Harthoorn, Lucien F; de Jonge, Wouter J; Smout, Andreas J P M; Bredenoord, Albert J

    2017-07-01

    The esophageal mucosal integrity is impaired in eosinophilic esophagitis (EoE) and it has been suggested that the duodenal permeability is increased. The absence of food allergens may restore the integrity. The aims of this study were to assess duodenal permeability in EoE and to evaluate the effect of an elemental diet on the esophageal and duodenal integrity. In this prospective study 17 adult EoE patients and 8 healthy controls (HC) were included. Esophageal biopsy specimens were sampled before and after 4 weeks of elemental diet to measure eosinophil counts and gene expression of tight junction and barrier integrity proteins. Esophageal and duodenal impedance were measured by electrical tissue impedance spectroscopy and Ussing chambers were used to measure transepithelial resistance (TER) and transepithelial molecule flux. Small intestinal permeability was measured using a test, measuring lactulose/mannitol (L/M) ratios. In EoE patients, the esophageal but not the duodenal integrity was impaired, compared with HC. We observed no significant difference between L/M ratios of HC and EoE patients. After diet, eosinophil counts decreased significantly, which was paralleled by normalization of esophageal impedance and transepithelial molecule flux. The esophageal TER improved significantly, but did not reach values seen in HC. Esophageal expression of genes encoding for barrier integrity proteins filaggrin and desmoglein-1 was impaired at baseline and restored after diet. An elemental diet restores esophageal integrity, suggesting that it is at least partly secondary to allergen exposure. Duodenal integrity seems not to be affected in EoE, and possibly plays a minor role in its pathophysiology.

  13. A Strategy for Integrating a Large Finite Element Model: X-33 Lessons Learned

    NASA Technical Reports Server (NTRS)

    McGhee, David S.

    2000-01-01

    The X-33 vehicle is an advanced technology demonstrator sponsored by NASA. For the past three years the Structural Dynamics & Loads Group of NASA's Marshall Space Flight Center has had the task of integrating the X-33 vehicle structural finite element model. In that time, five versions of the integrated vehicle model have been produced and a strategy has evolved that would benefit anyone given the task of integrating structural finite element models that have been generated by various modelers and companies. The strategy that has been presented here consists of six decisions that need to be made. These six decisions are: purpose of model, units, common material list, model numbering, interface control, and archive format. This strategy has been proved and expanded from experience on the X-33 vehicle.

  14. Finite element analysis of nano-scale Timoshenko beams using the integral model of nonlocal elasticity

    NASA Astrophysics Data System (ADS)

    Norouzzadeh, A.; Ansari, R.

    2017-04-01

    Stress-strain relation in Eringen's nonlocal elasticity theory was originally formulated within the framework of an integral model. Due to difficulty of working with that integral model, the differential model of nonlocal constitutive equation is widely used for nanostructures. However, paradoxical results may be obtained by the differential model for some boundary and loading conditions. Presented in this article is a finite element analysis of Timoshenko nano-beams based on the integral model of nonlocal continuum theory without employing any simplification in the model. The entire procedure of deriving equations of motion is carried out in the matrix form of representation, and hence, they can be easily used in the finite element analysis. For comparison purpose, the differential counterparts of equations are also derived. To study the outcome of analysis based on the integral and differential models, some case studies are presented in which the influences of boundary conditions, nonlocal length scale parameter and loading factor are analyzed. It is concluded that, in contrast to the differential model, there is no paradox in the numerical results of developed integral model of nonlocal continuum theory for different situations of problem characteristics. So, resolving the mentioned paradoxes by means of a purely numerical approach based on the original integral form of nonlocal elasticity theory is the major contribution of present study.

  15. Thermalization away from integrability and the role of operator off-diagonal elements.

    PubMed

    Konstantinidis, N P

    2015-05-01

    We investigate the rate of thermalization of local operators in the one-dimensional anisotropic antiferromagnetic Heisenberg model with next-nearest neighbor interactions that break integrability. This is done by calculating the scaling of the difference of the diagonal and canonical thermal ensemble values as a function of system size, and by directly calculating the time evolution of the expectation values of the operators with the Chebyshev polynomial expansion. Spatial and spin symmetry is exploited and the Hamiltonian is divided into subsectors according to their symmetry. The rate of thermalization depends on the proximity to the integrable limit. When integrability is weakly broken thermalization is slow, and becomes faster the stronger the next-nearest neighbor interaction is. Three different regimes for the rate of thermalization with respect to the strength of the integrability breaking parameter are identified. These are shown to be directly connected with the relative strength of the low and higher energy difference off-diagonal operator matrix elements in the symmetry eigenbasis of the Hamiltonian. Close to the integrable limit the off-diagonal matrix elements peak at higher energies and high-frequency fluctuations are important and slow down thermalization. Away from the integrable limit a strong low-energy peak gradually develops that takes over the higher frequency fluctuations and leads to quicker thermalization.

  16. An integrated digital silicon micro-accelerometer with MOSFET-type sensing elements

    NASA Astrophysics Data System (ADS)

    Yee, Youngjoo; Bu, Jong Uk; Chun, Kukjin; Lee, Joong-Won

    2000-09-01

    A fully digital integrated accelerometer having a new sensing element is designed and fabricated based on CMOS processes and micromachining. The sensing elements of this accelerometer are constructed on the bulk silicon proof mass with metal air-gap MOSFETs (MAMOS) whose drain current is dependent on the applied acceleration. A current-controlled oscillator converts the change of this drain current to a digital pulse train. A 20-bit synchronous binary counter is monolithically integrated to digitize the output pulse of the oscillator. A bulk micromachined silicon proof mass provides perfect electrical isolation of the MOSFET sensing elements from a peripheral CMOS readout circuit. The suspension springs of this accelerometer are formed from thick MEMS (microelectromechanical systems) polysilicon. A CMOS compatible doping and annealing process for the MEMS polysilicon is developed to optimize the trade-off between the mechanical properties and the electrical requirements. The shift in the overall device characteristics of CMOS circuitry integrated with MEMS polysilicon is well below 5% of those fabricated by a standard CMOS process. Using the slightly modified 1.5 µm CMOS circuit process followed by an anisotropic silicon etch, an integrated digital silicon accelerometer is fabricated. The measured sensitivity of the fabricated MAMOS accelerometer is 63 kHz G-1.

  17. Multi-Element Integration Test on ISS components under way in the SSPF

    NASA Technical Reports Server (NTRS)

    1999-01-01

    In The Space Station Processing Facility, a Multi-Element Integration Test (MEIT) is underway to ensure components of the International Space Station work together before they are launched into orbit. Within the framework at right is the U.S. Lab, called Destiny; at left is the Z-1 truss. The current MEIT combines the P-6 photovoltaic module, the Z-1 truss and the Pressurized Mating Adapter 3. Electrical and fluid connections are being hooked up to verify how the ISS elements operate together.

  18. James Webb Space Telescope Optical Telescope Element Integrated Science Instrument Module (OTIS) Status

    NASA Technical Reports Server (NTRS)

    Feinberg, Lee; Voyton, Mark; Lander, Julie; Keski-Kuha, Ritva; Matthews, Gary

    2016-01-01

    The James Webb Space Telescope Optical Telescope Element (OTE) and Integrated ScienceInstrument Module (ISIM)are integrated together to form the OTIS. Once integrated, the OTIS undergoes primary mirrorcenter of curvatureoptical tests, electrical and operational tests, acoustics and vibration testing at the Goddard SpaceFlight Center beforebeing shipped to the Johnson Space Center for cryogenic optical testing of the OTIS. In preparationfor the cryogenicoptical testing, the JWST project has built a Pathfinder telescope and has completed two OpticalGround SystemEquipment (OGSE) cryogenic optical tests with the Pathfinder. In this paper, we will summarize opticaltest results todate and status the final Pathfinder test and the OTIS integration and environmental test preparations

  19. James Webb Space Telescope Optical Telescope Element/Integrated Science Instrument Module (OTIS) Status

    NASA Technical Reports Server (NTRS)

    Feinberg, Lee; Voyton, Mark; Lander, Juli; Keski-Kuha, Ritva; Matthews, Gary

    2016-01-01

    The James Webb Space Telescope Optical Telescope Element (OTE) and Integrated Science Instrument Module (ISIM) are integrated together to form the OTIS. Once integrated, the OTIS undergoes primary mirror center of curvature optical tests, electrical and operational tests, acoustics and vibration testing at the Goddard Space Flight Center before being shipped to the Johnson Space Center for cryogenic optical testing of the OTIS. In preparation for the cryogenic optical testing, the JWST project has built a Pathfinder telescope and has completed two Optical Ground System Equipment (OGSE) cryogenic optical tests with the Pathfinder. In this paper, we will summarize optical test results to date and status the final Pathfinder test and the OTIS integration and environmental test preparations

  20. Intermediate elemental image reconstruction for refocused three-dimensional images in integral imaging by convolution with δ-function sequences

    NASA Astrophysics Data System (ADS)

    Yoo, Hoon; Jang, Jae-Young

    2017-10-01

    We propose a novel approach for intermediate elemental image reconstruction in integral imaging. To reconstruct intermediate elemental images, we introduce a null elemental image whose pixels are all zero. In the proposed method a number of null elemental images are inserted into a given elemental image array. The elemental image array with null elemental images is convolved with the δ-function sequence. The convolution result shows that the proposed method provides an efficient structure to expand an elemental image array. The resulting elemental image array from the proposed method can supply three-dimensional information for an object at a specific depth. In addition, the proposed method provides adjustable parameters, which can be utilized in design of integral imaging systems. The feasibility of the proposed method has been confirmed through preliminary experiments and theoretical analysis.

  1. Directly laser-written integrated photonics devices including diffractive optical elements

    NASA Astrophysics Data System (ADS)

    Choi, Jiyeon; Ramme, Mark; Richardson, Martin

    2016-08-01

    Femtosecond laser-written integrated devices involving Fresnel Zone Plates (FZPs) and waveguide arrays are demonstrated as built-in optical couplers. These structures were fabricated in borosilicate glass using a direct laser writing technique. The optical properties of these integrated photonic structures were investigated using CW lasers and high-resolution CCDs. For a single FZP coupled to a single waveguide, the overall coupling efficiency was 9%. A multiplexed optical coupler composed of three FZP layers was demonstrated to couple three waveguides simultaneously in a waveguide array. Structures of this type can be used as platforms for multichannel waveguide coupling elements or as microfluidic sensors that require higher light collecting efficiency.

  2. An integrated approach to identify normal tissue expression of targets for antibody-drug conjugates: case study of TENB2

    PubMed Central

    Boswell, C Andrew; Mundo, Eduardo E; Firestein, Ron; Zhang, Crystal; Mao, Weiguang; Gill, Herman; Young, Cynthia; Ljumanovic, Nina; Stainton, Shannon; Ulufatu, Sheila; Fourie, Aimee; Kozak, Katherine R; Fuji, Reina; Polakis, Paul; Khawli, Leslie A; Lin, Kedan

    2013-01-01

    Background and Purpose The success of antibody-drug conjugates (ADCs) depends on the therapeutic window rendered by the differential expression between normal and pathological tissues. The ability to identify and visualize target expression in normal tissues could reveal causes for target-mediated clearance observed in pharmacokinetic characterization. TENB2 is a prostate cancer target associated with the progression of poorly differentiated and androgen-independent tumour types, and ADCs specific for TENB2 are candidate therapeutics. The objective of this study was to locate antigen expression of TENB2 in normal tissues, thereby elucidating the underlying causes of target-mediated clearance. Experimental Approach A series of pharmacokinetics, tissue distribution and mass balance studies were conducted in mice using a radiolabelled anti-TENB2 ADC. These data were complemented by non-invasive single photon emission computed tomography – X-ray computed tomography imaging and immunohistochemistry. Key Results The intestines were identified as a saturable and specific antigen sink that contributes, at least in part, to the rapid target-mediated clearance of the anti-TENB2 antibody and its drug conjugate in rodents. As a proof of concept, we also demonstrated the selective disposition of the ADC in a tumoural environment in vivo using the LuCaP 77 transplant mouse model. High tumour uptake was observed despite the presence of the antigen sink, and antigen specificity was confirmed by antigen blockade. Conclusions and Implications Our findings provide the anatomical location and biological interpretation of target-mediated clearance of anti-TENB2 antibodies and corresponding drug conjugates. Further investigations may be beneficial in addressing the relative contributions to ADC disposition from antigen expression in both normal and pathological tissues. PMID:22889168

  3. An integrated approach to identify normal tissue expression of targets for antibody-drug conjugates: case study of TENB2.

    PubMed

    Boswell, C Andrew; Mundo, Eduardo E; Firestein, Ron; Zhang, Crystal; Mao, Weiguang; Gill, Herman; Young, Cynthia; Ljumanovic, Nina; Stainton, Shannon; Ulufatu, Sheila; Fourie, Aimee; Kozak, Katherine R; Fuji, Reina; Polakis, Paul; Khawli, Leslie A; Lin, Kedan

    2013-01-01

    The success of antibody-drug conjugates (ADCs) depends on the therapeutic window rendered by the differential expression between normal and pathological tissues. The ability to identify and visualize target expression in normal tissues could reveal causes for target-mediated clearance observed in pharmacokinetic characterization. TENB2 is a prostate cancer target associated with the progression of poorly differentiated and androgen-independent tumour types, and ADCs specific for TENB2 are candidate therapeutics. The objective of this study was to locate antigen expression of TENB2 in normal tissues, thereby elucidating the underlying causes of target-mediated clearance. A series of pharmacokinetics, tissue distribution and mass balance studies were conducted in mice using a radiolabelled anti-TENB2 ADC. These data were complemented by non-invasive single photon emission computed tomography - X-ray computed tomography imaging and immunohistochemistry. The intestines were identified as a saturable and specific antigen sink that contributes, at least in part, to the rapid target-mediated clearance of the anti-TENB2 antibody and its drug conjugate in rodents. As a proof of concept, we also demonstrated the selective disposition of the ADC in a tumoural environment in vivo using the LuCaP 77 transplant mouse model. High tumour uptake was observed despite the presence of the antigen sink, and antigen specificity was confirmed by antigen blockade. Our findings provide the anatomical location and biological interpretation of target-mediated clearance of anti-TENB2 antibodies and corresponding drug conjugates. Further investigations may be beneficial in addressing the relative contributions to ADC disposition from antigen expression in both normal and pathological tissues. © 2012 Genentech, Inc.. British Journal of Pharmacology © 2012 The British Pharmacological Society.

  4. An Integrated Finite Element-based Simulation Framework: From Hole Piercing to Hole Expansion

    SciTech Connect

    Hu, Xiaohua; Sun, Xin; Golovashchenko, Segey F.

    2016-02-01

    An integrated finite element-based modeling framework is developed to predict the hole expansion ratio (HER) of AA6111-T4 sheet by considering the piercing-induced damages around the hole edge. Using damage models and parameters calibrated from previously reported tensile stretchability studies, the predicted HER correlates well with experimentally measured HER values for different hole piercing clearances. The hole piercing model shows burrs are not generated on the sheared surface for clearances less than 20%, which corresponds well with the experimental data on pierced holes cross-sections. Finite-element-calculated HER also is not especially sensitive to piercing clearances less than this value. However, as clearances increase to 30% and further to 40%, the HER values are predicted to be considerably smaller, also consistent with experimental measurements. Upon validation, the integrated modeling framework is used to examine the effects of different hole piercing and hole expansion conditions on the critical HERs for AA6111-T4.

  5. Optical frequency selective surface design using a GPU accelerated finite element boundary integral method

    NASA Astrophysics Data System (ADS)

    Ashbach, Jason A.

    Periodic metallodielectric frequency selective surface (FSS) designs have historically seen widespread use in the microwave and radio frequency spectra. By scaling the dimensions of an FSS unit cell for use in a nano-fabrication process, these concepts have recently been adapted for use in optical applications as well. While early optical designs have been limited to wellunderstood geometries or optimized pixelated screens, nano-fabrication, lithographic and interconnect technology has progressed to a point where it is possible to fabricate metallic screens of arbitrary geometries featuring curvilinear or even three-dimensional characteristics that are only tens of nanometers wide. In order to design an FSS featuring such characteristics, it is important to have a robust numerical solver that features triangular elements in purely two-dimensional geometries and prismatic or tetrahedral elements in three-dimensional geometries. In this dissertation, a periodic finite element method code has been developed which features prismatic elements whose top and bottom boundaries are truncated by numerical integration of the boundary integral as opposed to an approximate representation found in a perfectly matched layer. However, since no exact solution exists for the calculation of triangular elements in a boundary integral, this process can be time consuming. To address this, these calculations were optimized for parallelization such that they may be done on a graphics processor, which provides a large increase in computational speed. Additionally, a simple geometrical representation using a Bezier surface is presented which provides generality with few variables. With a fast numerical solver coupled with a lowvariable geometric representation, a heuristic optimization algorithm has been used to develop several optical designs such as an absorber, a circular polarization filter, a transparent conductive surface and an enhanced, optical modulator.

  6. On the accuracy and convergence of implicit numerical integration of finite element generated ordinary differential equations

    NASA Technical Reports Server (NTRS)

    Baker, A. J.; Soliman, M. O.

    1978-01-01

    A study of accuracy and convergence of linear functional finite element solution to linear parabolic and hyperbolic partial differential equations is presented. A variable-implicit integration procedure is employed for the resultant system of ordinary differential equations. Accuracy and convergence is compared for the consistent and two lumped assembly procedures for the identified initial-value matrix structure. Truncation error estimation is accomplished using Richardson extrapolation.

  7. An Integrated Support and Alignment System for Large ILC Lattice Elements

    SciTech Connect

    Viola, Robert

    2013-05-15

    The manipulators used to support and position lattice elements are critical components of all particle accelerators. The increased use of large superconducting magnets and accelerator modules places even greater demands on these manipulators. However, the performance of these support systems has not kept pace with the advances made in other areas of accelerator technology. This results in accelerators that are difficult to align and may not be capable of achieving target luminosities. An innovative new type of positioning mechanism tailored to the requirements of the International Linear Collider is proposed. The Tri-Sphere System provides secure support for large lattice elements and precision adjustment in six degrees of freedom. Integrated target sockets allow the support system to be rapidly pre-aligned. The system's kinematic design passively guides lattice elements into their correct location during installation. A complimentary Portable Actuation Unit provides the advantages of automated adjustment and allows these adjustments to be completely decoupled from surveying.

  8. Determining the DNA sequence elements required for binding integration host factor to two different target sites.

    PubMed Central

    Hales, L M; Gumport, R I; Gardner, J F

    1994-01-01

    Binding sites for the Escherichia coli protein integration host factor (IHF) include a set of conserved bases that can be summarized by the consensus sequence WATCAANNNNTTR (W is dA or dT, R is dA or dG, and N is any nucleotide). However, additional 5'-proximal bases, whose common feature is a high dA+dT content, are also thought to be required for binding at some sites. We examine the relative contribution of these two sequence elements to IHF binding to the H' and H1 sites in attP of bacteriophage lambda by using the bacteriophage P22-based challenge-phage system. IHF was unable to act as a repressor in the challenge-phage assay at H' sites containing the core consensus element but lacking the dA+dT-rich element. This indicates that both elements are required for IHF to bind to the H' site. In contrast, the core consensus determinant alone is sufficient for IHF binding to the H1 site, which lacks an upstream dA+dT-rich region. Fifty mutants that decreased or eliminated IHF binding to the H1 site were isolated. Sequence analysis showed changes in the bases in the core consensus element only, further indicating that this determinant is sufficient for IHF binding to the H1 site. We found that placement of a dA+dT-rich element upstream of the H1 core consensus element significantly increased the affinity, suggesting that the presence of a dA+dT-rich element enhances IHF binding. PMID:8188600

  9. Integration of local pattern elements into a global shape in human vision

    PubMed Central

    Saarinen, Jukka; Levi, Dennis M.; Shen, Bridgitte

    1997-01-01

    The spatial extent of the cortical filters selective for different spatial frequencies and orientations is limited. We studied psychophysically how information from the local filters is integrated into global pattern shapes, i.e., whether performance in the identification of a global pattern consisting of small, locally oriented Gabor elements depends on the orientations of those elements. The observer was presented with an E-like stimulus pattern shape comprised of oriented Gabor patches on a blank background, and the performance measure was the threshold contrast for identifying the orientation of the E pattern (four possible rotated orientations). The results showed that contrast thresholds were significantly lower when the local elements all shared the same orientation (e.g., all horizontal) compared with the condition in which the elements had mixed orientations (both horizontal and vertical). The enhancement effect due to uniform local orientations can be explained by two factors: One is local facilitatory interactions between the orientation selective filters, and the other is second-order information integration across the filters. PMID:9223350

  10. Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus.

    PubMed

    Valente, Guilherme; Kocher, Thomas; Eickbush, Thomas; Simões, Rafael P; Martins, Cesar

    2016-06-01

    Integration of cytogenetics and genomics has become essential to a better view of architecture and function of genomes. Although the advances on genomic sequencing have contributed to study genes and genomes, the repetitive DNA fraction of the genome is still enigmatic and poorly understood. Among repeated DNAs, transposable elements (TEs) are major components of eukaryotic chromatin and their investigation has been hindered even after the availability of whole sequenced genomes. The cytogenetic mapping of TEs in chromosomes has proved to be of high value to integrate information from the micro level of nucleotide sequence to a cytological view of chromosomes. Different TEs have been cytogenetically mapped in cichlids; however, neither details about their genomic arrangement nor appropriated copy number are well defined by these approaches. The current study integrates TEs distribution in Nile tilapia Oreochromis niloticus genome based on cytogenetic and genomics/bioinformatics approach. The results showed that some elements are not randomly distributed and that some are genomic dependent on each other. Moreover, we found extensive overlap between genomics and cytogenetics data and that tandem duplication may be the major mechanism responsible for the genomic dynamics of TEs here analyzed. This paper provides insights in the genomic organization of TEs under an integrated view based on cytogenetics and genomics.

  11. Interrater reliability and discriminative validity of the structural elements of the Ayres Sensory Integration Fidelity Measure.

    PubMed

    May-Benson, Teresa A; Roley, Susanne Smith; Mailloux, Zoe; Parham, L Diane; Koomar, Jane; Schaaf, Roseann C; Jaarsveld, Annamarie Van; Cohn, Ellen

    2014-01-01

    This study examined the reliability and validity of the structural section of the Ayres Sensory Integration® Fidelity Measure© (ASIFM), which provides a method for monitoring the extent to which an intervention was implemented as conceptualized in studies of occupational therapy using sensory integration intervention methods (OT-SI). We examined the structural elements of the measure, including content of assessment reports, availability of specific equipment and adequate space, safety monitoring, and integration of communication with parents and other team members, such as collaborative goal setting with parents or family and teacher education, into the intervention program. Analysis of self-report ratings by 259 occupational therapists from 185 different facilities indicated that the structural section of the ASIFM has acceptable interrater reliability (r ≥ .82) and significantly differentiates between settings in which therapists reportedly do and do not practice OT-SI (p < .001).

  12. Construction of an integrative regulatory element and variation map of the murine Tst locus.

    PubMed

    Beltram, Jasmina; Morton, Nicholas M; Kunej, Tanja; Horvat, Simon

    2016-06-11

    Given the abundance of new genomic projects and gene annotations, researchers trying to pinpoint causal genetic variants are faced with a challenging task of how to efficiently integrate all current genomic information. The objective of the study was to develop an approach to integrate various genomic annotations for a recently positionally-cloned Tst gene (Thiosulfate Sulfur Transferase, synonym Rhodanese) responsible for the Fob3b2 QTL effect on leanness and improved metabolic parameters. The second aim was to identify and prioritize Tst genetic variants that may be causal for the phenotypic effects. A bioinformatics approach was developed to integrate existing knowledge of regulatory elements of the Tst gene. The entire Tst locus along with flanking segments was sequenced between our unique polygenic mouse Fat and Lean strains that were generated by divergent selection on adiposity for over 60 generations. The bioinformatics-generated regulatory element map of the Tst locus was then combined with genetic variants between the Fat and Lean mice and with comparative analyses of polymorphisms across 17 mouse strains in order to prioritise likely causal polymorphisms. Two candidate regulatory variants were identified, one overlapping an evolutionary constrained Tst intronic element and the other residing in the seed region of a predicted 3'UTR miRNA binding site. This study developed a map of regulatory elements for the Tst locus in mice and identified candidate genetic variants with increased causal likelihood. This map provides a basis for experimental validation and functional analyses of this novel candidate leanness and antidiabetic gene. Our methodological approach is of general utility for analyzing regulation of loci that have limited annotations and experimental evidence and for identifying candidate causal regulatory genetic variants in post-GWAS or post-QTL- cloning studies.

  13. Contour integration and aging: the effects of element spacing, orientation alignment and stimulus duration.

    PubMed

    Roudaia, Eugenie; Bennett, Patrick J; Sekuler, Allison B

    2013-01-01

    The ability to extract contours in cluttered visual scenes, which is a crucial step in visual processing, declines with healthy aging, but the reasons for this decline are not well understood. In three experiments, we examined how the effect of aging on contour discrimination varies as a function of contour and distracter inter-element spacing, collinearity, and stimulus duration. Spiral-shaped contours composed of Gabors were embedded within a field of distracter Gabors of uniform density. In a four alternative forced-choice task, younger and older subjects were required to report the global orientation of the contour. In Experiment 1, the absolute contour element spacing varied from two to eight times the Gabor wavelength and contour element collinearity was disrupted with five levels of orientation jitter. Contour discrimination accuracy was lower in older subjects, but the effect of aging did not vary with contour spacing or orientation jitter. Experiment 2 found that decreasing stimulus durations from 0.8 to 0.04 s had a greater effect on older subjects' performance, but only for less salient contours. Experiment 3 examined the effect of the background on contour discrimination by varying the spacing and orientation of the distracter elements for contours with small and large absolute spacing. As in Experiment, the effect of aging did not vary with absolute contour spacing. Decreasing the distracter spacing, however, had a greater detrimental effect on accuracy in older subjects compared to younger subjects. Finally, both groups showed equally high accuracy when all distracters were iso-oriented. In sum, these findings suggest that aging does not affect the sensitivity of contour integration to proximity or collinearity. However, contour integration in older adults is slower and is especially vulnerable when distracters are denser than contour elements.

  14. Common elements in self-management of HIV and other chronic illnesses: an integrative framework.

    PubMed

    Swendeman, Dallas; Ingram, Barbara L; Rotheram-Borus, Mary Jane

    2009-10-01

    HIV/AIDS is widely recognized as a chronic illness within HIV care, but is often excluded from chronic disease lists outside the field. Similar to other chronic diseases, HIV requires lifetime changes in physical health, psychological functioning, social relations, and adoption of disease-specific regimens. The shift from acute to chronic illness requires a self-management model in which patients assume an active and informed role in healthcare decision making to change behaviors and social relations to optimize health and proactively address predictable challenges of chronic diseases generally and HIV specifically. This article reviews literature on chronic disease self-management to identify factors common across chronic diseases, highlight HIV-specific challenges, and review recent developments in self-management interventions for people living with HIV (PLH) and other chronic diseases. An integrated framework of common elements or tasks in chronic disease self-management is presented that outlines 14 elements in three broad categories: physical health; psychological functioning; and social relationships. Common elements for physical health include: a framework for understanding illness and wellness; health promoting behaviors; treatment adherence; self-monitoring of physical status; accessing appropriate treatment and services; and preventing transmission. Elements related to psychological functioning include: self-efficacy and empowerment; cognitive skills; reducing negative emotional states; and managing identity shifts. Social relationship elements include: collaborative relationships with healthcare providers; social support; disclosure and stigma management; and positive social and family relationships. There is a global need to scale up chronic disease self-management services, including for HIV, but there are significant challenges related to healthcare system and provider capacities, and stigma is a significant barrier to HIV-identified service

  15. Integrated learning in practical machine element design course: a case study of V-pulley design

    NASA Astrophysics Data System (ADS)

    Tantrabandit, Manop

    2014-06-01

    To achieve an effective integrated learning in Machine Element Design course, it is of importance to bridge the basic knowledge and skills of element designs. The multiple core learning leads the pathway which consists of two main parts. The first part involves teaching documents of which the contents are number of V-groove formulae, standard of V-grooved pulleys, and parallel key dimension's formulae. The second part relates to the subjects that the students have studied prior to participating in this integrated learning course, namely Material Selection, Manufacturing Process, Applied Engineering Drawing, CAD (Computer Aided Design) animation software. Moreover, an intensive cooperation between a lecturer and students is another key factor to fulfill the success of integrated learning. Last but not least, the students need to share their knowledge within the group and among the other groups aiming to gain knowledge of and skills in 1) the application of CAD-software to build up manufacture part drawings, 2) assembly drawing, 3) simulation to verify the strength of loaded pulley by method of Finite Element Analysis (FEA), 4) the software to create animation of mounting and dismounting of a pulley to a shaft, and 5) an instruction manual. The end product of this integrated learning, as a result of the above 1 to 5 knowledge and skills obtained, the participating students can create an assembly derived from manufacture part drawings and a video presentation with bilingual (English-Thai) audio description of Vpulley with datum diameter of 250 mm, 4 grooves, and type of groove: SPA.

  16. Element Library for Three-Dimensional Stress Analysis by the Integrated Force Method

    NASA Technical Reports Server (NTRS)

    Kaljevic, Igor; Patnaik, Surya N.; Hopkins, Dale A.

    1996-01-01

    The Integrated Force Method, a recently developed method for analyzing structures, is extended in this paper to three-dimensional structural analysis. First, a general formulation is developed to generate the stress interpolation matrix in terms of complete polynomials of the required order. The formulation is based on definitions of the stress tensor components in term of stress functions. The stress functions are written as complete polynomials and substituted into expressions for stress components. Then elimination of the dependent coefficients leaves the stress components expressed as complete polynomials whose coefficients are defined as generalized independent forces. Such derived components of the stress tensor identically satisfy homogenous Navier equations of equilibrium. The resulting element matrices are invariant with respect to coordinate transformation and are free of spurious zero-energy modes. The formulation provides a rational way to calculate the exact number of independent forces necessary to arrive at an approximation of the required order for complete polynomials. The influence of reducing the number of independent forces on the accuracy of the response is also analyzed. The stress fields derived are used to develop a comprehensive finite element library for three-dimensional structural analysis by the Integrated Force Method. Both tetrahedral- and hexahedral-shaped elements capable of modeling arbitrary geometric configurations are developed. A number of examples with known analytical solutions are solved by using the developments presented herein. The results are in good agreement with the analytical solutions. The responses obtained with the Integrated Force Method are also compared with those generated by the standard displacement method. In most cases, the performance of the Integrated Force Method is better overall.

  17. Cis-element mutated in GATA2-dependent immunodeficiency governs hematopoiesis and vascular integrity

    PubMed Central

    Johnson, Kirby D.; Hsu, Amy P.; Ryu, Myung-Jeom; Wang, Jinyong; Gao, Xin; Boyer, Meghan E.; Liu, Yangang; Lee, Youngsook; Calvo, Katherine R.; Keles, Sunduz; Zhang, Jing; Holland, Steven M.; Bresnick, Emery H.

    2012-01-01

    Haploinsufficiency for GATA2 causes human immunodeficiency syndromes characterized by mycobacterial infection, myelodysplasia, lymphedema, or aplastic anemia that progress to myeloid leukemia. GATA2 encodes a master regulator of hematopoiesis that is also linked to endothelial biology. Though the disease-causing mutations commonly occur in the GATA-2 DNA binding domain, we identified a patient with mycobacterial infection and myelodysplasia who had an uncharacterized heterozygous deletion in a GATA2 cis-element consisting of an E-box and a GATA motif. Targeted deletion of the equivalent murine element to yield homozygous mutant mice revealed embryonic lethality later than occurred with global Gata2 knockout, hematopoietic stem/progenitor cell depletion, and impaired vascular integrity. Heterozygous mutant mice were viable, but embryos exhibited deficits in definitive, but not primitive, hematopoietic stem/progenitor activity and reduced expression of Gata2 and its target genes. Mechanistic analysis revealed disruption of the endothelial cell transcriptome and loss of vascular integrity. Thus, the composite element disrupted in a human immunodeficiency is essential for establishment of the murine hematopoietic stem/progenitor cell compartment in the fetal liver and for essential vascular processes. PMID:22996659

  18. Implementation of a finite element method for the vertical discretization of KIAPS Integrated Model (KIM)

    NASA Astrophysics Data System (ADS)

    Park, J. R.; Choi, S. J.

    2016-12-01

    As an attempt to improve numerical accuracy of the global numerical forecast model developed in Korea Institute of Atmospheric Prediction Systems (KIAPS), named as KIAPS Integrated Model (KIM) (Choi and Hong 2016), we have tried to implement the finite element method (FEM) for the vertical discretization. The main modifications are involved in the derivative and integral operators and the vertically no staggering grids. The vertical operators are defined using the linear and cubic splines as basis functions, the numerical accuracy of which is examined by using several idealized test cases. With combination of the horizontal spectral element and vertical FEM, the simulated results reveal that benefit of the high accuracy by FEM mainly appeared in inner domain away from the boundaries compared to the finite difference method (FDM). In 3D Hadley-like meridional advection test, for example, error norms produced by using FEM are much smaller. ReferenceChoi, S.-J. and S.-Y. Hong, 2016: A global non-hydrostatic dynamical core using the spectral element method on a cubed-sphere grid, Asia-Pac. J. Atmos. Sci., 52(3), 291-307.

  19. An adjustable RF tuning element for microwave, millimeter wave, and submillimeter wave integrated circuits

    NASA Technical Reports Server (NTRS)

    Lubecke, Victor M.; Mcgrath, William R.; Rutledge, David B.

    1991-01-01

    Planar RF circuits are used in a wide range of applications from 1 GHz to 300 GHz, including radar, communications, commercial RF test instruments, and remote sensing radiometers. These circuits, however, provide only fixed tuning elements. This lack of adjustability puts severe demands on circuit design procedures and materials parameters. We have developed a novel tuning element which can be incorporated into the design of a planar circuit in order to allow active, post-fabrication tuning by varying the electrical length of a coplanar strip transmission line. It consists of a series of thin plates which can slide in unison along the transmission line, and the size and spacing of the plates are designed to provide a large reflection of RF power over a useful frequency bandwidth. Tests of this structure at 1 GHz to 3 Ghz showed that it produced a reflection coefficient greater than 0.90 over a 20 percent bandwidth. A 2 GHz circuit incorporating this tuning element was also tested to demonstrate practical tuning ranges. This structure can be fabricated for frequencies as high as 1000 GHz using existing micromachining techniques. Many commercial applications can benefit from this micromechanical RF tuning element, as it will aid in extending microwave integrated circuit technology into the high millimeter wave and submillimeter wave bands by easing constraints on circuit technology.

  20. Tipping elements and climate-economic shocks: Pathways toward integrated assessment

    NASA Astrophysics Data System (ADS)

    Kopp, Robert E.; Shwom, Rachael L.; Wagner, Gernot; Yuan, Jiacan

    2016-08-01

    The literature on the costs of climate change often draws a link between climatic "tipping points" and large economic shocks, frequently called "catastrophes." The phrase "tipping points" in this context can be misleading. In popular and social scientific discourse, "tipping points" involve abrupt state changes. For some climatic "tipping points," the commitment to a state change may occur abruptly, but the change itself may be rate-limited and take centuries or longer to realize. Additionally, the connection between climatic "tipping points" and economic losses is tenuous, although emerging empirical and process-model-based tools provide pathways for investigating it. We propose terminology to clarify the distinction between "tipping points" in the popular sense, the critical thresholds exhibited by climatic and social "tipping elements," and "economic shocks." The last may be associated with tipping elements, gradual climate change, or nonclimatic triggers. We illustrate our proposed distinctions by surveying the literature on climatic tipping elements, climatically sensitive social tipping elements, and climate-economic shocks, and we propose a research agenda to advance the integrated assessment of all three.

  1. Element-free precise integration method and its applications in seismic modelling and imaging

    NASA Astrophysics Data System (ADS)

    Jia, Xiaofeng; Hu, Tianyue

    2006-07-01

    In this paper the theory of the element-free precise integration method (EFPIM) is presented as well as its applications in seismic modelling and imaging. The key point of this method is the absence of elements, which makes nodes free from the elemental restraint. Due to the moving least-squares (MLS) fitting instead of interpolation, the EFPIM results in high accuracy for both the dependent variable and its gradient. The EFPIM improves the implicit element-free method (EFM) by cutting the computational cost significantly. At the same time, the accuracy of this method keeps as good as that of the implicit EFM. The scheme of EFPIM is shown for the full scalar wave equation. Numerical stability is examined for the scheme subsequently. Based on the theory, a simple example of vibrant film is discussed in details to indicate the effectivity of the EFPIM. Main factors affecting the accuracy of the method are illustrated. Furthermore, we show some synthetic examples to demonstrate good performance of the EFPIM in seismic modelling and imaging problems. Both post-stack and pre-stack cases are considered. Combined with appropriate absorbing boundary conditions, the EFPIM can generate sections with accurate traveltimes and amplitudes. Complex structures can be imaged clearly such as high-angle dip and embedded high-velocity anomalies.

  2. Genetic engineering in Actinoplanes sp. SE50/110 - development of an intergeneric conjugation system for the introduction of actinophage-based integrative vectors.

    PubMed

    Gren, Tetiana; Ortseifen, Vera; Wibberg, Daniel; Schneiker-Bekel, Susanne; Bednarz, Hanna; Niehaus, Karsten; Zemke, Till; Persicke, Marcus; Pühler, Alfred; Kalinowski, Jörn

    2016-08-20

    The α-glucosidase inhibitor acarbose is used for treatment of diabetes mellitus type II, and is manufactured industrially with overproducing derivatives of Actinoplanes sp. SE50/110, reportedly obtained by conventional mutagenesis. Despite of high industrial significance, only limited information exists regarding acarbose metabolism, function and regulation of these processes, due to the absence of proper genetic engineering methods and tools developed for this strain. Here, a basic toolkit for genetic engineering of Actinoplanes sp. SE50/110 was developed, comprising a standardized protocol for a DNA transfer through Escherichia coli-Actinoplanes intergeneric conjugation and applied for the transfer of ϕC31, ϕBT1 and VWB actinophage-based integrative vectors. Integration sites, occurring once per genome for all vectors, were sequenced and characterized for the first time in Actinoplanes sp. SE50/110. Notably, in case of ϕC31 based vector pSET152, the integration site is highly conserved, while for ϕBT1 and the VWB based vectors pRT801 and pSOK804, respectively, no sequence similarities to those in other bacteria were detected. The studied plasmids were proven to be stable and neutral with respect to strain morphology and acarbose production, enabling future use for genetic manipulations of Actinoplanes sp. SE50/110. To further broaden the spectrum of available tools, a GUS reporter system, based on the pSET152 derived vector, was also established in Actinoplanes sp. SE50/110.

