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Sample records for integrating conjugative element

  1. Conjugative Transfer of the Integrative Conjugative Elements ICESt1 and ICESt3 from Streptococcus thermophilus▿ †

    PubMed Central

    Bellanger, Xavier; Roberts, Adam P.; Morel, Catherine; Choulet, Frédéric; Pavlovic, Guillaume; Mullany, Peter; Decaris, Bernard; Guédon, Gérard

    2009-01-01

    Integrative and conjugative elements (ICEs), also called conjugative transposons, are genomic islands that excise, self-transfer by conjugation, and integrate in the genome of the recipient bacterium. The current investigation shows the intraspecies conjugative transfer of the first described ICEs in Streptococcus thermophilus, ICESt1 and ICESt3. Mitomycin C, a DNA-damaging agent, derepresses ICESt3 conjugative transfer almost 25-fold. The ICESt3 host range was determined using various members of the Firmicutes as recipients. Whereas numerous ICESt3 transconjugants of Streptococcus pyogenes and Enterococcus faecalis were recovered, only one transconjugant of Lactococcus lactis was obtained. The newly incoming ICEs, except the one from L. lactis, are site-specifically integrated into the 3′ end of the fda gene and are still able to excise in these transconjugants. Furthermore, ICESt3 was retransferred from E. faecalis to S. thermophilus. Recombinant plasmids carrying different parts of the ICESt1 recombination module were used to show that the integrase gene is required for the site-specific integration and excision of the ICEs, whereas the excisionase gene is required for the site-specific excision only. PMID:19181800

  2. 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

  3. Conjugative transposons: an unusual and diverse set of integrated gene transfer elements.

    PubMed Central

    Salyers, A A; Shoemaker, N B; Stevens, A M; Li, L Y

    1995-01-01

    Conjugative transposons are integrated DNA elements that excise themselves to form a covalently closed circular intermediate. This circular intermediate can either reintegrate in the same cell (intracellular transposition) or transfer by conjugation to a recipient and integrate into the recipient's genome (intercellular transposition). Conjugative transposons were first found in gram-positive cocci but are now known to be present in a variety of gram-positive and gram-negative bacteria also. Conjugative transposons have a surprisingly broad host range, and they probably contribute as much as plasmids to the spread of antibiotic resistance genes in some genera of disease-causing bacteria. Resistance genes need not be carried on the conjugative transposon to be transferred. Many conjugative transposons can mobilize coresident plasmids, and the Bacteroides conjugative transposons can even excise and mobilize unlinked integrated elements. The Bacteroides conjugative transposons are also unusual in that their transfer activities are regulated by tetracycline via a complex regulatory network. PMID:8531886

  4. A novel streptococcal integrative conjugative element involved in iron acquisition

    PubMed Central

    Heather, Zoe; Holden, Matthew T G; Steward, Karen F; Parkhill, Julian; Song, Lijiang; Challis, Gregory L; Robinson, Carl; Davis-Poynter, Nicholas; Waller, Andrew S

    2008-01-01

    In this study, we determined the function of a novel non-ribosomal peptide synthetase (NRPS) system carried by a streptococcal integrative conjugative element (ICE), ICESe2. The NRPS shares similarity with the yersiniabactin system found in the high-pathogenicity island of Yersinia sp. and is the first of its kind to be identified in streptococci. We named the NRPS product ‘equibactin’ and genes of this locus eqbA–N. ICESe2, although absolutely conserved in Streptococcus equi, the causative agent of equine strangles, was absent from all strains of the closely related opportunistic pathogen Streptococcus zooepidemicus. Binding of EqbA, a DtxR-like regulator, to the eqbB promoter was increased in the presence of cations. Deletion of eqbA resulted in a small-colony phenotype. Further deletion of the irp2 homologue eqbE, or the genes eqbH, eqbI and eqbJ encoding a putative ABC transporter, or addition of the iron chelator nitrilotriacetate, reversed this phenotype, implicating iron toxicity. Quantification of 55Fe accumulation and sensitivity to streptonigrin suggested that equibactin is secreted by S. equi and that the eqbH, eqbI and eqbJ genes are required for its associated iron import. In agreement with a structure-based model of equibactin synthesis, supplementation of chemically defined media with salicylate was required for equibactin production. PMID:18990191

  5. 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. PMID:27303400

  6. 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

  7. 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. PMID:26347724

  8. SXT-Related Integrating Conjugative Element in New World Vibrio cholerae

    PubMed Central

    Burrus, Vincent; Quezada-Calvillo, Roberto; Marrero, Joeli; Waldor, Matthew K.

    2006-01-01

    SXT-related integrating conjugative elements (ICEs) became prevalent in Asian Vibrio cholerae populations after V. cholerae O139 emerged. Here, we describe an SXT-related ICE, ICEVchMex1, in a Mexican environmental V. cholerae isolate. Identification of ICEVchMex1 represents the first description of an SXT-related ICE in the Western Hemisphere. The significant differences between the SXT and ICEVchMex1 genomes suggest that these ICEs have evolved independently. PMID:16598018

  9. ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.

    PubMed

    Bi, Dexi; Xu, Zhen; Harrison, Ewan M; Tai, Cui; Wei, Yiqing; He, Xinyi; Jia, Shiru; Deng, Zixin; Rajakumar, Kumar; Ou, Hong-Yu

    2012-01-01

    ICEberg (http://db-mml.sjtu.edu.cn/ICEberg/) is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. We propose that ICEberg will facilitate efficient, multi-disciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community.

  10. 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

  11. Biology of ICEBs1, an integrative and conjugative element in Bacillus subtilis.

    PubMed

    Auchtung, Jennifer M; Aleksanyan, Naira; Bulku, Artemisa; Berkmen, Melanie B

    2016-07-01

    Horizontal gene transfer plays a profound role in bacterial evolution by propelling the rapid transfer of genes and gene cassettes. Integrative and conjugative elements (ICEs) are one important mechanism driving horizontal gene transfer. ICEs, also known as conjugative transposons, reside on the host chromosome but can excise to form a conjugative DNA circle that is capable of transfer to other cells. Analysis of the large number of completed bacterial genome sequences has revealed many previously unrecognized ICEs, including ICEBs1, found in the Gram-positive model bacterium Bacillus subtilis. The discovery of ICEBs1 in an organism with such an impressive array of molecular tools for genetics and molecular biology was fortuitous. Significant insights into ICE biology have resulted since its discovery <15years ago. In this review, we describe aspects of ICEBs1 biology, such as excision, conjugative transfer, and reintegration, likely to be conserved across many ICEs. We will also highlight some of the more unexpected aspects of ICEBs1 biology, such as its ability to undergo plasmid-like replication after excision and its ability to mobilize plasmids lacking dedicated mobilization functions. A molecular understanding of ICEBs1 has led to additional insights into signals and mechanisms that promote horizontal gene transfer and shape bacterial evolution. PMID:27381852

  12. 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

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

    PubMed Central

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

    2016-01-01

    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. PMID:26779141

  14. 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.

  15. 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

  16. 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.

  17. Worldwide occurrence of integrative conjugative element encoding multidrug resistance determinants in epidemic Vibrio cholerae O1.

    PubMed

    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.

  18. Integrative conjugative element ICE-βox confers oxidative stress resistance to Legionella pneumophila in vitro and in macrophages.

    PubMed

    Flynn, Kaitlin J; Swanson, Michele S

    2014-01-01

    ABSTRACT Integrative conjugative elements (ICEs) are mobile blocks of DNA that can contribute to bacterial evolution by self-directed transmission of advantageous traits. Here, we analyze the activity of a putative 65-kb ICE harbored by Legionella pneumophila using molecular genetics, conjugation assays, a phenotype microarray screen, and macrophage infections. The element transferred to a naive L. pneumophila strain, integrated site-specifically, and conferred increased resistance to oxacillin, penicillin, hydrogen peroxide, and bleach. Furthermore, the element increased survival of L. pneumophila within restrictive mouse macrophages. In particular, this ICE protects L. pneumophila from phagocyte oxidase activity, since mutation of the macrophage NADPH oxidase eliminated the fitness difference between strains that carried and those that lacked the mobile element. Renamed ICE-βox (for β-lactam antibiotics and oxidative stress), this transposable element is predicted to contribute to the emergence of L. pneumophila strains that are more fit in natural and engineered water systems and in macrophages. IMPORTANCE Bacteria evolve rapidly by acquiring new traits via horizontal gene transfer. Integrative conjugative elements (ICEs) are mobile blocks of DNA that encode the machinery necessary to spread among bacterial populations. ICEs transfer antibiotic resistance and other bacterial survival factors as cargo genes carried within the element. Here, we show that Legionella pneumophila, the causative agent of Legionnaires' disease, carries ICE-βox, which enhances the resistance of this opportunistic pathogen to bleach and β-lactam antibiotics. Moreover, L. pneumophila strains encoding ICE-βox are more resistant to macrophages that carry phagocyte oxidase. Accordingly, ICE-βox is predicted to increase the fitness of L. pneumophila in natural and engineered waters and in humans. To our knowledge, this is the first description of an ICE that confers oxidative

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

    PubMed Central

    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. PMID:26106378

  20. Integrative Conjugative Element ICE-βox Confers Oxidative Stress Resistance to Legionella pneumophila In Vitro and in Macrophages

    PubMed Central

    Flynn, Kaitlin J.