  3. Integration Of The Security Sub-Modules Elements In The Automotive Industry

    SciTech Connect

    Gallego, C.; Fernandez, M.; Caires, A. S.; Canibano, E.

    2007-05-17

    This study is addressed to obtain a design methodology for integrated security sub-modules (constituting the suspension and steering modules) in the car manufacturing industry. The sub-modules are made up of a steel structure and anchorage elements (rubber-metal or plastic-metal), which undergo separate surface treatments to prevent corrosion. Afterwards, the elements are traditionally joined by means of adhesives and screws. This process involves a great number of stages, low quality union methods and generation of corrosion areas that shorten its useful life.This methodology provides automotive suppliers an additional added value and cost reduction, allowing them to increase its competitiveness in a sector that faces the transition from the traditional supply chain to a strategic value chain.

  4. STARS: An integrated general-purpose finite element structural, aeroelastic, and aeroservoelastic analysis computer program

    NASA Technical Reports Server (NTRS)

    Gupta, Kajal K.

    1991-01-01

    The details of an integrated general-purpose finite element structural analysis computer program which is also capable of solving complex multidisciplinary problems is presented. Thus, the SOLIDS module of the program possesses an extensive finite element library suitable for modeling most practical problems and is capable of solving statics, vibration, buckling, and dynamic response problems of complex structures, including spinning ones. The aerodynamic module, AERO, enables computation of unsteady aerodynamic forces for both subsonic and supersonic flow for subsequent flutter and divergence analysis of the structure. The associated aeroservoelastic analysis module, ASE, effects aero-structural-control stability analysis yielding frequency responses as well as damping characteristics of the structure. The program is written in standard FORTRAN to run on a wide variety of computers. Extensive graphics, preprocessing, and postprocessing routines are also available pertaining to a number of terminals.

  5. Altering genomic integrity: heavy metal exposure promotes trans-posable element-mediated damage

    PubMed Central

    Morales, Maria E.; Servant, Geraldine; Ade, Catherine; Roy-Enge, Astrid M.

    2015-01-01

    Maintenance of genomic integrity is critical for cellular homeostasis and survival. The active transposable elements (TEs) composed primarily of three mobile element lineages LINE-1, Alu, and SVA comprise approximately 30% of the mass of the human genome. For the past two decades, studies have shown that TEs significantly contribute to genetic instability and that TE-caused damages are associated with genetic diseases and cancer. Different environmental exposures, including several heavy metals, influence how TEs interact with its host genome increasing their negative impact. This mini-review provides some basic knowledge on TEs, their contribution to disease and an overview of the current knowledge on how heavy metals influence TE-mediated damage. PMID:25774044

  6. A computerized symbolic integration technique for development of triangular and quadrilateral composite shallow-shell finite elements

    NASA Technical Reports Server (NTRS)

    Anderson, C. M.; Noor, A. K.

    1975-01-01

    Computerized symbolic integration was used in conjunction with group-theoretic techniques to obtain analytic expressions for the stiffness, geometric stiffness, consistent mass, and consistent load matrices of composite shallow shell structural elements. The elements are shear flexible and have variable curvature. A stiffness (displacement) formulation was used with the fundamental unknowns consisting of both the displacement and rotation components of the reference surface of the shell. The triangular elements have six and ten nodes; the quadrilateral elements have four and eight nodes and can have internal degrees of freedom associated with displacement modes which vanish along the edges of the element (bubble modes). The stiffness, geometric stiffness, consistent mass, and consistent load coefficients are expressed as linear combinations of integrals (over the element domain) whose integrands are products of shape functions and their derivatives. The evaluation of the elemental matrices is divided into two separate problems - determination of the coefficients in the linear combination and evaluation of the integrals. The integrals are performed symbolically by using the symbolic-and-algebraic-manipulation language MACSYMA. The efficiency of using symbolic integration in the element development is demonstrated by comparing the number of floating-point arithmetic operations required in this approach with those required by a commonly used numerical quadrature technique.

  7. Optical Testing and Verification Methods for the James Webb Space Telescope Integrated Science Instrument Module Element

    NASA Technical Reports Server (NTRS)

    Antonille, Scott R.; Miskey, Cherie L.; Ohl, Raymond G.; Rohrbach, Scott O.; Aronstein, David L.; Bartoszyk, Andrew E.; Bowers, Charles W.; Cofie, Emmanuel; Collins, Nicholas R.; Comber, Brian J.; Eichhorn, William L.; Glasse, Alistair C.; Gracey, Renee; Hartig, George F.; Howard, Joseph M.; Kelly, Douglas M.; Kimble, Randy A.; Kirk, Jeffrey R.; Kubalak, David A.; Landsman, Wayne B.; Lindler, Don J.; Malumuth, Eliot M.; Maszkiewicz, Michael; Rieke, Marcia J.; Rowlands, Neil; Sabatke, Derek S.; Smith, Corbett T.; Smith, J. Scott; Sullivan, Joseph F.; Telfer, Randal C.; Plate, Maurice Te; Vila, M. Begona; Warner, Gerry D.; Wright, Raymond H.; Wright, David; Zhou, Julia; Zielinski, Thomas P.

    2016-01-01

    NASA's James Webb Space Telescope (JWST) is a 6.6m diameter, segmented, deployable telescope for cryogenic IR space astronomy (40K). The JWST Observatory includes the Optical Telescope Element (OTE) and the Integrated Science Instrument Module (ISIM) that contains four science instruments (SI) and the fine guider. The SIs are mounted to a composite metering structure. The SI and guider units were integrated to the ISIM structure and optically tested at the NASA Goddard Space Flight Center as a suite using the Optical Telescope Element SIMulator (OSIM). OSIM is a full field, cryogenic JWST telescope simulator. SI performance, including alignment and wave front error, were evaluated using OSIM. We describe test and analysis methods for optical performance verification of the ISIM Element, with an emphasis on the processes used to plan and execute the test. The complexity of ISIM and OSIM drove us to develop a software tool for test planning that allows for configuration control of observations, associated scripts, and management of hardware and software limits and constraints, as well as tools for rapid data evaluation, and flexible re-planning in response to the unexpected. As examples of our test and analysis approach, we discuss how factors such as the ground test thermal environment are compensated in alignment. We describe how these innovative methods for test planning and execution and post-test analysis were instrumental in the verification program for the ISIM element, with enough information to allow the reader to consider these innovations and lessons learned in this successful effort in their future testing for other programs.

  8. A paradigm for human body finite element model integration from a set of regional models.

    PubMed

    Thompson, A B; Gayzik, F S; Moreno, D P; Rhyne, A C; Vavalle, N A; Stitzel, J D

    2012-01-01

    Computational modeling offers versatility, scalability, and cost advantages to researchers in the trauma and injury biomechanics communities. The Global Human Body Models Consortium (GHBMC) is a group of government, industry, and academic researchers developing human body models (HBMs) that aim to become the standard tool to meet this growing research need. The objective of this study is to present the methods used to develop the average seated male occupant model (M50, weight = 78 kg, height = 175 cm) from five separately validated body region models (BRMs). BRMs include the head, neck, thorax, abdomen, and a combined pelvis and lower extremity model. Modeling domains were split at the atlanto-occipital joint, C7-T1 boundary, diaphragm, abdominal cavity (peritoneum/retroperitoneum), and the acetabulum respectively. BRM meshes are based on a custom CAD model of the seated male built from a multi-modality imaging protocol of a volunteer subject found in literature.[1] Various meshing techniques were used to integrate the full body model (FBM) including 1-D beam and discrete element connections (e.g. ligamentous structures), 2D shell nodal connections (e.g. inferior vena cava to right atrium), 3D hexahedral nodal connections (e.g. soft tissue envelope connections between regions), and contact definitions varying from tied (muscle insertions) to sliding (liver and diaphragm contact). The model was developed in a general-purpose finite element code, LS-Dyna (LTSC, Livermore, CA) R4.2.1., and consists of 1.95 million elements and 1.3 million nodes. The element breakdown by type is 41% hexahedral, 33.7% tetrahedral, 19.5% quad shells and 5% tria shell. The integration methodology presented highlights the viability of using a collaborative development paradigm for the construction of HBMs, and will be used as template for expanding the suite of GHBMC models.

  9. Optical testing and verification methods for the James Webb Space Telescope Integrated Science Instrument Module element

    NASA Astrophysics Data System (ADS)

    Antonille, Scott R.; Miskey, Cherie L.; Ohl, Raymond G.; Rohrbach, Scott O.; Aronstein, David L.; Bartoszyk, Andrew E.; Bowers, Charles W.; Cofie, Emmanuel; Collins, Nicholas R.; Comber, Brian J.; Eichhorn, William L.; Glasse, Alistair C.; Gracey, Renee; Hartig, George F.; Howard, Joseph M.; Kelly, Douglas M.; Kimble, Randy A.; Kirk, Jeffrey R.; Kubalak, David A.; Landsman, Wayne B.; Lindler, Don J.; Malumuth, Eliot M.; Maszkiewicz, Michael; Rieke, Marcia J.; Rowlands, Neil; Sabatke, Derek S.; Smith, Corbett T.; Smith, J. Scott; Sullivan, Joseph F.; Telfer, Randal C.; Te Plate, Maurice; Vila, M. Begoña.; Warner, Gerry D.; Wright, David; Wright, Raymond H.; Zhou, Julia; Zielinski, Thomas P.

    2016-09-01

    NASA's James Webb Space Telescope (JWST) is a 6.5m diameter, segmented, deployable telescope for cryogenic IR space astronomy. The JWST Observatory includes the Optical Telescope Element (OTE) and the Integrated Science Instrument Module (ISIM), that contains four science instruments (SI) and the Fine Guidance Sensor (FGS). The SIs are mounted to a composite metering structure. The SIs and FGS were integrated to the ISIM structure and optically tested at NASA's Goddard Space Flight Center using the Optical Telescope Element SIMulator (OSIM). OSIM is a full-field, cryogenic JWST telescope simulator. SI performance, including alignment and wavefront error, was evaluated using OSIM. We describe test and analysis methods for optical performance verification of the ISIM Element, with an emphasis on the processes used to plan and execute the test. The complexity of ISIM and OSIM drove us to develop a software tool for test planning that allows for configuration control of observations, implementation of associated scripts, and management of hardware and software limits and constraints, as well as tools for rapid data evaluation, and flexible re-planning in response to the unexpected. As examples of our test and analysis approach, we discuss how factors such as the ground test thermal environment are compensated in alignment. We describe how these innovative methods for test planning and execution and post-test analysis were instrumental in the verification program for the ISIM element, with enough information to allow the reader to consider these innovations and lessons learned in this successful effort in their future testing for other programs.

  10. Number-conserving random phase approximation with analytically integrated matrix elements

    SciTech Connect

    Kyotoku, M. ); Schmid, K.W. ); Gruemmer, F. ); Faessler, A. )

    1990-01-01

    In the present paper a number conserving random phase approximation is derived as a special case of the recently developed random phase approximation in general symmetry projected quasiparticle mean fields. All the occurring integrals induced by the number projection are performed analytically after writing the various overlap and energy matrices in the random phase approximation equation as polynomials in the gauge angle. In the limit of a large number of particles the well-known pairing vibration matrix elements are recovered. We also present a new analytically number projected variational equation for the number conserving pairing problem.

  11. Error analysis for a sinh transformation used in evaluating nearly singular boundary element integrals

    NASA Astrophysics Data System (ADS)

    Elliott, David; Johnston, Peter R.

    2007-06-01

    In the two-dimensional boundary element method, one often needs to evaluate numerically integrals of the form where j2 is a quadratic, g is a polynomial and f is a rational, logarithmic or algebraic function with a singularity at zero. The constants a and b are such that -1[less-than-or-equals, slant]a[less-than-or-equals, slant]1 and 0integration. In this case the direct application of Gauss-Legendre quadrature can give large truncation errors. By making the transformation x=a+bsinh([mu]u-[eta]), where the constants [mu] and [eta] are chosen so that the interval of integration is again [-1,1], it is found that the truncation errors arising, when the same Gauss-Legendre quadrature is applied to the transformed integral, are much reduced. The asymptotic error analysis for Gauss-Legendre quadrature, as given by Donaldson and Elliott [A unified approach to quadrature rules with asymptotic estimates of their remainders, SIAM J. Numer. Anal. 9 (1972) 573-602], is then used to explain this phenomenon and justify the transformation.

  12. JAC2D: A two-dimensional finite element computer program for the nonlinear quasi-static response of solids with the conjugate gradient method; Yucca Mountain Site Characterization Project

    SciTech Connect

    Biffle, J.H.; Blanford, M.L.

    1994-05-01

    JAC2D is a two-dimensional finite element program designed to solve quasi-static nonlinear mechanics problems. A set of continuum equations describes the nonlinear mechanics involving large rotation and strain. A nonlinear conjugate gradient method is used to solve the equations. The method is implemented in a two-dimensional setting with various methods for accelerating convergence. Sliding interface logic is also implemented. A four-node Lagrangian uniform strain element is used with hourglass stiffness to control the zero-energy modes. This report documents the elastic and isothermal elastic/plastic material model. Other material models, documented elsewhere, are also available. The program is vectorized for efficient performance on Cray computers. Sample problems described are the bending of a thin beam, the rotation of a unit cube, and the pressurization and thermal loading of a hollow sphere.

  13. JAC3D -- A three-dimensional finite element computer program for the nonlinear quasi-static response of solids with the conjugate gradient method; Yucca Mountain Site Characterization Project

    SciTech Connect

    Biffle, J.H.

    1993-02-01

    JAC3D is a three-dimensional finite element program designed to solve quasi-static nonlinear mechanics problems. A set of continuum equations describes the nonlinear mechanics involving large rotation and strain. A nonlinear conjugate gradient method is used to solve the equation. The method is implemented in a three-dimensional setting with various methods for accelerating convergence. Sliding interface logic is also implemented. An eight-node Lagrangian uniform strain element is used with hourglass stiffness to control the zero-energy modes. This report documents the elastic and isothermal elastic-plastic material model. Other material models, documented elsewhere, are also available. The program is vectorized for efficient performance on Cray computers. Sample problems described are the bending of a thin beam, the rotation of a unit cube, and the pressurization and thermal loading of a hollow sphere.

  14. TraY and Integration Host Factor oriT Binding Sites and F Conjugal Transfer: Sequence Variations, but Not Altered Spacing, Are Tolerated▿ †

    PubMed Central

    Williams, Sarah L.; Schildbach, Joel F.

    2007-01-01

    Bacterial conjugation is the process by which a single strand of a conjugative plasmid is transferred from donor to recipient. For F plasmid, TraI, a relaxase or nickase, binds a single plasmid DNA strand at its specific origin of transfer (oriT) binding site, sbi, and cleaves at a site called nic. In vitro studies suggest TraI is recruited to sbi by its accessory proteins, TraY and integration host factor (IHF). TraY and IHF bind conserved oriT sites sbyA and ihfA, respectively, and bend DNA. The resulting conformational changes may propagate to nic, generating the single-stranded region that TraI can bind. Previous deletion studies performed by others showed transfer efficiency of a plasmid containing F oriT decreased progressively as increasingly longer segments, ultimately containing both sbyA and ihfA, were deleted. Here we describe our efforts to more precisely define the role of sbyA and ihfA by examining the effects of multiple base substitutions at sbyA and ihfA on binding and plasmid mobilization. While we observed significant decreases in in vitro DNA-binding affinities, we saw little effect on plasmid mobilization even when sbyA and ihfA variants were combined. In contrast, when half or full helical turns were inserted between the relaxosome protein-binding sites, mobilization was dramatically reduced, in some cases below the detectable limit of the assay. These results are consistent with TraY and IHF recognizing sbyA and ihfA with limited sequence specificity and with relaxosome proteins requiring proper spacing and orientation with respect to each other. PMID:17351033

  15. A Modified Method for Evaluating the Invariant J-Integral in Finite-Element Models of Prismatic Bodies

    NASA Astrophysics Data System (ADS)

    Bazhenov, V. A.; Sakharov, A. S.; Maksimyuk, Yu. V.; Shkryl', A. A.

    2016-03-01

    Numerical experiments are performed to analyze the invariance and reliability of the results of evaluation of the J-integral by the modified method of reactions in problems of mixed fracture. Bodies with cracks undergoing elastoplastic deformation under static loading are considered. To demonstrate the universality of the method to finite-element schemes, prismatic bodies are considered. This allows using not only conventional finite-element schemes, but also the semi-analytical finite-element method

  16. Glutathione Conjugation

    PubMed Central

    Shimabukuro, R. H.; Swanson, H. R.; Walsh, W. C.

    1970-01-01

    Glutathione conjugation (GS-atrazine) of the herbicide, 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (atrazine) is another major detoxication mechanism in leaf tissue of corn (Zea mays, L.). The identification of GS-atrazine is the first example of glutathione conjugation as a biotransformation mechanism of a pesticide in plants. Recovery of atrazine-inhibited photosynthesis was accompanied by a rapid conversion of atrazine to GS-atrazine when the herbicide was introduced directly into leaf tissue. N-De-alkylation pathway is relatively inactive in both roots and shoots. The nonenzymatic detoxication of atrazine to hydroxyatrazine is negligible in leaf tissue. The hydroxylation pathway contributed significantly to the total detoxication of atrazine only when the herbicide was introduced into the plant through the roots. The metabolism of atrazine to GS-atrazine may be the primary factor in the resistance of corn to atrazine. PMID:16657398

  17. Textile antenna integrated with compact AMC and parasitic elements for WLAN/WBAN applications

    NASA Astrophysics Data System (ADS)

    Lago, Herwansyah; Soh, Ping Jack; Jamlos, Mohd Faizal; Shohaimi, Nursuriati; Yan, Sen; Vandenbosch, Guy A. E.

    2016-12-01

    A wearable antenna fully designed and fabricated using textile is presented. Both antenna and artificial magnetic conductor plane are designed for operation in the wireless local area network (WLAN)/wireless body area network (WBAN) band from 2.4 to 2.5 GHz. The AMC unit element is designed based on the rectangular patch structure, which is then integrated using slots and slits for bandwidth broadening. Meanwhile, the combination of the slits and L-shaped parasitic elements applied at four edges of the rectangular antenna structure enabled unidirectional radiation outwards from the body. The structure is coaxially fed using a rectangular ring slot centered on the radiating element. Simulated and measured reflection and radiation performance indicate a satisfactory agreement, fulfilling the requirements for WLAN/WBAN applications both in free space and on body. The shielding effectiveness provided by the AMC plane is also evaluated numerically in terms of specific absorption rate, indicating levels below the European regulatory limit of 2 W/kg.

  18. Integrating Epigenomic Elements and GWASs Identifies BDNF Gene Affecting Bone Mineral Density and Osteoporotic Fracture Risk

    PubMed Central

    Guo, Yan; Dong, Shan-Shan; Chen, Xiao-Feng; Jing, Ying-Aisha; Yang, Man; Yan, Han; Shen, Hui; Chen, Xiang-Ding; Tan, Li-Jun; Tian, Qing; Deng, Hong-Wen; Yang, Tie-Lin

    2016-01-01

    To identify susceptibility genes for osteoporosis, we conducted an integrative analysis that combined epigenomic elements and previous genome-wide association studies (GWASs) data, followed by validation at population and functional levels, which could identify common regulatory elements and predict new susceptibility genes that are biologically meaningful to osteoporosis. By this approach, we found a set of distinct epigenomic elements significantly enriched or depleted in the promoters of osteoporosis-associated genes, including 4 transcription factor binding sites, 27 histone marks, and 21 chromatin states segmentation types. Using these epigenomic marks, we performed reverse prediction analysis to prioritize the discovery of new candidate genes. Functional enrichment analysis of all the prioritized genes revealed several key osteoporosis related pathways, including Wnt signaling. Genes with high priority were further subjected to validation using available GWASs datasets. Three genes were significantly associated with spine bone mineral density, including BDNF, PDE4D, and SATB2, which all closely related to bone metabolism. The most significant gene BDNF was also associated with osteoporotic fractures. RNA interference revealed that BDNF knockdown can suppress osteoblast differentiation. Our results demonstrated that epigenomic data could be used to indicate common epigenomic marks to discover additional loci with biological functions for osteoporosis. PMID:27465306

  19. Integrating Epigenomic Elements and GWASs Identifies BDNF Gene Affecting Bone Mineral Density and Osteoporotic Fracture Risk.

    PubMed

    Guo, Yan; Dong, Shan-Shan; Chen, Xiao-Feng; Jing, Ying-Aisha; Yang, Man; Yan, Han; Shen, Hui; Chen, Xiang-Ding; Tan, Li-Jun; Tian, Qing; Deng, Hong-Wen; Yang, Tie-Lin

    2016-07-28

    To identify susceptibility genes for osteoporosis, we conducted an integrative analysis that combined epigenomic elements and previous genome-wide association studies (GWASs) data, followed by validation at population and functional levels, which could identify common regulatory elements and predict new susceptibility genes that are biologically meaningful to osteoporosis. By this approach, we found a set of distinct epigenomic elements significantly enriched or depleted in the promoters of osteoporosis-associated genes, including 4 transcription factor binding sites, 27 histone marks, and 21 chromatin states segmentation types. Using these epigenomic marks, we performed reverse prediction analysis to prioritize the discovery of new candidate genes. Functional enrichment analysis of all the prioritized genes revealed several key osteoporosis related pathways, including Wnt signaling. Genes with high priority were further subjected to validation using available GWASs datasets. Three genes were significantly associated with spine bone mineral density, including BDNF, PDE4D, and SATB2, which all closely related to bone metabolism. The most significant gene BDNF was also associated with osteoporotic fractures. RNA interference revealed that BDNF knockdown can suppress osteoblast differentiation. Our results demonstrated that epigenomic data could be used to indicate common epigenomic marks to discover additional loci with biological functions for osteoporosis.

  20. Biomechanical properties in titanium implants with integrated maintenance free shock absorbing elements.

    PubMed

    Gaggl, A; Schultes, G

    2001-11-01

    Good functional properties are essential in dental implantology. Bio-kinetic elements are imitating dental resilience. In this study a new kind of implants with maintenance free shock absorbing elements will be introduced and their bio-mechanic properties reported. The mobile implant (SIS Inc., Klagenfurt, Austria) is a self-cutting conical screw implant with an integrated bio-kinetic element. The shock absorber is a central part of the implant and a titanium ring closes the shock absorbing unit within the implant. The resilience of the implant was tested by axial and horizontal loading in a special testing unit. Furthermore, a survival test of the elastic titanium ring in the most exposed cervical part of the implant was performed. The region was examined by electron microscopy after 12 million movements in the axial and horizontal direction. A progressive shock absorption was registered during horizontal and axial movements. The maximum movements were 0.06 mm in the axial and 0.16 mm in the horizontal direction. There were seen no signs of material destruction in the electron microscopic analysis. A maintenance-free bio-kinetic implant with progressive shock absorbing qualities was registered.

  1. [Resilience behavior of titanium implants with integrated maintenance-free biokinetic elements].

    PubMed

    Gaggl, A; Schultes, G

    2000-01-01

    Good functional properties are essential in dental implantology. Bio-kinetics elements are imitating dental resilience. In this study a new kind of implants with maintenance-free shock-absorbing elements was introduced and their bio-mechanic properties were tested. The mobile implant (SIS Inc, Klagenfurt, Austria) is a self-cutting conical screw implant with an integrated bio-kinetic element. The shock absorber is a central part of the implant and a titanium ring obturates the shock absorbing unit in the implant. The resilience of the implant was tested by axial and excentric loading in a special testing unit. Furthermore a survival test of the elastic titanium ring in the most exposed cervical part of the implant was performed. The region was examined by scanning electron microscopy after 12 million loading cycles in the axial and radial direction. A progressive shock absorption was registered during radial and axial loading. The maximum movements were 0.06 mm in the axial and 0.16 mm in the radial direction. No signs of material destruction were seen in the electron microscopic analysis. Thus a maintenance-free bio-kinetic implant with progressive shock-absorbing qualities is presented.

  2. Integrated force method - Compatibility conditions of structural mechanics for finite element analysis

    NASA Technical Reports Server (NTRS)

    Patnaik, Surya N.; Berke, Laszlo; Gallagher, Richard H.

    1991-01-01

    The equilibrium equations and the compatibility conditions are fundamental to the analyses of structures. However, anyone who undertakes even a cursory generic study of the compatibility conditions can discover, with little effort, that historically this facet of structural mechanics had not been adequately researched by the profession. Now the compatibility conditions (CC's) have been researched and are understood to a great extent. For finite element discretizations, the CC's are banded and can be divided into three distinct categories: (1) the interface CC's, (2) the cluster or field CC's, and (3) the external CC's. The generation of CC's requires the separating of a local region, then writing the deformation displacement relation (ddr) for the region, and finally, the eliminating of the displacements from the ddr. The procedure to generate all three types of CC's is presented and illustrated through examples of finite element models. The uniqueness of the CC's thus generated is shown. The utilization of CC's has resulted in the novel integrated force method (IFM). The solution that is obtained by the IFM converges with a significantly fewer number of elements, compared to the stiffness and the hybrid methods.

  3. Hybrid Finite Element-Fast Spectral Domain Multilayer Boundary Integral Modeling of Doubly Periodic Structures

    SciTech Connect

    T.F. Eibert; J.L. Volakis; Y.E. Erdemli

    2002-03-03

    Hybrid finite element (FE)--boundary integral (BI) analysis of infinite periodic arrays is extended to include planar multilayered Green's functions. In this manner, a portion of the volumetric dielectric region can be modeled via the finite element method whereas uniform multilayered regions can be modeled using a multilayered Green's function. As such, thick uniform substrates can be modeled without loss of efficiency and accuracy. The multilayered Green's function is analytically computed in the spectral domain and the resulting BI matrix-vector products are evaluated via the fast spectral domain algorithm (FSDA). As a result, the computational cost of the matrix-vector products is kept at O(N). Furthermore, the number of Floquet modes in the expansion are kept very few by placing the BI surfaces within the computational unit cell. Examples of frequency selective surface (FSS) arrays are analyzed with this method to demonstrate the accuracy and capability of the approach. One example involves complicated multilayered substrates above and below an inhomogeneous filter element and the other is an optical ring-slot array on a substrate several hundred wavelengths in thickness. Comparisons with measurements are included.

  4. Alignment of the James Webb Space Telescope Integrated Science Instrument Module Element

    NASA Astrophysics Data System (ADS)

    Hadjimichael, Theo; Ohl, Raymond G.; Antonille, Scott; Aronstein, David L.; Bartoszyk, Andrew; Berrier, Josh; Cofie, Emmanuel; Coulter, Phil; Gracey, Renee; Hayden, Joseph; Howard, Joseph; Hylan, Jason; Kubalak, David; McLean, Kyle; Miskey, Cherie; Redman, Kevin; Rohrbach, Scott; Sabatke, Derek; Telfer, Randal; Wenzel, Greg; Zielinski, Thomas; Sullivan, Joseph; Hartig, George; Eichhorn, William

    2016-10-01

    NASA's James Webb Space Telescope (JWST) is a 6.6m diameter, segmented, deployable telescope for cryogenic IR space astronomy. The JWST Observatory architecture includes the Optical Telescope Element (OTE) and the Integrated Science Instrument Module (ISIM) element which contains four science instruments (SI), including a guider. The SIs and guider are mounted to a composite metering structure with outer envelope approximate measurements of 2.2x2.2x1.7m. These SI units are integrated to the ISIM structure and optically tested at NASA Goddard Space Flight Center as an instrument suite using an Optical telescope element SIMulator (OSIM). OSIM is a high-fidelity, cryogenic JWST simulator that features a 1.5m diameter powered mirror. The SIs are aligned to the flight structure's coordinate system under ambient, clean room conditions using opto-mechanical metrology and customized interfaces. OSIM is aligned to the ISIM mechanical coordinate system at the cryogenic operating temperature via internal mechanisms and feedback from alignment sensors and metrology in six degrees of freedom. SI performance, including focus, pupil shear, pupil roll, boresight, wavefront error, and image quality, is evaluated at the operating temperature using OSIM. This work reports on the as-run ambient assembly and ambient alignment steps for the flight ISIM, including SI interface fixtures and customization and kinematic mount adjustment. The ISIM alignment plan consists of multiple steps to meet the "absolute" alignment requirements of the SIs and OSIM to the flight coordinate system. In this paper, we focus on key aspects of absolute, optical-mechanical alignment. We discuss various metrology and alignment techniques. In addition, we summarize our approach for dealing with and the results of ground-test factors, such as gravity.

  5. Development and Calibration of a System-Integrated Rotorcraft Finite Element Model for Impact Scenarios

    NASA Technical Reports Server (NTRS)

    Annett, Martin S.; Horta, Lucas G.; Jackson, Karen E.; Polanco, Michael A.; Littell, Justin D.

    2012-01-01

    Two full-scale crash tests of an MD-500 helicopter were conducted in 2009 and 2010 at NASA Langley's Landing and Impact Research Facility in support of NASA s Subsonic Rotary Wing Crashworthiness Project. The first crash test was conducted to evaluate the performance of an externally mounted composite deployable energy absorber (DEA) under combined impact conditions. In the second crash test, the energy absorber was removed to establish baseline loads that are regarded as severe but survivable. The presence of this energy absorbing device reduced the peak impact acceleration levels by a factor of three. Accelerations and kinematic data collected from the crash tests were compared to a system-integrated finite element model of the test article developed in parallel with the test program. In preparation for the full-scale crash test, a series of sub-scale and MD-500 mass simulator tests were conducted to evaluate the impact performances of various components and subsystems, including new crush tubes and the DEA blocks. Parameters defined for the system-integrated finite element model were determined from these tests. Results from 19 accelerometers placed throughout the airframe were compared to finite element model responses. The model developed for the purposes of predicting acceleration responses from the first crash test was inadequate when evaluating more severe conditions seen in the second crash test. A newly developed model calibration approach that includes uncertainty estimation, parameter sensitivity, impact shape orthogonality, and numerical optimization was used to calibrate model results for the full-scale crash test without the DEA. This combination of heuristic and quantitative methods identified modeling deficiencies, evaluated parameter importance, and proposed required model changes. The multidimensional calibration techniques presented here are particularly effective in identifying model adequacy. Acceleration results for the calibrated model were

  6. Addressable test matrix for measuring analog transfer characteristics of test elements used for integrated process control and device evaluation

    NASA Technical Reports Server (NTRS)

    Buehler, Martin G. (Inventor)

    1988-01-01

    A set of addressable test structures, each of which uses addressing schemes to access individual elements of the structure in a matrix, is used to test the quality of a wafer before integrated circuits produced thereon are diced, packaged and subjected to final testing. The electrical characteristic of each element is checked and compared to the electrical characteristic of all other like elements in the matrix. The effectiveness of the addressable test matrix is in readily analyzing the electrical characteristics of the test elements and in providing diagnostic information.

  7. Grassmann integral and Balian-Brézin decomposition in Hartree-Fock-Bogoliubov matrix elements

    NASA Astrophysics Data System (ADS)

    Mizusaki, Takahiro; Oi, Makito; Chen, Fang-Qi; Sun, Yang

    2013-08-01

    We present a new formula to calculate matrix elements of a general unitary operator with respect to Hartree-Fock-Bogoliubov states allowing multiple quasi-particle excitations. The Balian-Brézin decomposition of the unitary operator [R. Balian, E. Brézin, Il Nuovo Cimento B 64 (1969) 37] is employed in the derivation. We found that this decomposition is extremely suitable for an application of Fermion coherent state and Grassmann integrals in the quasi-particle basis. The resultant formula is compactly expressed in terms of the Pfaffian, and shows the similar bipartite structure to the formula that we have previously derived in the bare-particles basis [T. Mizusaki, M. Oi, Phys. Lett. B 715 (2012) 219].

  8. Top Quark Mass Measurement Using a Matrix Element Method with Quasi-Monte Carlo Integration

    SciTech Connect

    Lujan, Paul J.

    2008-10-01

    We report an updated measurement of the top quark mass obtained from ppbar collisions at sqrt(s) = 1.96 TeV at the Fermilab Tevatron using the CDF II detector. Our measurement uses a matrix element integration method to obtain a signal likelihood, with a neural network used to identify background events and a likelihood cut applied to reduce the effect of badly reconstructed events. We use a 2.7 fb{sup -1} sample and observe 422 events passing all of our cuts. We find m{sub t} = 172.2 +/- 1.0 (stat.) +/- 0.9 (JES) +/- 1.0 (syst.) GeV/c{sup 2}, or m{sub t} = 172.2 +/- 1.7 (total) GeV/c{sup 2}.

  9. Cutting force predication based on integration of symmetric fuzzy number and finite element method.

    PubMed

    Wang, Zhanli; Hu, Yanjuan; Wang, Yao; Dong, Chao; Pang, Zaixiang

    2014-01-01

    In the process of turning, pointing at the uncertain phenomenon of cutting which is caused by the disturbance of random factors, for determining the uncertain scope of cutting force, the integrated symmetric fuzzy number and the finite element method (FEM) are used in the prediction of cutting force. The method used symmetric fuzzy number to establish fuzzy function between cutting force and three factors and obtained the uncertain interval of cutting force by linear programming. At the same time, the change curve of cutting force with time was directly simulated by using thermal-mechanical coupling FEM; also the nonuniform stress field and temperature distribution of workpiece, tool, and chip under the action of thermal-mechanical coupling were simulated. The experimental result shows that the method is effective for the uncertain prediction of cutting force.

  10. Cutting Force Predication Based on Integration of Symmetric Fuzzy Number and Finite Element Method

    PubMed Central

    Wang, Zhanli; Hu, Yanjuan; Wang, Yao; Dong, Chao; Pang, Zaixiang

    2014-01-01

    In the process of turning, pointing at the uncertain phenomenon of cutting which is caused by the disturbance of random factors, for determining the uncertain scope of cutting force, the integrated symmetric fuzzy number and the finite element method (FEM) are used in the prediction of cutting force. The method used symmetric fuzzy number to establish fuzzy function between cutting force and three factors and obtained the uncertain interval of cutting force by linear programming. At the same time, the change curve of cutting force with time was directly simulated by using thermal-mechanical coupling FEM; also the nonuniform stress field and temperature distribution of workpiece, tool, and chip under the action of thermal-mechanical coupling were simulated. The experimental result shows that the method is effective for the uncertain prediction of cutting force. PMID:24790556

  11. Activation of the cell integrity pathway is channelled through diverse signalling elements in fission yeast.

    PubMed

    Barba, Gregorio; Soto, Teresa; Madrid, Marisa; Núñez, Andrés; Vicente, Jeronima; Gacto, Mariano; Cansado, José

    2008-04-01

    MAPK Pmk1p is the central element of a cascade involved in the maintenance of cell integrity and other functions in Schizosaccharomyces pombe. Pmk1p becomes activated by multiple stressing situations and also during cell separation. GTPase Rho2p acts upstream of the protein kinase C homolog Pck2p to activate the Pmk1 signalling pathway through direct interaction with MAPKKK Mkh1p. In this work we analyzed the functional significance of both Rho2p and Pck2p in the transduction of various stress signals by the cell integrity pathway. The results indicate that basal Pmk1p activity can be positively regulated by alternative mechanisms which are independent on the control by Rho2p and/or Pck2p. Unexpectedly, Pck1p, another protein kinase C homolog, negatively modulates Pmk1p basal activity by an unknown mechanism. Moreover, different elements appear to regulate the stress-induced activation of Pmk1p depending on the nature of the triggering stimuli. Whereas Pmk1p activation induced by hyper- or hypotonic stresses is channeled through Rho2p-Pck2p, other stressors, like glucose deprivation or cell wall disturbance, are transduced via other pathways in addition to that of Rho2p-Pck2p. On the contrary, Pmk1p activation observed during cell separation or after treatment with hydrogen peroxide does not involve Rho2p-Pck2p. Finally, Pck2p function is critical to maintain a Pmk1p basal activity that allows Pmk1p activation induced by heat stress. These data demonstrate the existence of a complex signalling network modulating Pmk1p activation in response to a variety of stresses in fission yeast.

  12. Fabrication of Diffractive Optical Elements for an Integrated Compact Optical-MEMS Laser Scanner

    SciTech Connect

    WENDT,JOEL R.; KRYGOWSKI,T.W.; VAWTER,GREGORY A.; SPAHN,OLGA B.; SWEATT,WILLIAM C.; WARREN,MIAL E.; REYES,DAVID NMN

    2000-07-13

    The authors describe the microfabrication of a multi-level diffractive optical element (DOE) onto a micro-electromechanical system (MEMS) as a key element in an integrated compact optical-MEMS laser scanner. The DOE is a four-level off-axis microlens fabricated onto a movable polysilicon shuttle. The microlens is patterned by electron beam lithography and etched by reactive ion beam etching. The DOE was fabricated on two generations of MEMS components. The first generation design uses a shuttle suspended on springs and displaced by a linear rack. The second generation design uses a shuttle guided by roller bearings and driven by a single reciprocating gear. Both the linear rack and the reciprocating gear are driven by a microengine assembly. The compact design is based on mounting the MEMS module and a vertical cavity surface emitting laser (VCSEL) onto a fused silica substrate that contains the rest of the optical system. The estimated scan range of the system is {+-}4{degree} with a spot size of 0.5 mm.

  13. Path Integral Monte Carlo Simulations of Warm Dense Plasmas with mid-Z Elements

    NASA Astrophysics Data System (ADS)

    Driver, Kevin; Soubiran, Francois; Zhang, Shuai; Militzer, Burkhard

    2016-10-01

    Theoretical studies of warm dense plasmas are crucial for improving our knowledge of giant planets, astrophysics, shock physics, and new plasma energy technologies, such as inertial confined fusion. Path integral Monte Carlo (PIMC) and density functional theory molecular dynamics (DFT-MD) provide consistent, first-principles descriptions of warm, dense matter over a wide range of density and temperature conditions. Here, we report simulation results for a variety of first- and second-row elements. DFT-MD algorithms are well-suited for low temperatures, while PIMC has been restricted to relatively high temperatures due to the free-particle approximation of the nodal surface. For heavier, second-row elements, we have developed a new, localized nodal surface, which allows us to treat bound states within the PIMC formalism. By combining PIMC and DFT-MD pressures and internal energies, we produce a coherent, first-principles equation of state, bridging the entire warm dense matter regime. Pair-correlation functions and the density of electronic states reveal an evolving plasma structure. The degree of ionization is affected by both temperature and density. Finally, shock Hugoniot curves show an increase in compression as the first and second shells are ionized. Funding provided by the DOE (DE-SC0010517). Computational resources provided by the NCAR/CISL, NERSC, and NASA.