    2014-01-01

    ABSTRACT Integrative conjugative elements (ICEs) are mobile blocks of DNA that can contribute to bacterial evolution by self-directed transmission of advantageous traits. Here, we analyze the activity of a putative 65-kb ICE harbored by Legionella pneumophila using molecular genetics, conjugation assays, a phenotype microarray screen, and macrophage infections. The element transferred to a naive L. pneumophila strain, integrated site-specifically, and conferred increased resistance to oxacillin, penicillin, hydrogen peroxide, and bleach. Furthermore, the element increased survival of L. pneumophila within restrictive mouse macrophages. In particular, this ICE protects L. pneumophila from phagocyte oxidase activity, since mutation of the macrophage NADPH oxidase eliminated the fitness difference between strains that carried and those that lacked the mobile element. Renamed ICE-βox (for β-lactam antibiotics and oxidative stress), this transposable element is predicted to contribute to the emergence of L. pneumophila strains that are more fit in natural and engineered water systems and in macrophages. PMID:24781744

  1. 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. PMID:27379024

  2. 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

  3. Characterization of a New CAMP Factor Carried by an Integrative and Conjugative Element in Streptococcus agalactiae and Spreading in Streptococci

    PubMed Central

    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 tRNALys encoding gene. In strain 515 of S. agalactiae, an invasive neonate human pathogen, the ICE (called 515_tRNALys) 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 tRNALys gene. This work thus describes a CAMP factor that is carried by a mobile genetic element and has spread to different streptococcal species. PMID:23152820

  4. 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

  5. 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

  6. 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

  7. Rapid detection by multiplex PCR of Genomic Islands, prophages and Integrative Conjugative Elements in V. cholerae 7th pandemic variants.

    PubMed

    Spagnoletti, Matteo; Ceccarelli, Daniela; Colombo, Mauro M

    2012-01-01

    Vibrio cholerae poses a threat to human health, and new epidemic variants have been reported so far. Seventh pandemic V. cholerae strains are characterized by highly related genomic sequences but can be discriminated by a large set of Genomic Islands, phages and Integrative Conjugative Elements. Classical serotyping and biotyping methods do not easily discriminate among new variants arising worldwide, therefore the establishment of new methods for their identification is required. We developed a multiplex PCR assay for the rapid detection of the major 7th pandemic variants of V. cholerae O1 and O139. Three specific genomic islands (GI-12, GI-14 and GI-15), two phages (Kappa and TLC), Vibrio Seventh Pandemic Island 2 (VSP-II), and the ICEs of the SXT/R391 family were selected as targets of our multiplex PCR based on a comparative genomic approach. The optimization and specificity of the multiplex PCR was assessed on 5 V. cholerae 7th pandemic reference strains, and other 34 V. cholerae strains from various epidemic events were analyzed to validate the reliability of our method. This assay had sufficient specificity to identify twelve different V. cholerae genetic profiles, and therefore has the potential to be used as a rapid screening method.

  8. Self-transmissibility of the integrative and conjugative element ICEPm1 between clinical isolates requires a functional integrase, relaxase, and type IV secretion system.

    PubMed

    Flannery, Erika L; Antczak, Samantha M; Mobley, Harry L T

    2011-08-01

    Integrative and conjugative elements (ICEs), which are chromosomal mobile elements, can conjugatively transfer between bacteria. Recently, we identified a genomic island of Proteus mirabilis, a common agent of catheter-associated urinary tract infection (UTI), that possesses all the properties consistent with an ICE. This element, designated ICEPm1, is highly conserved in other causative agents of UTI, suggesting its mobility. We demonstrate that ICEPm1 can actively excise from the chromosome in a clonal population of bacteria and that this excision is integrase dependent. Although in P. mirabilis HI4320, ICEPm1 is annotated as integrated into the phenylalanine tRNA gene pheV, we show that ICEPm1 can integrate into either pheV or pheU. We determined that ICEPm1 transfers at a frequency of 1.35 × 10(-5) transconjugants/donor to ICEPm1-deficient P. mirabilis using plate mating assays with clinical isolates. Insertional inactivation of a putative integrase gene on ICEPm1 decreased transfer frequencies of ICEPm1 to below the limit of detection. Mutation of the relaxase of ICEPm1 also eliminates transfer and demonstrates that this element is indeed self-transmissible and not transferred in trans, as are some mobilizable genomic islands. Together, these findings clearly demonstrate that ICEPm1 can actively excise from the chromosome in an integrase-dependent manner, dynamically integrate into both phenylalanine tRNA genes, and transfer into clinical strains using its own conjugation machinery. PMID:21665966

  9. Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element

    PubMed Central

    Delavat, François; Mitri, Sara; Pelet, Serge; van der Meer, Jan Roelof

    2016-01-01

    Horizontal gene transfer is an important evolutionary mechanism for bacterial adaptation. However, given the typical low transfer frequencies in a bacterial population, little is known about the fate and interplay of donor cells and the mobilized DNA during transfer. Here we study transfer of an integrative and conjugative element (ICE) among individual live bacterial cells. ICEs are widely distributed mobile DNA elements that are different than plasmids because they reside silent in the host chromosome and are maintained through vertical descent. Occasionally, ICEs become active, excise, and transmit their DNA to a new recipient, where it is reintegrated. We develop a fluorescent tool to differentiate excision, transfer, and reintegration of a model ICE named ICEclc (for carrying the clc genes for chlorocatechol metabolism) among single Pseudomonas cells by using time-lapse microscopy. We find that ICEclc activation is initiated in stationary phase cells, but excision and transfer predominantly occur only when such cells have been presented with new nutrients. Donors with activated ICE develop a number of different states, characterized by reduced cell division rates or growth arrest, persistence, or lysis, concomitant with ICE excision, and likely, ICE loss or replication. The donor cell state transitions can be described by using a stochastic model, which predicts that ICE fitness is optimal at low initiation rates in stationary phase. Despite highly variable donor cell fates, ICE transfer is remarkably robust overall, with 75% success after excision. Our results help to better understand ICE behavior and shed a new light on bacterial cellular differentiation during horizontal gene transfer. PMID:27247406

  10. Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element.

    PubMed

    Delavat, François; Mitri, Sara; Pelet, Serge; van der Meer, Jan Roelof

    2016-06-14

    Horizontal gene transfer is an important evolutionary mechanism for bacterial adaptation. However, given the typical low transfer frequencies in a bacterial population, little is known about the fate and interplay of donor cells and the mobilized DNA during transfer. Here we study transfer of an integrative and conjugative element (ICE) among individual live bacterial cells. ICEs are widely distributed mobile DNA elements that are different than plasmids because they reside silent in the host chromosome and are maintained through vertical descent. Occasionally, ICEs become active, excise, and transmit their DNA to a new recipient, where it is reintegrated. We develop a fluorescent tool to differentiate excision, transfer, and reintegration of a model ICE named ICEclc (for carrying the clc genes for chlorocatechol metabolism) among single Pseudomonas cells by using time-lapse microscopy. We find that ICEclc activation is initiated in stationary phase cells, but excision and transfer predominantly occur only when such cells have been presented with new nutrients. Donors with activated ICE develop a number of different states, characterized by reduced cell division rates or growth arrest, persistence, or lysis, concomitant with ICE excision, and likely, ICE loss or replication. The donor cell state transitions can be described by using a stochastic model, which predicts that ICE fitness is optimal at low initiation rates in stationary phase. Despite highly variable donor cell fates, ICE transfer is remarkably robust overall, with 75% success after excision. Our results help to better understand ICE behavior and shed a new light on bacterial cellular differentiation during horizontal gene transfer. PMID:27247406

  11. 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

  12. 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. PMID:26643344

  13. Characterization of the integration and modular excision of the integrative conjugative element PAISt in Streptomyces turgidiscabies Car8.

    PubMed

    Huguet-Tapia, Jose C; Bignell, Dawn R D; Loria, Rosemary

    2014-01-01

    PAISt is a large genomic island located in the chromosome of the plant pathogen Streptomyces turgidiscabies Car8. The island carries clustered virulence genes, transfers to other Streptomyces species, and integrates by site-specific recombination at the 8 bp palindrome TTCATGAA. The palindrome is located at the 3' end of the bacitracin resistance gene (bacA). We demonstrate that PAISt is able to excise in modules by recombination of one internal and two flanking palindromic direct repeats. The gene intSt located at the 3( end of PAISt encodes a tyrosine recombinase. Site-specific recombination activity of intSt was tested and confirmed by heterologous expression in Streptomyces coelicolor. Comparative analysis of PAISt homologues in Streptomyces scabies 87-22 and Streptomyces acidiscabies 84-104 indicates that these islands have been fixed by sequence erosion of intSt and the recombination sites. PMID:24927117

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  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. PMID:27215217

  1. 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

  2. Cloning and physical characterization of chromosomal conjugative elements in streptococci

    SciTech Connect

    Vijayakumar, M.N.; Priebe, S.D.; Pozzi, G.; Hageman, J.M.; Guild, W.R.

    1986-06-01

    A directed insertion method was used to introduce a nonreplicating vector plasmid into the large conjugative cat-tet element found in the chromosome of Streptococcus pneumoniae BM6001 and derivatives. To direct insertion preferentially to the conjugative element, we transferred it by conjugation to Streptococcus faecalis and then used DNA from this strain as a source of restriction nuclease fragments for ligation to digests of the vector pVA891, which can replicate in Escherichia coli but not in streptococci. This ligation mix was used to transform pneumococcal cells carrying the cat-tet element, with selection for the erythromycin resistance carried by pVA891. Eight such isolates were found, and transformation and conjugation tests showed that in each case the vector had inserted into the conjugative element, as expected. DNA from these pneumococcal strains generated a variety of E. coli plasmids which provide tools for obtaining a detailed restriction map and for defining other structural features of the streptococcal conjugative element.

  3. 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.

  4. 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

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

    PubMed

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

    2016-08-01

    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. PMID:27344980

  6. Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer

    PubMed Central

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

    2014-01-01

    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. PMID:25474706

  7. 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.

  8. Genomic islands are dynamic, ancient integrative elements in bacterial evolution.

    PubMed

    Boyd, E Fidelma; Almagro-Moreno, Salvador; Parent, Michelle A

    2009-02-01

    Acquisition of genomic islands plays a central part in bacterial evolution as a mechanism of diversification and adaptation. Genomic islands are non-self-mobilizing integrative and excisive elements that encode diverse functional characteristics but all contain a recombination module comprised of an integrase, associated attachment sites and, in some cases, a recombination directionality factor. Here, we discuss how a group of related genomic islands are evolutionarily ancient elements unrelated to plasmids, phages, integrons and integrative conjugative elements. In addition, we explore the diversity of genomic islands and their insertion sites among Gram-negative bacteria and discuss why they integrate at a limited number of tRNA genes.

  9. Genomic islands are dynamic, ancient integrative elements in bacterial evolution.

    PubMed

    Boyd, E Fidelma; Almagro-Moreno, Salvador; Parent, Michelle A

    2009-02-01

    Acquisition of genomic islands plays a central part in bacterial evolution as a mechanism of diversification and adaptation. Genomic islands are non-self-mobilizing integrative and excisive elements that encode diverse functional characteristics but all contain a recombination module comprised of an integrase, associated attachment sites and, in some cases, a recombination directionality factor. Here, we discuss how a group of related genomic islands are evolutionarily ancient elements unrelated to plasmids, phages, integrons and integrative conjugative elements. In addition, we explore the diversity of genomic islands and their insertion sites among Gram-negative bacteria and discuss why they integrate at a limited number of tRNA genes. PMID:19162481

  10. Make conjugation simple: a facile approach to integrated nanostructures.

    PubMed

    Xu, Yaolin; Palchoudhury, Soubantika; Qin, Ying; Macher, Thomas; Bao, Yuping

    2012-06-12

    We report a facile approach to the conjugation of protein-encapsulated gold fluorescent nanoclusters to the iron oxide nanoparticles through catechol reaction. This method eliminates the use of chemical linkers and can be readily extended to the conjugation of biological molecules and other nanomaterials onto nanoparticle surfaces. The key to the success was producing water-soluble iron oxide nanoparticles with active catechol groups. Further, advanced electron microscopy analysis of the integrated gold nanoclusters and iron oxide nanoparticles provided direct evidence of the presence of a single fluorescent nanocluster per protein template. Interestingly, the integrated nanoparticles exhibited enhanced fluorescent emission in biological media. These studies will provide significantly practical value in chemical conjugation, the development of multifunctional nanostructures, and exploration of multifunctional nanoparticles for biological applications.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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. PMID:19025575

  16. Integral volumetric imaging using decentered elemental lenses.

    PubMed

    Sawada, Shimpei; Kakeya, Hideki

    2012-11-01

    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.

  17. Integrative mobile elements exploiting Xer recombination.

    PubMed

    Das, Bhabatosh; Martínez, Eriel; Midonet, Caroline; Barre, François-Xavier

    2013-01-01

    Integrative mobile genetic elements directly participate in the rapid response of bacteria to environmental challenges. They generally encode their own dedicated recombination machineries. CTXφ, a filamentous bacteriophage that harbors the genes encoding cholera toxin in Vibrio cholerae provided the first notable exception to this rule: it hijacks XerC and XerD, two chromosome-encoded tyrosine recombinases for lysogenic conversion. XerC and XerD are highly conserved in bacteria because of their role in the topological maintenance of circular chromosomes and, with the advent of high throughput sequencing, numerous other integrative mobile elements exploiting them have been discovered. Here, we review our understanding of the molecular mechanisms of integration of the different integrative mobile elements exploiting Xer (IMEXs) so far described. PMID:23127381

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

    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 percent for sufficiently large problems.

  19. 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.

  20. Spectral element-Fourier method for unsteady conjugate heat transfer in complex geometry flows

    NASA Astrophysics Data System (ADS)

    Amon, Cristina H.

    1995-04-01

    A spectral-element Fourier method (SEFM) is presented for the direct numerical simulation of forced convective heat transfer and conjugate conduction/convection in transitional internal flows in complex geometries. The SEFM is employed for the spatial discretization of the unsteady, incompressible, three-dimensional Navier-Stokes and energy equations. The resulting discrete equations are solved by a semi-implicit method in time treating explicitly the convection operator and implicitly the remaining pressure and viscous contributions. This methodology is illustrated by performing direct numerical simulations to investigate forced convective heat transfer in supercritical self-sustained oscillatory flows and conjugate effects in multimaterial domains. Highly unsteady flows in complex geometries are considered, including modified channels with periodic inhomogeneities such as spanwise rectangular and triangular grooves encountered in electronic equipment and compact heat exchangers.

  1. Functional Analysis of a Bacitracin Resistance Determinant Located on ICECp1, a Novel Tn916-Like Element from a Conjugative Plasmid in Clostridium perfringens

    PubMed Central

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

    2015-01-01

    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. PMID:26282424

  2. Integration of erm(B)-containing elements through large chromosome fragment exchange in Clostridium difficile

    PubMed Central

    Wasels, François; Spigaglia, Patrizia; Barbanti, Fabrizio; Monot, Marc; Villa, Laura; Dupuy, Bruno; Carattoli, Alessandra; Mastrantonio, Paola

    2015-01-01

    In Clostridium difficile, erm(B) genes are located on mobile elements like Tn5398 and Tn6215. In previous studies, some of these elements were transferred by conjugation-like mechanisms, mobilized in trans by helper conjugative systems. In this study, we analyzed the genomes of several recipient strains that acquired either Tn5398 or Tn6215-like elements. We demonstrated that the integration of the transposons in the genome of the recipient cell was always due to homologous recombination events, involving exchange of large chromosomal segments. We did not observed transposon transfer to a C. difficile strain in presence of DNAse, suggesting that a possible transformation-like mechanism occurred in this recipient. PMID:26442177

  3. 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.

  4. Integrated transient thermal-structural finite element analysis

    NASA Technical Reports Server (NTRS)

    Thornton, E. A.; Dechaumphai, P.; Wieting, A. R.; Tamma, K. K.

    1981-01-01

    An integrated thermal structural finite element approach for efficient coupling of transient thermal and structural analysis is presented. Integrated thermal structural rod and one dimensional axisymmetric elements considering conduction and convection are developed and used in transient thermal structural applications. The improved accuracy of the integrated approach is illustrated by comparisons with exact transient heat conduction elasticity solutions and conventional finite element thermal finite element structural analyses.

  5. 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.

  6. 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.

  7. Integrated transient thermal-structural finite element analysis

    NASA Technical Reports Server (NTRS)

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

    1981-01-01

    An integrated thermal-structural finite element approach for efficient coupling of transient thermal and structural analysis is presented. New integrated thermal-structural rod and one dimensional axisymmetric elements considering conduction and convection are developed and used in transient thermal-structural applications. The improved accuracy of the integrated approach is illustrated by comparisons with exact transient heat conduction-elasticity solutions and conventional finite element thermal-finite element structural analyses. Results indicate that the approach offers significant potential for further development with other elements.

  8. 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.

  9. 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.