  14. A velocity-pressure integrated, mixed interpolation, Galerkin finite element method for high Reynolds number laminar flows

    NASA Technical Reports Server (NTRS)

    Kim, Sang-Wook

    1988-01-01

    A velocity-pressure integrated, mixed interpolation, Galerkin finite element method for the Navier-Stokes equations is presented. In the method, the velocity variables were interpolated using complete quadratic shape functions and the pressure was interpolated using linear shape functions. For the two dimensional case, the pressure is defined on a triangular element which is contained inside the complete biquadratic element for velocity variables; and for the three dimensional case, the pressure is defined on a tetrahedral element which is again contained inside the complete tri-quadratic element. Thus the pressure is discontinuous across the element boundaries. Example problems considered include: a cavity flow for Reynolds number of 400 through 10,000; a laminar backward facing step flow; and a laminar flow in a square duct of strong curvature. The computational results compared favorable with those of the finite difference methods as well as experimental data available. A finite elememt computer program for incompressible, laminar flows is presented.

  15. Integrated remodeling-to-fracture finite element model of human proximal femur behavior.

    PubMed

    Hambli, Ridha; Lespessailles, Eric; Benhamou, Claude-Laurent

    2013-01-01

    The purpose of this work was to develop an integrated remodeling-to-fracture finite element model allowing for the combined simulation of (i) simulation of a human proximal femur remodeling under a given boundary conditions, (ii) followed by the simulation of its fracture behavior (force-displacement curve and fracture pattern) under quasi-static load. The combination of remodeling and fracture simulation into one unified model consists in considering that the femur properties resulting from the remodeling simulation correspond to the initial state for the fracture prediction. The remodeling model is based on phenomenological one based on a coupled strain and fatigue damage stimulus. The fracture model is based on continuum damage mechanics in order to predict the progressive fracturing process which allows to predict the fracture pattern and the complete force-displacement curve under quasi-static load. To prevent mesh-dependence that generally affects the damage propagation rate, regularization technique was applied in the current work. To investigate the potential of the proposed unified remodeling-to-fracture model, we performed remodeling simulations on a 3D proximal femur model for a duration of 365 days under five different daily loading conditions followed by a side fall fracture simulation reproducing previously published experimental tests (de Bakker et al. (2009), case C, male, 72 years old). We show here that the implementation of an integrated remodeling-to-fracture model provides more realistic prediction strategy to assess the bone remodeling effects on the fracture risk of bone.

  16. Finite element modelling of process-integrated powder coating by radial axial rolling of rings

    NASA Astrophysics Data System (ADS)

    Frischkorn, J.; Kebriaei, R.; Reese, S.; Moll, H.; Theisen, W.; Husmann, T.; Meier, H.

    2011-05-01

    The process-integrated powder coating by radial axial rolling of rings represents a new hybrid production technique applied in the manufacturing of large ring-shaped work pieces with functional layers. It is thought to break some limitations that come along with the hot isostatic pressing (HIP) which is used nowadays to apply the powdery layer material onto the rolled substrate ring. Within the new process the compaction of the layer material is integrated into the ring rolling and HIP becomes dispensable. Following this approach the rolling of such compound rings brings up some new challenges. The volume of a solid ring stays nearly constant during the rolling. This behaviour can be exploited to determine the infeed of the rollers needed to reach the desired ring shape. Since volume consistency cannot be guaranteed for the rolling of a compound ring the choice of appropriate infeed of the rollers is still an open question. This paper deals with the finite element (FE) simulation of this new process. First, the material model that is used to describe the compaction of the layer material is shortly reviewed. The main focus of the paper is then put on a parameterized FE ring rolling model that incorporates a control system in order to stabilize the process. Also the differences in the behaviour during the rolling stage between a compound and a solid ring will be discussed by means of simulation results.

  17. Finite element and integral equation formulations for high-performance micromagnetic and electromagnetic solvers

    NASA Astrophysics Data System (ADS)

    Chang, Ruinan

    The ability to have a good understanding of and to manipulate electromagnetic elds has been increasingly important for many hardware technologies. There is a strong need for advanced numeric algorithms that yield fast and accuracy controllable solvers for electromagnetic and micromagnetic simulations. The first part of the dissertation presents methods constituting the core of the high-performance simulator FastMag. FastMag derives its high speed from three aspects. First, it leverages the state-of-the-art graphics processing unit computational architectures, which can be hundreds of times faster than a single central processing unit. Moreover, ecient and and accurate implementations of numeric quadrature was invoked. Thirdly, we provide an analytic method for Jacobian vector products. Some advanced features are provided in FastMag. Quadratic basis functions are used to provide better accuracy. Hexahedral elements were also implemented because they are more accurate, consume less memory. The second part of the dissertation is devoted to electromagnetic scattering problems. We developed new algorithms that signicantly improved the traditional methods. First of all, potential volume integral equations were implemented, where the potential quantities (vector and scalar potential). Another important contribution of this disertation is quadrilateral barycentric basis functions (QBBFs). The QBBFs can serve as a fundamental block for primary basis functions (PBFs) and dual basis functions (DBFs). The PBFs and DBFs, when applied in combination into traditional electric and magnetic eld integral equations (EFIE and MFIE), give rise to accurate and robust results. Moreover, the DBFs make the famous Calderon preconditioner multiplicative.

  18. STARS: An Integrated, Multidisciplinary, Finite-Element, Structural, Fluids, Aeroelastic, and Aeroservoelastic Analysis Computer Program

    NASA Technical Reports Server (NTRS)

    Gupta, K. K.

    1997-01-01

    A multidisciplinary, finite element-based, highly graphics-oriented, linear and nonlinear analysis capability that includes such disciplines as structures, heat transfer, linear aerodynamics, computational fluid dynamics, and controls engineering has been achieved by integrating several new modules in the original STARS (STructural Analysis RoutineS) computer program. Each individual analysis module is general-purpose in nature and is effectively integrated to yield aeroelastic and aeroservoelastic solutions of complex engineering problems. Examples of advanced NASA Dryden Flight Research Center projects analyzed by the code in recent years include the X-29A, F-18 High Alpha Research Vehicle/Thrust Vectoring Control System, B-52/Pegasus Generic Hypersonics, National AeroSpace Plane (NASP), SR-71/Hypersonic Launch Vehicle, and High Speed Civil Transport (HSCT) projects. Extensive graphics capabilities exist for convenient model development and postprocessing of analysis results. The program is written in modular form in standard FORTRAN language to run on a variety of computers, such as the IBM RISC/6000, SGI, DEC, Cray, and personal computer; associated graphics codes use OpenGL and IBM/graPHIGS language for color depiction. This program is available from COSMIC, the NASA agency for distribution of computer programs.

  19. Finite element modelling of process-integrated powder coating by radial axial rolling of rings

    SciTech Connect

    Frischkorn, J.; Kebriaei, R.; Reese, S.; Moll, H.; Theisen, W.; Husmann, T.; Meier, H.

    2011-05-04

    The process-integrated powder coating by radial axial rolling of rings represents a new hybrid production technique applied in the manufacturing of large ring-shaped work pieces with functional layers. It is thought to break some limitations that come along with the hot isostatic pressing (HIP) which is used nowadays to apply the powdery layer material onto the rolled substrate ring. Within the new process the compaction of the layer material is integrated into the ring rolling and HIP becomes dispensable. Following this approach the rolling of such compound rings brings up some new challenges. The volume of a solid ring stays nearly constant during the rolling. This behaviour can be exploited to determine the infeed of the rollers needed to reach the desired ring shape. Since volume consistency cannot be guaranteed for the rolling of a compound ring the choice of appropriate infeed of the rollers is still an open question. This paper deals with the finite element (FE) simulation of this new process. First, the material model that is used to describe the compaction of the layer material is shortly reviewed. The main focus of the paper is then put on a parameterized FE ring rolling model that incorporates a control system in order to stabilize the process. Also the differences in the behaviour during the rolling stage between a compound and a solid ring will be discussed by means of simulation results.

  20. True Concurrent Thermal Engineering Integrating CAD Model Building with Finite Element and Finite Difference Methods

    NASA Technical Reports Server (NTRS)

    Panczak, Tim; Ring, Steve; Welch, Mark

    1999-01-01

    Thermal engineering has long been left out of the concurrent engineering environment dominated by CAD (computer aided design) and FEM (finite element method) software. Current tools attempt to force the thermal design process into an environment primarily created to support structural analysis, which results in inappropriate thermal models. As a result, many thermal engineers either build models "by hand" or use geometric user interfaces that are separate from and have little useful connection, if any, to CAD and FEM systems. This paper describes the development of a new thermal design environment called the Thermal Desktop. This system, while fully integrated into a neutral, low cost CAD system, and which utilizes both FEM and FD methods, does not compromise the needs of the thermal engineer. Rather, the features needed for concurrent thermal analysis are specifically addressed by combining traditional parametric surface based radiation and FD based conduction modeling with CAD and FEM methods. The use of flexible and familiar temperature solvers such as SINDA/FLUINT (Systems Improved Numerical Differencing Analyzer/Fluid Integrator) is retained.

  1. True Concurrent Thermal Engineering Integrating CAD Model Building with Finite Element and Finite Difference Methods

    NASA Technical Reports Server (NTRS)

    Panczak, Tim; Ring, Steve; Welch, Mark

    1999-01-01

    Thermal engineering has long been left out of the concurrent engineering environment dominated by CAD (computer aided design) and FEM (finite element method) software. Current tools attempt to force the thermal design process into an environment primarily created to support structural analysis, which results in inappropriate thermal models. As a result, many thermal engineers either build models "by hand" or use geometric user interfaces that are separate from and have little useful connection, if any, to CAD and FEM systems. This paper describes the development of a new thermal design environment called the Thermal Desktop. This system, while fully integrated into a neutral, low cost CAD system, and which utilizes both FEM and FD methods, does not compromise the needs of the thermal engineer. Rather, the features needed for concurrent thermal analysis are specifically addressed by combining traditional parametric surface based radiation and FD based conduction modeling with CAD and FEM methods. The use of flexible and familiar temperature solvers such as SINDA/FLUINT (Systems Improved Numerical Differencing Analyzer/Fluid Integrator) is retained.

  2. Orthoscopic real image reconstruction in integral imaging by rotating an elemental image based on the reference point of object space.

    PubMed

    Jang, Jae-Young; Cho, Myungjin

    2015-06-20

    We propose a new approach for depth conversion of three-dimensional (3D) reconstruction from pseudoscopic to orthoscopic real images in resolution priority integral imaging. In integral imaging, depth of field is recorded in an elemental image array. In the proposed method, the depth information is converted by a 180° rotation of each elemental image in an elemental image array based on a reference point of conversion, which is caused by a reference point of object space. Orthoscopic real images can be reconstructed in 3D space by using the depth conversion of an elemental image array. The feasibility of the proposed method has been confirmed through preliminary experiments as well as ray optical analysis.

  3. A general algorithm for evaluating nearly strong-singular (and beyond) integrals in three-dimensional boundary element analysis

    NASA Astrophysics Data System (ADS)

    Gu, Yan; Gao, Hongwei; Chen, Wen; Wang, Huijuan; Zhang, Chuanzeng

    2017-05-01

    One of the typical and most significant issues of almost all boundary element analyses is the accurate evaluation of nearly singular boundary element integrals. In this study, we review some numerical techniques used currently to calculate nearly singular integrals and propose an improved algorithm to calculate integrals with nearly strong (and beyond) singularities. This new method has full generally and can be easily included in any existing computer code. The method is tested in general three-dimensional boundary element analysis. Comparison of this method with some of the existing methods is also presented. It is shown that several orders of magnitude improvement in relative errors can be obtained using the proposed method when compared to a straightforward implementation of Gaussian quadrature.

  4. Assembly, integration, and verification (AIV) in ALMA: series processing of array elements

    NASA Astrophysics Data System (ADS)

    Lopez, Bernhard; Jager, Rieks; Whyborn, Nicholas D.; Knee, Lewis B. G.; McMullin, Joseph P.

    2012-09-01

    The Atacama Large Millimeter/submillimeter Array (ALMA) is a joint project between astronomical organizations in Europe, North America, and East Asia, in collaboration with the Republic of Chile. ALMA will consist of at least 54 twelve-meter antennas and 12 seven-meter antennas operating as an aperture synthesis array in the (sub)millimeter wavelength range. It is the responsibility of ALMA AIV to deliver the fully assembled, integrated, and verified antennas (array elements) to the telescope array. After an initial phase of infrastructure setup AIV activities began when the first ALMA antenna and subsystems became available in mid 2008. During the second semester of 2009 a project-wide effort was made to put in operation a first 3- antenna interferometer at the Array Operations Site (AOS). In 2010 the AIV focus was the transition from event-driven activities towards routine series production. Also, due to the ramp-up of operations activities, AIV underwent an organizational change from an autonomous department into a project within a strong matrix management structure. When the subsystem deliveries stabilized in early 2011, steady-state series processing could be achieved in an efficient and reliable manner. The challenge today is to maintain this production pace until completion towards the end of 2013. This paper describes the way ALMA AIV evolved successfully from the initial phase to the present steady-state of array element series processing. It elaborates on the different project phases and their relationships, presents processing statistics, illustrates the lessons learned and relevant best practices, and concludes with an outlook of the path towards completion.

  5. Integrated Project Teams - An Essential Element of Project Management during Project Planning and Execution - 12155

    SciTech Connect

    Burritt, James G.; Berkey, Edgar

    2012-07-01

    Managing complex projects requires a capable, effective project manager to be in place, who is assisted by a team of competent assistants in various relevant disciplines. This team of assistants is known as the Integrated Project Team (IPT). he IPT is composed of a multidisciplinary group of people who are collectively responsible for delivering a defined project outcome and who plan, execute, and implement over the entire life-cycle of a project, which can be a facility being constructed or a system being acquired. An ideal IPT includes empowered representatives from all functional areas involved with a project-such as engineering design, technology, manufacturing, test and evaluation, contracts, legal, logistics, and especially, the customer. Effective IPTs are an essential element of scope, cost, and schedule control for any complex, large construction project, whether funded by DOE or another organization. By recently assessing a number of major, on-going DOE waste management projects, the characteristics of high performing IPTs have been defined as well as the reasons for potential IPT failure. Project managers should use IPTs to plan and execute projects, but the IPTs must be properly constituted and the members capable and empowered. For them to be effective, the project manager must select the right team, and provide them with the training and guidance for them to be effective. IPT members must treat their IPT assignment as a primary duty, not some ancillary function. All team members must have an understanding of the factors associated with successful IPTs, and the reasons that some IPTs fail. Integrated Project Teams should be used by both government and industry. (authors)

  6. ROAM mutations causing increased expression of yeast genes: their activation by signals directed toward conjugation functions and their formation by insertion of tyl repetitive elements

    SciTech Connect

    Errede, B.; Cardillo, T.S.; Wever, G.; Sherman, F.

    1980-01-01

    Mechanisms available to eukaryotic organisms for the coordinate regulation of gene expression are being examined by genetic and biochemical characterization of an unusual mutation, CYC7-H2, which causes overproduction of iso-2-cytochrome c in the yeast Saccharomyces cerevisiae. The CYC7-H2 mutation causes approximately a twenty fold overproduction of iso-2-cytochrome c in haploid strains but only a one to four fold overproduction in MATa/MAT..cap alpha.. diploid strains. This regulation of overproduction has been characterized as a response to signals controlling conjugation in yeast. The CYC7-H2 mutation is closely related to other regulatory mutations occurring at the cargA, cargB and DUR1,2 loci which are the structural genes for arginase, ornithine transaminase and urea amidolyase, respectively. Similar to the CYC7-H2 mutation, the mutations designated cargA/sup +/O/sup h/, cargB/sup +/O/sup h/ and durO/sup h/ cause constitutive production of their respective gene products at much lower levels in MATa/MAT..cap alpha.. diploid strains than in the corresponding haploid strains. Observations characterizing the regulation of overproduction in the CYC7-H2 mutant are presented with the additional and parallel observations for the O/sup h/ mutants.

  7. Is 20/20 vision good enough? Visual acuity differences within the normal range predict contour element detection and integration.

    PubMed

    Keane, Brian P; Kastner, Sabine; Paterno, Danielle; Silverstein, Steven M

    2015-02-01

    Contour integration (CI) combines appropriately aligned and oriented elements into continuous boundaries. Collinear facilitation (CF) occurs when a low-contrast oriented element becomes more visible when flanked by collinear high-contrast elements. Both processes rely at least partly on long-range horizontal connections in early visual cortex, and thus both have been extensively studied to understand visual cortical functioning in aging, development, and clinical disorders. Here, we ask: Can acuity differences within the normal range predict CI or CF? To consider this question, we measured binocular visual acuity and compared subjects with 20/20 vision to those with better-than-20/20 vision (SharpPerceivers) on two tasks. In the CI task, subjects located an integrated shape embedded in varying amounts of noise; in the CF task, subjects detected a low-contrast element flanked by collinear or orthogonal high-contrast elements. In each case, displays were scaled in size to modulate element visibility and spatial frequency (4-12 cycles/deg). SharpPerceivers could integrate contours under noisier conditions than the 20/20 group (p = .0002), especially for high spatial frequency displays. Moreover, although the two groups exhibited similar collinear facilitation, SharpPerceivers could detect the central target with lower contrast at high spatial frequencies (p <. 05). These results suggest that small acuity differences within the normal range--corresponding to about a one line difference on a vision chart--strongly predict element detection and integration. Furthermore, simply ensuring that subjects have normal or corrected-to-normal vision is not sufficient when comparing groups on contour tasks; visual acuity confounds also need to be ruled out.

  8. Conjugation of PEG-hexadecane markedly increases the immunogenicity of pneumococcal polysaccharide conjugate vaccine.

    PubMed

    Chang, Xin; Yu, Weili; Ji, Shaoyang; Shen, Lijuan; Tan, Aijuan; Hu, Tao

    2017-02-24

    Streptococcus pneumoniae is a serious Gram-positive pathogen that can lead to an invasive pneumococcal disease with high mortality rate. Pneumococcal capsular polysaccharide (PS) is a key virulence determinant and its immunogenicity can be increased by conjugation with a carrier protein. However, the PS-specific cellular and humoral immunity of pneumococcal conjugate vaccine needs further improvement. Hexadecane (HD) is an element of lipid that decorates the surface of nearly all microbial classes. Polyethylene glycol (PEG)-HD conjugate (PEG-HD) is soluble and can act as an adjuvant. In the present study, a novel pneumococcal polysaccharide conjugate vaccine was prepared by conjugation of tetanus toxoid (TT) portion of PS-TT conjugate (PS-TT) with PEG-HD. As compared with PS-TT, conjugation with PEG-HD led to an 8.0-fold increase in the PS-specific IgG titers. Conjugation with PEG-HD also gave rise to 34.9-, 3.6- and 7.7-fold increase in the IFN-γ, TNF-α and IL-5 levels, respectively. Thus, the conjugated PEG-HD has a stimulatory adjuvant activity to potentiate a robust humoral and cellular immunity. Our proposed conjugate was expected to act as an effective pneumococcal conjugate vaccine for prevention of S. pneumoniae infections.

  9. Precise integration of inducible transcriptional elements (PrIITE) enables absolute control of gene expression

    PubMed Central

    Pinto, Rita; Hansen, Lars; Hintze, John; Almeida, Raquel; Larsen, Sylvester; Coskun, Mehmet; Davidsen, Johanne; Mitchelmore, Cathy; David, Leonor; Troelsen, Jesper Thorvald

    2017-01-01

    Abstract Tetracycline-based inducible systems provide powerful methods for functional studies where gene expression can be controlled. However, the lack of tight control of the inducible system, leading to leakiness and adverse effects caused by undesirable tetracycline dosage requirements, has proven to be a limitation. Here, we report that the combined use of genome editing tools and last generation Tet-On systems can resolve these issues. Our principle is based on precise integration of inducible transcriptional elements (coined PrIITE) targeted to: (i) exons of an endogenous gene of interest (GOI) and (ii) a safe harbor locus. Using PrIITE cells harboring a GFP reporter or CDX2 transcription factor, we demonstrate discrete inducibility of gene expression with complete abrogation of leakiness. CDX2 PrIITE cells generated by this approach uncovered novel CDX2 downstream effector genes. Our results provide a strategy for characterization of dose-dependent effector functions of essential genes that require absence of endogenous gene expression. PMID:28472465

  10. A time-domain finite element boundary integral approach for elastic wave scattering

    NASA Astrophysics Data System (ADS)

    Shi, F.; Lowe, M. J. S.; Skelton, E. A.; Craster, R. V.

    2017-08-01

    The response of complex scatterers, such as rough or branched cracks, to incident elastic waves is required in many areas of industrial importance such as those in non-destructive evaluation and related fields; we develop an approach to generate accurate and rapid simulations. To achieve this we develop, in the time domain, an implementation to efficiently couple the finite element (FE) method within a small local region, and the boundary integral (BI) globally. The FE explicit scheme is run in a local box to compute the surface displacement of the scatterer, by giving forcing signals to excitation nodes, which can lie on the scatterer itself. The required input forces on the excitation nodes are obtained with a reformulated FE equation, according to the incident displacement field. The surface displacements computed by the local FE are then projected, through time-domain BI formulae, to calculate the scattering signals with different modes. This new method yields huge improvements in the efficiency of FE simulations for scattering from complex scatterers. We present results using different shapes and boundary conditions, all simulated using this approach in both 2D and 3D, and then compare with full FE models and theoretical solutions to demonstrate the efficiency and accuracy of this numerical approach.

  11. A DNase encoded by integrated element CJIE1 inhibits natural transformation of Campylobacter jejuni.

    PubMed

    Gaasbeek, Esther J; Wagenaar, Jaap A; Guilhabert, Magalie R; Wösten, Marc M S M; van Putten, Jos P M; van der Graaf-van Bloois, Linda; Parker, Craig T; van der Wal, Fimme J

    2009-04-01

    The species Campylobacter jejuni is considered naturally competent for DNA uptake and displays strong genetic diversity. Nevertheless, nonnaturally transformable strains and several relatively stable clonal lineages exist. In the present study, the molecular mechanism responsible for the nonnatural transformability of a subset of C. jejuni strains was investigated. Comparative genome hybridization indicated that C. jejuni Mu-like prophage integrated element 1 (CJIE1) was more abundant in nonnaturally transformable C. jejuni strains than in naturally transformable strains. Analysis of CJIE1 indicated the presence of dns (CJE0256), which is annotated as a gene encoding an extracellular DNase. DNase assays using a defined dns mutant and a dns-negative strain expressing Dns from a plasmid indicated that Dns is an endogenous DNase. The DNA-hydrolyzing activity directly correlated with the natural transformability of the knockout mutant and the dns-negative strain expressing Dns from a plasmid. Analysis of a broader set of strains indicated that the majority of nonnaturally transformable strains expressed DNase activity, while all naturally competent strains lacked this activity. The inhibition of natural transformation in C. jejuni via endogenous DNase activity may contribute to the formation of stable lineages in the C. jejuni population.

  12. A novel finite element method for the modeling of multiple reflections in photonic integrated circuits

    NASA Astrophysics Data System (ADS)

    Ging, John A.; O'Dowd, Ronan

    2006-04-01

    The complex transverse waveguide geometries of integrated photonic devices warrant the application of intricate Numerical Methods when modelling these types of Planar Lightwave Circuits (PLC). To aggravate the problem, difficulties also arise when dealing with back-reflections at interfaces, counter-propagating signals and other associated losses. Routines such as the Finite Element Method (FEM) and Finite Difference Method (FDM) are utilised in simulating the propagation of light through the core waveguide structures of these PLCs. In this paper a novel FEM reliant upon device cross-sectional symmetry is proposed, developed and discussed in regards to its advantages in precision over other procedures. Upon completion of this analysis, the propagation constant and effective refractive indices are known and extensions may be employed to accurately model propagation through the device and outline any reflections or losses that may ensue. A clear and concise review of some of the foremost available schemes is also presented here. These techniques, such as the Bidirectional Eigenmode Propagation Method (BEP) and the Beam Propagation Method (BPM) will be discussed and an effective and precise 3-dimensional model is presented. Due to the myriad of available techniques and algorithms, a comparative study is drawn, listing the advantages and failures of the major methods while suggesting improvements to their application. Necessary considerations such as simulation time and the trade-off between computer memory requirements and accuracy of the solution are also acknowledged.

  13. Volcano Deformation Sources at Tungurahua Volcano from Finite Element Methods and Multidisciplinary Data Integration

    NASA Astrophysics Data System (ADS)

    Morales Rivera, A. M.; Albino, F.; Amelug, F.; Gregg, P. M.; Mothes, P. A.

    2015-12-01

    Tungurahua volcano has been intermittently erupting since 1999, with observed deformation between 2007-2011 using Interferometric Synthetic Aperture Radar (InSAR) from the ALOS satellite of the Japanese Aerospace Exploration Agency. Our recent analysis during that time period has provided insights into the characteristics of the subsurface, suggesting multiple connected magma chambers underneath the edifice with distinct temporal and spatial behaviors. However, the previous source models are too simplistic and fail to incorporate realistic physical properties and forces acting within the volcano that would generate the observed deformation. We use deformation data from InSAR and solve for the optimal deformation source parameters with Finite Element Methods (FEM) by incorporating into the models the material heterogeneities (e.g. temperature, density, elastic, viscoelastic), and stresses (e.g. background stresses, edifice loading, magma chamber overpressure) acting on the volcano. We attempt to integrate previous multidisciplinary volcanological studies with our results to constrain the subsurface characteristics and understand the volcanic processes generating the observed deformation.

  14. The Language Element in the Somerset Mode III Integrated European Studies Syllabus and Its Relevance to the Less Able Pupil

    ERIC Educational Resources Information Center

    King, Barrie

    1974-01-01

    The Somerset CSE Mode III integrated European Studies syllabus, which contains a French language course, is aimed at the lower and below CSE candidate. The second language element of the course is described and reasons for constructing such a course for less able students are discussed. (RM)

  15. Portable waveguide display system with a large field of view by integrating freeform elements and volume holograms.

    PubMed

    Han, Jian; Liu, Juan; Yao, Xincheng; Wang, Yongtian

    2015-02-09

    A compact waveguide display system integrating freeform elements and volume holograms is presented here for the first time. The use of freeform elements can broaden the field of view, which limits the applications of a holographic waveguide. An optimized system can achieve a diagonal field of view of 45° when the thickness of the waveguide planar is 3mm. Freeform-elements in-coupler and the volume holograms out-coupler were designed in detail in our study, and the influence of grating configurations on diffraction efficiency was analyzed thoroughly. The off-axis aberrations were well compensated by the in-coupler and the diffraction efficiency of the optimized waveguide display system could reach 87.57%. With integrated design, stability and reliability of this monochromatic display system were achieved and the alignment of the system was easily controlled by the record of the volume holograms, which makes mass production possible.

  16. A finite element-boundary integral method for scattering and radiation by two- and three-dimensional structures

    NASA Technical Reports Server (NTRS)

    Jin, Jian-Ming; Volakis, John L.; Collins, Jeffery D.

    1991-01-01

    A review of a hybrid finite element-boundary integral formulation for scattering and radiation by two- and three-dimensional composite structures is presented. In contrast to other hybrid techniques involving the finite element method, the proposed one is in principle exact and can be implemented using a low O(N) storage. This is of particular importance for large scale applications and is a characteristic of the boundary chosen to terminate the finite element mesh, usually as close to the structure as possible. A certain class of these boundaries lead to convolutional boundary integrals which can be evaluated via the fast Fourier transform (FFT) without a need to generate a matrix; thus, retaining the O(N) storage requirement. The paper begins with a general description of the method. A number of two- and three-dimensional applications are then given, including numerical computations which demonstrate the method's accuracy, efficiency, and capability.

  17. Portable waveguide display system with a large field of view by integrating freeform elements and volume holograms

    PubMed Central

    Han, Jian; Liu, Juan; Yao, Xincheng; Wang, Yongtian

    2015-01-01

    A compact waveguide display system integrating freeform elements and volume holograms is presented here for the first time. The use of freeform elements can broaden the field of view, which limits the applications of a holographic waveguide. An optimized system can achieve a diagonal field of view of 45° when the thickness of the waveguide planar is 3mm. Freeform-elements in-coupler and the volume holograms out-coupler were designed in detail in our study, and the influence of grating configurations on diffraction efficiency was analyzed thoroughly. The off-axis aberrations were well compensated by the in-coupler and the diffraction efficiency of the optimized waveguide display system could reach 87.57%. With integrated design, stability and reliability of this monochromatic display system were achieved and the alignment of the system was easily controlled by the record of the volume holograms, which makes mass production possible. PMID:25836207

  18. A Strategy for Integrating a Large Finite Element Model Using MSC NASTRAN/PATRAN: X-33 Lessons Learned

    NASA Technical Reports Server (NTRS)

    McGhee, D. S.

    1999-01-01

    The X-33 vehicle is an advanced technology demonstrator sponsored by NASA. For the past 3 years the Structural Dynamics and Loads Branch of NASA's Marshall Space Flight Center has had the task of integrating the X-33 vehicle structural finite element model. In that time, five versions of the integrated vehicle model have been produced and a strategy has evolved that would benefit anyone given the task of integrating structural finite element models that have been generated by various modelers and companies. The strategy that has been presented here consists of six decisions that need to be made: purpose of models, units, common materials list, model numbering, interface control, and archive format. This strategy has been proven and expanded from experience on the X-33 vehicle.

  19. The SMART Theory and Modeling Team: an Integrated Element of Mission Development and Science Analysis

    NASA Astrophysics Data System (ADS)

    Hesse, M.; Birn, J.; Denton, R.; Drake, J.; Gombosi, T.; Hoshino, M.; Matthaeus, B.; Sibeck, D.

    2005-12-01

    When targeting physical understanding of space plasmas, our focus is gradually shifting away from discovery-type investigations to missions and studies that address our basic understanding of processes we know to be important. For these studies, theory and models provide physical predictions that need to be verified or falsified by empirical evidence. Within this paradigm, a tight integration between theory, modeling, and space flight mission design and execution is essential. NASA's Magnetospheric MultiScale (MMS) mission is a pathfinder in this new era of space research. The prime objective of MMS is to understand magnetic reconnection, arguably the most fundamental of plasma processes. In particular, MMS targets the microphysical processes, which permit magnetic reconnection to operate in the collisionless plasmas that permeate space and astrophysical systems. More specifically, MMS will provide closure to such elemental questions as how particles become demagnetized in the reconnection diffusion region, which effects determine the reconnection rate, and how reconnection is coupled to environmental conditions such as magnetic shear angles. Solutions to these problems have remained elusive in past and present spacecraft missions primarily due to instrumental limitations - yet they are fundamental to the large-scale dynamics of collisionless plasmas. Owing to the lack of measurements, most of our present knowledge of these processes is based on results from modern theory and modeling studies of the reconnection process. Proper design and execution of a mission targeting magnetic reconnection should include this knowledge and have to ensure that all relevant scales and effects can be resolved by mission measurements. The SMART mission has responded to this need through a tight integration between instrument and theory and modeling teams. Input from theory and modeling is fed into all aspects of science mission design, and theory and modeling activities are tailored

  20. The SMART Theory and Modeling Team: An Integrated Element of Mission Development and Science Analysis

    NASA Technical Reports Server (NTRS)

    Hesse, Michael; Birn, J.; Denton, Richard E.; Drake, J.; Gombosi, T.; Hoshino, M.; Matthaeus, B.; Sibeck, D.

    2005-01-01

    When targeting physical understanding of space plasmas, our focus is gradually shifting away from discovery-type investigations to missions and studies that address our basic understanding of processes we know to be important. For these studies, theory and models provide physical predictions that need to be verified or falsified by empirical evidence. Within this paradigm, a tight integration between theory, modeling, and space flight mission design and execution is essential. NASA's Magnetospheric MultiScale (MMS) mission is a pathfinder in this new era of space research. The prime objective of MMS is to understand magnetic reconnection, arguably the most fundamental of plasma processes. In particular, MMS targets the microphysical processes, which permit magnetic reconnection to operate in the collisionless plasmas that permeate space and astrophysical systems. More specifically, MMS will provide closure to such elemental questions as how particles become demagnetized in the reconnection diffusion region, which effects determine the reconnection rate, and how reconnection is coupled to environmental conditions such as magnetic shear angles. Solutions to these problems have remained elusive in past and present spacecraft missions primarily due to instrumental limitations - yet they are fundamental to the large-scale dynamics of collisionless plasmas. Owing to the lack of measurements, most of our present knowledge of these processes is based on results from modern theory and modeling studies of the reconnection process. Proper design and execution of a mission targeting magnetic reconnection should include this knowledge and have to ensure that all relevant scales and effects can be resolved by mission measurements. The SMART mission has responded to this need through a tight integration between instrument and theory and modeling teams. Input from theory and modeling is fed into all aspects of science mission design, and theory and modeling activities are tailored

  1. The SMART Theory and Modeling Team: An Integrated Element of Mission Development and Science Analysis

    NASA Technical Reports Server (NTRS)

    Hesse, Michael; Birn, J.; Denton, Richard E.; Drake, J.; Gombosi, T.; Hoshino, M.; Matthaeus, B.; Sibeck, D.

    2005-01-01

    When targeting physical understanding of space plasmas, our focus is gradually shifting away from discovery-type investigations to missions and studies that address our basic understanding of processes we know to be important. For these studies, theory and models provide physical predictions that need to be verified or falsified by empirical evidence. Within this paradigm, a tight integration between theory, modeling, and space flight mission design and execution is essential. NASA's Magnetospheric MultiScale (MMS) mission is a pathfinder in this new era of space research. The prime objective of MMS is to understand magnetic reconnection, arguably the most fundamental of plasma processes. In particular, MMS targets the microphysical processes, which permit magnetic reconnection to operate in the collisionless plasmas that permeate space and astrophysical systems. More specifically, MMS will provide closure to such elemental questions as how particles become demagnetized in the reconnection diffusion region, which effects determine the reconnection rate, and how reconnection is coupled to environmental conditions such as magnetic shear angles. Solutions to these problems have remained elusive in past and present spacecraft missions primarily due to instrumental limitations - yet they are fundamental to the large-scale dynamics of collisionless plasmas. Owing to the lack of measurements, most of our present knowledge of these processes is based on results from modern theory and modeling studies of the reconnection process. Proper design and execution of a mission targeting magnetic reconnection should include this knowledge and have to ensure that all relevant scales and effects can be resolved by mission measurements. The SMART mission has responded to this need through a tight integration between instrument and theory and modeling teams. Input from theory and modeling is fed into all aspects of science mission design, and theory and modeling activities are tailored

  2. Population responses to contour integration: early encoding of discrete elements and late perceptual grouping.

    PubMed

    Gilad, Ariel; Meirovithz, Elhanan; Slovin, Hamutal

    2013-04-24

    The neuronal mechanisms underlying perceptual grouping of discrete, similarly oriented elements are not well understood. To investigate this, we measured neural population responses using voltage-sensitive dye imaging in V1 of monkeys trained on a contour-detection task. By mapping the contour and background elements onto V1, we could study their neural processing. Population response early in time showed activation patches corresponding to the contour/background individual elements. However, late increased activity in the contour elements, along with suppressed activity in the background elements, enabled us to visualize in single trials a salient continuous contour "popping out" from a suppressed background. This modulated activity in the contour and in background extended beyond the cortical representation of individual contour or background elements. Finally, the late modulation was correlated with behavioral performance of contour saliency and the monkeys' perceptual report. Thus, opposing responses in the contour and background may underlie perceptual grouping in V1.

  3. [Integrity].

    PubMed

    Gómez Rodríguez, Rafael Ángel

    2014-01-01

    To say that someone possesses integrity is to claim that that person is almost predictable about responses to specific situations, that he or she can prudentially judge and to act correctly. There is a closed interrelationship between integrity and autonomy, and the autonomy rests on the deeper moral claim of all humans to integrity of the person. Integrity has two senses of significance for medical ethic: one sense refers to the integrity of the person in the bodily, psychosocial and intellectual elements; and in the second sense, the integrity is the virtue. Another facet of integrity of the person is la integrity of values we cherish and espouse. The physician must be a person of integrity if the integrity of the patient is to be safeguarded. The autonomy has reduced the violations in the past, but the character and virtues of the physician are the ultimate safeguard of autonomy of patient. A field very important in medicine is the scientific research. It is the character of the investigator that determines the moral quality of research. The problem arises when legitimate self-interests are replaced by selfish, particularly when human subjects are involved. The final safeguard of moral quality of research is the character and conscience of the investigator. Teaching must be relevant in the scientific field, but the most effective way to teach virtue ethics is through the example of the a respected scientist.

  4. A study of methods to predict and measure the transmission of sound through the walls of light aircraft. Integration of certain singular boundary element integrals for applications in linear acoustics

    NASA Technical Reports Server (NTRS)

    Zimmerle, D.; Bernhard, R. J.

    1985-01-01

    An alternative method for performing singular boundary element integrals for applications in linear acoustics is discussed. The method separates the integral of the characteristic solution into a singular and nonsingular part. The singular portion is integrated with a combination of analytic and numerical techniques while the nonsingular portion is integrated with standard Gaussian quadrature. The method may be generalized to many types of subparametric elements. The integrals over elements containing the root node are considered, and the characteristic solution for linear acoustic problems are examined. The method may be generalized to most characteristic solutions.

  5. Challenges in Integrating Nondestructive Evaluation and Finite Element Methods for Realistic Structural Analysis

    NASA Technical Reports Server (NTRS)

    Abdul-Aziz, Ali; Baaklini, George Y.; Zagidulin, Dmitri; Rauser, Richard W.

    2000-01-01

    Capabilities and expertise related to the development of links between nondestructive evaluation (NDE) and finite element analysis (FEA) at Glenn Research Center (GRC) are demonstrated. Current tools to analyze data produced by computed tomography (CT) scans are exercised to help assess the damage state in high temperature structural composite materials. A utility translator was written to convert velocity (an image processing software) STL data file to a suitable CAD-FEA type file. Finite element analyses are carried out with MARC, a commercial nonlinear finite element code, and the analytical results are discussed. Modeling was established by building MSC/Patran (a pre and post processing finite element package) generated model and comparing it to a model generated by Velocity in conjunction with MSC/Patran Graphics. Modeling issues and results are discussed in this paper. The entire process that outlines the tie between the data extracted via NDE and the finite element modeling and analysis is fully described.