  10. A new regulatory element modulates homoserine lactone-mediated autoinduction of Ti plasmid conjugal transfer.

    PubMed Central

    Hwang, I; Cook, D M; Farrand, S K

    1995-01-01

    Conjugal transfer of the Agrobacterium tumefaciens nopaline-type Ti plasmid pTiC58 is induced by agrocinopines A and B, opines secreted by crown gall tumors induced by the bacterium. This regulation functions through the transcriptional repressor, AccR. However, actual transcription of the tra genes is regulated by autoinduction through the activator TraR and the substituted homoserine lactone second messenger, Agrobacterium autoinducer (AAI). We have identified a new regulatory element that modulates the response of TraR to AAI. The gene, called traM, suppresses TraR-AAI activation of transcription of tra genes carried on recombinant clones. The suppression could be relieved by increasing the expression of TraR but not by increasing AAI levels. traM is located between traR and traAF on pTiC58 and is transcribed in the clockwise direction. The 306-bp gene encodes an 11.2-kDa protein showing no significant relatedness to other proteins in the databases. Mutations in traM in pTiC58 conferred a transfer-constitutive phenotype, and strains harboring the Ti plasmid produced easily detectable amounts of AAI. These same mutations engineered into the transfer-constitutive Ti plasmid pTiC58 delta accR conferred a hyperconjugal phenotype and very high levels of AAI production. Expression of traM required TraR, indicating that transcription of the gene is regulated by the autoinduction system. TraM had no effect on the expression of traR, demonstrating that the suppressive effect is not due to repression of the gene encoding the activator. These results suggest that TraM is not a direct transcriptional regulator. Since the suppressive effect is demonstrable only when traM is overexpressed with respect to traR, we suggest that TraM functions to sequester TraR from the very small amounts of AAI produced under conditions when the agrocinopines are not present. PMID:7814335

  11. 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

  12. 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.

  13. Finite Element Analysis for Pseudo Hyperbolic Integral-Differential Equations

    NASA Astrophysics Data System (ADS)

    Cui, Xia

    The finite element method and its analysis for pseudo-hyperbolic integral-differential equations with nonlinear boundary conditions is considered. A new projection is introduced to obtain optimal L2 convergence estimates. The present techniques can be applied to treat elastic wave problems with absorbing boundary conditions in porous media. Keywords: pseudo-hyperbolic integral-differential equation, finite element, Sobolev-Volterra projection, convergence analysis

  14. 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.

  15. 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.

  16. 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

  17. Analysis of the mobilization functions of the vancomycin resistance transposon Tn1549, a member of a new family of conjugative elements.

    PubMed

    Tsvetkova, Krassimira; Marvaud, Jean-Christophe; Lambert, Thierry

    2010-02-01

    Conjugative transfer from Clostridium symbiosum to enterococci of Tn1549, which confers VanB-type vancomycin resistance, has been reported. This indicates the presence of a transfer origin (oriT) in the element. Transcription analysis of Tn1549 indicated that orf29, orf28, orfz, and orf27 were cotranscribed. A pACYC184 derivative containing 250 bp intergenic to orf29-orf30 of Tn1549 was mobilized in Escherichia coli recA::RP4::Delta nic provided that orf28 and orf29 were delivered simultaneously. These open reading frame (ORF) genes were able to promote mobilization in trans, but a cis-acting preference was observed. On the basis of a mobilization assay, a minimal 28-bp oriT was delimited, although the frequency of transfer was significantly reduced compared to that of a 130-bp oriT fragment. The minimal oriT contained an inverted repeat and a core, which was homologous to the cleavage sequence found in certain Gram-positive rolling-circle replicating (RCR) plasmids. While Orf29 was a mobilization accessory component similar to MobC proteins, Orf28 was identified as a relaxase belonging to a new phyletic cluster of the MOB(p) superfamily. The nick site was identified within oriT by an oligonucleotide cleavage assay. Closely related oriTs linked to mobilization genes were detected in data banks; they were found in various integrative and conjugative elements (ICEs) originating mainly from anaerobes. These results support the notion that Tn1549 is a member of a MOB(p) clade. Interestingly, the Tn1549-derived constructs were mobilized by RP4 in E. coli, suggesting that a relaxosome resulting from DNA cleavage by Orf28 interacted with the coupling protein TraG. This demonstrates the capacity of Tn1549 to be mobilized by a heterologous transfer system.

  18. 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

  19. A non-integral, axial-force measuring element

    NASA Astrophysics Data System (ADS)

    Ringel, M.; Levin, D.; Seginer, A.

    1989-10-01

    A new approach to the measurement of the axial force is presented. A nonintegral axial-force measuring element, housed within the wind-tunnel model, avoids the interactions that are caused by nonlinear elastic phenomena characteristic of integral balances. The new design overcomes other problems, such as friction, misalignment and relative motion between metric elements, that plagued previous attempts at separate measurement of the axial force. Calibration and test results prove the ability of the new approach to duplicate and even surpass the results of much more complicated and expensive integral balances. The advantages of the new design make it the best known solution for particular measurement problems.

  20. A 90-Kilobase Conjugative Chromosomal Element Coding for Biphenyl and Salicylate Catabolism in Pseudomonas putida KF715

    PubMed Central

    Nishi, Akito; Tominaga, Kiyomi; Furukawa, Kensuke

    2000-01-01

    The biphenyl and salicylate metabolic pathways in Pseudomonas putida KF715 are chromosomally encoded. The bph gene cluster coding for the conversion of biphenyl to benzoic acid and the sal gene cluster coding for the salicylate meta-pathway were obtained from the KF715 genomic cosmid libraries. These two gene clusters were separated by 10-kb DNA and were highly prone to deletion when KF715 was grown in nutrient medium. Two types of deletions took place at the region including only the bph genes (ca. 40 kb) or at the region including both the bph and sal genes (ca. 70 kb). A 90-kb DNA region, including both the bph and sal genes (termed the bph-sal element), was transferred by conjugation from KF715 to P. putida AC30. Such transconjugants gained the ability to grow on biphenyl and salicylate as the sole sources of carbon. The bph and sal element was located on the chromosome of the recipient. The bph-sal element in strain AC30 was also highly prone to deletion; however, it could be mobilized to the chromosome of P. putida KT2440 and the two deletion mutants of KF715. PMID:10715002

  1. A multilevel finite element method for Fredholm integral eigenvalue problems

    NASA Astrophysics Data System (ADS)

    Xie, Hehu; Zhou, Tao

    2015-12-01

    In this work, we proposed a multigrid finite element (MFE) method for solving the Fredholm integral eigenvalue problems. The main motivation for such studies is to compute the Karhunen-Loève expansions of random fields, which play an important role in the applications of uncertainty quantification. In our MFE framework, solving the eigenvalue problem is converted to doing a series of integral iterations and eigenvalue solving in the coarsest mesh. Then, any existing efficient integration scheme can be used for the associated integration process. The error estimates are provided, and the computational complexity is analyzed. It is noticed that the total computational work of our method is comparable with a single integration step in the finest mesh. Several numerical experiments are presented to validate the efficiency of the proposed numerical method.

  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 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. Elements for successful sensor-based process control {Integrated Metrology}

    NASA Astrophysics Data System (ADS)

    Butler, Stephanie Watts

    1998-11-01

    Current productivity needs have stimulated development of alternative metrology, control, and equipment maintenance methods. Specifically, sensor applications provide the opportunity to increase productivity, tighten control, reduce scrap, and improve maintenance schedules and procedures. Past experience indicates a complete integrated solution must be provided for sensor-based control to be used successfully in production. In this paper, Integrated Metrology is proposed as the term for an integrated solution that will result in a successful application of sensors for process control. This paper defines and explores the perceived four elements of successful sensor applications: business needs, integration, components, and form. Based upon analysis of existing successful commercially available controllers, the necessary business factors have been determined to be strong, measurable industry-wide business needs whose solution is profitable and feasible. This paper examines why the key aspect of integration is the decision making process. A detailed discussion is provided of the components of most importance to sensor based control: decision-making methods, the 3R's of sensors, and connectivity. A metric for one of the R's (resolution) is proposed to allow focus on this important aspect of measurement. A form for these integrated components which synergistically partitions various aspects of control at the equipment and MES levels to efficiently achieve desired benefits is recommended.

  8. 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

  9. 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.

  10. 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. PMID:27173524

  11. 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

  12. 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.

  13. 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

  14. 49 CFR 192.911 - What are the elements of an integrity management program?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 3 2010-10-01 2010-10-01 false What are the elements of an integrity management... Transmission Pipeline Integrity Management § 192.911 What are the elements of an integrity management program? An operator's initial integrity management program begins with a framework (see § 192.907)...

  15. 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.

  16. 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.

  17. 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

  18. Bacterial conjugation protein MobA mediates integration of complex DNA structures into plant cells.

    PubMed

    Bravo-Angel, A M; Gloeckler, V; Hohn, B; Tinland, B

    1999-09-01

    Agrobacterium tumefaciens transfers T-DNA to plant cells, where it integrates into the genome, a property that is ensured by bacterial proteins VirD2 and VirE2. Under natural conditions, the protein MobA mobilizes its encoding plasmid, RSF1010, between different bacteria. A detailed analysis of MobA-mediated DNA mobilization by Agrobacterium to plants was performed. We compared the ability of MobA to transfer DNA and integrate it into the plant genome to that of pilot protein VirD2. MobA was found to be about 100-fold less efficient than VirD2 in conducting the DNA from the pTi plasmid to the plant cell nucleus. However, interestingly, DNAs transferred by the two proteins were integrated into the plant cell genome with similar efficiencies. In contrast, most of the integrated DNA copies transferred from a MobA-containing strain were truncated at the 5' end. Isolation and analysis of the most conserved 5' ends revealed patterns which resulted from the illegitimate integration of one transferred DNA within another. These complex integration patterns indicate a specific deficiency in MobA. The data conform to a model according to which efficiency of T-DNA integration is determined by plant enzymes and integrity is determined by bacterial proteins. PMID:10482518

  19. 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.

  20. 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.

  1. 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.

  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. 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.

  4. 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.

  5. Integrating conjugated polymer microactuators with CMOS sensing circuitry for studying living cells

    NASA Astrophysics Data System (ADS)

    Urdaneta, Mario; Liu, Yingkai; Christophersen, Marc; Prakash, Somashekar; Abshire, Pamela; Smela, Elisabeth

    2005-05-01

    We present the use of electroactive polymer actuators as components of a biolab-on-a-chip, which has potential applications in cell-based sensing. This technology takes full advantage of the properties of polypyrrole actuators as well as the wide range of CMOS sensors that can be created. System integration becomes an important issue when developing real applications of EAP technologies. The requirements of the application and the constraints imposed by the various components must be considered in the context of the whole system, along with any opportunities that present themselves. In this paper, we discuss some of these challenges, including actuator design, the use of complementary actuation techniques, miniaturization, and packaging.

  6. 49 CFR 192.1007 - What are the required elements of an integrity management plan?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... management plan? 192.1007 Section 192.1007 Transportation Other Regulations Relating to Transportation... Distribution Pipeline Integrity Management (IM) § 192.1007 What are the required elements of an integrity management plan? A written integrity management plan must contain procedures for developing and...

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

    PubMed

    2012-09-01

    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.

  8. 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

  9. Coupling finite element and integral equation solutions using decoupled boundary meshes

    NASA Technical Reports Server (NTRS)

    Cwik, Tom

    1992-01-01

    A method is outlined for calculating scattered fields from inhomogeneous penetrable objects using a coupled finite element-integral equation solution. The finite element equation can efficiently model fields in penetrable and inhomogeneous regions, while the integral equation exactly models fields on the finite element mesh boundary and in the exterior region. By decoupling the interior finite element and exterior integral equation meshes, considerable flexibility is found in both the number of field expansion points as well as their density. Only the nonmetal portions of the object need be modeled using a finite element expansion; exterior perfect conducting surfaces are modeled using an integral equation with a single unknown field since E(tan) is identically zero on these surfaces. Numerical convergence, accuracy, and stability at interior resonant frequencies are studied in detail.

  10. Integrative annotation of chromatin elements from ENCODE data

    PubMed Central

    Hoffman, Michael M.; Ernst, Jason; Wilder, Steven P.; Kundaje, Anshul; Harris, Robert S.; Libbrecht, Max; Giardine, Belinda; Ellenbogen, Paul M.; Bilmes, Jeffrey A.; Birney, Ewan; Hardison, Ross C.; Dunham, Ian; Kellis, Manolis; Noble, William Stafford

    2013-01-01

    The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of regulatory elements, their interrelations contain much richer information for the systematic annotation of regulatory elements. To uncover these interrelations and to generate an interpretable summary of the massive datasets of the ENCODE Project, we apply unsupervised learning methodologies, converting dozens of chromatin datasets into discrete annotation maps of regulatory regions and other chromatin elements across the human genome. These methods rediscover and summarize diverse aspects of chromatin architecture, elucidate the interplay between chromatin activity and RNA transcription, and reveal that a large proportion of the genome lies in a quiescent state, even across multiple cell types. The resulting annotation of non-coding regulatory elements correlate strongly with mammalian evolutionary constraint, and provide an unbiased approach for evaluating metrics of evolutionary constraint in human. Lastly, we use the regulatory annotations to revisit previously uncharacterized disease-associated loci, resulting in focused, testable hypotheses through the lens of the chromatin landscape. PMID:23221638

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Evaluation of integrated tuning elements with SIS devices

    NASA Technical Reports Server (NTRS)

    Dierichs, M. M. T. M.; Honingh, C. E.; Panhuyzen, R. A.; Feenstra, B. J.; Skalare, A.; Wijnbergen, J. J.; Vanderstadt, H.; Degraauw, T.

    1992-01-01

    The resonance of integrated tuning stubs in combination with SIS detectors is measured and modeled. The predicted resonances are compared with measurements of stubs integrated with Nb/Al2O3/Nb junctions in a log-periodic antenna using a Michelson interferometer. Different stub lengths were made on different substrates (on 200 micron thick quartz and on a 7 micron thick silicon membrane) and the results show a fairly good agreement with the model calculations. Quartz substrates showed resonances up to 580 GHz, silicon membrane stub resonances reach as high as 480 GHz. An observed resonance at 560 GHz is probably a substrate effect from the membrane. The gap frequency for all the samples is 650 GHz and no resonances are detected above this frequency. Up to the maximum detected frequency dispersion is found to be negligible.

  16. 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.

  17. 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).

  18. 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.

  19. Intergeneric conjugation in Streptomyces peucetius and Streptomyces sp. strain C5: chromosomal integration and expression of recombinant plasmids carrying the chiC gene.

    PubMed

    Paranthaman, Senthamaraikannan; Dharmalingam, Kuppamuthu

    2003-01-01

    Intergeneric conjugal transfer of plasmid DNA from Escherichia coli to Streptomyces circumvents problems such as host-controlled restriction and instability of foreign DNA during the transformation of Streptomyces protoplasts. The anthracycline antibiotic-producing strains Streptomyces peucetius and Streptomyces sp. strain C5 were transformed using E. coli ET12567(pUZ8002) as a conjugal donor. When this donor species, carrying pSET152, was mated with Streptomyces strains, the resident plasmid was mobilized to the recipient and the transferred DNA was also integrated into the recipient chromosome. Analysis of the exconjugants showed stable integration of the plasmid at a single chromosomal site (attB) of the Streptomyces genome. The DNA sequence of the chromosomal integration site was determined and shown to be conserved. However, the core sequence, where the crossover presumably occurred in C5 and S. peucetius, is TTC. These results also showed that the phiC31 integrative recombination is active and the phage attP site is functional in S. peucetius as well as in C5. The efficiency and specificity of phiC31-mediated site-specific integration of the plasmid in the presence of a 3.7-kb homologous DNA sequence indicates that integrative recombination is preferred under these conditions. The integration of plasmid DNA did not affect antibiotic biosynthesis or biosynthesis of essential amino acids. Integration of a single copy of a mutant chiC into the wild-type S. peucetius chromosome led to the production of 30-fold more chitinase.

  20. 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.

  1. 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.

  2. Gaussian and finite-element Coulomb method for the fast evaluation of Coulomb integrals

    NASA Astrophysics Data System (ADS)

    Kurashige, Yuki; Nakajima, Takahito; Hirao, Kimihiko

    2007-04-01

    The authors propose a new linear-scaling method for the fast evaluation of Coulomb integrals with Gaussian basis functions called the Gaussian and finite-element Coulomb (GFC) method. In this method, the Coulomb potential is expanded in a basis of mixed Gaussian and finite-element auxiliary functions that express the core and smooth Coulomb potentials, respectively. Coulomb integrals can be evaluated by three-center one-electron overlap integrals among two Gaussian basis functions and one mixed auxiliary function. Thus, the computational cost and scaling for large molecules are drastically reduced. Several applications to molecular systems show that the GFC method is more efficient than the analytical integration approach that requires four-center two-electron repulsion integrals. The GFC method realizes a near linear scaling for both one-dimensional alanine α-helix chains and three-dimensional diamond pieces.

  3. 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.

  4. 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.

  5. 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'.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Segment-based vs. element-based integration for mortar methods in computational contact mechanics

    NASA Astrophysics Data System (ADS)

    Farah, Philipp; Popp, Alexander; Wall, Wolfgang A.

    2015-01-01

    Mortar finite element methods provide a very convenient and powerful discretization framework for geometrically nonlinear applications in computational contact mechanics, because they allow for a variationally consistent treatment of contact conditions (mesh tying, non-penetration, frictionless or frictional sliding) despite the fact that the underlying contact surface meshes are non-matching and possibly also geometrically non-conforming. However, one of the major issues with regard to mortar methods is the design of adequate numerical integration schemes for the resulting interface coupling terms, i.e. curve integrals for 2D contact problems and surface integrals for 3D contact problems. The way how mortar integration is performed crucially influences the accuracy of the overall numerical procedure as well as the computational efficiency of contact evaluation. Basically, two different types of mortar integration schemes, which will be termed as segment-based integration and element-based integration here, can be found predominantly in the literature. While almost the entire existing literature focuses on either of the two mentioned mortar integration schemes without questioning this choice, the intention of this paper is to provide a comprehensive and unbiased comparison. The theoretical aspects covered here include the choice of integration rule, the treatment of boundaries of the contact zone, higher-order interpolation and frictional sliding. Moreover, a new hybrid scheme is proposed, which beneficially combines the advantages of segment-based and element-based mortar integration. Several numerical examples are presented for a detailed and critical evaluation of the overall performance of the different schemes within several well-known benchmark problems of computational contact mechanics.