  6. Finite element-integral simulation of static and flight fan noise radiation from the JT15D turbofan engine

    NASA Technical Reports Server (NTRS)

    Baumeister, K. J.; Horowitz, S. J.

    1982-01-01

    An iterative finite element integral technique is used to predict the sound field radiated from the JT15D turbofan inlet. The sound field is divided into two regions: the sound field within and near the inlet which is computed using the finite element method and the radiation field beyond the inlet which is calculated using an integral solution technique. The velocity potential formulation of the acoustic wave equation was employed in the program. For some single mode JT15D data, the theory and experiment are in good agreement for the far field radiation pattern as well as suppressor attenuation. Also, the computer program is used to simulate flight effects that cannot be performed on a ground static test stand.

  7. Integral equations and boundary-element solution for static potential in a general piece-wise homogeneous volume conductor.

    PubMed

    Stenroos, Matti

    2016-11-21

    Boundary element methods (BEM) are used for forward computation of bioelectromagnetic fields in multi-compartment volume conductor models. Most BEM approaches assume that each compartment is in contact with at most one external compartment. In this work, I present a general surface integral equation and BEM discretization that remove this limitation and allow BEM modeling of general piecewise-homogeneous medium. The new integral equation allows positioning of field points at junctioned boundary of more than two compartments, enabling the use of linear collocation BEM in such a complex geometry. A modular BEM implementation is presented for linear collocation and Galerkin approaches, starting from the standard formulation. The approach and resulting solver are verified in four ways, including comparisons of volume and surface potentials to those obtained using the finite element method (FEM), and the effect of a hole in skull on electroencephalographic scalp potentials is demonstrated.

  8. A finite element-boundary integral formulation for scattering by three-dimensional cavity-backed apertures

    NASA Technical Reports Server (NTRS)

    Jin, Jian-Ming; Volakis, John L.

    1990-01-01

    A numerical technique is proposed for the electromagnetic characterization of the scattering by a three-dimensional cavity-backed aperture in an infinite ground plane. The technique combines the finite element and boundary integral methods to formulate a system of equations for the solution of the aperture fields and those inside the cavity. Specifically, the finite element method is employed to formulate the fields in the cavity region and the boundary integral approach is used in conjunction with the equivalence principle to represent the fields above the ground plane. Unlike traditional approaches, the proposed technique does not require knowledge of the cavity's Green's function and is, therefore, applicable to arbitrary shape depressions and material fillings. Furthermore, the proposed formulation leads to a system having a partly full and partly sparse as well as symmetric and banded matrix which can be solved efficiently using special algorithms.

  9. Integral equations and boundary-element solution for static potential in a general piece-wise homogeneous volume conductor

    NASA Astrophysics Data System (ADS)

    Stenroos, Matti

    2016-11-01

    Boundary element methods (BEM) are used for forward computation of bioelectromagnetic fields in multi-compartment volume conductor models. Most BEM approaches assume that each compartment is in contact with at most one external compartment. In this work, I present a general surface integral equation and BEM discretization that remove this limitation and allow BEM modeling of general piecewise-homogeneous medium. The new integral equation allows positioning of field points at junctioned boundary of more than two compartments, enabling the use of linear collocation BEM in such a complex geometry. A modular BEM implementation is presented for linear collocation and Galerkin approaches, starting from the standard formulation. The approach and resulting solver are verified in four ways, including comparisons of volume and surface potentials to those obtained using the finite element method (FEM), and the effect of a hole in skull on electroencephalographic scalp potentials is demonstrated.

  10. Composite mobile genetic elements disseminating macrolide resistance in Streptococcus pneumoniae

    PubMed Central

    Chancey, Scott T.; Agrawal, Sonia; Schroeder, Max R.; Farley, Monica M.; Tettelin, Hervé; Stephens, David S.

    2015-01-01

    Macrolide resistance in Streptococcus pneumoniae emerged in the U.S. and globally during the early 1990's. The RNA methylase encoded by erm(B) and the macrolide efflux genes mef(E) and mel were identified as the resistance determining factors. These genes are disseminated in the pneumococcus on mobile, often chimeric elements consisting of multiple smaller elements. To better understand the variety of elements encoding macrolide resistance and how they have evolved in the pre- and post-conjugate vaccine eras, the genomes of 121 invasive and ten carriage isolates from Atlanta from 1994 to 2011 were analyzed for mobile elements involved in the dissemination of macrolide resistance. The isolates were selected to provide broad coverage of the genetic variability of antibiotic resistant pneumococci and included 100 invasive isolates resistant to macrolides. Tn916-like elements carrying mef(E) and mel on the Macrolide Genetic Assembly (Mega) and erm(B) on the erm(B) element and Tn917 were integrated into the pneumococcal chromosome backbone and into larger Tn5253-like composite elements. The results reported here include identification of novel insertion sites for Mega and characterization of the insertion sites of Tn916-like elements in the pneumococcal chromosome and in larger composite elements. The data indicate that integration of elements by conjugation was infrequent compared to recombination. Thus, it appears that conjugative mobile elements allow the pneumococcus to acquire DNA from distantly related bacteria, but once integrated into a pneumococcal genome, transformation and recombination is the primary mechanism for transmission of novel DNA throughout the pneumococcal population. PMID:25709602

  11. Numerical Treatment of Differential and Integral Equations by the P and H-P Versions of the Finite Element Method

    DTIC Science & Technology

    1992-01-01

    mathematical papers which describe various locking effects and analyze methods (mainly mixed methods ) to overcome it. However, the treatment in these...finite element method in various areas, such as the numerical approximation of three-dimensional PDEs anu integral equations, the investigation of mixed ... methods for these versions and, most importantly, the uniform approximation of parameter-dependent problems by these versions. By the p version, we

  12. Iterative methods for elliptic finite element equations on general meshes

    NASA Technical Reports Server (NTRS)

    Nicolaides, R. A.; Choudhury, Shenaz

    1986-01-01

    Iterative methods for arbitrary mesh discretizations of elliptic partial differential equations are surveyed. The methods discussed are preconditioned conjugate gradients, algebraic multigrid, deflated conjugate gradients, an element-by-element techniques, and domain decomposition. Computational results are included.

  13. Incremental motion encoder: a sensor for the integrated condition monitoring of rolling element bearings in machine tools

    NASA Astrophysics Data System (ADS)

    Ayandokun, Kayode A.; Orton, P. A.; Sherkat, Nasser; Thomas, Peter D.; Poliakoff, Janet F.

    1995-12-01

    Modern industry increasingly demands that machine tools operate continuously as elements within computer integrated manufacturing cells. Accurate monitoring of machine condition is the key to predicting failures that would result in quality defects or costly unplanned production stoppages. This paper presents research into the use of a novel rotary motion sensor for the condition monitoring of rolling element bearings. This sensor, the incremental motion encoder (IME), is based upon a patented development of the optical encoder commonly used in machine tools for sensing angular position and rotational speed. The IME combines these measurements with that of shaft center position in two dimensions. This motion of the shaft center is directly related to the condition of the bearings supporting the shaft. To illustrate the IME principle experimental results showing the ability of the sensor to distinguish between bearing defects and external sources of vibration are presented. Measurement of shaft loading with the sensor is also described. Currently machine tool condition is most often measured by external sensors, such as accelerometers or acoustic emission transducers, which are not parts of the machine itself. The IME is ideally suited to being designed into a machine tool so as to integrate a condition monitoring facility into the computer control of the machine. The paper concludes by describing the current technology which allows sensors based on the IME principle to be integrated directly into rolling element bearings for this purpose.

  14. Design of time-pulse coded optoelectronic neuronal elements for nonlinear transformation and integration

    NASA Astrophysics Data System (ADS)

    Krasilenko, Vladimir G.; Nikolsky, Alexander I.; Lazarev, Alexander A.; Lazareva, Maria V.

    2008-03-01

    In the paper the actuality of neurophysiologically motivated neuron arrays with flexibly programmable functions and operations with possibility to select required accuracy and type of nonlinear transformation and learning are shown. We consider neurons design and simulation results of multichannel spatio-time algebraic accumulation - integration of optical signals. Advantages for nonlinear transformation and summation - integration are shown. The offered circuits are simple and can have intellectual properties such as learning and adaptation. The integrator-neuron is based on CMOS current mirrors and comparators. The performance: consumable power - 100...500 μW, signal period- 0.1...1ms, input optical signals power - 0.2...20 μW time delays - less 1μs, the number of optical signals - 2...10, integration time - 10...100 of signal periods, accuracy or integration error - about 1%. Various modifications of the neuron-integrators with improved performance and for different applications are considered in the paper.

  15. 3-D imaging using row-column-addressed arrays with integrated apodization - part i: apodization design and line element beamforming.

    PubMed

    Rasmussen, Morten Fischer; Christiansen, Thomas Lehrmann; Thomsen, Erik Vilain; Jensen, Jørgen Arendt

    2015-05-01

    This paper investigates the effect of transducerintegrated apodization in row-column-addressed arrays and presents a beamforming approach specific for such arrays. Row-column addressing 2-D arrays greatly reduces the number of active channels needed to acquire a 3-D volume. A disadvantage of row-column-addressed arrays is an apparent ghost effect in the point spread function caused by edge waves. This paper investigates the origin of the edge waves and the effect of introducing an integrated apodization to reduce the ghost echoes. The performance of a λ/2-pitch 5-MHz 128 + 128 row-column-addressed array with different apodizations is simulated. A Hann apodization is shown to decrease imaging performance away from the center axis of the array because of a decrease in main lobe amplitude. Instead, a static roll-off apodization region located at the ends of the line elements is proposed. In simulations, the peak ghost echo intensity of a scatterer at (x,y, z) = (8, 3, 30) mm was decreased by 43 dB by integrating roll-off apodization into the array. The main lobe was unaffected by the apodization. Simulations of a 3-mm-diameter anechoic blood vessel at 30 mm depth showed that applying the transducer-integrated apodization increased the apparent diameter of the vessel from 2.0 mm to 2.4 mm, corresponding to an increase from 67% to 80% of the true vessel diameter. The line element beamforming approach is shown to be essential for achieving correct time-of-flight calculations, and hence avoid geometrical distortions. In Part II of this work, experimental results from a capacitive micromachined ultrasonic transducer with integrated roll-off apodization are given to validate the effect of integrating apodization into the line elements.

  16. Application of the Integrated Product Support Elements by the F-35 Joint Program Office

    DTIC Science & Technology

    2014-08-01

    Product Support (IPS) elements, outlined in the Department of Defense’s Product Support Manager ( PSM ) Guidebook. This article aims to promote...in Figure 1, the two additional elements, product support management and sustaining engineering, were added to reflect the PSM and life-cycle...logistician’s enhanced enterprise roles and responsibilities, which transcend the traditional logistics domain. The PSM is a key leadership position for

  17. A New Integrated Slot Element Feed Array for Multi-beam Systems

    NASA Technical Reports Server (NTRS)

    Yngvesson, K. S.; Johansson, J. F.; Kollberg, E. L.

    1985-01-01

    A feed array consisting of constant width slot antennas (CWSA's), fed from a block containing fin-line transitions, has been developed. The array has a two-dimensional configuration, with five elements each on five parallel substrates. Beam-widths are compatible with use in f/D-1.0 multi-beam systems, with optimum taper. Array element spacings are close to a factor of two smaller than for other typical arrays, and spill-over efficiency is about 65%.

  18. Occurrence, transport, and fate of trace elements, Blue River Basin, Summit County, Colorado: an integrated approach

    USGS Publications Warehouse

    Apodaca, L.E.; Driver, N.E.; Bails, J.B.

    2000-01-01

    Mining activities in the Blue River Basin, Summit County, Colorado, have affected the trace-element chemistry and biota along French Gulch and the Blue River. Elevated concentrations of As, Cd, Cu, Pb, and Zn were present in the bed and suspended sediments. Bed sediment trace-element concentrations were high in the streams in and near mining activities in the basin and remained high as water flowed into Dillon Reservoir about 3.5 km downstream. Bed-sediment (< 63 μm) data were useful in assessing the distribution of trace elements in the basin. Suspended-sediment measurements provided information as to the transport of the trace elements. Filtered (< 0.45 μm) water-column trace-element concentrations were orders of magnitude less than the sediment concentrations. Concentrations of Cd and Zn in the water column at some sites exceeded stream water-quality standards. Elevated trace-element concentrations in the sediment and water column are a source of contamination and must be considered in water-quality management of the Blue River Basin.

  19. A combined finite element-boundary element formulation for solution of two-dimensional problems via CGFFT

    NASA Technical Reports Server (NTRS)

    Collins, Jeffery D.; Jin, Jian-Ming; Volakis, John L.

    1990-01-01

    A method for the computation of electromagnetic scattering from arbitrary two-dimensional bodies is presented. The method combines the finite element and boundary element methods leading to a system for solution via the conjugate gradient Fast Fourier Transform (FFT) algorithm. Two forms of boundaries aimed at reducing the storage requirement of the boundary integral are investigated. It is shown that the boundary integral becomes convolutional when a circular enclosure is chosen, resulting in reduced storage requirement when the system is solved via the conjugate gradient FFT method. The same holds for the ogival enclosure, except that some of the boundary integrals are not convolutional and must be carefully treated to maintain O(N) memory requirement. Results for several circular and ogival structures are presented and shown to be in excellent agreement with those obtained by traditional methods.

  20. Autonomous Replication of the Conjugative Transposon Tn916

    PubMed Central

    Wright, Laurel D.

    2016-01-01

    ABSTRACT Integrative and conjugative elements (ICEs), also known as conjugative transposons, are self-transferable elements that are widely distributed among bacterial phyla and are important drivers of horizontal gene transfer. Many ICEs carry genes that confer antibiotic resistances to their host cells and are involved in the dissemination of these resistance genes. ICEs reside in host chromosomes but under certain conditions can excise to form a plasmid that is typically the substrate for transfer. A few ICEs are known to undergo autonomous replication following activation. However, it is not clear if autonomous replication is a general property of many ICEs. We found that Tn916, the first conjugative transposon identified, replicates autonomously via a rolling-circle mechanism. Replication of Tn916 was dependent on the relaxase encoded by orf20 of Tn916. The origin of transfer of Tn916, oriT(916), also functioned as an origin of replication. Using immunoprecipitation and mass spectrometry, we found that the relaxase (Orf20) and the two putative helicase processivity factors (Orf22 and Orf23) encoded by Tn916 likely interact in a complex and that the Tn916 relaxase contains a previously unidentified conserved helix-turn-helix domain in its N-terminal region that is required for relaxase function and replication. Lastly, we identified a functional single-strand origin of replication (sso) in Tn916 that we predict primes second-strand synthesis during rolling-circle replication. Together these results add to the emerging data that show that several ICEs replicate via a conserved, rolling-circle mechanism. IMPORTANCE Integrative and conjugative elements (ICEs) drive horizontal gene transfer and the spread of antibiotic resistances in bacteria. ICEs reside integrated in a host genome but can excise to create a plasmid that is the substrate for transfer to other cells. Here we show that Tn916, an ICE with broad host range, undergoes autonomous rolling

  1. Nuclear microprobe - synchrotron synergy: towards integrated quantitative real-time elemental imaging using PIXE and SCRF.

    SciTech Connect

    Ryan, C. G.; Etschmann, B. E.; Vogt, S.; Maser, J.; Harland, C. L.; van Achterbergh, E.; Legnini, D.; Experimental Facilities Division; CSIRO Exploration and Mining; Australian Synchrotron Research Program, ANSTO

    2005-01-01

    The Dynamic Analysis (DA) method, for the projection of quantitative elemental images using Proton Induced X-ray Emission (PIXE), has been extended for use with energy-dispersive Synchrotron X-ray Fluorescence (SXRF) data collected with the X-ray microprobe by making use of similarities and synergy with nuclear microscopy. The broad element sensitivity of PIXE is complemented by the selective nature of SXRF, where the beam energy can be tuned to optimize the sensitivity in a portion of the periodic table. PIXE combined with Proton Induced {gamma}-ray Emission (PIGE) in this study provided images of geological samples of 25 elements, including characteristic X-rays up to the energy of the Nd K lines (37 keV). Maximum sensitivity was achieved for elements around Z {approx} 33 with detection limits of {approx}250 ppb (in 5 h). SXRF using a 16.1 keV photon microbeam provided images of 16 elements, with optimum sensitivity around Z {approx} 35 with detection limits of {approx}70 ppb (in 11 h), an improvement of {approx}2.4 times when corrected for acquisition time.

  2. Developing data elements for research information system in health; a starting point for systems integration.

    PubMed

    Ghorbani, Nr; Ahmadi, M; Sadoughi, F; Ghanei, M

    2012-01-01

    This study defines necessary data elements required for the research information system in the domain of health, and its level of accountability to national health research indicators from the experts' perspective is being explored. This qualitative study was conducted based on comparative approach using the focus group method. Data were collected through 6 semi-structured group discussions held at the Undersecretary for Research and Technology, Ministry of Health and Medical Education, Tehran, Iran. For this study, 48 researchers were selected for the group discussions. All interviews and group discussions were recorded and transcribed. The Data analysis was performed simultaneously using Strauss and Corbin method. BASED ON CONTENT ANALYSIS, THE NECESSARY DATA ELEMENTS IDENTIFIED FOR THE NATIONAL HEALTH RESEARCH INFORMATION SYSTEM DESIGNED FOR ALL DATABASES WERE THE FOLLOWING: organizations, researchers, journals, articles, research projects and dissertations. Also, extracted from the focus group discussion were three main themes regarding data elements of these databases for the National Health Research Information System: 1) essential elements for each database 2) the system's data elements accountability to the national indicators in the domain of health research and 3) recommendations in the direction of optimizing the data. The results obtained from this study can serve as a valuable source in designing research information system in the domain of health within the country and in the region as well.

  3. Developing Data Elements for Research Information System in Health; a Starting Point for Systems Integration

    PubMed Central

    Ghorbani, NR; Ahmadi, M; Sadoughi, F; Ghanei, M

    2012-01-01

    Background: This study defines necessary data elements required for the research information system in the domain of health, and its level of accountability to national health research indicators from the experts’ perspective is being explored. Methods: This qualitative study was conducted based on comparative approach using the focus group method. Data were collected through 6 semi-structured group discussions held at the Undersecretary for Research and Technology, Ministry of Health and Medical Education, Tehran, Iran. For this study, 48 researchers were selected for the group discussions. All interviews and group discussions were recorded and transcribed. The Data analysis was performed simultaneously using Strauss and Corbin method. Results: Based on content analysis, the necessary data elements identified for the National Health Research Information System designed for all databases were the following: organizations, researchers, journals, articles, research projects and dissertations. Also, extracted from the focus group discussion were three main themes regarding data elements of these databases for the National Health Research Information System: 1) essential elements for each database 2) the system’s data elements accountability to the national indicators in the domain of health research and 3) recommendations in the direction of optimizing the data. Conclusions: The results obtained from this study can serve as a valuable source in designing research information system in the domain of health within the country and in the region as well. PMID:23641388

  4. Development of an integrated BEM (Boundary Element Mesh) for hot fluid-structure interaction

    NASA Technical Reports Server (NTRS)

    Dargush, G. F.; Banerjee, P. K.

    1987-01-01

    A boundary integral representation for a coupled approach to fluid flow and solid deformation problems associated with the design of hot-section components such as those in the Space Shuttle Main Engine is discussed. The formulation is based on the fundamental analytical solution of the Navier-Stokes equation for fluid velocity in an infinite domain. This fundamental solution was obtained by decomposing a Navier-Stokes equation into vorticity and dilation transport equations. A boundary integral involving convolutions in time was then constructed in which the convective terms appear in the volume integral.

  5. Thermomechanical stability and integrability of an embedded ceramic antenna with an integrated sensor element for wireless reading in harsh environments

    NASA Astrophysics Data System (ADS)

    Sturesson, P.; Khaji, Z.; Knaust, S.; Sundqvist, J.; Klintberg, L.; Thornell, G.

    2013-12-01

    This paper reports on the design, manufacturing and evaluation of a small, wirelessly powered and read resonating antenna circuit with an integrated pressure sensor. The work aims at developing miniature devices suitable for harsh environments, where high temperature prevents the use of conventional, silicon-based microdevices. Here, the device is made of alumina with platinum as conducting material. Ceramic green tapes were structured using high-precision milling, metallized using screen printing, and subsequently laminated to form stacks before they were sintered. The device's frequency shift as a function of temperature was studied up to 900°C. The contributions to the shift both from the thermomechanical deformation of the device at large, and from the integrated and, so far, self-pressurized sensor were sorted out. A total frequency shift of 3200 ppm was observed for the pressure sensor for heating over the whole range. Negligible levels of thermally induced radius of curvature were observed. With three-point bending, a frequency shift of 180 ppm was possible to induce with a curvature of radius of 220 m at a 10 N load. The results indicate that a robust pressure sensor node, which can register pressure changes of a few bars at 900°C and wirelessly transmit the signal, is viable.

  6. Revisiting conjugate schedules.

    PubMed

    MacAleese, Kenneth R; Ghezzi, Patrick M; Rapp, John T

    2015-07-01

    The effects of conjugate reinforcement on the responding of 13 college students were examined in three experiments. Conjugate reinforcement was provided via key presses that changed the clarity of pictures displayed on a computer monitor in a manner proportional to the rate of responding. Experiment 1, which included seven parameters of clarity change per response, revealed that responding decreased as the percentage clarity per response increased for all five participants. These results indicate that each participant's responding was sensitive to intensity change, which is a parameter of conjugate reinforcement schedules. Experiment 2 showed that responding increased during conjugate reinforcement phases and decreased during extinction phases for all four participants. Experiment 3 also showed that responding increased during conjugate reinforcement and further showed that responding decreased during a conjugate negative punishment condition for another four participants. Directions for future research with conjugate schedules are briefly discussed.

  7. A new boundary element formulation for two- and three-dimensional thermoelasticity using particular integrals

    NASA Technical Reports Server (NTRS)

    Henry, Donald P., Jr.; Banerjee, Prasanta K.

    1988-01-01

    New two- and three-dimensional BEM formulations are developed for steady-state and transient uncoupled thermoelasticity. These new procedures differ from previous work in that additional surface of volume integration is not required to incorporate thermal loads in the analysis. Instead, thermal body forces are introduced in the BEM system via particular integrals. The present formulation is implemented in a general-purpose multiregion system, and examples are presented to demonstrate the accuracy and versatility of the method.

  8. A new boundary element formulation for two- and three-dimensional thermoelasticity using particular integrals

    NASA Technical Reports Server (NTRS)

    Henry, Donald P., Jr.; Banerjee, Prasanta K.

    1988-01-01

    New two- and three-dimensional BEM formulations are developed for steady-state and transient uncoupled thermoelasticity. These new procedures differ from previous work in that additional surface of volume integration is not required to incorporate thermal loads in the analysis. Instead, thermal body forces are introduced in the BEM system via particular integrals. The present formulation is implemented in a general-purpose multiregion system, and examples are presented to demonstrate the accuracy and versatility of the method.

  9. Cryogenic optical test planning using the Optical Telescope Element Simulator with the James Webb Space Telescope Integrated Science Instrument Module

    NASA Astrophysics Data System (ADS)

    Reichard, Timothy A.; Bond, Nicholas A.; Greeley, Bradford W.; Malumuth, Eliot M.; Melendez, Marcio; Shiri, Ron; Alves de Oliveira, Catarina; Antonille, Scott R.; Birkmann, Stephan; Davis, Clinton; Dixon, William V.; Martel, André R.; Miskey, Cherie L.; Ohl, Raymond G.; Sabatke, Derek; Sullivan, Joseph

    2016-09-01

    NASA's James Webb Space Telescope (JWST) is a 6.5 m diameter, segmented, deployable telescope for cryogenic infrared space astronomy ( 40 K). The JWST Observatory architecture includes the Optical Telescope Element (OTE) and the Integrated Science Instrument Module (ISIM) element that contains four science instruments (SIs), including a guider. The SI and guider units are integrated to the ISIM structure and optically tested at NASA Goddard Space Flight Center as an instrument suite using a telescope simulator (Optical Telescope Element SIMulator; OSIM). OSIM is a high-fidelity, cryogenic JWST telescope simulator that features a 1.5m diameter powered mirror. The SIs are aligned to the flight structure's coordinate system under ambient, clean room conditions using optomechanical metrology and customized interfaces. OSIM is aligned to the ISIM mechanical coordinate system at the cryogenic operating temperature via internal mechanisms and feedback from alignment sensors and metrology in six degrees of freedom. SI performance, including focus, pupil shear, pupil roll, boresight, wavefront error, and image quality, is evaluated at the operating temperature using OSIM. The comprehensive optical test plans include drafting OSIM source configurations for thousands of exposures ahead of the start of a cryogenic test campaign. We describe how we predicted the performance of OSIM light sources illuminating the ISIM detectors to aide in drafting these optical tests before a test campaign began. We also discuss the actual challenges and successes of those exposure predictions encountered during a test campaign to fulfill the demands of the ISIM optical performance verification.

  10. System-Integrated Finite Element Analysis of a Full-Scale Helicopter Crash Test with Deployable Energy Absorbers

    NASA Technical Reports Server (NTRS)

    Annett, Martin S.; Polanco, Michael A.

    2010-01-01

    A full-scale crash test of an MD-500 helicopter was conducted in December 2009 at NASA Langley's Landing and Impact Research facility (LandIR). The MD-500 helicopter was fitted with a composite honeycomb Deployable Energy Absorber (DEA) and tested under vertical and horizontal impact velocities of 26-ft/sec and 40-ft/sec, respectively. The objectives of the test were to evaluate the performance of the DEA concept under realistic crash conditions and to generate test data for validation of a system integrated finite element model. In preparation for the full-scale crash test, a series of sub-scale and MD-500 mass simulator tests was conducted to evaluate the impact performances of various components, including a new crush tube and the DEA blocks. Parameters defined within the system integrated finite element model were determined from these tests. The objective of this paper is to summarize the finite element models developed and analyses performed, beginning with pre-test predictions and continuing through post-test validation.

  11. Integration of finite element modeling with solid modeling through a dynamic interface

    NASA Technical Reports Server (NTRS)

    Shephard, Mark S.

    1987-01-01

    Finite element modeling is dominated by geometric modeling type operations. Therefore, an effective interface to geometric modeling requires access to both the model and the modeling functionality used to create it. The use of a dynamic interface that addresses these needs through the use of boundary data structures and geometric operators is discussed.

  12. Integration Of Heat Transfer Coefficient In Glass Forming Modeling With Special Interface Element

    SciTech Connect

    Moreau, P.; Gregoire, S.; Lochegnies, D.; Cesar de Sa, J.

    2007-05-17

    Numerical modeling of the glass forming processes requires the accurate knowledge of the heat exchange between the glass and the forming tools. A laboratory testing is developed to determine the evolution of the heat transfer coefficient in different glass/mould contact conditions (contact pressure, temperature, lubrication...). In this paper, trials are performed to determine heat transfer coefficient evolutions in experimental conditions close to the industrial blow-and-blow process conditions. In parallel of this work, a special interface element is implemented in a commercial Finite Element code in order to deal with heat transfer between glass and mould for non-meshing meshes and evolutive contact. This special interface element, implemented by using user subroutines, permits to introduce the previous heat transfer coefficient evolutions in the numerical modelings at the glass/mould interface in function of the local temperatures, contact pressures, contact time and kind of lubrication. The blow-and-blow forming simulation of a perfume bottle is finally performed to assess the special interface element performance.

  13. Integration Of Heat Transfer Coefficient In Glass Forming Modeling With Special Interface Element

    NASA Astrophysics Data System (ADS)

    Moreau, P.; César de Sá, J.; Grégoire, S.; Lochegnies, D.

    2007-05-01

    Numerical modeling of the glass forming processes requires the accurate knowledge of the heat exchange between the glass and the forming tools. A laboratory testing is developed to determine the evolution of the heat transfer coefficient in different glass/mould contact conditions (contact pressure, temperature, lubrication…). In this paper, trials are performed to determine heat transfer coefficient evolutions in experimental conditions close to the industrial blow-and-blow process conditions. In parallel of this work, a special interface element is implemented in a commercial Finite Element code in order to deal with heat transfer between glass and mould for non-meshing meshes and evolutive contact. This special interface element, implemented by using user subroutines, permits to introduce the previous heat transfer coefficient evolutions in the numerical modelings at the glass/mould interface in function of the local temperatures, contact pressures, contact time and kind of lubrication. The blow-and-blow forming simulation of a perfume bottle is finally performed to assess the special interface element performance.

  14. Compensation of reflector surface distortions using conjugate field matching

    NASA Technical Reports Server (NTRS)

    Acosta, R. J.

    1986-01-01

    The feasibility of compensating for reflector surface distortions has been investigated. The performance characteristics (gain, sidelobe level, null location, beamwidth, etc.) of space communication reflector antenna systems degrade as the reflector surface distorts due to thermal effects from a varying solar flux. The technique reported here will maintain the design radiation performance independently of thermal effects on the reflector surface. With the advent of monolithic microwave integrated circuits (MMIC), a greater flexibility in array-fed reflector system design can be achieved. MMIC arrays provides independent control of amplitude and phase for each of many radiating elements of the feed array. The conjugate field matching technique provide a basis for obtaining the required element excitations under surface distortion for maintaining the design radiation performance. It is assumed that the surface characteristics (x, y, z, first derivatives, and second derivatives) under distortion are known.

  15. An efficient formulation of the coupled finite element-integral equation technique for solving large 3D scattering problems

    NASA Technical Reports Server (NTRS)

    Cwik, T.; Jamnejad, V.; Zuffada, C.

    1993-01-01

    It is often desirable to calculate the electromagnetic fields inside and about a complicated system of scattering bodies, as well as in their far-field region. The finite element method (FE) is well suited to solving the interior problem, but the domain has to be limited to a manageable size. At the truncation of the FE mesh one can either impose approximate (absorbing) boundary conditions or set up an integral equation (IE) for the fields scattered from the bodies. The latter approach is preferable since it results in higher accuracy. Hence, the two techniques can be successfully combined by introducing a surface that encloses the scatterers, applying a FE model to the inner volume and setting up an IE for the tangential fields components on the surface. Here the continuity of the tangential fields is used bo obtain a consistent solution. A few coupled FE-IE methods have recently appeared in the literature. The approach presented here has the advantage of using edge-based finite elements, a type of finite elements with degrees of freedom associated with edges of the mesh. Because of their properties, they are better suited than the conventional node based elements to represent electromagnetic fields, particularly when inhomogeneous regions are modeled, since the node based elements impose an unnatural continuity of all field components across boundaries of mesh elements. Additionally, our approach is well suited to handle large size problems and lends itself to code parallelization. We will discuss the salient features that make our approach very efficient from the standpoint of numerical computation, and the fields and RCS of a few objects are illustrated as examples.

  16. Fiber bundle phase conjugate mirror

    DOEpatents

    Ward, Benjamin G.

    2012-05-01

    An improved method and apparatus for passively conjugating the phases of a distorted wavefronts resulting from optical phase mismatch between elements of a fiber laser array are disclosed. A method for passively conjugating a distorted wavefront comprises the steps of: multiplexing a plurality of probe fibers and a bundle pump fiber in a fiber bundle array; passing the multiplexed output from the fiber bundle array through a collimating lens and into one portion of a non-linear medium; passing the output from a pump collection fiber through a focusing lens and into another portion of the non-linear medium so that the output from the pump collection fiber mixes with the multiplexed output from the fiber bundle; adjusting one or more degrees of freedom of one or more of the fiber bundle array, the collimating lens, the focusing lens, the non-linear medium, or the pump collection fiber to produce a standing wave in the non-linear medium.

  17. The SXT Conjugative Element and Linear Prophage N15 Encode Toxin-Antitoxin-Stabilizing Systems Homologous to the tad-ata Module of the Paracoccus aminophilus Plasmid pAMI2▿ †

    PubMed Central

    Dziewit, Lukasz; Jazurek, Magdalena; Drewniak, Lukasz; Baj, Jadwiga; Bartosik, Dariusz

    2007-01-01

    A group of proteic toxin-antitoxin (TA) cassettes whose representatives are widely distributed among bacterial genomes has been identified. These cassettes occur in chromosomes, plasmids, bacteriophages, and noncomposite transposons, as well as in the SXT conjugative element of Vibrio cholerae. The following four homologous loci were subjected to detailed comparative studies: (i) tad-ata from plasmid pAMI2 of Paracoccus aminophilus (the prototype of this group), (ii) gp49-gp48 from the linear bacteriophage N15 of Escherichia coli, (iii) s045-s044 from SXT, and (iv) Z3230-Z3231 from the genomic island of enterohemorrhagic Escherichia coli O157:H7 strain EDL933. Functional analysis revealed that all but one of these loci (Z3230-Z3231) are able to stabilize heterologous replicons, although the host ranges varied. The TA cassettes analyzed have the following common features: (i) the toxins are encoded by the first gene of each operon; (ii) the antitoxins contain a predicted helix-turn-helix motif of the XRE family; and (iii) the cassettes have two promoters that are different strengths, one which is located upstream of the toxin gene and one which is located upstream of the antitoxin gene. All four toxins tested are functional in E. coli; overexpression of the toxins (in the absence of antitoxin) results in a bacteriostatic effect manifested by elongation of bacterial cells and growth arrest. The toxins have various effects on cell viability, which suggests that they may recognize different intracellular targets. Preliminary data suggest that different cellular proteases are involved in degradation of antitoxins encoded by the loci analyzed. PMID:17158670

  18. Integrating the human element into the systems engineering process and MBSE methodology.

    SciTech Connect

    Tadros, Michael Samir.

    2013-12-01

    In response to the challenges related to the increasing size and complexity of systems, organizations have recognized the need to integrate human considerations in the beginning stages of systems development. Human Systems Integration (HSI) seeks to accomplish this objective by incorporating human factors within systems engineering (SE) processes and methodologies, which is the focus of this paper. A representative set of HSI methods from multiple sources are organized, analyzed, and mapped to the systems engineering Vee-model. These methods are then consolidated and evaluated against the SE process and Models-Based Systems Engineering (MBSE) methodology to determine where and how they could integrate within systems development activities in the form of specific enhancements. Overall conclusions based on these evaluations are presented and future research areas are proposed.

  19. An Integrated Magnetic Circuit Model and Finite Element Model Approach to Magnetic Bearing Design

    NASA Technical Reports Server (NTRS)

    Provenza, Andrew J.; Kenny, Andrew; Palazzolo, Alan B.

    2003-01-01

    A code for designing magnetic bearings is described. The code generates curves from magnetic circuit equations relating important bearing performance parameters. Bearing parameters selected from the curves by a designer to meet the requirements of a particular application are input directly by the code into a three-dimensional finite element analysis preprocessor. This means that a three-dimensional computer model of the bearing being developed is immediately available for viewing. The finite element model solution can be used to show areas of magnetic saturation and make more accurate predictions of the bearing load capacity, current stiffness, position stiffness, and inductance than the magnetic circuit equations did at the start of the design process. In summary, the code combines one-dimensional and three-dimensional modeling methods for designing magnetic bearings.

  20. Integrated Nondestructive Evaluation and Finite Element Analysis Predicts Crack Location and Shape

    NASA Technical Reports Server (NTRS)

    Abdul-Azia, Ali; Baaklini, George Y.; Trudell, Jeffrey J.

    2002-01-01

    This study describes the finite-element analyses and the NDE modality undertaken on two flywheel rotors that were spun to burst speed. Computed tomography and dimensional measurements were used to nondestructively evaluate the rotors before and/or after they were spun to the first crack detection. Computed tomography data findings of two- and three-dimensional crack formation were used to conduct finite-element (FEA) and fracture mechanics analyses. A procedure to extend these analyses to estimate the life of these components is also outlined. NDE-FEA results for one of the rotors are presented in the figures. The stress results, which represent the radial stresses in the rim, clearly indicate that the maximum stress region is within the section defined by the computed tomography scan. Furthermore, the NDE data correlate well with the FEA results. In addition, the measurements reported show that the NDE and FEA data are in parallel.

  1. Integration of Large Deformation Finite Element Formulations in Flexible Multibody System Algorithms

    DTIC Science & Technology

    2010-07-01

    important ANCF feature was demonstrated by using the general large deformation Neo-Hookean and Mooney - Rivlin constitutive models [5]. The results...applications will include belt drives and rubber chain tracked vehicles. In the applications considered in this research project, the important features of...nonlinear dynamic rubber chains and belt drives models are developed using ANCF finite elements that allow for a straight forward implementation of

  2. The accuracy of the Gaussian-and-finite-element-Coulomb (GFC) method for the calculation of Coulomb integrals

    NASA Astrophysics Data System (ADS)

    Przybytek, Michal; Helgaker, Trygve

    2013-08-01

    We analyze the accuracy of the Coulomb energy calculated using the Gaussian-and-finite-element-Coulomb (GFC) method. In this approach, the electrostatic potential associated with the molecular electronic density is obtained by solving the Poisson equation and then used to calculate matrix elements of the Coulomb operator. The molecular electrostatic potential is expanded in a mixed Gaussian-finite-element (GF) basis set consisting of Gaussian functions of s symmetry centered on the nuclei (with exponents obtained from a full optimization of the atomic potentials generated by the atomic densities from symmetry-averaged restricted open-shell Hartree-Fock theory) and shape functions defined on uniform finite elements. The quality of the GF basis is controlled by means of a small set of parameters; for a given width of the finite elements d, the highest accuracy is achieved at smallest computational cost when tricubic (n = 3) elements are used in combination with two (γH = 2) and eight (γ1st = 8) Gaussians on hydrogen and first-row atoms, respectively, with exponents greater than a given threshold (α _min^G=0.5). The error in the calculated Coulomb energy divided by the number of atoms in the system depends on the system type but is independent of the system size or the orbital basis set, vanishing approximately like d4 with decreasing d. If the boundary conditions for the Poisson equation are calculated in an approximate way, the GFC method may lose its variational character when the finite elements are too small; with larger elements, it is less sensitive to inaccuracies in the boundary values. As it is possible to obtain accurate boundary conditions in linear time, the overall scaling of the GFC method for large systems is governed by another computational step—namely, the generation of the three-center overlap integrals with three Gaussian orbitals. The most unfavorable (nearly quadratic) scaling is observed for compact, truly three-dimensional systems

  3. The accuracy of the Gaussian-and-finite-element-Coulomb (GFC) method for the calculation of Coulomb integrals.

    PubMed

    Przybytek, Michal; Helgaker, Trygve

    2013-08-07

    We analyze the accuracy of the Coulomb energy calculated using the Gaussian-and-finite-element-Coulomb (GFC) method. In this approach, the electrostatic potential associated with the molecular electronic density is obtained by solving the Poisson equation and then used to calculate matrix elements of the Coulomb operator. The molecular electrostatic potential is expanded in a mixed Gaussian-finite-element (GF) basis set consisting of Gaussian functions of s symmetry centered on the nuclei (with exponents obtained from a full optimization of the atomic potentials generated by the atomic densities from symmetry-averaged restricted open-shell Hartree-Fock theory) and shape functions defined on uniform finite elements. The quality of the GF basis is controlled by means of a small set of parameters; for a given width of the finite elements d, the highest accuracy is achieved at smallest computational cost when tricubic (n = 3) elements are used in combination with two (γ(H) = 2) and eight (γ(1st) = 8) Gaussians on hydrogen and first-row atoms, respectively, with exponents greater than a given threshold (αmin (G)=0.5). The error in the calculated Coulomb energy divided by the number of atoms in the system depends on the system type but is independent of the system size or the orbital basis set, vanishing approximately like d(4) with decreasing d. If the boundary conditions for the Poisson equation are calculated in an approximate way, the GFC method may lose its variational character when the finite elements are too small; with larger elements, it is less sensitive to inaccuracies in the boundary values. As it is possible to obtain accurate boundary conditions in linear time, the overall scaling of the GFC method for large systems is governed by another computational step-namely, the generation of the three-center overlap integrals with three Gaussian orbitals. The most unfavorable (nearly quadratic) scaling is observed for compact, truly three-dimensional systems

  4. A peptide nucleic acid-aminosugar conjugate targeting transactivation response element of HIV-1 RNA genome shows a high bioavailability in human cells and strongly inhibits tat-mediated transactivation of HIV-1 transcription.