  12. CTnscr94, a conjugative transposon found in enterobacteria.

    PubMed Central

    Hochhut, B; Jahreis, K; Lengeler, J W; Schmid, K

    1997-01-01

    Conjugational transposons are important for horizontal gene transfer in gram-positive and gram-negative bacteria, but have not been reported yet for enteric bacteria. Salmonella senftenberg 5494-57 has previously been shown to transfer by conjugation genes for a sucrose fermentation pathway which were located on a DNA element called scr-94. We report here that the corresponding scr genes for a phosphoenolpyruvate-dependent sucrose:phosphotransferase system and a sucrose metabolic pathway are located on a large (ca. 100 kb) conjugative transposon renamed CTnscr94. The self-transmissible element integrates at two specific attachment sites in a RecA-independent way into the chromosome of Escherichia coli K-12 strains. One site was identified within pheV, the structural gene for a tRNA(Phe). Sequencing of both ends of CTnscr94 revealed the presence of the 3' part of pheV on one end such that after integration of the element, a complete pheV gene is retained. CTnscr94 represents, to our knowledge, the first conjugational transposon found in enteric bacteria. PMID:9079891

  13. Analytical finite element matrix elements and global matrix assembly for hierarchical 3-D vector basis functions within the hybrid finite element boundary integral method

    NASA Astrophysics Data System (ADS)

    Li, L.; Wang, K.; Li, H.; Eibert, T. F.

    2014-11-01

    A hybrid higher-order finite element boundary integral (FE-BI) technique is discussed where the higher-order FE matrix elements are computed by a fully analytical procedure and where the gobal matrix assembly is organized by a self-identifying procedure of the local to global transformation. This assembly procedure applys to both, the FE part as well as the BI part of the algorithm. The geometry is meshed into three-dimensional tetrahedra as finite elements and nearly orthogonal hierarchical basis functions are employed. The boundary conditions are implemented in a strong sense such that the boundary values of the volume basis functions are directly utilized within the BI, either for the tangential electric and magnetic fields or for the asssociated equivalent surface current densities by applying a cross product with the unit surface normals. The self-identified method for the global matrix assembly automatically discerns the global order of the basis functions for generating the matrix elements. Higher order basis functions do need more unknowns for each single FE, however, fewer FEs are needed to achieve the same satisfiable accuracy. This improvement provides a lot more flexibility for meshing and allows the mesh size to raise up to λ/3. The performance of the implemented system is evaluated in terms of computation time, accuracy and memory occupation, where excellent results with respect to precision and computation times of large scale simulations are found.

  14. 49 CFR 192.1007 - What are the required elements of an integrity management plan?

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... (Continued) PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF NATURAL AND OTHER GAS BY PIPELINE: MINIMUM FEDERAL SAFETY STANDARDS Gas Distribution Pipeline Integrity Management (IM) § 192.1007 What are the required elements of an...

  15. 49 CFR 192.1007 - What are the required elements of an integrity management plan?

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... (Continued) PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF NATURAL AND OTHER GAS BY PIPELINE: MINIMUM FEDERAL SAFETY STANDARDS Gas Distribution Pipeline Integrity Management (IM) § 192.1007 What are the required elements of an...

  16. 49 CFR 192.1007 - What are the required elements of an integrity management plan?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... (Continued) PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF NATURAL AND OTHER GAS BY PIPELINE: MINIMUM FEDERAL SAFETY STANDARDS Gas Distribution Pipeline Integrity Management (IM) § 192.1007 What are the required elements of an...

  17. 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.

  18. 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.

  19. Social behavior and decision making in bacterial conjugation

    PubMed Central

    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. PMID:24809026

  20. 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.

  1. 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.

  2. Developmental timing of mRNA translation--integration of distinct regulatory elements.

    PubMed

    MacNicol, Melanie C; MacNicol, Angus M

    2010-08-01

    Targeted mRNA translation is emerging as a critical mechanism to control gene expression during developmental processes. Exciting new findings have revealed a critical role for regulatory elements within the mRNA untranslated regions to direct the timing of mRNA translation. Regulatory elements can be targeted by sequence-specific binding proteins to direct either repression or activation of mRNA translation in response to developmental signals. As new regulatory elements continue to be identified it has become clear that targeted mRNAs can contain multiple regulatory elements, directing apparently contradictory translational patterns. How is this complex regulatory input integrated? In this review, we focus on a new challenge area-how sequence-specific RNA binding proteins respond to developmental signals and functionally integrate to regulate the extent and timing of target mRNA translation. We discuss current understanding with a particular emphasis on the control of cell cycle progression that is mediated through a complex interplay of distinct mRNA regulatory elements during Xenopus oocyte maturation.

  3. 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

  4. James Webb Space Telescope optical telescope element/integrated science instrument module (OTIS) status

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    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.

  5. 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

  6. 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.

  7. Finite element-integral acoustic simulation of JT15D turbofan engine

    NASA Astrophysics Data System (ADS)

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

    1984-07-01

    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.

  8. A mathematical boundary integral equation for analysis of the heterogeneous media, using the functionally graded elements

    NASA Astrophysics Data System (ADS)

    Ashrafi, H.; Shariyat, M.

    2015-09-01

    In the present research, a functionally graded (FG) boundary integral equation method capable of modeling quasistatic behavior of heterogeneous media fabricated from functionally graded materials (FGMs) whose distributions of the material properties obey either power or exponential laws is developed. Two heterogeneous material gradation models were employed to present the numerical formulations and solution algorithm. Somigliana's identity in 2D displacement fields of the isotropic heterogeneous domains is numerically implemented, employing FG elements. Based on the constitutive and governing equations and the weighted residual technique, the proposed boundary integral equation formulations are implemented for behavior analysis of the elastic heterogeneous isotropic solid structures. Results are verified and the proposed boundary element (BE) formulation is employed for behavior analysis of the plates and cylinders to demonstrate the proposed procedure more adequately.

  9. 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.

  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. PMID:26860923

  11. Partial extensions of jets and the polar distribution on Grassmannians of non-maximal integral elements

    NASA Astrophysics Data System (ADS)

    Bächtold, Michael

    2016-02-01

    We study an intrinsic distribution, called polar, on the space of l-dimensional integral elements of the higher order contact structure on jet spaces. The main result establishes that this exterior differential system is the prolongation of a natural system of PDEs, named pasting conditions, on sections of the bundle of partial jet extensions. Informally, a partial jet extension is a kth order jet with additional (k + 1)st order information along l of the n possible directions. A choice of partial extensions of a jet into all possible l-directions satisfies the pasting conditions if the extensions coincide along pairwise intersecting l-directions. We further show that prolonging the polar distribution once more yields the space of (l , n)-dimensional integral flags with its double fibration distribution. When l > 1 the exterior differential system is holonomic, stabilizing after one further prolongation. The proof starts form the space of integral flags, constructing the tower of prolongations by reduction.

  12. 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.

  13. 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.

  14. 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.

  15. Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements

    PubMed Central

    Levy, Asaf; Schwartz, Schraga; Ast, Gil

    2010-01-01

    Throughout evolution, eukaryotic genomes have been invaded by transposable elements (TEs). Little is known about the factors leading to genomic proliferation of TEs, their preferred integration sites and the molecular mechanisms underlying their insertion. We analyzed hundreds of thousands nested TEs in the human genome, i.e. insertions of TEs into existing ones. We first discovered that most TEs insert within specific ‘hotspots’ along the targeted TE. In particular, retrotransposed Alu elements contain a non-canonical single nucleotide hotspot for insertion of other Alu sequences. We next devised a method for identification of integration sequence motifs of inserted TEs that are conserved within the targeted TEs. This method revealed novel sequences motifs characterizing insertions of various important TE families: Alu, hAT, ERV1 and MaLR. Finally, we performed a global assessment to determine the extent to which young TEs tend to nest within older transposed elements and identified a 4-fold higher tendency of TEs to insert into existing TEs than to insert within non-TE intergenic regions. Our analysis demonstrates that TEs are highly biased to insert within certain TEs, in specific orientations and within specific targeted TE positions. TE nesting events also reveal new characteristics of the molecular mechanisms underlying transposition. PMID:20008508

  16. Boundary integral spectral element method analyses of extreme ultraviolet multilayer defects.

    PubMed

    Niu, Jun; Luo, Ma; Fang, Yuan; Liu, Qing Huo

    2014-10-01

    Extreme ultraviolet (EUV) lithography is an emerging technology for high-density semiconductor patterning. Multilayer distortion caused by mask defects is regarded as one of the critical challenges of EUV lithography. To simulate the influence of the defected nanoscale structures with high accuracy and efficiency, we have developed a boundary integral spectral element method (BI-SEM) that combines the SEM with a set of surface integral equations. The SEM is used to solve the interior computational domain, while the open boundaries are truncated by the surface integral equations. Both two-dimensional (2D) and three-dimensional (3D) EUV cases are simulated. Through comparing the performance of this method with the conventional finite element method (FEM), it is shown that the proposed BI-SEM can greatly decrease both the memory cost and the computation time. For typical 2D problems, we show that the BI-SEM is 11 and 1.25 times more efficient than the FEM in terms of memory and CPU time, respectively, while for 3D problems, these factors are over 14 and 2, respectively, for smaller problems; realistic 3D problems that cannot be solved by the conventional FEM can be accurately simulated by the BI-SEM. PMID:25401246

  17. 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.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Gallego, C.; Fernández, M.; Caires, A. S.; Cañibano, E.