    PubMed

    Das, Indrajit; Désiré, Jérôme; Manvar, Dinesh; Baussanne, Isabelle; Pandey, Virendra N; Décout, Jean-Luc

    2012-07-12

    The 6-aminoglucosamine ring of the aminoglycoside antibiotic neomycin B (ring II) was conjugated to a 16-mer peptide nucleic acid (PNA) targeting HIV-1 TAR RNA. For this purpose, we prepared the aminoglucosamine monomer 15 and attached it to the protected PNA prior to its cleavage from the solid support. We found that the resulting PNA-aminoglucosamine conjugate is stable under acidic conditions, efficiently taken up by the human cells and fairly distributed in both cytosol and nucleus without endosomal entrapment because cotreatment with endosome-disrupting agent had no effect on its cellular distribution. The conjugate displayed very high target specificity in vitro and strongly inhibited Tat mediated transactivation of HIV-1 LTR transcription in a cell culture system. The unique properties of this new class of PNA conjugate suggest it to be a potential candidate for therapeutic application.

  5. A Peptide Nucleic Acid-Aminosugar Conjugate Targeting Transactivation Response Element of HIV-1 RNA Genome Shows a High Bioavailability in Human Cells and Strongly Inhibits Tat-mediated Transactivation of HIV-1 Transcription

    PubMed Central

    Das, Indrajit; Désiré, Jérôme; Manvar, Dinesh; Baussanne, Isabelle; Pandey, Virendra N.; Décout, Jean-Luc

    2012-01-01

    The 6-aminoglucosamine ring of the aminoglycoside antibiotic neomycin B (ring II) was conjugated to a 16 mer peptide nucleic acid (PNA) targeting HIV-1 TAR RNA. For this purpose we prepared the aminoglucosamine monomer 15 and attached it to the protected PNA prior to its cleavage from the solid support. We found that the resulting PNA-aminoglucosamine conjugate is stable under acidic condition, efficiently taken up by the human cells and fairly distributed in both cytosol and nucleus without endosomal entrapment since co-treatment with endosome-disrupting agent had no effect on its cellular distribution. The conjugate displayed very high target specificity in vitro and strongly inhibited Tat mediated transactivation of HIV-1 LTR transcription in cell culture system. The unique properties of this new class of PNA conjugate suggest it to be a potential candidate for therapeutic application. PMID:22698070

  6. Process improvement and supply and demand: the elements that underlie integration.

    PubMed

    Murray, Mark

    2009-01-01

    Integration relies on a series of key change strategies connected by a fundamental dynamic: system capacity has to match demand or it will ultimately result in expanding delay and system failure. A balance of supply and demand is necessary for successful system performance. If demand and capacity are balanced, then delays are not required.

  7. Integrating Literature with Craft in a Learning Process with Creative Elements

    ERIC Educational Resources Information Center

    Aerila, Juli-Anna; Rönkkö, Marja-Leena

    2015-01-01

    Art-related learning should be the central way of doing and playing in preschool, because the high quality of art-related education has a positive effect on children's well-being, identity development, and creative thinking. In our study we tested an integrated learning process where reading literature and telling stories is combined with the…

  8. 49 CFR 192.911 - What are the elements of an integrity management program?

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... threats to each covered pipeline segment, which must include data integration and a risk assessment. An operator must use the threat identification and risk assessment to prioritize covered segments for... assessment is being conducted in a manner that minimizes environmental and safety risks. (p) A process...

  9. 49 CFR 192.911 - What are the elements of an integrity management program?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... threats to each covered pipeline segment, which must include data integration and a risk assessment. An operator must use the threat identification and risk assessment to prioritize covered segments for... assessment is being conducted in a manner that minimizes environmental and safety risks. (p) A process...

  10. Academic Use of Social Media Technologies as an Integral Element of Informatics Program Delivery in Malaysia

    ERIC Educational Resources Information Center

    Lim, Jane See Yin; Harper, Barry; Chicharo, Joe F.

    2014-01-01

    Higher education institutions are currently examining how the current emerging technologies and social media applications can be integrated with the appropriate teaching pedagogies adopted by higher education institutions to provide students with learning experiences that take advantage of these new affordances. Due to the continuous and pervasive…

  11. Integrating Literature with Craft in a Learning Process with Creative Elements

    ERIC Educational Resources Information Center

    Aerila, Juli-Anna; Rönkkö, Marja-Leena

    2015-01-01

    Art-related learning should be the central way of doing and playing in preschool, because the high quality of art-related education has a positive effect on children's well-being, identity development, and creative thinking. In our study we tested an integrated learning process where reading literature and telling stories is combined with the…

  12. Mathematical Treats Form the Stars: Integrating Curricular Elements through Partnerships between NASA and Math Methods Faculty.

    ERIC Educational Resources Information Center

    Crawford, Caroline M.; Brown, Evelyn; Chilelli, Chris

    Mathematics methods coursework can be an innovative environment through which to emphasize the integration of real-world data structures and opportunities. These opportunities can create instructionally informative opportunities for learners, as well as inform teacher candidates of innovative teaching tools at their fingertips. NASA offers…

  13. A novel method for the design of diffractive optical elements based on the Rayleigh-Sommerfeld integral

    NASA Astrophysics Data System (ADS)

    Pang, Hui; Yin, Shaoyun; Deng, Qiling; Qiu, Qi; Du, Chunlei

    2015-07-01

    The original design method for diffractive optical elements (DOEs) is limited to cases of small-angle diffraction due to the Fresnel or Fraunhofer diffraction integral. In this paper, we propose a new method based on the Rayleigh-Sommerfeld diffraction integral, which does not have this limit. In this method, the target intensity distribution is first modified via coordinate transformation and intensity adjustment. Then, the modified Gerchberg-Saxton algorithm is used to achieve the phase distribution of the DOE. To verify this method, simulations and experiments are performed. The results show that the original method is effective only when the full diffraction angle of the DOE is below 25°. Conversely, this method can achieve the target with both small and large diffraction angles.

  14. J-integral patch for finite element analysis of dynamic fracture due to impact of pressure vessels

    NASA Technical Reports Server (NTRS)

    Kunin, Boris I.

    1993-01-01

    Prediction of whether a pressurized cylinder will fail catastrophically when impacted by a projectile has important applications ranging from perforation of an airplane's skin by a failed turbine blade to meteorite impact of a space station habitation module. This report summarizes the accomplishment of one task for a project whose aim is to simulate numerically the outcome of a high velocity impact of pressure vessels. A finite element patch covering the vicinity of a growing crack has been constructed to estimate the J-integral (crack driving force) during the impact. Explicit expressions for the J-integral through the nodal values of displacement, strain, and stress have been written. The patch is to be used repeatedly to estimate the amount of crack growth during the time of the impact. The resulting crack size is to be compared to an estimated critical crack size for the pressurized cylinder.

  15. Geomechanical Simulations of CO2 Storage Integrity using the Livermore Distinct Element Method

    SciTech Connect

    Morris, J P; Johnson, S M; Friedmann, S J

    2008-07-11

    Large-scale carbon capture and sequestration (CCS) projects involving annual injections of millions of tons of CO{sub 2} are a key infrastructural element needed to substantially reduce greenhouse gas emissions. The large rate and volume of injection will induce pressure and stress gradients within the formation that could activate existing fractures and faults, or drive new fractures through the caprock. We will present results of an ongoing investigation to identify conditions that will activate existing fractures/faults or make new fractures within the caprock using the Livermore Distinct Element Code (LDEC). LDEC is a multiphysics code, developed at LLNL, capable of simulating dynamic fracture of rock masses under a range of conditions. As part of a recent project, LDEC has been extended to consider fault activation and dynamic fracture of rock masses due to pressurization of the pore-space. We will present several demonstrations of LDEC functionality and applications of LDEC to CO{sub 2} injection scenarios including injection into an extensively fractured rockmass. These examples highlight the advantages of explicitly including the geomechanical response of each interface within the rockmass. We present results from our investigations of Teapot Dome using LDEC to study the potential for fault activation during injection. Using this approach, we built finite element models of the rock masses surrounding bounding faults and explicitly simulated the compression and shear on the fault interface. A CO{sub 2} injection source was introduced and the area of fault activation was predicted as a function of injection rate. This work presents an approach where the interactions of all locations on the fault are considered in response to specific injection scenarios. For example, with LDEC, as regions of the fault fail, the shear load is taken up elsewhere on the fault. The results of this study are consistent with previous studies of Teapot Dome and indicate

  16. Geomechanical Simulations of Caprock Integrity Using the Livermore Distinict Element Method

    SciTech Connect

    Morris, J; Johnson, S; Friedmann, S J

    2008-04-17

    Large-scale carbon capture and sequestration (CCS) projects involving annual injections of millions of tons of CO2 are a key infrastructural element needed to substantially reduce greenhouse gas emissions. The large rate and volume of injection will induce pressure and stress gradients within the formation that could activate existing fractures and faults, or drive new fractures through the caprock. We will present results of an ongoing investigation to identify conditions that will activate existing fractures/faults or make new fractures within the caprock using the Livermore Distinct Element Code (LDEC). LDEC is a multiphysics code, developed at LLNL, capable of simulating dynamic fracture of rock masses under a range of conditions. As part of a recent project, LDEC has been extended to consider fault activation and dynamic fracture of rock masses due to pressurization of the pore-space. We will present several demonstrations of LDEC functionality and an application of LDEC to a CO2 injection scenario. We present results from our investigations of Teapot Dome using LDEC to study the potential for fault activation during injection. Using this approach, we built finite element models of the rock masses surrounding bounding faults and explicitly simulated the compression and shear on the fault interface. A CO2 injection source was introduced and the area of fault activation was predicted as a function of injection rate. This work presents an approach where the interactions of all locations on the fault are considered in response to specific injection scenarios. For example, with LDEC, as regions of the fault fail, the shear load is taken up elsewhere on the fault. The results of this study are consistent with previous studies of Teapot Dome and indicate significantly elevated pore pressures are required to activate the bounding faults, given the assumed in situ stress state on the faults.

  17. Carbonate fracture stratigraphy: An integrated outcrop and 2D discrete element modelling study

    NASA Astrophysics Data System (ADS)

    Spence, Guy; Finch, Emma

    2013-04-01

    Constraining fracture stratigraphy is important as natural fractures control primary fluid flow in low matrix permeability naturally fractured carbonate hydrocarbon reservoirs. Away from the influence of folds and faults, stratigraphic controls are known to be the major control on fracture networks. The fracture stratigraphy of carbonate nodular-chert rhythmite successions are investigated using a Discrete Element Modelling (DEM) technique and validated against observations from outcrops. Comparisons are made to the naturally fractured carbonates of the Eocene Thebes Formation exposed in the west central Sinai of Egypt, which form reservoir rocks in the nearby East Ras Budran Field. DEM allows mechanical stratigraphy to be defined as the starting conditions from which forward numerical modelling can generate fracture stratigraphy. DEM can incorporate both stratigraphic and lateral heterogeneity, and enable mechanical and fracture stratigraphy to be characterised separately. Stratally bound stratified chert nodules below bedding surfaces generate closely spaced lateral heterogeneity in physical properties at stratigraphic mechanical interfaces. This generates extra complexity in natural fracture networks in addition to that caused by bed thickness and lithological physical properties. A series of representative geologically appropriate synthetic mechanical stratigraphic models were tested. Fracture networks generated in 15 DEM experiments designed to isolate and constrain the effects of nodular chert rhythmites on carbonate fracture stratigraphy are presented. The discrete element media used to model the elastic strengths of rocks contain 72,866 individual elements. Mechanical stratigraphies and the fracture networks generated are placed in a sequence stratigraphic framework. Nodular chert rhythmite successions are shown to be a distinct type of naturally fractured carbonate reservoir. Qualitative stratigraphic rules for predicting the distribution, lengths, spacing

  18. The Role of Heterologous Chloroplast Sequence Elements in Transgene Integration and Expression1[W][OA

    PubMed Central

    Ruhlman, Tracey; Verma, Dheeraj; Samson, Nalapalli; Daniell, Henry

    2010-01-01

    Heterologous regulatory elements and flanking sequences have been used in chloroplast transformation of several crop species, but their roles and mechanisms have not yet been investigated. Nucleotide sequence identity in the photosystem II protein D1 (psbA) upstream region is 59% across all taxa; similar variation was consistent across all genes and taxa examined. Secondary structure and predicted Gibbs free energy values of the psbA 5′ untranslated region (UTR) among different families reflected this variation. Therefore, chloroplast transformation vectors were made for tobacco (Nicotiana tabacum) and lettuce (Lactuca sativa), with endogenous (Nt-Nt, Ls-Ls) or heterologous (Nt-Ls, Ls-Nt) psbA promoter, 5′ UTR and 3′ UTR, regulating expression of the anthrax protective antigen (PA) or human proinsulin (Pins) fused with the cholera toxin B-subunit (CTB). Unique lettuce flanking sequences were completely eliminated during homologous recombination in the transplastomic tobacco genomes but not unique tobacco sequences. Nt-Ls or Ls-Nt transplastomic lines showed reduction of 80% PA and 97% CTB-Pins expression when compared with endogenous psbA regulatory elements, which accumulated up to 29.6% total soluble protein PA and 72.0% total leaf protein CTB-Pins, 2-fold higher than Rubisco. Transgene transcripts were reduced by 84% in Ls-Nt-CTB-Pins and by 72% in Nt-Ls-PA lines. Transcripts containing endogenous 5′ UTR were stabilized in nonpolysomal fractions. Stromal RNA-binding proteins were preferentially associated with endogenous psbA 5′ UTR. A rapid and reproducible regeneration system was developed for lettuce commercial cultivars by optimizing plant growth regulators. These findings underscore the need for sequencing complete crop chloroplast genomes, utilization of endogenous regulatory elements and flanking sequences, as well as optimization of plant growth regulators for efficient chloroplast transformation. PMID:20130101

  19. Phase-Conjugated Fluorescence

    DTIC Science & Technology

    1991-01-01

    reverse if necessary and identify by block number)FIELD GROUP SUB-GROUP PHASE-CONJUGATED FLUORESCENCE EMITTED POWER FOUR -WAVE MIXING THREE CONTRIBUTIONS...atom near a phase conjugator (PC) based on four -wave mixing is studied from first principles. The MaxwellLeisenberg equations are solved for the...Fronczak Hall State University of New York at Buffalo Buffalo, New York 14260 Fluorescent emission by an atom near a phase conjugator (PC) based on four -wave

  20. A DNA-Fullerene Conjugate as a Template for Supramolecular Chromophore Assemblies: Towards DNA-Based Solar Cells.

    PubMed

    Ensslen, Philipp; Gärtner, Stefan; Glaser, Konstantin; Colsmann, Alexander; Wagenknecht, Hans-Achim

    2016-01-26

    A fullerene was covalently attached to a (dA)20 template that serves as structural scaffold to self-assemble an ordered and mixed array of ethynyl-pyrene- and ethynyl-Nile-red-nucleoside conjugates. Fluorescence spectroscopy revealed evidence for energy transfer between the two different chromophores. Moreover, fluorescence quenching is significantly enhanced by the attached fullerene in mixed assemblies of different chromophore ratios. This indicates exciton dissociation by electron transfer from the photo-generated exciton on the chromophore stack to the fullerene. The fullerene-DNA-conjugate was integrated as a photo-active layer in solar cells that showed charge-carrier generation in the spectral regime of all three components of the conjugate. This work clearly demonstrates that DNA is suitable as structural element for chromophore assemblies in future organic optoelectronic devices, such as solar cells.

  1. Integrating finite elements with optimal control to simulate active vibrations attenuation

    NASA Astrophysics Data System (ADS)

    Woods, S.; Szyszkowski, W.

    2016-12-01

    Continuous mechanical systems controlled by discrete actuators are inherently under-actuated and involve second-order non-holonomic constraints. A method of simulating optimal vibrations attenuation for such systems is proposed, in which the system is modeled by the finite elements (with possibly a large number of DOFs) and Pontryagin's Principle is applied to control several significant vibration modes by a small number of discrete actuators. For an assumed set of actuators the complete dynamic response of the system can be obtained, as well as the rate and effort parameters to evaluate efficiency of the whole attenuation process.

  2. The master regulator of IncA/C plasmids is recognized by the Salmonella Genomic island SGI1 as a signal for excision and conjugal transfer.

    PubMed

    Kiss, János; Papp, Péter Pál; Szabó, Mónika; Farkas, Tibor; Murányi, Gábor; Szakállas, Erik; Olasz, Ferenc

    2015-10-15

    The genomic island SGI1 and its variants, the important vehicles of multi-resistance in Salmonella strains, are integrative elements mobilized exclusively by the conjugative IncA/C plasmids. Integration and excision of the island are carried out by the SGI1-encoded site-specific recombinase Int and the recombination directionality factor Xis. Chromosomal integration ensures the stable maintenance and vertical transmission of SGI1, while excision is the initial step of horizontal transfer, followed by conjugation and integration into the recipient. We report here that SGI1 not only exploits the conjugal apparatus of the IncA/C plasmids but also utilizes the regulatory mechanisms of the conjugation system for the exact timing and activation of excision to ensure efficient horizontal transfer. This study demonstrates that the FlhDC-family activator AcaCD, which regulates the conjugation machinery of the IncA/C plasmids, serves as a signal of helper entry through binding to SGI1 xis promoter and activating SGI1 excision. Promoters of int and xis genes have been identified and the binding site of the activator has been located by footprinting and deletion analyses. We prove that expression of xis is activator-dependent while int is constitutively expressed, and this regulatory mechanism is presumably responsible for the efficient transfer and stable maintenance of SGI1.

  3. The master regulator of IncA/C plasmids is recognized by the Salmonella Genomic island SGI1 as a signal for excision and conjugal transfer

    PubMed Central

    Kiss, János; Papp, Péter Pál; Szabó, Mónika; Farkas, Tibor; Murányi, Gábor; Szakállas, Erik; Olasz, Ferenc

    2015-01-01

    The genomic island SGI1 and its variants, the important vehicles of multi-resistance in Salmonella strains, are integrative elements mobilized exclusively by the conjugative IncA/C plasmids. Integration and excision of the island are carried out by the SGI1-encoded site-specific recombinase Int and the recombination directionality factor Xis. Chromosomal integration ensures the stable maintenance and vertical transmission of SGI1, while excision is the initial step of horizontal transfer, followed by conjugation and integration into the recipient. We report here that SGI1 not only exploits the conjugal apparatus of the IncA/C plasmids but also utilizes the regulatory mechanisms of the conjugation system for the exact timing and activation of excision to ensure efficient horizontal transfer. This study demonstrates that the FlhDC-family activator AcaCD, which regulates the conjugation machinery of the IncA/C plasmids, serves as a signal of helper entry through binding to SGI1 xis promoter and activating SGI1 excision. Promoters of int and xis genes have been identified and the binding site of the activator has been located by footprinting and deletion analyses. We prove that expression of xis is activator-dependent while int is constitutively expressed, and this regulatory mechanism is presumably responsible for the efficient transfer and stable maintenance of SGI1. PMID:26209134

  4. Establishing the Structural Integrity of Core-Shell Nanoparticles against Elemental Migration using Luminescent Lanthanide Probes.

    PubMed

    Chen, Bing; Peng, Dengfeng; Chen, Xian; Qiao, Xvsheng; Fan, Xianping; Wang, Feng

    2015-10-19

    Core-shell structured nanoparticles are increasingly used to host luminescent lanthanide ions but the structural integrity of these nanoparticles still lacks sufficient understanding. Herein, we present a new approach to detect the diffusion of dopant ions in core-shell nanostructures using luminescent lanthanide probes whose emission profile and luminescence lifetime are sensitive to the chemical environment. We show that dopant ions in solution-synthesized core-shell nanoparticles are firmly confined in the designed locations. However, annealing at certain temperatures (greater than circa 350 °C) promotes diffusion of the dopant ions and leads to degradation of the integrity of the nanoparticles. These insights into core-shell nanostructures should enhance our ability to understand and use lanthanide-doped luminescent nanoparticles.

  5. Inter-element orientation and distance influence the duration of persistent contour integration.

    PubMed

    Strother, Lars; Alferov, Danila

    2014-01-01

    Contour integration is a fundamental form of perceptual organization. We introduce a new method of studying the mechanisms responsible for contour integration. This method capitalizes on the perceptual persistence of contours under conditions of impending camouflage. Observers viewed arrays of randomly arranged line segments upon which circular contours comprised of similar line segments were superimposed via abrupt onset. Crucially, these contours remained visible for up to a few seconds following onset, but eventually disappeared due to the camouflaging effects of surrounding background line segments. Our main finding was that the duration of contour visibility depended on the distance and degree of co-alignment between adjacent contour segments such that relatively dense smooth contours persisted longest. The stimulus-related effects reported here parallel similar results from contour detection studies, and complement previous reported top-down influences on contour persistence (Strother et al., 2011). We propose that persistent contour visibility reflects the sustained activity of recurrent processing loops within and between visual cortical areas involved in contour integration and other important stages of visual object recognition.

  6. Finite Element Analysis of Single Cell Stiffness Measurements Using PZT-Integrated Buckling Nanoneedles

    PubMed Central

    Rad, Maryam Alsadat; Tijjani, Auwal Shehu; Ahmad, Mohd Ridzuan; Auwal, Shehu Muhammad

    2016-01-01

    This paper proposes a new technique for real-time single cell stiffness measurement using lead zirconate titanate (PZT)-integrated buckling nanoneedles. The PZT and the buckling part of the nanoneedle have been modelled and validated using the ABAQUS software. The two parts are integrated together to function as a single unit. After calibration, the stiffness, Young’s modulus, Poisson’s ratio and sensitivity of the PZT-integrated buckling nanoneedle have been determined to be 0.7100 N·m−1, 123.4700 GPa, 0.3000 and 0.0693 V·m·N−1, respectively. Three Saccharomyces cerevisiae cells have been modelled and validated based on compression tests. The average global stiffness and Young’s modulus of the cells are determined to be 10.8867 ± 0.0094 N·m−1 and 110.7033 ± 0.0081 MPa, respectively. The nanoneedle and the cell have been assembled to measure the local stiffness of the single Saccharomyces cerevisiae cells The local stiffness, Young’s modulus and PZT output voltage of the three different size Saccharomyces cerevisiae have been determined at different environmental conditions. We investigated that, at low temperature the stiffness value is low to adapt to the change in the environmental condition. As a result, Saccharomyces cerevisiae becomes vulnerable to viral and bacterial attacks. Therefore, the proposed technique will serve as a quick and accurate process to diagnose diseases at early stage in a cell for effective treatment. PMID:28025571

  7. Finite Element Analysis of Single Cell Stiffness Measurements Using PZT-Integrated Buckling Nanoneedles.

    PubMed

    Rad, Maryam Alsadat; Tijjani, Auwal Shehu; Ahmad, Mohd Ridzuan; Auwal, Shehu Muhammad

    2016-12-23

    This paper proposes a new technique for real-time single cell stiffness measurement using lead zirconate titanate (PZT)-integrated buckling nanoneedles. The PZT and the buckling part of the nanoneedle have been modelled and validated using the ABAQUS software. The two parts are integrated together to function as a single unit. After calibration, the stiffness, Young's modulus, Poisson's ratio and sensitivity of the PZT-integrated buckling nanoneedle have been determined to be 0.7100 N·m(-1), 123.4700 GPa, 0.3000 and 0.0693 V·m·N(-1), respectively. Three Saccharomyces cerevisiae cells have been modelled and validated based on compression tests. The average global stiffness and Young's modulus of the cells are determined to be 10.8867 ± 0.0094 N·m(-1) and 110.7033 ± 0.0081 MPa, respectively. The nanoneedle and the cell have been assembled to measure the local stiffness of the single Saccharomyces cerevisiae cells The local stiffness, Young's modulus and PZT output voltage of the three different size Saccharomyces cerevisiae have been determined at different environmental conditions. We investigated that, at low temperature the stiffness value is low to adapt to the change in the environmental condition. As a result, Saccharomyces cerevisiae becomes vulnerable to viral and bacterial attacks. Therefore, the proposed technique will serve as a quick and accurate process to diagnose diseases at early stage in a cell for effective treatment.

  8. Characterization and modes of occurrence of elements in feed coal and fly ash; an integrated approach

    USGS Publications Warehouse

    Brownfield, M.E.

    2002-01-01

    Despite certain environmental concerns, coal is likely to remain an important component of the United States energy supply, partly because it is the most abundant domestically available fossil fuel. One of the concerns about coal combustion for electricity production is the potential release of elements from coal and coal combustion products (CCPs) - fly ash - to the environment. This concern prompted the need for accurate, reliable, and comprehensive information on the contents and modes of occurrence of selected elements in power-plant feed coal and fly ash. The U.S. Geological Survey (USGS) is collaborating with several electric utilities to determine the chemical and mineralogical properties of feed coal and fly ash. Our first study analyzed coal and fly ash from a Kentucky power plant, which uses many different bituminous coals from the Appalachian and Illinois Basins. Sulfur content of these feed coals rangedfrom 2.5 to 3.5 percent. The second study analyzed coal and fly ash from an Indiana power plant, which uses subbituminous coal from the Powder River Basin (fig. 1). Sulfur content of this feed coal ranged from 0.23 to 0.47 percent. A summary of important aspects of our approach and results are presented in this report. 

  9. Semi-implicit time-integrators for a scalable spectral element atmospheric model

    NASA Astrophysics Data System (ADS)

    Giraldo, Francis X.

    2005-07-01

    The Naval Research Laboratory's spectral element atmospheric model (NSEAM) for scalable computer architectures is presented. This new dynamical core is based on a high-order spectral element (SE) method in space and uses semi-implicit methods in time based on either the traditional second-order leapfrog (LF2) or second-order backward difference formulas (BDF2). The novelties of NSEAM are: it is geometrically flexible and thereby can accommodate any type of grid; LF2 or BDF2 are used to construct the semi-implicit method; and the horizontal operators are written, discretized, and solved in three-dimensional Cartesian space. The semi-implicit NSEAM is validated using: five baroclinic test cases; direct comparisons to the explicit version of NSEAM which has been extensively tested and the results previously reported in the literature; and comparisons with operational weather prediction and well-established climate models. A comparison with the US Navy's spectral transform global forecast model illustrates that NSEAM is 60% faster on an IBM SP4 using 96 processors for the current operational resolution of T239 L30. However, NSEAM can accommodate many more processors while continuing to scale efficiently even at higher grid resolutions. In fact, we show that at T498 L60, NSEAM scales linearly up to 384 processors.

  10. Three dimensional fabrication of optical waveguiding elements for on-chip integration

    NASA Astrophysics Data System (ADS)

    Parsi Sreenivas, V. V.; Bülters, M.; Schröder, M.; Bergmann, R. B.

    2014-05-01

    We present micro polymer optical waveguide elements fabricated using femtosecond laser and two-photon absorption (TPA) process. The POWs are constructed by tightly focusing a laser beam in SU-8 based resists transparent to the laser wavelength for single-photon absorption. The TPA process enables the patterning of the resist in three dimensions at a resolution of 100-200 nm, which provides a high degree of freedom for POW designs. Using this technology, we provide a novel approach to fabricate Three dimensional Polymer Optical Waveguides (3D-POW) and coupling with single mode fibers in the visible wavelength regions. Our research is also focused on fabricating passive micro optical elements such as splitters, combiners and simple logical gates. For this reason we are aiming to achieve optimum coupling efficiency between the 3D-POW and fibers. The technology also facilitates 3D-POW fabrication independent of the substrate material. We present these fabrication techniques and designs, along with supporting numerical simulations and its transmission properties. With a length of 270 μm and polymer core diameter of 9 μm with air cladding, the waveguides possess a total loss of 12 dB. This value also includes the external in and out mode coupling and in continuously being improved upon by design optimization and simulations. We verify the overall feasibility of the design and coupling mechanisms that can be exploited to execute waveguide based optical functions such as filtering and logical operations.

  11. Identification of a gene encoding the replication initiator protein of the Streptomyces integrating element, pSAM2.

    PubMed

    Hagège, J; Boccard, F; Smokvina, T; Pernodet, J L; Friedmann, A; Guérineau, M

    1994-03-01

    pSAM2 is an 11-kilobase integrating element from Streptomyces ambofaciens which was previously shown to generate single-stranded DNA during replication, indicating that it probably replicates by a rolling-circle replication (RCR) mechanism. Two separate regions are involved in its replication, one of which was shown to contain the plus origin of replication (ds origin). We report here the study of the second region. Its nucleotide sequence was determined and analysed for open reading frames (ORFs). Three putative ORFs were identified: orf183 (183 amino acids (aa)), orf50 (50 aa), and repSA (459 aa). orf183 is not necessary for replication. The function of orf50 is unknown. repSA is essential for pSAM2 replication; it could encode a protein, RepSA, presenting similarities to the replication initiator proteins (Rep) of elements that replicate by an RCR mechanism. A derivative consisting of repSA, the region containing ds origin, a Streptomyces antibiotic resistance marker, and pBR322, could replicate in Streptomyces, further demonstrating that this ORF encodes the major replication protein of pSAM2. repSA might be co-transcribed with the genes involved in integration and excision of pSAM2.

  12. Extended displacement discontinuity boundary integral equation and boundary element method for cracks in thermo-magneto-electro-elastic media

    NASA Astrophysics Data System (ADS)

    Li, Yuan; Dang, HuaYang; Xu, GuangTao; Fan, CuiYing; Zhao, MingHao

    2016-08-01

    The extended displacement discontinuity boundary integral equation (EDDBIE) and boundary element method is developed for the analysis of planar cracks of arbitrary shape in the isotropic plane of three-dimensional (3D) transversely isotropic thermo-magneto-electro-elastic (TMEE) media. The extended displacement discontinuities (EDDs) include conventional displacement discontinuity, electric potential discontinuity, magnetic potential discontinuity, as well as temperature discontinuity across crack faces; correspondingly, the extended stresses represent conventional stress, electric displacement, magnetic induction and heat flux. Employing a Hankel transformation, the fundamental solutions for unit point EDDs in 3D transversely isotropic TMEE media are derived. The EDDBIEs for a planar crack of arbitrary shape in the isotropic plane of a 3D transversely isotropic TMEE medium are then established. Using the boundary integral equation method, the singularities of near-crack border fields are obtained and the extended stress field intensity factors are expressed in terms of the EDDs on crack faces. According to the analogy between the EDDBIEs for an isotropic thermoelastic material and TMEE medium, an analogical solution method for crack problems of a TMEE medium is proposed for coupled multi-field loadings. Employing constant triangular elements, the EDDBIEs are discretized and numerically solved. As an application, the problems of an elliptical crack subjected to combined mechanical-electric-magnetic-thermal loadings are investigated.

  13. Definition, technology readiness, and development cost of the orbit transfer vehicle engine integrated control and health monitoring system elements

    NASA Technical Reports Server (NTRS)

    Cannon, I.; Balcer, S.; Cochran, M.; Klop, J.; Peterson, S.

    1991-01-01

    An Integrated Control and Health Monitoring (ICHM) system was conceived for use on a 20 Klb thrust baseline Orbit Transfer Vehicle (OTV) engine. Considered for space used, the ICHM was defined for reusability requirements for an OTV engine service free life of 20 missions, with 100 starts and a total engine operational time of 4 hours. Functions were derived by flowing down requirements from NASA guidelines, previous OTV engine or ICHM documents, and related contracts. The elements of an ICHM were identified and listed, and these elements were described in sufficient detail to allow estimation of their technology readiness levels. These elements were assessed in terms of technology readiness level, and supporting rationale for these assessments presented. The remaining cost for development of a minimal ICHM system to technology readiness level 6 was estimated. The estimates are within an accuracy range of minus/plus 20 percent. The cost estimates cover what is needed to prepare an ICHM system for use on a focussed testbed for an expander cycle engine, excluding support to the actual test firings.

  14. A Fully Integrated RF-Powered Contact Lens With a Single Element Display.

    PubMed

    Pandey, J; Yu-Te Liao; Lingley, Andrew; Mirjalili, R; Parviz, B; Otis, B

    2010-12-01

    We present progress toward a wirelessly-powered active contact lens comprised of a transparent polymer substrate, loop antenna, power harvesting IC, and micro-LED. The fully integrated radio power harvesting and power management system was fabricated in a 0.13 μm CMOS process with a total die area of 0.2 mm(2). It utilizes a small on-chip capacitor for energy storage to light up a micro-LED pixel. We have demonstrated wireless power transfer at 10 cm distance using the custom IC and on-lens antenna.

  15. DelftShell - integrated modeling environment with elements of GIS, Data Management and OpenMI support

    NASA Astrophysics Data System (ADS)

    Donchyts, G.; Baart, F.; Jagers, B.

    2008-12-01

    Many efforts have been made in the past years promoting solutions aimed at integrating different numerical models with each other as well as at simplifying the way to set them up, entering the data, and running them. Meanwhile the development of many modeling frameworks concentrated on the interoperability of different model engines, several standards were introduced such as ESMF, OMS and OpenMI. In this work we will focus on another aspect of model integration, namely, the design of a higher level integrated modeling system targeting the interaction with the end user via a graphical user interface. In many cases these user interface is only available as commercial software tool that has been built to work only with a specific model; in this case functionality is usually hardcoded and limited to that particular model. On the other hand many generic GIS systems are available that can be used to process data, concentrating mainly on a spatial aspect. We will present an integrated modeling environment that combines elements of the GIS environment with running a modular framework of OpenMI-compliant models. Another important part is related to management of the model data in a unified way as well as providing generic tools to help user visualize and process such a data, such that the system no longer provides a user interface for just one model but for a whole range of similar models. The environment will be presented as a tool available for the general community; it includes a plug-in API that allows for the integration of a custom plug-ins providing either new model engines, modeling frameworks or new types of visualization and data processing tools.

  16. Conjugation in Gram-Positive Bacteria.

    PubMed

    Goessweiner-Mohr, Nikolaus; Arends, Karsten; Keller, Walter; Grohmann, Elisabeth

    2014-08-01

    Conjugative transfer is the most important means of spreading antibiotic resistance and virulence factors among bacteria. The key vehicles of this horizontal gene transfer are a group of mobile genetic elements, termed conjugative plasmids. Conjugative plasmids contain as minimum instrumentation an origin of transfer (oriT), DNA-processing factors (a relaxase and accessory proteins), as well as proteins that constitute the trans-envelope transport channel, the so-called mating pair formation (Mpf) proteins. All these protein factors are encoded by one or more transfer (tra) operons that together form the DNA transport machinery, the Gram-positive type IV secretion system. However, multicellular Gram-positive bacteria belonging to the streptomycetes appear to have evolved another mechanism for conjugative plasmid spread reminiscent of the machinery involved in bacterial cell division and sporulation, which transports double-stranded DNA from donor to recipient cells. Here, we focus on the protein key players involved in the plasmid spread through the two different modes and present a new secondary structure homology-based classification system for type IV secretion protein families. Moreover, we discuss the relevance of conjugative plasmid transfer in the environment and summarize novel techniques to visualize and quantify conjugative transfer in situ.

  17. Autonomous Replication of the Conjugative Transposon Tn916.

    PubMed

    Wright, Laurel D; Grossman, Alan D

    2016-12-15

    Integrative and conjugative elements (ICEs), also known as conjugative transposons, are self-transferable elements that are widely distributed among bacterial phyla and are important drivers of horizontal gene transfer. Many ICEs carry genes that confer antibiotic resistances to their host cells and are involved in the dissemination of these resistance genes. ICEs reside in host chromosomes but under certain conditions can excise to form a plasmid that is typically the substrate for transfer. A few ICEs are known to undergo autonomous replication following activation. However, it is not clear if autonomous replication is a general property of many ICEs. We found that Tn916, the first conjugative transposon identified, replicates autonomously via a rolling-circle mechanism. Replication of Tn916 was dependent on the relaxase encoded by orf20 of Tn916 The origin of transfer of Tn916, oriT(916), also functioned as an origin of replication. Using immunoprecipitation and mass spectrometry, we found that the relaxase (Orf20) and the two putative helicase processivity factors (Orf22 and Orf23) encoded by Tn916 likely interact in a complex and that the Tn916 relaxase contains a previously unidentified conserved helix-turn-helix domain in its N-terminal region that is required for relaxase function and replication. Lastly, we identified a functional single-strand origin of replication (sso) in Tn916 that we predict primes second-strand synthesis during rolling-circle replication. Together these results add to the emerging data that show that several ICEs replicate via a conserved, rolling-circle mechanism.

  18. Manufacturing and characterization of a ceramic microcombustor with integrated oxygen storage and release element

    NASA Astrophysics Data System (ADS)

    Khaji, Z.; Sturesson, P.; Klintberg, L.; Hjort, K.; Thornell, G.

    2015-10-01

    A microscale ceramic high-temperature combustor with a built-in temperature sensor and source of oxygen has been designed, manufactured and characterized. The successful in situ electroplating and oxidation of copper, and the use of copper oxide as the source of oxygen were demonstrated. It was shown that residual stresses from electroplating, copper oxidation and oxide decomposition did not cause much deformation of the substrate but influenced mainly the integrity and adhesion of the metal films. The process had influence on the electrical resistances, however. Calibration of the temperature sensor and correlation with IR thermography up to 1000 °C revealed a nearly linear sensor behavior. Demonstration of combustion in a vacuum chamber proved that no combustion had occurred before release of oxygen from the metal oxide resource.

  19. Multimode interference structures as sensing elements integrated into Mach-Zehnder interferometers in polymer foils

    NASA Astrophysics Data System (ADS)

    Xiao, Yanfen; Langenecker, Alexa; Hofmann, Meike; Sherman, Stanislav; Gleissner, Uwe; Mueller, Claas; Zappe, Hans

    2016-11-01

    Integrated Mach-Zehnder interferometers (MZIs) based on flexible polymer materials have been demonstrated as evanescent field sensors for the detection of refractive indices and molecule concentrations. The used application of a measurement window in classical MZIs is difficult in a roll-to-roll fabrication process. We have previously demonstrated foil-based asymmetric MZIs with different widths in sensing and reference arm which do not need a measurement window. Here we present the use of a multimode interference structure (MMI) inserted into the sensing arm of the interferometer to increase the sensitivity. We consider the expected interference signal from numerical simulations and optimize the system in terms of sensitivity, dimensions and absorption losses. The fabricated MMI-MZI foils are tested experimentally to demonstrate the function of the MMI-MZI system by applying water/glucose solutions with different refractive indices.

  20. Integrating 128-element linear imager for the 1 to 5 microns region

    NASA Technical Reports Server (NTRS)

    Bailey, G. C.

    1982-01-01

    Useful charge integration has been achieved in high quality photovoltaic InSb diodes when combined with a FET multiplexing (MUX) scheme. An experimental detector assembly with a linear array of 128 InSb diodes coupled to a FEX MUX has been developed. The first stage J-FET preamp, pixel reset switch, MUX, and the InSb array are contained in a hybrid microcircuit of compact dimensions. A low noise preamplifier topology which capitalizes on the low video line capacitance inherent with hybrid fabrication techniques is also utilized. Measurements indicate a signal-to-noise ratio of over 1000:1 and response uniformity of + or - 2 percent. Sample images show subtle detail which supports the estimated radiometric sensitivity of 0.01 K.

  1. Space Station Freedom airlock - The integration of IVA and EVA capabilities in an orbital element

    NASA Astrophysics Data System (ADS)

    Moore, Thomas O., Jr.; Matthews, Anthony P.

    1992-07-01

    In order to meet mission goals, the Space Station Freedom (SSF) airlock must maximize crew efficiency while supporting a range of extravehicular activity (EVA) and intravehicular activity (IVA) operations. EVA will be a frequently planned occurrence on SSF. In order to maximize the usefulness of the limited EVA resource, overhead times must be minimized. This paper discusses how the SSF airlock outfitting design responds to both IVA and EVA requirements. An overview of the SSF airlock and the missions it must accomplish are also provided. The focus of this paper is on how the outfitting and man systems designs provide solutions to multiple requirements, explicitly stated as well as derived requirements. The Space Station airlock is evaluated as an integrated system in the functional assessments of the EVA task, and this paper explains how station common hardware and systems are adapted to the unique airlock environment.

  2. Accessibility, continuity and appropriateness: key elements in assessing integration of perinatal services.

    PubMed

    D'Amour, Danielle; Goulet, Lise; Labadie, Jean-François; Bernier, Liette; Pineault, Raynald

    2003-09-01

    A trend toward the reduction in the length of hospital stays has been widely observed. This increasing shift is particularly evident in perinatal care. A stay of less than 48 hours after delivery has been shown to have no negative effects on the health of either the mother or the baby as long as they receive an adequate follow-up. This implies a close integration between hospital and community health services. The present article addresses the following questions: To what extent are postnatal services accessible to mothers and neonates? Are postnatal services in the community in continuity with those of the hospital? Are the services provided by the appropriate source of care? The authors conducted a telephone survey among 1158 mothers in a large urban area in the province of Quebec, Canada. The results were compared to clinical guidelines widely recognised by professionals. The results show serious discrepancies with these guidelines. The authors found a low accessibility to services: less than half of the mothers received a home visit by a nurse. In terms of continuity of care, less than 10% of the mothers received a follow-up telephone call within the recommended time frame and only 18% benefited from a home visit within the recommended period. Finally, despite guidelines to the contrary, hospitals continue to intervene after discharge. This results in a duplication of services for 44.7% of the new-borns. On the other hand, 40.7% are not seen in the recommended period after hospital discharge at all. These results raise concerns about the integration of services between agencies. Following earlier work, the present authors have grouped explanatory factors under four dimensions: the strategic dimension, particularly leadership; the structural dimension, including the size of the network; the technological dimension, with respect to information transmission system; and the cultural dimension, which concerns the collaboration process and the development of

  3. Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes

    USDA-ARS?s Scientific Manuscript database

    Background: Mannheimia haemolytica typically resides in cattle as a commensal member of the upper respiratory tract microbiome. However, some strains can invade their lungs and cause respiratory disease and death, including those with multi-drug resistance. A nucleotide polymorphism typing system ...

  4. Micromechanics-Based Inelastic Finite Element Analysis Accomplished Via Seamless Integration of MAC/GMC

    NASA Technical Reports Server (NTRS)

    Arnold, Steven M.; Trowbridge, D.

    2001-01-01

    A critical issue in the micromechanics-based analysis of composite structures becomes the availability of a computationally efficient homogenization technique: one that is 1) Capable of handling the sophisticated, physically based, viscoelastoplastic constitutive and life models for each constituent; 2) Able to generate accurate displacement and stress fields at both the macro and the micro levels; 3) Compatible with the finite element method. The Generalized Method of Cells (GMC) developed by Paley and Aboudi is one such micromechanical model that has been shown to predict accurately the overall macro behavior of various types of composites given the required constituent properties. Specifically, the method provides "closed-form" expressions for the macroscopic composite response in terms of the properties, size, shape, distribution, and response of the individual constituents or phases that make up the material. Furthermore, expressions relating the internal stress and strain fields in the individual constituents in terms of the macroscopically applied stresses and strains are available through strain or stress concentration matrices. These expressions make possible the investigation of failure processes at the microscopic level at each step of an applied load history.

  5. An integrated finite element simulation of cardiomyocyte function based on triphasic theory

    PubMed Central

    Hatano, Asuka; Okada, Jun-Ichi; Washio, Takumi; Hisada, Toshiaki; Sugiura, Seiryo

    2015-01-01

    In numerical simulations of cardiac excitation-contraction coupling, the intracellular potential distribution and mobility of cytosol and ions have been mostly ignored. Although the intracellular potential gradient is small, during depolarization it can be a significant driving force for ion movement, and is comparable to diffusion in terms of net flux. Furthermore, fluid in the t-tubules is thought to advect ions to facilitate their exchange with the extracellular space. We extend our previous finite element model that was based on triphasic theory to examine the significance of these factors in cardiac physiology. Triphasic theory allows us to study the behavior of solids (proteins), fluids (cytosol) and ions governed by mechanics and electrochemistry in detailed subcellular structures, including myofibrils, mitochondria, the sarcoplasmic reticulum, membranes, and t-tubules. Our simulation results predicted an electrical potential gradient inside the t-tubules at the onset of depolarization, which corresponded to the Na+ channel distribution therein. Ejection and suction of fluid between the t-tubules and the extracellular compartment during isometric contraction were observed. We also examined the influence of t-tubule morphology and mitochondrial location on the electrophysiology and mechanics of the cardiomyocyte. Our results confirm that the t-tubule structure is important for synchrony of Ca2+ release, and suggest that mitochondria in the sub-sarcolemmal region might serve to cancel Ca2+ inflow through surface sarcolemma, thereby maintaining the intracellular Ca2+ environment in equilibrium. PMID:26539124

  6. Boundary element solution of unsteady magnetohydrodynamic duct flow with differential quadrature time integration scheme

    NASA Astrophysics Data System (ADS)

    Bozkaya, C.; Tezer-Sezgin, M.

    2006-06-01

    A numerical scheme which is a combination of the dual reciprocity boundary element method (DRBEM) and the differential quadrature method (DQM), is proposed for the solution of unsteady magnetohydrodynamic (MHD) flow problem in a rectangular duct with insulating walls. The coupled MHD equations in velocity and induced magnetic field are transformed first into the decoupled time-dependent convection-diffusion-type equations. These equations are solved by using DRBEM which treats the time and the space derivatives as nonhomogeneity and then by using DQM for the resulting system of initial value problems. The resulting linear system of equations is overdetermined due to the imposition of both boundary and initial conditions. Employing the least square method to this system the solution is obtained directly at any time level without the need of step-by-step computation with respect to time. Computations have been carried out for moderate values of Hartmann number (M50) at transient and the steady-state levels. As M increases boundary layers are formed for both the velocity and the induced magnetic field and the velocity becomes uniform at the centre of the duct. Also, the higher the value of M is the smaller the value of time for reaching steady-state solution.

  7. Single-Shell Tanks Leak Integrity Elements/ SX Farm Leak Causes and Locations - 12127

    SciTech Connect

    Girardot, Crystal; Harlow, Don; Venetz, Theodore; Washenfelder, Dennis; Johnson, Jeremy

    2012-07-01

    Washington River Protection Solutions, LLC (WRPS) developed an enhanced single-shell tank (SST) integrity project in 2009. An expert panel on SST integrity was created to provide recommendations supporting the development of the project. One primary recommendation was to expand the leak assessment reports (substitute report or LD-1) to include leak causes and locations. The recommendation has been included in the M-045-91F Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement) as one of four targets relating to SST leak integrity. The 241-SX Farm (SX Farm) tanks with leak losses were addressed on an individual tank basis as part of LD-1. Currently, 8 out of 23 SSTs that have been reported to having a liner leak are located in SX Farm. This percentage was the highest compared to other tank farms which is why SX Farm was analyzed first. The SX Farm is comprised of fifteen SSTs built 1953-1954. The tanks are arranged in rows of three tanks each, forming a cascade. Each of the SX Farm tanks has a nominal 1-million-gal storage capacity. Of the fifteen tanks in SX Farm, an assessment reported leak losses for the following tanks: 241-SX-107, 241-SX-108, 241-SX-109, 241-SX- 111, 241-SX-112, 241-SX-113, 241-SX-114 and 241-SX-115. The method used to identify leak location consisted of reviewing in-tank and ex-tank leak detection information. This provided the basic data identifying where and when the first leaks were detected. In-tank leak detection consisted of liquid level measurement that can be augmented with photographs which can provide an indication of the vertical leak location on the sidewall. Ex-tank leak detection for the leaking tanks consisted of soil radiation data from laterals and dry-wells near the tank. The in-tank and ex-tank leak detection can provide an indication of the possible leak location radially around and under the tank. Potential leak causes were determined using in-tank and ex-tank information that is not directly related to

  8. SINGLE-SHELL TANKS LEAK INTEGRITY ELEMENTS/SX FARM LEAK CAUSES AND LOCATIONS - 12127

    SciTech Connect

    VENETZ TJ; WASHENFELDER D; JOHNSON J; GIRARDOT C

    2012-01-25

    Washington River Protection Solutions, LLC (WRPS) developed an enhanced single-shell tank (SST) integrity project in 2009. An expert panel on SST integrity was created to provide recommendations supporting the development of the project. One primary recommendation was to expand the leak assessment reports (substitute report or LD-1) to include leak causes and locations. The recommendation has been included in the M-045-9IF Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement) as one of four targets relating to SST leak integrity. The 241-SX Farm (SX Farm) tanks with leak losses were addressed on an individual tank basis as part of LD-1. Currently, 8 out of 23 SSTs that have been reported to having a liner leak are located in SX Farm. This percentage was the highest compared to other tank farms which is why SX Farm was analyzed first. The SX Farm is comprised of fifteen SSTs built 1953-1954. The tanks are arranged in rows of three tanks each, forming a cascade. Each of the SX Farm tanks has a nominal I-million-gal storage capacity. Of the fifteen tanks in SX Farm, an assessment reported leak losses for the following tanks: 241-SX-107, 241-SX-108, 241-SX-109, 241-SX-111, 241-SX-112, 241-SX-113, 241-SX-114 and 241-SX-115. The method used to identify leak location consisted of reviewing in-tank and ex-tank leak detection information. This provided the basic data identifying where and when the first leaks were detected. In-tank leak detection consisted of liquid level measurement that can be augmented with photographs which can provide an indication of the vertical leak location on the sidewall. Ex-tank leak detection for the leaking tanks consisted of soil radiation data from laterals and drywells near the tank. The in-tank and ex-tank leak detection can provide an indication of the possible leak location radially around and under the tank. Potential leak causes were determined using in-tank and ex-tank information that is not directly related to

  9. Refinements in osteotomy design to improve structural integrity: a finite element analysis study.

    PubMed

    Bujtar, P; Simonovics, János; Váradi, Károly; Sándor, George K B; Pan, Jingzhe; Avery, C M E

    2013-09-01

    Osteotomy cuts are typically made using a saw, and the meeting point acts as a focus for the concentration of stress and failure. We have studied the impact of different designs of osteotomy cut. Cadaver sheep tibias were scanned by computed tomography (CT) and transformed into a computer-aided design (CAD) model. A standard marginal resection defect was created and then modified, and a finite element analysis made. The relative stress concentrations at the intersection of osteotomy cuts were recorded using principal stresses S1, S3, and von Mises stress, von Mises under both 4-point bending and torsion testing. The osteotomy designs studied were: right-angled and bevelled osteotomy end cuts, overcutting, and a stop drill hole. Peak stress values for 4-point bending and torsion were 24-30% greater at the right-angled osteotomy than the bevelled end cut. Overcutting dramatically increased peak stress values caused by bending and torsion by 48% and 71%, respectively. Substantially lower concentrations of stress were noted with a stop hole using both a 90° (bending 38% and torsion 56%), and a tangential (bending 58% and torsion 60%) cut. A bevelled osteotomy has substantially lower concentrations of stress than a right-angled osteotomy. It is important to avoid creating an overcut as this causes an appreciable increase in the concentration of stress, while a stop drill hole substantially reduces the stress. The creation of a stop hole and the use of judicious bevelling techniques are modifications in the design of an osteotomy that are readily applicable to surgical practice. Copyright © 2012 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

  10. Connecting Mechanics and Bone Cell Activities in the Bone Remodeling Process: An Integrated Finite Element Modeling

    PubMed Central

    Hambli, Ridha

    2014-01-01

    Bone adaptation occurs as a response to external loadings and involves bone resorption by osteoclasts followed by the formation of new bone by osteoblasts. It is directly triggered by the transduction phase by osteocytes embedded within the bone matrix. The bone remodeling process is governed by the interactions between osteoblasts and osteoclasts through the expression of several autocrine and paracrine factors that control bone cell populations and their relative rate of differentiation and proliferation. A review of the literature shows that despite the progress in bone remodeling simulation using the finite element (FE) method, there is still a lack of predictive models that explicitly consider the interaction between osteoblasts and osteoclasts combined with the mechanical response of bone. The current study attempts to develop an FE model to describe the bone remodeling process, taking into consideration the activities of osteoclasts and osteoblasts. The mechanical behavior of bone is described by taking into account the bone material fatigue damage accumulation and mineralization. A coupled strain–damage stimulus function is proposed, which controls the level of autocrine and paracrine factors. The cellular behavior is based on Komarova et al.’s (2003) dynamic law, which describes the autocrine and paracrine interactions between osteoblasts and osteoclasts and computes cell population dynamics and changes in bone mass at a discrete site of bone remodeling. Therefore, when an external mechanical stress is applied, bone formation and resorption is governed by cells dynamic rather than adaptive elasticity approaches. The proposed FE model has been implemented in the FE code Abaqus (UMAT routine). An example of human proximal femur is investigated using the model developed. The model was able to predict final human proximal femur adaptation similar to the patterns observed in a human proximal femur. The results obtained reveal complex spatio-temporal bone

  11. Connecting mechanics and bone cell activities in the bone remodeling process: an integrated finite element modeling.

    PubMed

    Hambli, Ridha

    2014-01-01

    Bone adaptation occurs as a response to external loadings and involves bone resorption by osteoclasts followed by the formation of new bone by osteoblasts. It is directly triggered by the transduction phase by osteocytes embedded within the bone matrix. The bone remodeling process is governed by the interactions between osteoblasts and osteoclasts through the expression of several autocrine and paracrine factors that control bone cell populations and their relative rate of differentiation and proliferation. A review of the literature shows that despite the progress in bone remodeling simulation using the finite element (FE) method, there is still a lack of predictive models that explicitly consider the interaction between osteoblasts and osteoclasts combined with the mechanical response of bone. The current study attempts to develop an FE model to describe the bone remodeling process, taking into consideration the activities of osteoclasts and osteoblasts. The mechanical behavior of bone is described by taking into account the bone material fatigue damage accumulation and mineralization. A coupled strain-damage stimulus function is proposed, which controls the level of autocrine and paracrine factors. The cellular behavior is based on Komarova et al.'s (2003) dynamic law, which describes the autocrine and paracrine interactions between osteoblasts and osteoclasts and computes cell population dynamics and changes in bone mass at a discrete site of bone remodeling. Therefore, when an external mechanical stress is applied, bone formation and resorption is governed by cells dynamic rather than adaptive elasticity approaches. The proposed FE model has been implemented in the FE code Abaqus (UMAT routine). An example of human proximal femur is investigated using the model developed. The model was able to predict final human proximal femur adaptation similar to the patterns observed in a human proximal femur. The results obtained reveal complex spatio-temporal bone

  12. Integrity of Lichen Cell Membranes in Relation to Concentration of Airborne Elements

    PubMed

    Garty; Kloog; Cohen

    1998-02-01

    This study dealt with the impact of air pollution on the integrity of cell membranes in the lichen Ramalina duriaei. The lichen was transplanted from a relatively unpolluted site in Israel to more polluted sites, adjacent to a 40-year-old town, for a period of 10 months. The concentrations of K, B, Al, Cr, Fe, Si, Ti, Zn, P, Ba, Cu, Mg, Na, Pb, Ca, Mn, Sr, and S in lichen thalli were compared with injury caused to the cell membranes. The study indicates that electric conductivity reflects adequately cellular injury to lichen thalli transplanted to sites near a motorway, an oil-fueled power plant and a rural community (a kibbutz). The concentrations of S, B, Al, Cr, Fe, Si, Ti, and Zn correlated with injury in cell membranes of R. duriaei retrieved from the biomonitoring sites, whereas the concentration of K in the thalli correlated inversely with the electric conductivity parameter. Leakage of K from lichen thalli as a result of air pollutants is suggested. This K leakage correlates positively with concentrations of S and Cr in transplants of R. duriaei to the Ashdod region.

  13. Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia

    PubMed Central

    Almamun, Md; Levinson, Benjamin T; van Swaay, Annette C; Johnson, Nathan T; McKay, Stephanie D; Arthur, Gerald L; Davis, J Wade; Taylor, Kristen H

    2015-01-01

    Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children under the age of 15. In addition to genetic aberrations, epigenetic modifications such as DNA methylation are altered in cancer and impact gene expression. To identify epigenetic alterations in ALL, genome-wide methylation profiles were generated using the methylated CpG island recovery assay followed by next-generation sequencing. More than 25,000 differentially methylated regions (DMR) were observed in ALL patients with ∼90% present within intronic or intergenic regions. To determine the regulatory potential of the DMR, whole-transcriptome analysis was performed and integrated with methylation data. Aberrant promoter methylation was associated with the altered expression of genes involved in transcriptional regulation, apoptosis, and proliferation. Novel enhancer-like sequences were identified within intronic and intergenic DMR. Aberrant methylation in these regions was associated with the altered expression of neighboring genes involved in cell cycle processes, lymphocyte activation and apoptosis. These genes include potential epi-driver genes, such as SYNE1, PTPRS, PAWR, HDAC9, RGCC, MCOLN2, LYN, TRAF3, FLT1, and MELK, which may provide a selective advantage to leukemic cells. In addition, the differential expression of epigenetic modifier genes, pseudogenes, and non-coding RNAs was also observed accentuating the role of erroneous epigenetic gene regulation in ALL. PMID:26308964

  14. Integrated Utilization of Sewage Sludge and Coal Gangue for Cement Clinker Products: Promoting Tricalcium Silicate Formation and Trace Elements Immobilization

    PubMed Central

    Yang, Zhenzhou; Zhang, Yingyi; Liu, Lili; Seetharaman, Seshadri; Wang, Xidong; Zhang, Zuotai

    2016-01-01

    The present study firstly proposed a method of integrated utilization of sewage sludge (SS) and coal gangue (CG), two waste products, for cement clinker products with the aim of heat recovery and environment protection. The results demonstrated that the incremental amounts of SS and CG addition was favorable for the formation of tricalcium silicate (C3S) during the calcinations, but excess amount of SS addition could cause the impediment effect on C3S formation. Furthermore, it was also observed that the C3S polymorphs showed the transition from rhombohedral to monoclinic structure as SS addition was increased to 15 wt %. During the calcinations, most of trace elements could be immobilized especially Zn and cannot be easily leached out. Given the encouraging results in the present study, the co-process of sewage sludge and coal gangue in the cement kiln can be expected with a higher quality of cement products and minimum pollution to the environment. PMID:28773400

  15. Reliable and efficient a posteriori error estimation for adaptive IGA boundary element methods for weakly-singular integral equations

    PubMed Central

    Feischl, Michael; Gantner, Gregor; Praetorius, Dirk

    2015-01-01

    We consider the Galerkin boundary element method (BEM) for weakly-singular integral equations of the first-kind in 2D. We analyze some residual-type a posteriori error estimator which provides a lower as well as an upper bound for the unknown Galerkin BEM error. The required assumptions are weak and allow for piecewise smooth parametrizations of the boundary, local mesh-refinement, and related standard piecewise polynomials as well as NURBS. In particular, our analysis gives a first contribution to adaptive BEM in the frame of isogeometric analysis (IGABEM), for which we formulate an adaptive algorithm which steers the local mesh-refinement and the multiplicity of the knots. Numerical experiments underline the theoretical findings and show that the proposed adaptive strategy leads to optimal convergence. PMID:26085698

  16. Reliable and efficient a posteriori error estimation for adaptive IGA boundary element methods for weakly-singular integral equations

    NASA Astrophysics Data System (ADS)

    Feischl, Michael; Gantner, Gregor; Praetorius, Dirk

    2015-06-01

    We consider the Galerkin boundary element method (BEM) for weakly-singular integral equations of the first-kind in 2D. We analyze some residual-type a posteriori error estimator which provides a lower as well as an upper bound for the unknown Galerkin BEM error. The required assumptions are weak and allow for piecewise smooth parametrizations of the boundary, local mesh-refinement, and related standard piecewise polynomials as well as NURBS. In particular, our analysis gives a first contribution to adaptive BEM in the frame of isogeometric analysis (IGABEM), for which we formulate an adaptive algorithm which steers the local mesh-refinement and the multiplicity of the knots. Numerical experiments underline the theoretical findings and show that the proposed adaptive strategy leads to optimal convergence.

  17. The Athlete Biological Passport: an integral element of innovative strategies in antidoping.

    PubMed

    Vernec, Alan R

    2014-05-01

    Concern for the health of athletes and integrity of sport resulted in the banning of specific substances although many years passed before analytical testing took place. Soon doping control programmes became synonymous with urine tests and adverse analytical findings. This system has its limits due to the detection window of prohibited substances, the timing of sample collections and the sophistication of some doping regimens. There have been a number of situations where these limits were demonstrated by athletes who proclaimed innocence based on passing their analytical tests only to later confess to doping. New strategies were called for to protect clean athletes. In the current World Anti-Doping Code, there are eight means to an Anti-Doping Rule Violation (ADRV). Article 2.2 states that the use of a prohibited substance may be established by any reliable means including witness statements, documentary evidence or evaluations of longitudinal profiling. In 2006, the World Anti-Doping Agency (WADA) with the support of some International Federations (IFs) gathered a group of experts to develop a harmonised programme on longitudinal profiling, or serial analysis of indirect biomarkers of doping, that was both scientifically and legally robust. This culminated in the WADA Athlete Biological Passport (ABP) Operating Guidelines and Technical Documents, published in 2009. The ABP is a paradigm that infers the use of prohibited substance (or method) by the monitoring of discriminant biomarkers over time. The haematological module detects blood manipulation by the use of erythropoietic stimulating agents or via blood transfusions. The steroidal module aims to identify endogenous anabolic androgenic steroids when administered exogenously and other indirect steroid doping substances or methods. Other ABP modules (endocrine, 'omics') are being developed. The term passport, first coined in 2000, is now defined in the ABP Guidelines as the longitudinal profile and all other

  18. Monolithic integration of elliptic-symmetry diffractive optical element on silicon-based 45 degrees micro-reflector.

    PubMed

    Lan, Hsiao-Chin; Hsiao, Hsu-Liang; Chang, Chia-Chi; Hsu, Chih-Hung; Wang, Chih-Ming; Wu, Mount-Learn

    2009-11-09

    A monolithically integrated micro-optical element consisting of a diffractive optical element (DOE) and a silicon-based 45 degrees micro-reflector is experimentally demonstrated to facilitate the optical alignment of non-coplanar fiber-to-fiber coupling. The slanted 45 degrees reflector with a depth of 216 microm is fabricated on a (100) silicon wafer by anisotropic wet etching. The DOE with a diameter of 174.2 microm and a focal length of 150 microm is formed by means of dry etching. Such a compact device is suitable for the optical micro-system to deflect the incident light by 90 degrees and to focus it on the image plane simultaneously. The measured light pattern with a spot size of 15 microm has a good agreement with the simulated result of the elliptic-symmetry DOE with an off-axis design for eliminating the strongly astigmatic aberration. The coupling efficiency is enhanced over 10-folds of the case without a DOE on the 45 degrees micro-reflector. This device would facilitate the optical alignment of non-coplanar light coupling and further miniaturize the volume of microsystem.

  19. Creep Life of Ceramic Components Using a Finite-Element-Based Integrated Design Program (CARES/CREEP)

    NASA Technical Reports Server (NTRS)

    Gyekenyesi, J. P.; Powers, L. M.; Jadaan, O. M.

    1998-01-01

    The desirable properties of ceramics at high temperatures have generated interest in their use for structural applications such as in advanced turbine systems. Design lives for such systems can exceed 10,000 hours. The long life requirement necessitates subjecting the components to relatively low stresses. The combination of high temperatures and low stresses typically places failure for monolithic ceramics in the creep regime. The objective of this paper is to present a design methodology for predicting the lifetimes of structural components subjected to creep rupture conditions. This methodology utilized commercially available finite element packages and takes into account the time-varying creep strain distributions (stress relaxation). The creep life of a component is discretized into short time steps, during which the stress and strain distributions are assumed constant. The damage is calculated for each time step based on a modified Monkman-Grant creep rupture criterion. Failure is assumed to occur when the normalized accumulated damage at any point in the component is greater than or equal to unity. The corresponding time will be the creep rupture life for that component. Examples are chosen to demonstrate the CARES/CREEP (Ceramics Analysis and Reliability Evaluation of Structures/CREEP) integrated design programs, which is written for the ANSYS finite element package. Depending on the component size and loading conditions, it was found that in real structures one of two competing failure modes (creep or slow crack growth) will dominate. Applications to benechmark problems and engine components are included.

  20. Creep Life of Ceramic Components Using a Finite-Element-Based Integrated Design Program (CARES/CREEP)

    NASA Technical Reports Server (NTRS)

    Powers, L. M.; Jadaan, O. M.; Gyekenyesi, J. P.

    1998-01-01

    The desirable properties of ceramics at high temperatures have generated interest in their use for structural application such as in advanced turbine engine systems. Design lives for such systems can exceed 10,000 hours. The long life requirement necessitates subjecting the components to relatively low stresses. The combination of high temperatures and low stresses typically places failure for monolithic ceramics in the creep regime. The objective of this paper is to present a design methodology for predicting the lifetimes of structural components subjected to creep rupture conditions. This methodology utilizes commercially available finite element packages and takes into account the time-varying creep strain distributions (stress relaxation). The creep life, of a component is discretized into short time steps, during which the stress and strain distributions are assumed constant. The damage is calculated for each time step based on a modified Monkman-Grant creep rupture criterion. Failure is assumed to occur when the normalized accumulated damage at any point in the component is greater than or equal to unity. The corresponding time will be the creep rupture life for that component. Examples are chosen to demonstrate the Ceramics Analysis and Reliability Evaluation of Structures/CREEP (CARES/CREEP) integrated design program, which is written for the ANSYS finite element package. Depending on the component size and loading conditions, it was found that in real structures one of two competing failure modes (creep or slow crack growth) will dominate. Applications to benchmark problems and engine components are included.

  1. Creep Life of Ceramic Components Using a Finite-Element-Based Integrated Design Program (CARES/CREEP)

    NASA Technical Reports Server (NTRS)

    Gyekenyesi, J. P.; Powers, L. M.; Jadaan, O. M.

    1998-01-01

    The desirable properties of ceramics at high temperatures have generated interest in their use for structural applications such as in advanced turbine systems. Design lives for such systems can exceed 10,000 hours. The long life requirement necessitates subjecting the components to relatively low stresses. The combination of high temperatures and low stresses typically places failure for monolithic ceramics in the creep regime. The objective of this paper is to present a design methodology for predicting the lifetimes of structural components subjected to creep rupture conditions. This methodology utilized commercially available finite element packages and takes into account the time-varying creep strain distributions (stress relaxation). The creep life of a component is discretized into short time steps, during which the stress and strain distributions are assumed constant. The damage is calculated for each time step based on a modified Monkman-Grant creep rupture criterion. Failure is assumed to occur when the normalized accumulated damage at any point in the component is greater than or equal to unity. The corresponding time will be the creep rupture life for that component. Examples are chosen to demonstrate the CARES/CREEP (Ceramics Analysis and Reliability Evaluation of Structures/CREEP) integrated design programs, which is written for the ANSYS finite element package. Depending on the component size and loading conditions, it was found that in real structures one of two competing failure modes (creep or slow crack growth) will dominate. Applications to benechmark problems and engine components are included.

  2. Creep Life of Ceramic Components Using a Finite-Element-Based Integrated Design Program (CARES/CREEP)

    NASA Technical Reports Server (NTRS)

    Powers, L. M.; Jadaan, O. M.; Gyekenyesi, J. P.

    1998-01-01

    The desirable properties of ceramics at high temperatures have generated interest in their use for structural application such as in advanced turbine engine systems. Design lives for such systems can exceed 10,000 hours. The long life requirement necessitates subjecting the components to relatively low stresses. The combination of high temperatures and low stresses typically places failure for monolithic ceramics in the creep regime. The objective of this paper is to present a design methodology for predicting the lifetimes of structural components subjected to creep rupture conditions. This methodology utilizes commercially available finite element packages and takes into account the time-varying creep strain distributions (stress relaxation). The creep life, of a component is discretized into short time steps, during which the stress and strain distributions are assumed constant. The damage is calculated for each time step based on a modified Monkman-Grant creep rupture criterion. Failure is assumed to occur when the normalized accumulated damage at any point in the component is greater than or equal to unity. The corresponding time will be the creep rupture life for that component. Examples are chosen to demonstrate the Ceramics Analysis and Reliability Evaluation of Structures/CREEP (CARES/CREEP) integrated design program, which is written for the ANSYS finite element package. Depending on the component size and loading conditions, it was found that in real structures one of two competing failure modes (creep or slow crack growth) will dominate. Applications to benchmark problems and engine components are included.

  3. Diagnosis System for Hepatocellular Carcinoma Based on Fractal Dimension of Morphometric Elements Integrated in an Artificial Neural Network

    PubMed Central

    Gheonea, Dan Ionuț; Streba, Costin Teodor; Vere, Cristin Constantin; Șerbănescu, Mircea; Pirici, Daniel; Comănescu, Maria; Streba, Letiția Adela Maria; Ciurea, Marius Eugen; Mogoantă, Stelian; Rogoveanu, Ion

    2014-01-01

    Background and Aims. Hepatocellular carcinoma (HCC) remains a leading cause of death by cancer worldwide. Computerized diagnosis systems relying on novel imaging markers gained significant importance in recent years. Our aim was to integrate a novel morphometric measurement—the fractal dimension (FD)—into an artificial neural network (ANN) designed to diagnose HCC. Material and Methods. The study included 21 HCC and 28 liver metastases (LM) patients scheduled for surgery. We performed hematoxylin staining for cell nuclei and CD31/34 immunostaining for vascular elements. We captured digital images and used an in-house application to segment elements of interest; FDs were calculated and fed to an ANN which classified them as malignant or benign, further identifying HCC and LM cases. Results. User intervention corrected segmentation errors and fractal dimensions were calculated. ANNs correctly classified 947/1050 HCC images (90.2%), 1021/1050 normal tissue images (97.23%), 1215/1400 LM (86.78%), and 1372/1400 normal tissues (98%). We obtained excellent interobserver agreement between human operators and the system. Conclusion. We successfully implemented FD as a morphometric marker in a decision system, an ensemble of ANNs designed to differentiate histological images of normal parenchyma from malignancy and classify HCCs and LMs. PMID:25025042

  4. Potential and limitations of finite element modelling in assessing structural integrity of coralline algae under future global change

    NASA Astrophysics Data System (ADS)

    Melbourne, L. A.; Griffin, J.; Schmidt, D. N.; Rayfield, E. J.

    2015-02-01

    Coralline algae are important habitat formers found on all rocky shores. While the impact of future ocean acidification on the physiological performance of the species has been well studied, little research has focussed on potential changes in structural integrity in response to climate change. A previous study using 2-D Finite Element Analysis (FEA), suggested increased vulnerability to fracture (by wave action or boring) in algae grown under high CO2 conditions. To assess how realistically 2-D simplified models represent structural performance, a series of increasingly biologically accurate 3-D FE-models that represent coralline algal growth were developed. Simplified geometric 3-D models of the genus Lithothamnion were compared to models created from computed tomography (CT) scan data of the same genus. The biologically accurate model and the simplified geometric model representing individual cells had similar average stresses and stress distributions, emphasizing the importance of the cell walls in dissipating the stress throughout the structure. In contrast models without the accurate representation of the cell geometry resulted in larger stress and strain results. Our more complex 3-D model reiterated the potential of climate change to diminish the structural integrity of the organism. This suggests that under future environmental conditions the weakening of the coralline algal skeleton along with increased external pressures (wave and bioerosion) may negatively influence the ability for coralline algae to maintain a habitat able to sustain high levels of biodiversity.

  5. Potential and limitations of finite element modelling in assessing structural integrity of coralline algae under future global change

    NASA Astrophysics Data System (ADS)

    Melbourne, L. A.; Griffin, J.; Schmidt, D. N.; Rayfield, E. J.

    2015-10-01

    Coralline algae are important habitat formers found on all rocky shores. While the impact of future ocean acidification on the physiological performance of the species has been well studied, little research has focused on potential changes in structural integrity in response to climate change. A previous study using 2-D Finite Element Analysis (FEA) suggested increased vulnerability to fracture (by wave action or boring) in algae grown under high CO2 conditions. To assess how realistically 2-D simplified models represent structural performance, a series of increasingly biologically accurate 3-D FE models that represent different aspects of coralline algal growth were developed. Simplified geometric 3-D models of the genus Lithothamnion were compared to models created from computed tomography (CT) scan data of the same genus. The biologically accurate model and the simplified geometric model representing individual cells had similar average stresses and stress distributions, emphasising the importance of the cell walls in dissipating the stress throughout the structure. In contrast models without the accurate representation of the cell geometry resulted in larger stress and strain results. Our more complex 3-D model reiterated the potential of climate change to diminish the structural integrity of the organism. This suggests that under future environmental conditions the weakening of the coralline algal skeleton along with increased external pressures (wave and bioerosion) may negatively influence the ability for coralline algae to maintain a habitat able to sustain high levels of biodiversity.

  6. Characterization of pra, a gene for replication control in pSAM2, the integrating element of Streptomyces ambofaciens.

    PubMed

    Sezonov, G; Hagège, J; Pernodet, J L; Friedmann, A; Guérineau, M

    1995-08-01

    pSAM2 is a genetic element found integrated in Streptomyces ambofaciens (B2) and additionally in a replicating form in two mutants B3 and B4. The presence of the pSAM2 replicating form in these mutants was the result of mutations located on pSAM2 in the pra locus, named pra3 and pra4, respectively. The pra gene is not directly involved in replication, but its inactivation led to the disappearance of the pSAM2 free form; therefore, it was considered as a replication regulator. The pra3 and pra4 mutations were located in the pra promoter and were shown to be point substitutions that increase the promoter strength. The replication regulator role of pra was demonstrated by the fact that its constitutive expression in cells harbouring pSAM2B2, which is normally only integrated, led to the appearance of the pSAM2 replicating form. Northern analysis showed that the pra gene transcript can be detected only for the replicating mutants B3 and B4 and that the three adjacent genes korSA, pra and traSA were transcribed separately. As replication of pSAM2 is not needed for its maintenance but is an indispensable stage of its transfer, the pra gene, described formally as an activator of pSAM2 replication, is patently involved in pSAM2 transfer.

  7. Finite element modeling simulation-assisted design of integrated microfluidic chips for heavy metal ion stripping analysis

    NASA Astrophysics Data System (ADS)

    Hong, Ying; Zou, Jianhua; Ge, Gang; Xiao, Wanyue; Gao, Ling; Shao, Jinjun; Dong, Xiaochen

    2017-10-01

    In this article, a transparent integrated microfluidic device composed of a 3D-printed thin-layer flow cell (3D-PTLFC) and an S-shaped screen-printed electrode (SPE) has been designed and fabricated for heavy metal ion stripping analysis. A finite element modeling (FEM) simulation is employed to optimize the shape of the electrode, the direction of the inlet pipeline, the thin-layer channel height and the sample flow rate to enhance the electron-enrichment efficiency for stripping analysis. The results demonstrate that the S-shaped SPE configuration matches the channel in 3D-PTLFC perfectly for the anodic stripping behavior of the heavy metal ions. Under optimized conditions, a wide linear range of 1–80 µg l‑1 is achieved for Pb2+ detection with a limit of 0.3 µg l‑1 for the microfluidic device. Thus, the obtained integrated microfluidic device proves to be a promising approach for heavy metal ions stripping analysis with low cost and high performance.

  8. Elemental Education.

    ERIC Educational Resources Information Center

    Daniel, Esther Gnanamalar Sarojini; Saat, Rohaida Mohd.