    2007-05-01

    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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. An independent refinement and integration procedure in multiregion finite element analysis

    NASA Technical Reports Server (NTRS)

    Krishnamurthy, T.; Raju, I. S.

    1992-01-01

    An independent refinement and integration procedure is developed to couple together independently modeled (global and local) regions in a single analysis. The models can have different levels of refinement and along the interface between them the finite element nodes need not coincide with one another. In the local model all the nodes except the nodes at the interface are statically condensed and the reduced stiffness matrix is obtained. For this static condensation a modified frontal solution technique is employed. A spline interpolation function that satisfies the linear isotropic plate bending differential equation is used to relate the local model interface nodal displacements to the global model interface displacements. The proposed independent refinement and integration procedure is evaluated by applying it to two- and three-dimensional cases involving inplane and out-of-plane deformation. The procedure yielded very accurate results for all the examples studied.

  8. Hybrid plasmon/dielectric waveguide for integrated silicon-on-insulator optical elements.

    PubMed

    Flammer, P D; Banks, J M; Furtak, T E; Durfee, C G; Hollingsworth, R E; Collins, R T

    2010-09-27

    VLSI compatible optical waveguides on silicon are currently of particular interest in order to integrate optical elements onto silicon chips, and for possible replacements of electrical cross-chip/inter-core interconnects. Here we present simulation and experimental verification of a hybrid plasmon/dielectric, single-mode, single-polarization waveguide for silicon-on-insulator wafers. Its fabrication is compatible with VLSI processing techniques, and it possesses desirable properties such as the absence of birefringence and low sensitivity to surface roughness and metallic losses. The waveguide structure naturally forms an MOS capacitor, possibly useful for active device integration. Simulations predict very long propagation lengths of millimeter scale with micron scale confinement, or sub-micron scale confinement with propagation lengths still in excess of 100 microns. The waveguide may be tuned continuously between these states using standard VLSI processing. Extremely long propagation lengths have been simulated: one configuration presented here has a simulated propagation length of 34 cm. PMID:20940996

  9. A finite element solution to conjugated heat transfer in tissue using magnetic resonance angiography to measure the in vitro velocity field

    NASA Astrophysics Data System (ADS)

    Dutton, Andrew William

    1993-12-01

    A combined numerical and experimental system for tissue heat transfer analysis was developed. The goal was to develop an integrated set of tools for studying the problem of providing accurate temperature estimation for use in hyperthermia treatment planning in a clinical environment. The completed system combines (1) Magnetic Resonance Angiography (MRA) to non-destructively measure the velocity field in situ, (2) the Streamwise Upwind Petrov-Galerkin finite element solution to the 3D steady state convective energy equation (CEE), (3) a medical image based automatic 3D mesh generator, and (4) a Gaussian type estimator to determine unknown thermal model parameters such as thermal conductivity, blood perfusion, and blood velocities from measured temperature data. The system was capable of using any combination of three thermal models (1) the Convective Energy Equation (CEE), (2) the Bioheat Transfer Equation (BHTE), and (3) the Effective Thermal Conductivity Equation (ETCE) Incorporation of the theoretically correct CEE was a significant theoretical advance over approximate models made possible by the use of MRA to directly measure the 3D velocity field in situ. Experiments were carried out in a perfused alcohol fixed canine liver with hyperthermia induced through scanned focused ultrasound Velocity fields were measured using Phase Contrast Angiography. The complete system was then used to (1) develop a 3D finite element model based upon user traced outlines over a series of MR images of the liver and (2) simulate temperatures at steady state using the CEE, BHTE, and ETCE thermal models in conjunction with the gauss estimator. Results of using the system on an in vitro liver preparation indicate the need for improved accuracy in the MRA scans and accurate spatial registration between the thermocouple junctions, the measured velocity field, and the scanned ultrasound power No individual thermal model was able to meet the desired accuracy of 0.5 deg C, the resolution

  10. 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

    2016-01-01

    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

  11. 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

  12. 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.

  13. 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.

  14. Clustering diagnosis of rolling element bearing fault based on integrated Autoregressive/Autoregressive Conditional Heteroscedasticity model

    NASA Astrophysics Data System (ADS)

    Wang, Guofeng; Liu, Chang; Cui, Yinhu

    2012-09-01

    Feature extraction plays an important role in the clustering analysis. In this paper an integrated Autoregressive (AR)/Autoregressive Conditional Heteroscedasticity (ARCH) model is proposed to characterize the vibration signal and the model coefficients are adopted as feature vectors to realize clustering diagnosis of rolling element bearings. The main characteristic is that the AR item and ARCH item are interrelated with each other so that it can depict the excess kurtosis and volatility clustering information in the vibration signal more accurately in comparison with two-stage AR/ARCH model. To testify the correctness, four kinds of bearing signals are adopted for parametric modeling by using the integrated and two-stage AR/ARCH model. The variance analysis of the model coefficients shows that the integrated AR/ARCH model can get more concentrated distribution. Taking these coefficients as feature vectors, K means based clustering is utilized to realize the automatic classification of bearing fault status. The results show that the proposed method can get more accurate results in comparison with two-stage model and discrete wavelet decomposition.

  15. 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

  16. Testing of Cis-Regulatory Elements by Targeted Transgene Integration in Zebrafish Using PhiC31 Integrase.

    PubMed

    Hadzhiev, Yavor; Miguel-Escalada, Irene; Balciunas, Darius; Müller, Ferenc

    2016-01-01

    Herein we present several strategies for testing the function of cis-regulatory elements using the PhiC31 integrase system. Firstly, we present two different strategies to analyze the activity of candidate enhancer elements. Targeted integration of candidate enhancers into the same genomic location circumvents the variability-associated random integration and position effects. This method is suitable for testing of candidate enhancers identified through computational or other analyses a priori. Secondly, we present methodology for targeted integration of BACs into the same genomic location(s). By using additional reporters integrated into a BAC, this enables experimental testing whether cis-regulatory elements are functional in the sequence inserted in the BAC. PMID:27464802

  17. 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.

  18. 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

  19. Prediction of metallic nano-optical trapping forces by finite element-boundary integral method.

    PubMed

    Pan, Xiao-Min; Xu, Kai-Jiang; Yang, Ming-Lin; Sheng, Xin-Qing

    2015-03-01

    The hybrid of finite element and boundary integral (FE-BI) method is employed to predict nano-optical trapping forces of arbitrarily shaped metallic nanostructures. A preconditioning strategy is proposed to improve the convergence of the iterative solution. Skeletonization is employed to speed up the design and optimization where iteration has to be repeated for each beam configuration. The radiation pressure force (RPF) is computed by vector flux of the Maxwell's stress tensor. Numerical simulations are performed to validate the developed method in analyzing the plasmonic effects as well as the optical trapping forces. It is shown that the proposed method is capable of predicting the trapping forces of complex metallic nanostructures accurately and efficiently.

  20. Evaluation of the current biased integrated optical processors based on bistable dode elements

    NASA Astrophysics Data System (ADS)

    Tang, C. L.; Swanson, P. D.; Parker, M. A.; Libby, S. I.

    1994-07-01

    Three optical switching elements have been designed, fabricated and tested for use in an integrated, optical signal processor. The first, and optical NOR logic gate, uses gain quenching as a means of allowing one (or more) light beam (s) to control the output light. This technique, along with the use of a two-pad bistable output laser, is used in the demonstration of the feasibility of the second device, an all optical RS flip-flop. The third device consists of a broad area orthogonal mode switch laser, whose corollary outputs correspond to the sign of the voltage difference between its two high impedance electrical inputs. This device also has possible memory applications if bistable mode switching within the broad area laser can be achieved.

  1. Enhanced plasmonic light absorption engineering of graphene: simulation by boundary-integral spectral element method.

    PubMed

    Niu, Jun; Luo, Ma; Zhu, Jinfeng; Liu, Qing Huo

    2015-02-23

    Graphene's relatively poor absorption is an essential obstacle for designing graphene-based photonic devices with satisfying photo-responsivity. To enhance the tunable light absorption of graphene, appropriate excitation of localized surface plasmon resonance is considered as a promising approach. In this work, the strategy of incorporating periodic cuboid gold nanoparticle (NP) cluster arrays and cylindrical gold NP arrays with Bragg reflectors into graphene-based photodetectors are theoretically studied by the boundary-integral spectral element method (BI-SEM). With the BI-SEM, the models can be numerically analyzed with excellent accuracy and efficiency. Numerical simulation shows that the proposed structures can effectively engineer the light absorption in graphene by tuning plasmon resonance. In the spectra of 300 nm to 1000 nm, a maximum light absorption of 67.54% is observed for the graphene layer with optimal parameters of the photodetector model.

  2. The numerical integration and 3-D finite element formulation of a viscoelastic model of glass

    SciTech Connect

    Chambers, R.S.