    2001-01-01

    Introduces a learning module integrating three disciplines--physics, chemistry, and biology--and based on four elements: carbon, oxygen, hydrogen, and silicon. Includes atomic model and silicon-based life activities. (YDS)

  9. Elemental Education.

    ERIC Educational Resources Information Center

    Daniel, Esther Gnanamalar Sarojini; Saat, Rohaida Mohd.

    2001-01-01

    Introduces a learning module integrating three disciplines--physics, chemistry, and biology--and based on four elements: carbon, oxygen, hydrogen, and silicon. Includes atomic model and silicon-based life activities. (YDS)

  10. Conjugate Gaze Palsies

    MedlinePlus

    ... version Home Brain, Spinal Cord, and Nerve Disorders Cranial Nerve Disorders Conjugate Gaze Palsies Horizontal gaze palsy Vertical ... Version. DOCTORS: Click here for the Professional Version Cranial Nerve Disorders Overview of the Cranial Nerves Internuclear Ophthalmoplegia ...

  11. Conjugal amyotrophic lateral sclerosis

    PubMed Central

    Dewitt, John D.; Kwon, Julia; Burton, Rebecca

    2012-01-01

    Amyotrophic lateral sclerosis (ALS) is a disease characterized by progressive degeneration of motor neurons in the motor cortex, brainstem, and spinal cord. The incidence of sporadic ALS is 1.5 to 2.7 in 100,000, and the prevalence is 5.2 to 6.0 in 100,000. Conjugal ALS is even rarer than sporadic ALS. We report a case of conjugal ALS encountered in our outpatient neurology clinic. PMID:22275781

  12. Conjugate field approaches for active array compensation

    NASA Technical Reports Server (NTRS)

    Acosta, R. J.

    1989-01-01

    Two approaches for calculating the compensating feed array complex excitations are namely, the indirect conjugate field matching (ICFM) and the direct conjugate field matching (DCFM) approach. In the ICFM approach the compensating feed array excitations are determined by considering the transmitting mode and the reciprocity principle. The DCF, in contrast calculates the array excitations by integrating directly the induced surface currents on the reflector under a receiving mode. DCFM allows the reflector to be illuminated by an incident plane wave with a tapered amplitude. The level of taper can effectively control the sidelobe level of the compensated antenna pattern. Both approaches are examined briefly.

  13. Calculation for path-domain independent J integral with elasto-viscoplastic consistent tangent operator concept-based boundary element methods

    NASA Astrophysics Data System (ADS)

    Yong, Liu; Qichao, Hong; Lihua, Liang

    1999-05-01

    This paper presents an elasto-viscoplastic consistent tangent operator (CTO) based boundary element formulation, and application for calculation of path-domain independent J integrals (extension of the classical J integrals) in nonlinear crack analysis. When viscoplastic deformation happens, the effective stresses around the crack tip in the nonlinear region is allowed to exceed the loading surface, and the pure plastic theory is not suitable for this situation. The concept of consistency employed in the solution of increment viscoplastic problem, plays a crucial role in preserving the quadratic rate asymptotic convergence of iteractive schemes based on Newton's method. Therefore, this paper investigates the viscoplastic crack problem, and presents an implicit viscoplastic algorithm using the CTO concept in a boundary element framework for path-domain independent J integrals. Applications are presented with two numerical examples for viscoplastic crack problems and J integrals.

  14. The sources and time-integrated evolution of diamond-forming fluids - Trace elements and isotopic evidence

    NASA Astrophysics Data System (ADS)

    Klein-BenDavid, Ofra; Pearson, D. Graham; Nowell, Geoff M.; Ottley, Chris; McNeill, John C. R.; Logvinova, Alla; Sobolev, Nikolay V.

    2014-01-01

    Sub-micrometer inclusions in fibrous diamond growth zones carry high-density fluids (HDF) from which the host diamonds have precipitated. The chemistry of these fluids is our best opportunity of characterizing the diamond-forming environment. The major and trace element patterns of diamond-forming fluids vary widely. Such elemental signatures can be easily modified by a variety of mantle processes whereas radiogenic isotopes give a clear fingerprint of the time-integrated evolution of the fluid source region. Thus, the combination of elemental and isotope data is a powerful tool in constraining the origin of fluids from which diamonds precipitate. Here we present combined trace element composition (34 diamonds) and Sr isotopic data (23 diamonds) for fluid-rich diamonds from six worldwide locations. The Nd and Pb isotopic composition of two of the diamonds were also obtained. Several of the samples were analyzed in at least 2 locations to investigate variations in the fluid during diamond growth. The data was acquired using an off-line laser sampling technique followed by solution ICPMS and TIMS analysis. The Sr isotopic compositions of diamond fluids from the different suites range between convecting mantle values for Udachnaya (87Sr/86Sr363 = 0.70300 ± 16 to 0.70361 ± 4), to highly enriched values, up to 87Sr/86Sr = 0.72330 ± 3, for a diamond from Congo. No isochronous relationships were observed in any of the suites. The lowest Nd isotopic composition recorded so far in a diamond is from Congo (εNd71 = -40.4), which also contains the most radiogenic Sr isotopic composition. In contrast, a less enriched but still rather unradiogenic Nd isotope composition (εNd540 = -11) was obtained for a diamond from Snap Lake, which has moderately radiogenic Sr isotopic enrichment (87Sr/86Sr540 = 0.70821 ± 1). The Pb isotopic system measured in one diamond indicates a complex evolution for the fluid source, with extreme 207Pb/204Pb ratio (15.810 ± 3) and moderate

  15. Diverse CRISPR-Cas responses and dramatic cellular DNA changes and cell death in pKEF9-conjugated Sulfolobus species.

    PubMed

    Liu, Guannan; She, Qunxin; Garrett, Roger A

    2016-05-19

    The Sulfolobales host a unique family of crenarchaeal conjugative plasmids some of which undergo complex rearrangements intracellularly. Here we examined the conjugation cycle of pKEF9 in the recipient strain Sulfolobus islandicus REY15A. The plasmid conjugated and replicated rapidly generating high average copy numbers which led to strong growth retardation that was coincident with activation of CRISPR-Cas adaptation. Simultaneously, intracellular DNA was extensively degraded and this also occurred in a conjugated Δcas6 mutant lacking a CRISPR-Cas immune response. Furthermore, the integrated forms of pKEF9 in the donor Sulfolobus solfataricus P1 and recipient host were specifically corrupted by transposable orfB elements, indicative of a dual mechanism for inactivating free and integrated forms of the plasmid. In addition, the CRISPR locus of pKEF9 was progressively deleted when conjugated into the recipient strain. Factors influencing activation of CRISPR-Cas adaptation in the recipient strain are considered, including the first evidence for a possible priming effect in Sulfolobus The 3-Mbp genome sequence of the donor P1 strain is presented. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Diverse CRISPR-Cas responses and dramatic cellular DNA changes and cell death in pKEF9-conjugated Sulfolobus species

    PubMed Central

    Liu, Guannan; She, Qunxin; Garrett, Roger A.

    2016-01-01

    The Sulfolobales host a unique family of crenarchaeal conjugative plasmids some of which undergo complex rearrangements intracellularly. Here we examined the conjugation cycle of pKEF9 in the recipient strain Sulfolobus islandicus REY15A. The plasmid conjugated and replicated rapidly generating high average copy numbers which led to strong growth retardation that was coincident with activation of CRISPR-Cas adaptation. Simultaneously, intracellular DNA was extensively degraded and this also occurred in a conjugated Δcas6 mutant lacking a CRISPR-Cas immune response. Furthermore, the integrated forms of pKEF9 in the donor Sulfolobus solfataricus P1 and recipient host were specifically corrupted by transposable orfB elements, indicative of a dual mechanism for inactivating free and integrated forms of the plasmid. In addition, the CRISPR locus of pKEF9 was progressively deleted when conjugated into the recipient strain. Factors influencing activation of CRISPR-Cas adaptation in the recipient strain are considered, including the first evidence for a possible priming effect in Sulfolobus. The 3-Mbp genome sequence of the donor P1 strain is presented. PMID:27098036

  17. Three-dimensional integral imaging displays using a quick-response encoded elemental image array: an overview

    NASA Astrophysics Data System (ADS)

    Markman, A.; Javidi, B.

    2016-06-01

    Quick-response (QR) codes are barcodes that can store information such as numeric data and hyperlinks. The QR code can be scanned using a QR code reader, such as those built into smartphone devices, revealing the information stored in the code. Moreover, the QR code is robust to noise, rotation, and illumination when scanning due to error correction built in the QR code design. Integral imaging is an imaging technique used to generate a three-dimensional (3D) scene by combining the information from two-dimensional (2D) elemental images (EIs) each with a different perspective of a scene. Transferring these 2D images in a secure manner can be difficult. In this work, we overview two methods to store and encrypt EIs in multiple QR codes. The first method uses run-length encoding with Huffman coding and the double-random-phase encryption (DRPE) to compress and encrypt an EI. This information is then stored in a QR code. An alternative compression scheme is to perform photon-counting on the EI prior to compression. Photon-counting is a non-linear transformation of data that creates redundant information thus improving image compression. The compressed data is encrypted using the DRPE. Once information is stored in the QR codes, it is scanned using a smartphone device. The information scanned is decompressed and decrypted and an EI is recovered. Once all EIs have been recovered, a 3D optical reconstruction is generated.

  18. Characterization of the attP site of the integrative element pSAM2 from Streptomyces ambofaciens.

    PubMed

    Raynal, Alain; Friedmann, Annick; Tuphile, Karine; Guerineau, Michel; Pernodet, Jean-Luc

    2002-01-01

    pSAM2 is integrated into the Streptomyces ambofaciens chromosome through site-specific recombination between the element (attP) and the chromosomal (attB) site. The 43 kDa integrase protein encoded by pSAM2 catalyses this recombination event. Tools have been developed to study site-specific recombination in Escherichia coli. In vivo studies showed that a 360 bp fragment of attP is required for efficient site-specific recombination and that int can be provided in trans. pSAM2 integrase was purified and overexpressed in E. coli and Int binding at the attP site was studied. DNaseI footprinting revealed two sites that bind integrase strongly and appear to be symmetrical with regard to the core site. These two P1/P2 arm-type sites both contain a 17 bp motif that is identical except at one position, GTCACGCAG(A/T)TAGACAC. P1 and P2 are essential for site-specific recombination.

  19. Yeast cytochrome c integrated with electronic elements: a nanoscopic and spectroscopic study down to single-molecule level

    NASA Astrophysics Data System (ADS)

    Delfino, I.; Bonanni, B.; Andolfi, L.; Baldacchini, C.; Bizzarri, A. R.; Cannistraro, S.

    2007-06-01

    Various aspects of redox protein integration with nano-electronic elements are addressed by a multi-technique investigation of different yeast cytochrome c (YCC)-based hybrid systems. Three different immobilization strategies on gold via organic linkers are explored, involving either covalent bonding or electrostatic interaction. Specifically, Au surfaces are chemically modified by self-assembled monolayers (SAMs) exposing thiol-reactive groups, or by acid-oxidized single-wall carbon nanotubes (SWNTs). Atomic force microscopy and scanning tunnelling microscopy are employed to characterize the morphology and the electronic properties of single YCC molecules adsorbed on the modified gold surfaces. In each hybrid system, the protein molecules are stably assembled, in a native configuration. A standing-up arrangement of YCC on SAMs is suggested, together with an enhancement of the molecular conduction, as compared to YCC directly assembled on gold. The electrostatic interaction with functionalized SWNTs allows several YCC adsorption geometries, with a preferential high-spin haem configuration, as outlined by Raman spectroscopy. Moreover, the conduction properties of YCC, explored in different YCC nanojunctions by conductive atomic force microscopy, indicate the effectiveness of electrical conduction through the molecule and its dependence on the electrode material. The joint employment of several techniques confirms the key role of a well-designed immobilization strategy, for optimizing biorecognition capabilities and electrical coupling with conductive substrates at the single-molecule level, as a starting point for advanced applications in nano-biotechnology.

  20. Designing the Ares I Crew Launch Vehicle Upper Stage Element and Integrating the Stack at NASA's Marshall Space Flight Center

    NASA Technical Reports Server (NTRS)

    Lyles, Garry; Otte, Neil E.

    2008-01-01

    transportation system for missions to the International Space Station in the next decade and to explore the Moon and establish an outpost around the 2020 timeframe.4 Based on this extensive study, NASA selected the Ares I crew launch vehicle configuration and the heavy-lift Ares V cargo launch vehicle (fig 1). This paper will give an overview of NASA's approach to integrating the Ares I vehicle stack using capabilities and assets that are resident in Marshall's Engineering Directorate, working in partnership with other NASA Centers and the U.S. aerospace industry. It also will provide top-level details on the progress of the in-house design of the Ares I vehicle's upper stage element.

  1. Importance of the structural integrity of a carbon conjugated mediator for photocatalytic hydrogen generation from water over a CdS-carbon nanotube-MoS2 composite.

    PubMed

    Meng-Jung Li, Molly; Mills, Poppy; Fairclough, Simon M; Robertson, Alex; Peng, Yung-Kang; Warner, Jamie; Nie, Chunyang; Flahaut, Emmanuel; Edman Tsang, Shik Chi

    2016-11-15

    Incorporation of CdS quantum dots is shown to significantly promote photocatalytic hydrogen production from water over single-layer MoS2 in a remote manner via their dispersions on a carbon nanotube as a nanocomposite: the hydrogen evolution rate is found to be critically dependent on the content and structural integrity of the carbon nanotube such that the double-walled carbon nanotube shows superior H2 production to a single-walled carbon nanotube because the inner carbon tubules survive from the structural damage during functionalization.

  2. Feasibility study of an Integrated Program for Aerospace vehicle Design (IPAD). Volume 5: Catalog of IPAD technical program elements

    NASA Technical Reports Server (NTRS)

    Gillette, W. B. (Editor); Southall, J. W. (Editor)

    1973-01-01

    The catalog is presented of technical program elements which are required to support the design activities for a subsonic and supersonic commercial transport. Information for each element consists of usage and storage information, ownership, status and an abstract describing the purpose of the element.

  3. M-step preconditioned conjugate gradient methods

    NASA Technical Reports Server (NTRS)

    Adams, L.

    1983-01-01

    Preconditioned conjugate gradient methods for solving sparse symmetric and positive finite systems of linear equations are described. Necessary and sufficient conditions are given for when these preconditioners can be used and an analysis of their effectiveness is given. Efficient computer implementations of these methods are discussed and results on the CYBER 203 and the Finite Element Machine under construction at NASA Langley Research Center are included.

  4. Polyamine conjugates of stigmasterol.

    PubMed

    Vida, Norbert; Svobodová, Hana; Rárová, Lucie; Drašar, Pavel; Saman, David; Cvačka, Josef; Wimmer, Zdeněk

    2012-10-01

    Three new polyamine conjugates with stigmasterol [(3β,22E)-stigmasta-5,22-dien-3-ol] were synthesized and subjected to basic antimicrobial and cytotoxic tests. The conjugate derived from spermine, (3β,22E)-stigmasta-5,22-dien-3-yl 4(12-amino-4,9-diaza-dodecylamino)-4-oxobutanoate (5c), displayed considerable antimicrobial activity on Staphylococcus aureus at low concentration (50 μg mL(-1)). The cytotoxic activity was tested on cells of human T-lymfoblastic leukemia (IC(50)=35.8 ± 10.3 μM (5c) and IC(50)=35.9 ± 5.7 μM (5b)) and normal human fibroblasts (IC(50)=38.0 ± 2.8 μM (5c) and IC(50)=45.5 ± 1.9 μM (5b)). Conjugate 5a displayed no activity in both tests.

  5. An updated view of plasmid conjugation and mobilization in Staphylococcus

    PubMed Central

    Ramsay, Joshua P.; Kwong, Stephen M.; Murphy, Riley J. T.; Yui Eto, Karina; Price, Karina J.; Nguyen, Quang T.; O'Brien, Frances G.; Grubb, Warren B.; Coombs, Geoffrey W.; Firth, Neville

    2016-01-01

    ABSTRACT The horizontal gene transfer facilitated by mobile genetic elements impacts almost all areas of bacterial evolution, including the accretion and dissemination of antimicrobial-resistance genes in the human and animal pathogen Staphylococcus aureus. Genome surveys of staphylococcal plasmids have revealed an unexpected paucity of conjugation and mobilization loci, perhaps suggesting that conjugation plays only a minor role in the evolution of this genus. In this letter we present the DNA sequences of historically documented staphylococcal conjugative plasmids and highlight that at least 3 distinct and widely distributed families of conjugative plasmids currently contribute to the dissemination of antimicrobial resistance in Staphylococcus. We also review the recently documented “relaxase-in trans” mechanism of conjugative mobilization facilitated by conjugative plasmids pWBG749 and pSK41, and discuss how this may facilitate the horizontal transmission of around 90% of plasmids that were previously considered non-mobilizable. Finally, we enumerate unique sequenced S. aureus plasmids with a potential mechanism of mobilization and predict that at least 80% of all non-conjugative S. aureus plasmids are mobilizable by at least one mechanism. We suggest that a greater research focus on the molecular biology of conjugation is essential if we are to recognize gene-transfer mechanisms from our increasingly in silico analyses. PMID:27583185

  6. Iii-V Compound Semiconductor Integrated Charge Storage Structures for Dynamic and Non-Volatile Memory Elements

    NASA Astrophysics Data System (ADS)

    Hetherington, Dale Laird

    This thesis presents an investigation into a novel group of GaAs charge storage devices. These devices, which are an integration of bipolar and junction field effect transistor structures were conceived, designed, fabricated, and tested within this study. The purpose was to analyse new types of charge storage devices, which are suitable for fabrication and lead to the development of dynamic and nonvolatile memories in III-V compound semiconductors. Currently, III-V semiconductor storage devices consist only of capacitors, where data is destroyed during reading and electrical erasure is difficult. In this work, four devices types were demonstrated that exhibit nondestructive reading, and three of the prototypes can be electrically erased. All types use the junction field effect transistor (JFET) for charge sensing, with each having different bipolar or epitaxial layer structure controlling the junction gate. The bottom epitaxial layer in each case served as the JFET channel. Two of the device types have three alternately doped layers, while the remaining two have four alternately doped layers. In all cases, removal of majority carriers from the middle layers constitutes stored charge. The missing carriers deplete the current carrying a region of the JFET channel. Drain current of the JFET becomes an indicator of stored charge. The basic function of each JFET memory element type is independent of interchanging n- and p- type doping within the structure type. Some performance advantage can be realized, however, by sensing with an n-type channel as compared to p- type due to increased carrier mobility. All device types exhibit storage time characteristics of order ten seconds. Devices are constructed in epitaxial layers grown by molecular beam epitaxy (MBE) reactors. The design of the epitaxial layers is an intrinsic part, together with the electrical design, of the storage device concept. These concepts are implemented first with photolithography masks which are used

  7. Synthesis of giant rigid pi-conjugated dendrimers.

    PubMed

    Jiang, Yang; Lu, Yi-Xuan; Cui, Yu-Xin; Zhou, Qi-Feng; Ma, Yuguo; Pei, Jian

    2007-10-25

    A novel family of giant pi-conjugated dendrimers (G0, G1, and G2) solely constructed by 5,5,10,10,15,15-hexahexyltruxene units has been developed in a convergent manner through a Suzuki cross-coupling reaction. The overall yields to such large rigid conjugated dendrimers are quite satisfying. The structures and purity of these nanosize rigid dendrimers are verified by 1H and 13C NMR, MALDI-TOF MS, and elemental analysis.

  8. Analysis of linear elastic wave propagation in piping systems by a combination of the boundary integral equations method and the finite element method

    NASA Astrophysics Data System (ADS)

    Søe-Knudsen, A.; Sorokin, S. V.

    2010-09-01

    The combined methodology of boundary integral equations and finite elements is formulated and applied to study the wave propagation phenomena in compound piping systems consisting of straight and curved pipe segments with compact elastic supports. This methodology replicates the concept of hierarchical boundary integral equations method proposed by L. I. Slepyan to model the time-harmonic wave propagation in wave guides, which have components of different dimensions. However, the formulation presented in this article is tuned to match the finite element format, and therefore, it employs the dynamical stiffness matrix to describe wave guide properties of all components of the assembled structure. This matrix may readily be derived from the boundary integral equations, and such a derivation is superior over the conventional derivation from the transfer matrix. The proposed methodology is verified in several examples and applied for analysis of periodicity effects in compound piping systems of several alternative layouts.

  9. Subgap Absorption in Conjugated Polymers

    DOE R&D Accomplishments Database

    Sinclair, M.; Seager, C. H.; McBranch, D.; Heeger, A. J; Baker, G. L.

    1991-01-01

    Along with X{sup (3)}, the magnitude of the optical absorption in the transparent window below the principal absorption edge is an important parameter which will ultimately determine the utility of conjugated polymers in active integrated optical devices. With an absorptance sensitivity of < 10{sup {minus}5}, Photothermal Deflection Spectroscopy (PDS) is ideal for determining the absorption coefficients of thin films of transparent'' materials. We have used PDS to measure the optical absorption spectra of the conjugated polymers poly(1,4-phenylene-vinylene) (and derivitives) and polydiacetylene-4BCMU in the spectral region from 0.55 eV to 3 eV. Our spectra show that the shape of the absorption edge varies considerably from polymer to polymer, with polydiacetylene-4BCMU having the steepest absorption edge. The minimum absorption coefficients measured varied somewhat with sample age and quality, but were typically in the range 1 cm{sup {minus}1} to 10 cm{sup {minus}1}. In the region below 1 eV, overtones of C-H stretching modes were observed, indicating that further improvements in transparency in this spectral region might be achieved via deuteration of fluorination.

  10. Integrated application of in situ non destructive techniques for the evaluation of the architectural elements of monumental structures.

    NASA Astrophysics Data System (ADS)

    Fais, Silvana; Casula, Giuseppe; Cuccuru, Francesco; Ligas, Paola; Bianchi, Maria Giovanna; Marraccini, Alessandro

    2017-04-01

    The need to integrate different non invasive geophysical datasets for an effective diagnostic process of the stone materials of cultural heritage buildings is due to the complexity of the intrinsic characteristics of the different types of stones and of their degradation process. Consequently integration between different geophysical techniques is required for the characterization of stone building materials. In order to perform the diagnostic process by different non-invasive techniques thus interpreting in a realistic way the different geophysical parameters, it is necessary to link the petrophysical characteristics of stones with the geophysical ones. In this study the complementary application of three different non invasive techniques (terrestrial laser scanner (TLS), infrared thermography and ultrasonic surface and tomography measurements) was carried out to analyse the conservation state and quality of the carbonate building materials of three inner columns of the old precious church of San Lorenzo in the historical city center of Cagliari (Sardinia). In previous works (Casula et al., 2009; Fais et al., 2015), especially the integrated application of TLS and ultrasonic techniques has been demonstrated to represent a powerful tool in evaluating the quality of the stone building materials by solving or limiting the uncertainties typical of all indirect methods. Thanks to the terrestrial laser scanner (TLS) technique it was possible to 3D model the investigated columns and their surface geometrical anomalies. The TLS measurements were complemented by several ultrasonic in situ and laboratory tests in the 24kHz - 54kHz range. The ultrasonic parameters, especially longitudinal and transversal velocities, allow to recover information on materials related with mechanical properties. A good correlation between TLS surface geometrical anomalies and the ultrasonic velocity ones is evident at the surface and in shallow parts of the investigated architectural elements

  11. Stabilized polyacrylic saccharide protein conjugates

    DOEpatents

    Callstrom, M.R.; Bednarski, M.D.; Gruber, P.R.

    1996-02-20

    This invention is directed to water soluble protein polymer conjugates which are stable in hostile environments. The conjugate comprises a protein which is linked to an acrylic polymer at multiple points through saccharide linker groups. 16 figs.

  12. Stabilized polyacrylic saccharide protein conjugates

    DOEpatents

    Callstrom, Matthew R.; Bednarski, Mark D.; Gruber, Patrick R.

    1996-01-01

    This invention is directed to water soluble protein polymer conjugates which are stabile in hostile environments. The conjugate comprises a protein which is linked to an acrylic polymer at multiple points through saccharide linker groups.

  13. Examining the contribution of a dA+dT element to the conformation of Escherichia coli integration host factor-DNA complexes.

    PubMed Central

    Hales, L M; Gumport, R I; Gardner, J F

    1996-01-01

    DNA binding proteins that induce structural changes in DNA are common in both prokaryotes and eukaryotes. Integration host factor (IHF) is a multi-functional DNA binding and bending protein of Escherichia coli that can mediate protein-protein and protein-DNA interactions by bending DNA. Previously we have shown that the presence of a dA+dT element 5'-proximal to an IHF consensus sequence can affect the binding of IHF to a particular site. In this study the contribution of various sequence elements to the formation of IHF-DNA complexes was examined. We show that IHF bends DNA more when it binds to a site containing a dA+dT element upstream of its core consensus element than to a site lacking a dA+dT element. We demonstrate that IHF can be specifically crosslinked to DNA with binding sites either containing or lacking this dA+dT element. These results indicate the importance of flanking DNA and a dA+dT element in the binding and bending of a site by IHF. PMID:8650000

  14. Examining the contribution of a dA+dT element to the conformation of Escherichia coli integration host factor-DNA complexes.

    PubMed

    Hales, L M; Gumport, R I; Gardner, J F

    1996-05-01

    DNA binding proteins that induce structural changes in DNA are common in both prokaryotes and eukaryotes. Integration host factor (IHF) is a multi-functional DNA binding and bending protein of Escherichia coli that can mediate protein-protein and protein-DNA interactions by bending DNA. Previously we have shown that the presence of a dA+dT element 5'-proximal to an IHF consensus sequence can affect the binding of IHF to a particular site. In this study the contribution of various sequence elements to the formation of IHF-DNA complexes was examined. We show that IHF bends DNA more when it binds to a site containing a dA+dT element upstream of its core consensus element than to a site lacking a dA+dT element. We demonstrate that IHF can be specifically crosslinked to DNA with binding sites either containing or lacking this dA+dT element. These results indicate the importance of flanking DNA and a dA+dT element in the binding and bending of a site by IHF.

  15. Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition1[OPEN

    PubMed Central

    Connolly, Erin L.

    2016-01-01

    Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. The identification of genes and alleles that modify element content in the grains of cereals, including sorghum (Sorghum bicolor), is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high-throughput work flow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel, representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome-wide association was demonstrated by implementing rank transformation and a multilocus mixed model to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc, manganese, nickel, calcium, and cadmium in sorghum seeds. In addition to strong candidates for these five elements, we provide a list of candidate loci for several other elements. Our approach enabled the identification of single-nucleotide polymorphisms in strong linkage disequilibrium with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement. PMID:26896393

  16. Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition.

    PubMed

    Shakoor, Nadia; Ziegler, Greg; Dilkes, Brian P; Brenton, Zachary; Boyles, Richard; Connolly, Erin L; Kresovich, Stephen; Baxter, Ivan

    2016-04-01

    Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. The identification of genes and alleles that modify element content in the grains of cereals, including sorghum (Sorghum bicolor), is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high-throughput work flow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel, representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome-wide association was demonstrated by implementing rank transformation and a multilocus mixed model to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc, manganese, nickel, calcium, and cadmium in sorghum seeds. In addition to strong candidates for these five elements, we provide a list of candidate loci for several other elements. Our approach enabled the identification of single-nucleotide polymorphisms in strong linkage disequilibrium with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement. © 2016 American Society of Plant Biologists. All Rights Reserved.

  17. Covalent polymer-drug conjugates.

    PubMed

    Elvira, Carlos; Gallardo, Alberto; Roman, Julio San; Cifuentes, Alejandro

    2005-01-31

    In this work, polymer-drugs conjugates used as drug delivery systems (DDS) are revised attending to their chemical conjugation. Namely, the classification of this type of DDS is based on the conjugation sites of the reactive groups (i.e., via end groups or pendant polymer groups). Advantages and limitations of these types of DDS are discussed through representative examples of polymer-drugs and polymer-proteins conjugates recently developed.

  18. Conjugate Silhouette Nets

    DTIC Science & Technology

    2000-01-01

    19) dv vEI 2 . Calling these curves the projective hodographs of p and q respectively, we can state Corollary. The Laplace transforms of a conjugate...silhouette net £ are the projective hodographs of the generating curves C1, C2 of L (considered as a projective translation surface). §3. Axial

  19. Conjugation in "Escherichia coli"

    ERIC Educational Resources Information Center

    Phornphisutthimas, Somkiat; Thamchaipenet, Arinthip; Panijpan, Bhinyo

    2007-01-01

    Bacterial conjugation is a genetic transfer that involves cell-to-cell between donor and recipient cells. With the current method used to teach students in genetic courses at the undergraduate level, the transconjugants are identified using bacterial physiology and/or antibiotic resistance. Using physiology, however, is difficult for both…

  20. DNA-cell conjugates

    DOEpatents

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  1. Conjugation in "Escherichia coli"

    ERIC Educational Resources Information Center

    Phornphisutthimas, Somkiat; Thamchaipenet, Arinthip; Panijpan, Bhinyo

    2007-01-01

    Bacterial conjugation is a genetic transfer that involves cell-to-cell between donor and recipient cells. With the current method used to teach students in genetic courses at the undergraduate level, the transconjugants are identified using bacterial physiology and/or antibiotic resistance. Using physiology, however, is difficult for both…

  2. pDGO100, a type 1 IncC plasmid from 1981 carrying ARI-A and a Tn1696-like transposon in a novel integrating element.

    PubMed

    Harmer, Christopher J; Partridge, Sally R; Hall, Ruth M

    2016-07-01

    Most A/C plasmids sequenced to date were recovered in the last two decades. To gain insight into the evolution of this group, the IncC plasmid pDGO100, found in a multiply antibiotic-resistant Escherichia coli strain isolated in 1981, was sequenced. pDGO100 belongs to the type 1 lineage and carries an ARI-A antibiotic resistance island but not an ARI-B island. The A/C2 backbone of pDGO100 has a deletion in the rhs1 gene previously found in pRMH760 and differs by only six single base pair substitutions from pRMH760, recovered at the same hospital 16years later. This confirms that the separation of type 1 and type 2 IncC plasmids is long standing. The ARI-A islands are also closely related, but pRMH760 contains Tn4352B in tniA of Tn402, while in pDGO100, Tn4352 has inserted into merA of pDUmer. pDGO100 also carries an additional 46kb insertion that includes a Tn1696-like transposon with the dfrB3 gene cassette. This insertion was identified as a novel integrating element, with an int gene at one end, and also includes the fec iron uptake operon that has been acquired from the E. coli chromosome. Related integrating elements carrying the same int gene were found in A/C2, IncHI1, and IncHI2 plasmids, and in the chromosomes of Enterobacter cloacae, Klebsiella oxytoca, and Cronobacter sakazakii isolates. In the Enterobacteriaceae chromosomes, these integrating elements appear to target a gene encoding a radical SAM superfamily protein. In the A/C2, IncHI1, and IncHI2 plasmids, genes encoding a phosphoadenosine phosphosulfate reductase were interrupted. The extremities of the integrating element are highly conserved, whilst the internal gene content varies. The detection of integrative elements in plasmids demonstrates an increased range of locations into which this type of mobile element can integrate and insertion in plasmids is likely to assist their spread.

  3. An integrated approach for risk object re-entry predictions in terms of KS elements and genetic algorithm

    NASA Astrophysics Data System (ADS)

    Sharma, R. K.; Anil Kumar, A. K.; Xavier James Raj, M.

    strategy (Sharma & Anilkumar 2003) adopted for the re-entry prediction of the risk objects by estimating the ballistic coefficient based on the TLEs. The estimation of the ballistic coefficient Bn = m/(CDA), where CD is the drag coefficient, A is the reference area, and m is the mass of the object, is done by minimizing a cost function (variation in the re-entry prediction time) using Genetic algorithm. The KS element equations of motion are numerically integrated with a suitable integration step size with the 4th - order Runge-Kutta-Gill method till the end of the orbital life, by including the Earth's oblateness with J2 to J6 terms, and modelling the air drag forces through an analytical oblate diurnal atmosphere with the density scale height varying with altitude. Jacchia (1977) atmospheric model, which takes into consideration the epoch, daily solar flux (F10.7) and geomagnetic index (Ap) for computation of density and density scale height, is utilized. The basic feature of the present approach is that the model and measurement errors are accountable in terms of adjusting the ballistic coefficient and hence the estimated Bn is not the actual ballistic coefficient but an effective ballistic coefficient. It is demonstrated that the inaccuracies or deficiencies in the inputs, like F10.7 and Ap values, are absorbed in the estimated Bn. The details of the re-entry results based on this approach, utilizing the TLE of debris objects, US Sat No. 25947 and SROSS-C2 Satellite, which re-entered the Earth's atmosphere on 4th March 2000 and 12th July 2001, are provided. Details of the re-entry predictions with respect to the 4th and 5th IADC re-entry campaigns, related to COSMOS 1043 rocket body and COSMOS 389 satellite, which re-entered the Earth's atmosphere on 19 January 2002 and 24 November 2003, respectively, are described. The predicted re-entries were found to be all along quite close to the actual re-entry time, with quite less uncertainties bands on the predictions. A

  4. On 3D Riesz systems of harmonic conjugates

    NASA Astrophysics Data System (ADS)

    Avetisyan, K.; Gürlebeck, K.; Morais, J.

    2012-11-01

    This note announces some results that will be presented in the forthcoming paper [10]. In continuation to these studies we discuss a constructive approach for the generation of harmonic conjugates to find nullsolutions to the Riesz system in R3. This class of solutions coincides with the subclass of monogenic functions with values in the reduced quaternions. The algorithm for harmonic conjugates is presented by means of an integral representation. Additionally, we discuss the weighted (monogenic) Hardy and Bergman spaces on the unit ball in R3 consisting of functions with values in the reduced quaternions. We end up showing the boundedness of the underlying harmonic conjugation operators in certain weighted spaces.

  5. Acoustic microscope based on magneto-elastic wave phase conjugator

    NASA Astrophysics Data System (ADS)

    Brysev, A.; Krutyansky, L.; Pernod, P.; Preobrazhensky, V.

    2000-05-01

    Acoustic C-scan imaging (acoustic microscopy) by means of supercritical parametric wave phase conjugation (WPC) is studied experimentally. A phase conjugator based on a magneto-acoustic active material is used for compensating phase distortions introduced by solid and polymer aberration layers covering objects (electronic integrated circuits as examples). Improvement of images is demonstrated on an acoustic microscope, operating at a frequency of 10 MHz.

  6. Synthesis of gold and silver nanoparticle S-ovalbumin protein conjugates by in situ conjugation process

    NASA Astrophysics Data System (ADS)

    Joshi, Deepti; Soni, R. K.

    2015-05-01

    Pure gold and silver nanoparticle (NP) generation and their conjugation with protein S-ovalbumin using in situ conjugation process have been reported. The in situ conjugation involves nanosecond pulse laser ablation of pure metal target in the protein S-ovalbumin solution. Transmission electron microscopy (TEM) and UV-Visible absorption results show decrease in mean NP size along with narrow particle size distribution on ablation in S-ovalbumin solution as compared to ablation in water for both Au and Ag NPs. Also, the NP size reduction was found to be dependent on the concentration of S-ovalbumin. For AuNPs, spherical NPs of mean size 4 nm with particle size distribution 2-6 nm were obtained at 300 nM S-ovalbumin concentration. Further, it has been observed that the resultant in situ-conjugated colloid gold and silver NP solutions were quite stable even in the presence of NaCl at physiological salt concentration (0.15 M). On post-laser irradiation (532 nm, 15 mJ) for 20 min, 9 nm red shift in surface plasmon resonance peak (SPR), along with increased broadening towards longer wavelength, was observed in the AuNPs-S-ovalbumin sample. Further increase in the time of irradiation showed shift in AuNPs-S-ovalbumin SPR towards lower wavelength. On laser irradiation (532 nm, 15 mJ) for 20 min, no significant change was observed in the line shape of the plasmon absorption band of the AgNPs-S-ovalbumin conjugate. FTIR spectra revealed that S-ovalbumin peptide backbone and secondary structure remain unchanged on laser irradiation during in situ conjugation process. Thus, integrity of S-ovalbumin does not get affected, and no degradation of S-ovalbumin takes place on laser-induced in situ conjugation. Raman results confirm that both Au and Ag NPs interact with S-ovalbumin via thiol-bearing cysteine residues of the disulfide bond.

  7. a Nonlinear Hybrid and VR Stepping Motor Analysis via AN Integrated Finite Element and Lumped Parameter Modeling Technique

    NASA Astrophysics Data System (ADS)

    Huard, Steven Roger

    The work involves the magnetic modeling of a variable reluctance and a hybrid stepping motor. The model combines two traditional methods for creating a magnetic model. Nonlinear two dimensional finite element analysis is combined with nonlinear lumped element modeling to create a three dimension lumped model. The two dimensional finite element analysis is used to numerically calculate the effective reluctance function of the motor tooth region. After the finite element analysis is completed, a two terminal tooth region reluctance element that is a function of both rotor angle and tooth region flux density results. The two terminal lumped element is then used to represent the tooth region of the motor in a lumped parameter model. The process by which the tooth region finite element field solution is transformed into the two terminal lumped reluctance is a new modeling approach; and, it is the foundation of the modeling method in this dissertation. Torque, back EMF, and inductance are some of the more important motor parameters predicted by the modeling method. The model predictions are compared to experimental data in the dissertation. The final motor parameter predictions from the model correlated quite well with experimental data. Also included in the dissertation is a unique derivation which defines the constraints that a region must satisfy such that a general three dimensional region of non-homogenous material can be modeled as a two terminal lumped reluctance element. The final restrictions imposed on the general three dimensional region are quite liberal. A method for solving any arbitrarily connected network of nonlinear lumped reluctances and sources is shown in detail. The method was developed specifically for use in this dissertation research, however, it is general enough to be applied to a wide variety of lumped element magnetic problems. The method explains how a Newton-Raphson iteration loop can be used to solve the nonlinear matrix equation created

  8. Why is entry exclusion an essential feature of conjugative plasmids?

    PubMed

    Garcillán-Barcia, M Pilar; de la Cruz, Fernando

    2008-07-01

    Entry exclusion is a property of plasmids by which the cells that contain them become bad recipients in additional conjugation rounds. This work reviews entry exclusion essential features and analyzes the mechanisms of action of the best studied systems. We searched for homologs of the proteins responsible for experimentally known exclusion systems. Results were used to classify exclusion systems in families of related elements. We arrive to the conclusion that all conjugative plasmids contain at least one entry exclusion gene. Although entry exclusion genes seem to be part of the plasmid conjugative machinery, they are systematically absent in phylogenetically related type IV protein exporting machines involved in virulence for plants and animals. We infer from this fact that entry exclusion is an essential feature of conjugative plasmid biology. Mathematical models suggest that plasmids expressing entry exclusion selectively eliminate plasmids lacking it, reinforcing its essential character and suggesting that entry exclusion plays a direct role in plasmid survival. Other experimental results confirm that entry exclusion is essential for the stability of a conjugative plasmid. We suggest that entry exclusion limits the damage of lethal zygosis (bacterial death produced by excessive rounds of conjugation). Additionally, it avoids competition in a host among identical plasmid backbones. Conversely, the lack of entry exclusion in conjugative transposons can be understood as a means of generating rapid evolutionary change.

  9. Novel Tn4371-ICE like element in Ralstonia pickettii and Genome mining for comparative elements

    PubMed Central

    2009-01-01

    Background Integrative Conjugative Elements (ICEs) are important factors in the plasticity of microbial genomes. An element related to the ICE Tn4371 was discovered during a bioinformatic search of the Ralstonia pickettii 12J genome. This element was analysed and further searches carried out for additional elements. A PCR method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight Ralstonia pickettii and Ralstonia insidiosa strains were analysed for the presence of the element. Results Comparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several β and γ- Proteobacteria. These elements vary in size, GC content, putative function and have a mosaic-like structure of plasmid- and phage-like sequences which is typical of Tn4371-like ICEs. These elements were found after a through search of the GenBank database. The elements, which are found in Ralstonia, Delftia, Acidovorax, Bordetella, Comamonas, Acidovorax, Congregibacter, Shewanella, Pseudomonas Stenotrophomonas, Thioalkalivibrio sp. HL-EbGR7, Polaromonas, Burkholderia and Diaphorobacter sp. share a common scaffold. A PCR method was designed (based on the Tn4371- like element detected in the Ralstonia pickettii 12J genome) to detect and characterise new elements of this type. Conclusion All elements found in this study possess a common scaffold of core genes but contain different accessory genes. A new uniform nomenclature is suggested for ICEs of the Tn4371 family. Two novel Tn4371-like ICE were discovered and characterised, using the novel PCR method described in two different isolates of Ralstonia pickettii from laboratory purified water. PMID:19941653

  10. Novel Tn4371-ICE like element in Ralstonia pickettii and genome mining for comparative elements.

    PubMed

    Ryan, Michael P; Pembroke, J Tony; Adley, Catherine C

    2009-11-26

    Integrative Conjugative Elements (ICEs) are important factors in the plasticity of microbial genomes. An element related to the ICE Tn4371 was discovered during a bioinformatic search of the Ralstonia pickettii 12J genome. This element was analysed and further searches carried out for additional elements.A PCR method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight Ralstonia pickettii and Ralstonia insidiosa strains were analysed for the presence of the element. Comparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several beta and gamma- Proteobacteria. These elements vary in size, GC content, putative function and have a mosaic-like structure of plasmid- and phage-like sequences which is typical of Tn4371-like ICEs. These elements were found after a through search of the GenBank database. The elements, which are found in Ralstonia, Delftia, Acidovorax, Bordetella, Comamonas, Acidovorax, Congregibacter, Shewanella, Pseudomonas Stenotrophomonas, Thioalkalivibrio sp. HL-EbGR7, Polaromonas, Burkholderia and Diaphorobacter sp. share a common scaffold. A PCR method was designed (based on the Tn4371- like element detected in the Ralstonia pickettii 12J genome) to detect and characterise new elements of this type. All elements found in this study possess a common scaffold of core genes but contain different accessory genes. A new uniform nomenclature is suggested for ICEs of the Tn4371 family. Two novel Tn4371-like ICE were discovered and characterised, using the novel PCR method described in two different isolates of Ralstonia pickettii from laboratory purified water.

  11. Gain of a New Exon by a Lineage-Specific Alu Element-Integration Event in the BCS1L Gene during Primate Evolution

    PubMed Central

    Park, Sang-Je; Kim, Young-Hyun; Lee, Sang-Rae; Choe, Se-Hee; Kim, Myung-Jin; Kim, Sun-Uk; Kim, Ji-Su; Sim, Bo-Woong; Song, Bong-Seok; Jeong, Kang-Jin; Jin, Yeung-Bae; Lee, Youngjeon; Park, Young-Ho; Park, Young Il; Huh, Jae-Won; Chang, Kyu-Tae

    2015-01-01

    BCS1L gene encodes mitochondrial protein and is a member of conserved AAA protein family. This gene is involved in the incorporation of Rieske FeS and Qcr10p into complex III of respiratory chain. In our previous study, AluYRa2-derived alternative transcript in rhesus monkey genome was identified. However, this transcript has not been reported in human genome. In present study, we conducted evolutionary analysis of AluYRa2-exonized transcript with various primate genomic DNAs and cDNAs from humans, rhesus monkeys, and crab-eating monkeys. Remarkably, our results show that AluYRa2 element has only been integrated into genomes of Macaca species. This Macaca lineage-specific integration of AluYRa2 element led to exonization event in the first intron region of BCS1L gene by producing a conserved 3′ splice site. Intriguingly, in rhesus and crab-eating monkeys, more diverse transcript variants by alternative splicing (AS) events, including exon skipping and different 5′ splice sites from humans, were identified. Alignment of amino acid sequences revealed that AluYRa2-exonized transcript has short N-terminal peptides. Therefore, AS events play a major role in the generation of various transcripts and proteins during primate evolution. In particular, lineage-specific integration of Alu elements and species-specific Alu-derived exonization events could be important sources of gene diversification in primates. PMID:26537194

  12. Conjugate flow action functionals

    SciTech Connect

    Venturi, Daniele

    2013-11-15

    We present a new general framework to construct an action functional for a non-potential field theory. The key idea relies on representing the governing equations relative to a diffeomorphic flow of curvilinear coordinates which is assumed to be functionally dependent on the solution field. Such flow, which will be called the conjugate flow, evolves in space and time similarly to a physical fluid flow of classical mechanics and it can be selected in order to symmetrize the Gâteaux derivative of the field equations with respect to suitable local bilinear forms. This is equivalent to requiring that the governing equations of the field theory can be derived from a principle of stationary action on a Lie group manifold. By using a general operator framework, we obtain the determining equations of such manifold and the corresponding conjugate flow action functional. In particular, we study scalar and vector field theories governed by second-order nonlinear partial differential equations. The identification of transformation groups leaving the conjugate flow action functional invariant could lead to the discovery of new conservation laws in fluid dynamics and other disciplines.

  13. Conjugate flow action functionals

    NASA Astrophysics Data System (ADS)

    Venturi, Daniele

    2013-11-01

    We present a new general framework to construct an action functional for a non-potential field theory. The key idea relies on representing the governing equations relative to a diffeomorphic flow of curvilinear coordinates which is assumed to be functionally dependent on the solution field. Such flow, which will be called the conjugate flow, evolves in space and time similarly to a physical fluid flow of classical mechanics and it can be selected in order to symmetrize the Gâteaux derivative of the field equations with respect to suitable local bilinear forms. This is equivalent to requiring that the governing equations of the field theory can be derived from a principle of stationary action on a Lie group manifold. By using a general operator framework, we obtain the determining equations of such manifold and the corresponding conjugate flow action functional. In particular, we study scalar and vector field theories governed by second-order nonlinear partial differential equations. The identification of transformation groups leaving the conjugate flow action functional invariant could lead to the discovery of new conservation laws in fluid dynamics and other disciplines.

  14. The Coupling of Finite Element and Integral Equation Representations for Efficient Three-Dimensional Modeling of Electromagnetic Scattering and Radiation

    NASA Technical Reports Server (NTRS)

    Cwik, Tom; Zuffada, Cinzia; Jamnejad, Vahraz

    1996-01-01

    Finite element modeling has proven useful for accurtely simulating scattered or radiated fields from complex three-dimensional objects whose geometry varies on the scale of a fraction of a wavelength.

  15. Conjugate phase plate use in analysis of the frequency response of imaging systems designed for extended depth of field.

    PubMed

    Ojeda-Castañeda, Jorge; Landgrave, J E A; Gómez-Sarabia, Cristina M

    2008-08-01

    We unveil a relationship between generating a point spread function with a pair of conjugate phase elements and visualizing the modulation transfer function (MTF) of a single phase element for a variable focus error, at a tunable spatial frequency. We show that the defocused MTF of a pair of conjugate phase elements can be expressed as the modulus of the second order ambiguity function of a single phase element. Finally, we propose a tunable wavefront coding technique with a pair of quartic (4th power) conjugate phase elements.

  16. Exciton transport in π-conjugated polymers with conjugation defects.

    PubMed

    Meng, Ruixuan; Li, Yuan; Li, Chong; Gao, Kun; Yin, Sun; Wang, Luxia

    2017-09-06

    In π-conjugated polymers for photovoltaic applications, intrinsic conjugation defects are known to play crucial roles in impacting exciton transport after photoexcitation. However, the understanding of the associated microscopic processes still remains limited. Here, we present a theoretical investigation of the effects of different conjugation defects on the dynamics of exciton transport in two linearly coupled poly(p-phenylene vinylene) (PPV) molecules. The model system is constructed by employing an extended version of the Su-Schrieffer-Heeger model and the exciton behaviors are simulated by means of a quantum nonadiabatic dynamics. We identify two types of conjugation defects, i.e., weakening conjugation and strengthening conjugation, which are demonstrated to play different roles in impacting the dynamics of exciton transport in the system. The weakening conjugation acts as an energy well inclined to trap a moving exciton, while the strengthening conjugation acts as an energy barrier inclined to block the exciton. We also systematically simulate both intrachain and interchain dynamics of exciton transport, and find that an exciton could experience a "short-time delaying", "trapping", "blocking", or "hopping" process, which is determined by the defect type, strength, and position. These findings provide a microscopic understanding of how the exciton transport dynamics can be impacted by conjugation defects in an actual polymer system.

  17. A two-dimensional flow sensor with integrated micro thermal sensing elements and a back propagation neural network.

    PubMed

    Que, Ruiyi; Zhu, Rong

    2013-12-31

    This paper demonstrates a novel flow sensor with two-dimensional 360° direction sensitivity achieved with a simple structure and a novel data fusion algorithm. Four sensing elements with roundabout wires distributed in four quadrants of a circle compose the sensor probe, and work in constant temperature difference (CTD) mode as both Joule heaters and temperature detectors. The magnitude and direction of a fluid flow are measured by detecting flow-induced temperature differences among the four elements. The probe is made of Ti/Au thin-film with a diameter of 2 mm, and is fabricated using micromachining techniques. When a flow goes through the sensor, the flow-induced temperature differences are detected by the sensing elements that also serve as the heaters of the sensor. By measuring the temperature differences among the four sensing elements symmetrically distributed in the sensing area, a full 360° direction sensitivity can be obtained. By using a BP neural network to model the relationship between the readouts of the four sensor elements and flow parameters and execute data fusion, the magnitude and direction of the flow can be deduced. Validity of the sensor design was proven through both simulations and experiments. Wind tunnel experimental results show that the measurement accuracy of the airflow speed reaches 0.72 m/s in the range of 3 m/s-30 m/s and the measurement accuracy of flow direction angle reaches 1.9° in the range of 360°.

  18. Structure of DRE, a retrotransposable element which integrates with position specificity upstream of Dictyostelium discoideum tRNA genes.

    PubMed Central

    Marschalek, R; Hofmann, J; Schumann, G; Gösseringer, R; Dingermann, T

    1992-01-01

    Different Dictyostelium discoideum strains contain between 2 and 200 copies of a retrotransposable element termed DRE (Dictyostelium repetitive element). From the analysis of more than 50 elements, it can be concluded that DRE elements always occur 50 +/- 3 nucleotides upstream of tRNA genes. All analyzed clones contain DRE in a constant orientation relative to the tRNA gene, implying orientation specificity as well as position specificity. DRE contains two open reading frames which are flanked by nonidentical terminal repeats. Long terminal repeats (LTRs) are composed of three distinct modules, called A, B, and C. The tRNA gene-proximal LTR is characterized by one or multiple A modules followed by a single B module (AnB). With respect to the distal LTR, two different subforms of DRE have been isolated. The majority of isolated clones contains a distal LTR composed of a B module followed by a C module (BC), whereas the distal LTR of the other subform contains a consecutive array of a B module, a C module, a slightly altered A module, another B module, and another C module (BC.ABC). Full-length as well as smaller transcripts from DRE elements have been detected, but in comparison with the high copy number in D. discoideum strains derived from the wild-type strain NC4, transcription is rather poor. Images PMID:1309589

  19. A Two-Dimensional Flow Sensor with Integrated Micro Thermal Sensing Elements and a Back Propagation Neural Network

    PubMed Central

    Que, Ruiyi; Zhu, Rong

    2014-01-01

    This paper demonstrates a novel flow sensor with two-dimensional 360° direction sensitivity achieved with a simple structure and a novel data fusion algorithm. Four sensing elements with roundabout wires distributed in four quadrants of a circle compose the sensor probe, and work in constant temperature difference (CTD) mode as both Joule heaters and temperature detectors. The magnitude and direction of a fluid flow are measured by detecting flow-induced temperature differences among the four elements. The probe is made of Ti/Au thin-film with a diameter of 2 mm, and is fabricated using micromachining techniques. When a flow goes through the sensor, the flow-induced temperature differences are detected by the sensing elements that also serve as the heaters of the sensor. By measuring the temperature differences among the four sensing elements symmetrically distributed in the sensing area, a full 360° direction sensitivity can be obtained. By using a BP neural network to model the relationship between the readouts of the four sensor elements and flow parameters and execute data fusion, the magnitude and direction of the flow can be deduced. Validity of the sensor design was proven through both simulations and experiments. Wind tunnel experimental results show that the measurement accuracy of the airflow speed reaches 0.72 m/s in the range of 3 m/s–30 m/s and the measurement accuracy of flow direction angle reaches 1.9° in the range of 360°. PMID:24385032

  20. Efficient compression scheme by use of the region division of elemental images on MALT in three-dimensional integral imaging

    NASA Astrophysics Data System (ADS)

    Kang, Ho-Hyun; Lee, Jung-Woo; Shin, Dong-Hak; Kim, Eun-Soo

    2010-02-01

    This paper addresses the efficient compression scheme of elemental image array (EIA) generated from the moving array lenslet technique (MALT) based on MPEG-4. The EIAs are picked-up by MALT controlling the spatial ray sampling of ray and which produces few EIAs that the positions of the lenslet arrays are rapidly vibrated in the lateral directions within the retention time of the afterimage of human eye. To enhance the similarity in each EIA picked-up by MALT, several EIAs obtained from MALT are regenerated by the collection of an elemental image occupied at the same position in each EIA. The newly generated each EIA has high similarity among adjacent elemental images. To illustrate the feasibility of the proposed scheme, some experiments are carried out to show the increased compression efficiency and we obtained the improved compression ratio of 12% compared to the unhandled compression scheme.

  1. Application of finite element and boundary integral methods in molecular collision theory. I - Introduction and model calculations

    NASA Astrophysics Data System (ADS)

    Sethuraman, V.; Hunt, P. M.

    1988-06-01

    The adaptive multigrid technique in the finite element method of the solution of partial differential equations is examined in the context of model problems in atom-atom and collinear atom-diatom collisions. For the problem leading to scattering along an L-shaped region, the technique yields accurate results for regions of energy far from the threshold for excitation of a new channel without inclusion of virtual states. Close to the threshold, the cusplike structure of the transition probability (vs. energy) and the time delay associated with the onset of a resonance are recovered only by inclusion of the new (closed) channel in the finite element solution. For atom-diatom collinear collisions, use of an orthogonal coordinate system facilitates dicretization and adds no extra labor in the finite element method, compared to the usual mass-weighted system.

  2. Elastic-Plastic J-Integral Solutions or Surface Cracks in Tension Using an Interpolation Methodology. Appendix C -- Finite Element Models Solution Database File, Appendix D -- Benchmark Finite Element Models Solution Database File

    NASA Technical Reports Server (NTRS)

    Allen, Phillip A.; Wells, Douglas N.

    2013-01-01

    No closed form solutions exist for the elastic-plastic J-integral for surface cracks due to the nonlinear, three-dimensional nature of the problem. Traditionally, each surface crack must be analyzed with a unique and time-consuming nonlinear finite element analysis. To overcome this shortcoming, the authors have developed and analyzed an array of 600 3D nonlinear finite element models for surface cracks in flat plates under tension loading. The solution space covers a wide range of crack shapes and depths (shape: 0.2 less than or equal to a/c less than or equal to 1, depth: 0.2 less than or equal to a/B less than or equal to 0.8) and material flow properties (elastic modulus-to-yield ratio: 100 less than or equal to E/ys less than or equal to 1,000, and hardening: 3 less than or equal to n less than or equal to 20). The authors have developed a methodology for interpolating between the goemetric and material property variables that allows the user to reliably evaluate the full elastic-plastic J-integral and force versus crack mouth opening displacement solution; thus, a solution can be obtained very rapidly by users without elastic-plastic fracture mechanics modeling experience. Complete solutions for the 600 models and 25 additional benchmark models are provided in tabular format.

  3. Elastic-Plastic J-Integral Solutions or Surface Cracks in Tension Using an Interpolation Methodology. Appendix C -- Finite Element Models Solution Database File, Appendix D -- Benchmark Finite Element Models Solution Database File

    NASA Technical Reports Server (NTRS)

    Allen, Phillip A.; Wells, Douglas N.

    2013-01-01

    No closed form solutions exist for the elastic-plastic J-integral for surface cracks due to the nonlinear, three-dimensional nature of the problem. Traditionally, each surface crack must be analyzed with a unique and time-consuming nonlinear finite element analysis. To overcome this shortcoming, the authors have developed and analyzed an array of 600 3D nonlinear finite element models for surface cracks in flat plates under tension loading. The solution space covers a wide range of crack shapes and depths (shape: 0.2 less than or equal to a/c less than or equal to 1, depth: 0.2 less than or equal to a/B less than or equal to 0.8) and material flow properties (elastic modulus-to-yield ratio: 100 less than or equal to E/ys less than or equal to 1,000, and hardening: 3 less than or equal to n less than or equal to 20). The authors have developed a methodology for interpolating between the goemetric and material property variables that allows the user to reliably evaluate the full elastic-plastic J-integral and force versus crack mouth opening displacement solution; thus, a solution can be obtained very rapidly by users without elastic-plastic fracture mechanics modeling experience. Complete solutions for the 600 models and 25 additional benchmark models are provided in tabular format.

  4. Frequency translating phase conjugation circuit for active retrodirective antenna array

    NASA Astrophysics Data System (ADS)

    Chernoff, R.

    1980-11-01

    An active retrodirective antenna array which has central phasing from a reference antenna element through a "tree" structured network of transmission lines utilizes a number of phase conjugate circuits (PCCs) at each node and a phase reference regeneration circuit (PRR) at each node except the initial node. Each node virtually coincides with an element of the array. A PCC generates the exact conjugate phase of an incident signal using a phase locked loop which combines the phases in an up converter, divides the sum by 2 and mixes the result with the phase in a down converter for phase detection. The PRR extracts the phase from the conjugate phase. Both the PCC and the PRR are not only exact but also free from mixer degeneracy.

  5. Integration of experiments across diverse environments identifies the genetic determinants of variation in Sorghum bicolor seed element composition

    USDA-ARS?s Scientific Manuscript database

    Increasing the bioavailable elemental nutrient content in the edible portions of the crop has the potential to increase the value of sorghum for human and animal nutrition. Seedling establishment and seed nutritional quality are in part determined by the sequestration of sufficient mineral nutrients...

  6. A Strategy for Preservice Teachers to Integrate Cultural Elements within Planning and Instruction: Cultural L.I.V.E.S.

    ERIC Educational Resources Information Center

    Salsbury, Denise E.

    2008-01-01

    The large percentages of teachers in the United States are white, middle class people who may not understand or identify their own cultural connections within the American culture, let alone elaborate their own ancestral cultural elements. Educators are expected to teach a diverse student population, and preservice teachers should be prepared to…

  7. Tandemly Integrated HPV16 Can Form a Brd4-Dependent Super-Enhancer-Like Element That Drives Transcription of Viral Oncogenes

    PubMed Central

    Dooley, Katharine E.; Warburton, Alix

    2016-01-01

    ABSTRACT In cancer cells associated with human papillomavirus (HPV) infections, the viral genome is very often found integrated into the cellular genome. The viral oncogenes E6 and E7 are transcribed from the viral promoter, and integration events that alter transcriptional regulation of this promoter contribute to carcinogenic progression. In this study, we detected highly enriched binding of the super-enhancer markers Brd4, MED1, and H3K27ac, visible as a prominent nuclear focus by immunofluorescence, at the tandemly integrated copies of HPV16 in cells of the cervical neoplasia cell line W12 subclone 20861. Tumor cells are often addicted to super-enhancer-driven oncogenes and are particularly sensitive to disruption of transcription factor binding to the enhancers. Treatment of 20861 cells with bromodomain inhibitors displaced Brd4 from the HPV integration site, greatly decreased E6/E7 transcription, and inhibited cellular proliferation. Thus, Brd4 activates viral transcription at this integration site, and strong selection for E6/E7 expression can drive the formation of a super-enhancer-like element to promote oncogenesis. PMID:27624132

  8. Conjugate and method for forming aminomethyl phosphorus conjugates

    SciTech Connect

    Katti, K.V.; Berning, D.E.; Volkert, W.A.; Ketring, A.R.; Churchill, R.

    1999-09-07

    A method of forming phosphine-amine conjugates includes reacting a hydroxymethyl phosphine group of an amine-free first molecule with at least one free amine group of a second molecule to covalently bond the first molecule with the second molecule through an aminomethyl phosphorus linkage and the conjugates formed thereby.

  9. Conjugate and method for forming aminomethyl phosphorus conjugates

    DOEpatents

    Katti, Kattesh V.; Berning, Douglas E.; Volkert, Wynn A.; Ketring, Alan R.; Churchill, Robert

    1999-01-01

    A method of forming phosphine-amine conjugates includes reacting a hydroxymethyl phosphine group of an amine-free first molecule with at least one free amine group of a second molecule to covalently bond the first molecule with the second molecule through an aminomethyl phosphorus linkage and the conjugates formed thereby.

  10. Potential for thermochemical conversion of biomass residues from the integrated sugar-ethanol process - Fate of ash and ash-forming elements.

    PubMed

    Dirbeba, Meheretu Jaleta; Brink, Anders; DeMartini, Nikolai; Zevenhoven, Maria; Hupa, Mikko

    2017-06-01

    In this work, potential for thermochemical conversion of biomass residues from an integrated sugar-ethanol process and the fate of ash and ash-forming elements in the process are presented. Ash, ash-forming elements, and energy flows in the process were determined using mass balances and analyses of eight different biomass samples for ash contents, elemental compositions, and heating values. The results show that the ash content increases from the sugarcane to the final residue, vinasse. The cane straw, which is left in the field, contains one-third of the energy and 25% of the K and Cl while the vinasse contains 2% of the energy and 40% of the K and Cl in the cane. K and Cl in biomass fuels cause corrosion and fouling problems in boilers and gasifiers. Over 85% of these elements in the straw are water soluble indicating that water leaching would improve it for utilization in thermochemical conversion. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Integration

    ERIC Educational Resources Information Center

    Kalyn, Brenda

    2006-01-01

    Integrated learning is an exciting adventure for both teachers and students. It is not uncommon to observe the integration of academic subjects such as math, science, and language arts. However, educators need to recognize that movement experiences in physical education also can be linked to academic curricula and, may even lead the…

  12. Conjugate heat transfer characterization in cooling channels

    NASA Astrophysics Data System (ADS)

    Cukurel, Beni; Arts, Tony; Selcan, Claudio

    2012-06-01

    Cooling technology of gas turbine blades, primarily ensured via internal forced convection, is aimed towards withdrawing thermal energy from the airfoil. To promote heat exchange, the walls of internal cooling passages are lined with repeated geometrical flow disturbance elements and surface non-uniformities. Raising the heat transfer at the expense of increased pressure loss; the goal is to obtain the highest possible cooling effectiveness at the lowest possible pressure drop penalty. The cooling channel heat transfer problem involves convection in the fluid domain and conduction in the solid. This coupled behavior is known as conjugate heat transfer. This experimental study models the effects of conduction coupling on convective heat transfer by applying iso-heat-flux boundary condition at the external side of a scaled serpentine passage. Investigations involve local temperature measurements performed by Infrared Thermography over flat and ribbed slab configurations. Nusselt number distributions along the wetted surface are obtained by means of heat flux distributions, computed from an energy balance within the metal domain. For the flat plate experiments, the effect of conjugate boundary condition on heat transfer is estimated to be in the order of 3%. In the ribbed channel case, the normalized Nusselt number distributions are compared with the basic flow features. Contrasting the findings with other conjugate and convective iso-heat-flux literature, a high degree of overall correlation is evident.

  13. Chiral Conjugated Corrals.

    PubMed

    Ball, Melissa; Fowler, Brandon; Li, Panpan; Joyce, Leo A; Li, Fang; Liu, Taifeng; Paley, Daniel; Zhong, Yu; Li, Hexing; Xiao, Shengxiong; Ng, Fay; Steigerwald, Michael L; Nuckolls, Colin

    2015-08-12

    We present here a new design motif for strained, conjugated macrocycles that incorporates two different aromatics into the cycle with an -A-B-A-B- pattern. In this study, we demonstrate the concept by alternating electron donors and acceptors in a conjugated cycle. The donor is a bithiophene, and the acceptor is a perylene diimide derivative. The macrocycle formed has a persistent elliptiform cavity that is lined with the sulfur atoms of the thiophenes and the π-faces of the perylene diimide. Due to the linkage of the perylene diimide subunits, the macrocycles exist in both chiral and achiral forms. We separate the three stereoisomers using chiral high-performance liquid chromatography and study their interconversion. The mechanism for interconversion involves an "intramolecular somersault" in which one of the PDIs rotates around its transverse axis, thereby moving one of its diimide heads through the plane of the cavity. These unusual macrocycles are black in color with an absorption spectrum that spans the visible range. Density functional theory calculations reveal a photoinduced electron transfer from the bithiophene to the perylene diimide.

  14. A novel fully conjugated phenanthroline-appended phthalocyanine: synthesis and characterisation.

    PubMed

    Rusanova, Julia; Pilkington, Melanie; Decurtins, Silvio

    2002-10-07

    The synthetic route to a new fully conjugated phenanthroline appended phthalocyanine is described. This compound has been fully characterised by elemental analysis, UV-VIS, IR, MS and 1H NMR spectroscopy.

  15. Improved recombinant antibody production by CHO cells using a production enhancer DNA element with repeated transgene integration at a predetermined chromosomal site.

    PubMed

    Kawabe, Yoshinori; Inao, Takanori; Komatsu, Shodai; Huang, Guan; Ito, Akira; Omasa, Takeshi; Kamihira, Masamichi

    2017-03-01

    Chinese hamster ovary (CHO) cells are one of the most useful host cell lines for the production of biopharmaceutical proteins. Although a series of production processes have been refined to improve protein productivity and cost performance, establishing producer cells is still time-consuming and labor-intensive. Recombinase-mediated site-specific gene integration into a predetermined chromosomal locus may enable predictable protein expression, reducing the laborious process of cell screening. We previously developed an accumulative site-specific gene integration system (AGIS) using Cre recombinase and mutated loxP sites for transgene integration and amplification in the CHO cell genome. Epigenetic modifier elements such as insulators are effective DNA cis-regulatory elements for stabilizing transgene expression. Here, we attempted to enhance transgene expression in recombinant CHO cells generated by AGIS using a production enhancer DNA element (PE) derived from the CHO genome. The PE was introduced into an expression unit for a recombinant scFv-Fc antibody. The effect on scFv-Fc productivity of PE position and orientation within the transgene was evaluated, while keeping the background chromosomal structure constant. For the optimal PE arrangement, scFv-Fc productivity was enhanced 2.6-fold compared with an expression unit without a PE. The enhancing effect of the PE on transgene expression was also observed when two or three PE-flanked expression units were inserted as tandem repeats. These results indicate that AGIS using the PE-flanked expression unit is a promising approach for establishing producer cell lines for biopharmaceutical protein production.

  16. Elemental distribution and sample integrity comparison of freeze-dried and frozen-hydrated biological tissue samples with nuclear microprobe

    NASA Astrophysics Data System (ADS)

    Vavpetič, P.; Vogel-Mikuš, K.; Jeromel, L.; Ogrinc Potočnik, N.; Pongrac, P.; Drobne, D.; Pipan Tkalec, Ž.; Novak, S.; Kos, M.; Koren, Š.; Regvar, M.; Pelicon, P.

    2015-04-01

    The analysis of biological samples in frozen-hydrated state with micro-PIXE technique at Jožef Stefan Institute (JSI) nuclear microprobe has matured to a point that enables us to measure and examine frozen tissue samples routinely as a standard research method. Cryotome-cut slice of frozen-hydrated biological sample is mounted between two thin foils and positioned on the sample holder. The temperature of the cold stage in the measuring chamber is kept below 130 K throughout the insertion of the samples and the proton beam exposure. Matrix composition of frozen-hydrated tissue is consisted mostly of ice. Sample deterioration during proton beam exposure is monitored during the experiment, as both Elastic Backscattering Spectrometry (EBS) and Scanning Transmission Ion Microscopy (STIM) in on-off axis geometry are recorded together with the events in two PIXE detectors and backscattered ions from the chopper in a single list-mode file. The aim of this experiment was to determine differences and similarities between two kinds of biological sample preparation techniques for micro-PIXE analysis, namely freeze-drying and frozen-hydrated sample preparation in order to evaluate the improvements in the elemental localisation of the latter technique if any. In the presented work, a standard micro-PIXE configuration for tissue mapping at JSI was used with five detection systems operating in parallel, with proton beam cross section of 1.0 × 1.0 μm2 and a beam current of 100 pA. The comparison of the resulting elemental distributions measured at the biological tissue prepared in the frozen-hydrated and in the freeze-dried state revealed differences in elemental distribution of particular elements at the cellular level due to the morphology alteration in particular tissue compartments induced either by water removal in the lyophilisation process or by unsatisfactory preparation of samples for cutting and mounting during the shock-freezing phase of sample preparation.

  17. Poro-viscoelastic constitutive modeling of unconfined creep of hydrogels using finite element analysis with integrated optimization method.

    PubMed

    Liu, Kaifeng; Ovaert, Timothy C

    2011-04-01

    Hydrogels are cross-linked polymer networks swollen with water and are being considered as potential replacements for deceased load bearing tissues such as cartilage. Hydrogels show nonlinear time dependent behavior, and are a challenge to model. A three-element poro-viscoelastic constitutive model was developed based on the structure and nature of the hydrogel. To identify the material parameters, an inverse finite element (FE) technique was used that combines experimental results with FE modeling and an optimization method. Unconfined compression creep tests were conducted on poly(vinyl alcohol) (PVA) and poly(ethylene-co-vinyl alcohol)-poly(vinyl pyrrolidone) (EVAL-PVP) hydrogels manufactured by injection molding. Results from the creep experiments showed that for PVA hydrogels, an increase in polymer concentration correlates with a decrease in the equilibrium water content (EWC) and the creep strain. In EVAL-PVP hydrogels, an increase in the hydrophobic segments (EVAL) correlates with a decrease in the EWC as well as the creep strain. An inverse FE method was used to identify the viscoelastic material parameters of the hydrogels in combination with creep testing using the poro-viscoelastic three-element constitutive model. The elastic modulus estimated from the inverse FE technique showed good agreement with the modulus estimated directly from the test data. Copyright © 2010 Elsevier Ltd. All rights reserved.

  18. Performance of an optical encoder based on a nondiffractive beam implemented with a specific photodetection integrated circuit and a diffractive optical element.

    PubMed

    Quintián, Fernando Perez; Calarco, Nicolás; Lutenberg, Ariel; Lipovetzky, José

    2015-09-01

    In this paper, we study the incremental signal produced by an optical encoder based on a nondiffractive beam (NDB). The NDB is generated by means of a diffractive optical element (DOE). The detection system is composed by an application specific integrated circuit (ASIC) sensor. The sensor consists of an array of eight concentric annular photodiodes, each one provided with a programmable gain amplifier. In this way, the system is able to synthesize a nonuniform detectivity. The contrast, amplitude, and harmonic content of the sinusoidal output signal are analyzed. The influence of the cross talk among the annular photodiodes is placed in evidence through the dependence of the signal contrast on the wavelength.

  19. Antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, J.F.

    1988-06-28

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be about 5.0 nm. Methods and reagents are disclosed in which antibodies or Fab' fragments thereof are covalently bound to a stable cluster of gold atoms. 2 figs.

  20. Is emergency management an integrated element of business continuity management? A case study with security professionals in Western Australia.

    PubMed

    Frohde, Kenny; Brooks, David J

    2014-01-01

    Emergency management (EM) and business continuity management (BCM) frameworks incorporate various strategic and operational measures. Defined within a number of national and international standards and guidelines, such concepts may be integrated within one another to provide increased resilience to disruptive events. Nevertheless, there is a degree of dispute regarding concept integration among security and EM professionals and bodies of knowledge. In line with cognitive psychology exemplar-based concepts, such disputes may be associated with a lack of precision in communality in the approach to EM and BCM. This paper presents a two-stage study, where stage 1 critiqued national and international literature and stage 2 applied semi-structured interviews with security managers in Western Australia. Findings indicate the existence of contradictory views on EM and its integration within BCM. As such, this study concludes that EM is considered a vital component of BCM by the majority of security managers. However, there is broader dispute regarding its degree of integration. Understanding the underpinnings of such disputes will aid in raising the standards and application of professionalism within security, EM and BCM domains, supporting clarification and definition of professional boundaries.

  1. Glutathione conjugation and contaminant transformation

    USGS Publications Warehouse

    Field, Jennifer A.; Thurman, E.M.

    1996-01-01

    The recent identification of a novel sulfonated metabolite of alachlor in groundwater and metolachlor in soil is likely the result of glutathione conjugation. Glutathione conjugation is an important biochemical reaction that leads, in the case of alachlor, to the formation of a rather difficult to detect, water-soluble, and therefore highly mobile, sulfonated metabolite. Research from weed science, toxicology, and biochemistry is discussed to support the hypothesis that glutathione conjugation is a potentially important detoxification pathway carried out by aquatic and terrestrial plants and soil microorganisms. A brief review of the biochemical basis for glutathione conjugation is presented. We recommend that multidisciplinary research focus on the occurrence and expression of glutathione and its attendant enzymes in plants and microorganisms, relationships between electrophilic substrate structure and enzyme activity, and the potential exploitation of plants and microorganisms that are competent in glutathione conjugation for phytoremediation and bioremediation.

  2. WARP3D-Release 10.8: Dynamic Nonlinear Analysis of Solids using a Preconditioned Conjugate Gradient Software Architecture

    NASA Technical Reports Server (NTRS)

    Koppenhoefer, Kyle C.; Gullerud, Arne S.; Ruggieri, Claudio; Dodds, Robert H., Jr.; Healy, Brian E.

    1998-01-01

    This report describes theoretical background material and commands necessary to use the WARP3D finite element code. WARP3D is under continuing development as a research code for the solution of very large-scale, 3-D solid models subjected to static and dynamic loads. Specific features in the code oriented toward the investigation of ductile fracture in metals include a robust finite strain formulation, a general J-integral computation facility (with inertia, face loading), an element extinction facility to model crack growth, nonlinear material models including viscoplastic effects, and the Gurson-Tver-gaard dilatant plasticity model for void growth. The nonlinear, dynamic equilibrium equations are solved using an incremental-iterative, implicit formulation with full Newton iterations to eliminate residual nodal forces. The history integration of the nonlinear equations of motion is accomplished with Newmarks Beta method. A central feature of WARP3D involves the use of a linear-preconditioned conjugate gradient (LPCG) solver implemented in an element-by-element format to replace a conventional direct linear equation solver. This software architecture dramatically reduces both the memory requirements and CPU time for very large, nonlinear solid models since formation of the assembled (dynamic) stiffness matrix is avoided. Analyses thus exhibit the numerical stability for large time (load) steps provided by the implicit formulation coupled with the low memory requirements characteristic of an explicit code. In addition to the much lower memory requirements of the LPCG solver, the CPU time required for solution of the linear equations during each Newton iteration is generally one-half or less of the CPU time required for a traditional direct solver. All other computational aspects of the code (element stiffnesses, element strains, stress updating, element internal forces) are implemented in the element-by- element, blocked architecture. This greatly improves

  3. Integration of a Finite Element Model with the DAP Bone Remodeling Model to Characterize Bone Response to Skeletal Loading

    NASA Technical Reports Server (NTRS)

    Werner, Christopher R.; Mulugeta, Lealem; Myers, J. G.; Pennline, J. A.

    2015-01-01

    NASA's Digital Astronaut Project (DAP) has developed a bone remodeling model that has been validated for predicting volumetric bone mineral density (vBMD) changes of trabecular and cortical bone in the absence of mechanical loading. The model was recently updated to include skeletal loading from exercise and free living activities to maintain healthy bone using a new daily load stimulus (DLS). This new formula was developed based on an extensive review of existing DLS formulas, as discussed in the abstract by Pennline et al. The DLS formula incorporated into the bone remodeling model utilizes strains and stress calculated from finite element model (FEM) of the bone region of interest. The proximal femur was selected for the initial application of the DLS formula, with a specific focus on the femoral neck. METHODS: The FEM was generated from CAD geometry of a femur using de-identified CT data. The femur was meshed using linear tetrahedral elements Figure (1) with higher mesh densities in the femoral neck region, which is the primary region of interest for the initial application of the DLS formula in concert with the DAP bone remodeling model. Nodal loads were applied to the femoral head and the greater trochanter and the base of the femur was held fixed. An L2 norm study was conducted to reduce the length of the femoral shaft without significantly impacting the stresses in the femoral neck. The material properties of the FEM of the proximal femur were separated between cortical and trabecular regions to work with the bone remodeling model. Determining the elements with cortical material properties in the FEM was based off of publicly available CT hip scans [4] that were segmented, cleaned, and overlaid onto the FEM.

  4. Non Linear Conjugate Gradient

    SciTech Connect

    Newman, Gregory A.; Commer, Michael

    2006-11-17

    Software that simulates and inverts electromagnetic field data for subsurface electrical properties (electrical conductivity) of geological media. The software treats data produced by a time harmonic source field excitation arising from the following antenna geometery: loops and grounded bipoles,