    1994-08-01

    The use of glasses is widespread in making hermetic, insulating seals for many electronic components. Flat panel displays and fiber optic connectors are other products utilizing glass as a structural element. When glass is cooled from sealing temperatures, residual stresses are generated due to mismatches in thermal shrinkage created by the dissimilar material properties of the adjoining materials. Because glass is such a brittle material at room temperature, tensile residual stresses must be kept small to ensure durability and avoid cracking. Although production designs and the required manufacturing process development can be deduced empirically, this is an expensive and time consuming process that does not necessarily lead to an optimal design. Agile manufacturing demands that analyses be used to reduce development costs and schedules by providing insight and guiding the design process through the development cycle. To make these gains, however, viscoelastic models of glass must be available along with the right tool to use them. A viscoelastic model of glass can be used to simulate the stress and volume relaxation that occurs at elevated temperatures as the molecular structure of the glass seeks to equilibrate to the state of the supercooled liquid. The substance of the numerical treatment needed to support the implementation of the model in a 3-D finite element program is presented herein. An accurate second-order, central difference integrator is proposed for the constitutive equations, and numerical solutions are compared to those obtained with other integrators. Inherent convergence problems are reviewed and fixes are described. The resulting algorithms are generally applicable to the broad class of viscoelastic material models. First-order error estimates are used as a basis for developing a scheme for automatic time step controls, and several demonstration problems are presented to illustrate the performance of the methodology.

  3. 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.

  4. Variable-node plate and shell elements with assumed natural strain and smoothed integration methods for nonmatching meshes

    NASA Astrophysics Data System (ADS)

    Sohn, Dongwoo; Im, Seyoung

    2013-06-01

    In this paper, novel finite elements that include an arbitrary number of additional nodes on each edge of a quadrilateral element are proposed to achieve compatible connection of neighboring nonmatching meshes in plate and shell analyses. The elements, termed variable-node plate elements, are based on two-dimensional variable-node elements with point interpolation and on the Mindlin-Reissner plate theory. Subsequently the flat shell elements, termed variable-node shell elements, are formulated by further extending the plate elements. To eliminate a transverse shear locking phenomenon, the assumed natural strain method is used for plate and shell analyses. Since the variable-node plate and shell elements allow an arbitrary number of additional nodes and overcome locking problems, they make it possible to connect two nonmatching meshes and to provide accurate solutions in local mesh refinement. In addition, the curvature and strain smoothing methods through smoothed integration are adopted to improve the element performance. Several numerical examples are presented to demonstrate the effectiveness of the elements in terms of the accuracy and efficiency of the analyses.

  5. Numerically stable approach for high-precision orbit integration using Encke's method and equinoctial elements

    NASA Astrophysics Data System (ADS)

    Ellmer, Matthias; Mayer-Gürr, Torsten

    2016-04-01

    Future gravity missions like GRACE-FO and beyond will deliver low-low satellite-to-satellite (ll-sst) ranging measurements of much increased precision. This necessitates a re-evaluation of the processes used in gravity field determination with an eye to numerical stability. When computing gravity fields from ll-sst data, precise positions of both satellites are needed in the setup of the observation equations. These positions thus have an immediate effect on the sought-after gravity field parameters. We use reduced-dynamic orbits which are computed through integration of all accelerations experienced by the satellite, as determined through a priori models and observed through the accelerometer. Our simulations showed that computing the orbit of the satellite through complete integration of all acting forces leads to numeric instabilities magnitudes larger than the expected ranging accuracy. We introduce a numerically stable approach employing a best-fit keplerian reference orbit based on Encke's method. Our investigations revealed that using canonical formulations for the evaluation of the reference keplerian orbit and accelerations lead to insufficient precision, necessitating an alternative formulation like the equinoctial elements.

  6. 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.

  7. A coupled finite-element, boundary-integral method for simulating ultrasonic flowmeters.

    PubMed

    Bezdĕk, Michal; Landes, Hermann; Rieder, Alfred; Lerch, Reinhard

    2007-03-01

    Today's most popular technology of ultrasonic flow measurement is based on the transit-time principle. In this paper, a numerical simulation technique applicable to the analysis of transit-time flowmeters is presented. A flowmeter represents a large simulation problem that also requires computation of acoustic fields in moving media. For this purpose, a novel boundary integral method, the Helmholtz integral-ray tracing method (HIRM), is derived and validated. HIRM is applicable to acoustic radiation problems in arbitrary mean flows at low Mach numbers and significantly reduces the memory demands in comparison with the finite-element method (FEM). It relies on an approximate free-space Green's function which makes use of the ray tracing technique. For simulation of practical acoustic devices, a hybrid simulation scheme consisting of FEM and HIRM is proposed. The coupling of FEM and HIRM is facilitated by means of absorbing boundaries in combination with a new, reflection-free, acoustic-source formulation. Using the coupled FEM-HIRM scheme, a full three-dimensional (3-D) simulation of a complete transit-time flowmeter is performed for the first time. The obtained simulation results are in good agreement with measurements both at zero flow and under flow conditions. PMID:17375833

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Free vibration analysis of laminated plate/shell structures based on FSDT with a stabilized nodal-integrated quadrilateral element

    NASA Astrophysics Data System (ADS)

    Nguyen-Van, H.; Mai-Duy, N.; Tran-Cong, T.

    2008-06-01

    This paper reports numerical analyses of free vibration of laminated composite plate/shell structures of various shapes, span-to-thickness ratios, boundary conditions and lay-up sequences. The method is based on a novel four-node quadrilateral element, namely MISQ20, within the framework of the first-order shear deformation theory (FSDT). The element is built by incorporating a strain smoothing method into the bilinear four-node quadrilateral finite element where the strain smoothing operation is based on mesh-free conforming nodal integration. The bending and membrane stiffness matrices are based on the boundaries of smoothing cells while the shear term is evaluated by 2×2 Gauss quadrature. Through several numerical examples, the capability, efficiency and simplicity of the element are demonstrated. Convergence studies and comparison with other existing solutions in the literature suggest that the present element is robust, computationally inexpensive and free of locking.

  13. 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)

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. Efficient compression of rearranged time-multiplexed elemental image arrays in MALT-based three-dimensional integral imaging

    NASA Astrophysics Data System (ADS)

    Kang, Ho-Hyun; Lee, Byung-Gook; Kim, Eun-Soo

    2011-06-01

    In this paper, an approach to efficiently compress the time-multiplexed EIAs picked up from the MALT-based integral imaging system is proposed. In this method, the time-multiplexed EIAs are rearranged by collecting the elemental images occupied at the same position in each EIA to enhance the similarity among the elemental images. Then, MPEG-4 is applied to these rearranged elemental images for compression. From the experimental results, it is shown that the average correlation quality ( ACQ) value representing a degree of similarity between the elemental images, and the resultant compression efficiency have been enhanced by 11.50% and 9.97%, respectively on the average for three kinds of test scenarios in the proposed method, compared to those of the conventional method. Good experimental results finally confirmed the feasibility of the proposed scheme.

  20. Filtering of high modal frequencies for stable real-time explicit integration of deformable objects using the Finite Element Method.

    PubMed

    Aguinaga, Iker; Fierz, Basil; Spillmann, Jonas; Harders, Matthias

    2010-12-01

    The behavior, performance, and run-time of mechanical simulations in interactive virtual surgery depend heavily on the type of numerical differential equation solver used to integrate in time the dynamic equations obtained from simulation methods, such as the Finite Element Method. Explicit solvers are fast but only conditionally stable. The condition number of the stiffness matrix limits the highest possible time step. This limit is related to the geometrical properties of the underlying mesh, such as element shape and size. In fact, it can be governed by a small set of ill-shaped elements. For many applications this issue can be solved a priori by a careful meshing. However, when meshes are cut during interactive surgery simulation, it is difficult and computationally expensive to control the quality of the resulting elements. As an alternative, we propose to modify the elemental stiffness matrices directly in order to ensure stability. In this context, we first investigate the behavior of the eigenmodes of the elemental stiffness matrix in a Finite Element Method. We then propose a simple filter to reduce high model frequencies and thus allow larger time steps, while maintaining the general mechanical behavior. PMID:20869390

  1. 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.

  2. Computation of dynamic stress intensity factors using the boundary element method based on Laplace transform and regularized boundary integral equations

    NASA Astrophysics Data System (ADS)

    Tanaka, Masataka; Nakamura, Masayuki; Aoki, Kazuhiko; Matsumoto, Toshiro

    1993-07-01

    This paper presents a computational method of dynamic stress intensity factors (DSIF) in two-dimensional problems. In order to obtain accurate numerical results of DSIF, the boundary element method based on the Laplace transform and regularized boundary integral equations is applied to the computation of transient elastodynamic responses. A computer program is newly developed for two-dimensional elastodynamics. Numerical computation of DSIF is carried out for a rectangular plate with a center crack under impact tension. Accuracy of the results is investigated from the viewpoint of computational conditions such as the number of sampling points of the inverse Laplace transform and the number of boundary elements.

  3. 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. PMID:26150349

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Long-term dynamic modeling of tethered spacecraft using nodal position finite element method and symplectic integration

    NASA Astrophysics Data System (ADS)

    Li, G. Q.; Zhu, Z. H.

    2015-12-01

    Dynamic modeling of tethered spacecraft with the consideration of elasticity of tether is prone to the numerical instability and error accumulation over long-term numerical integration. This paper addresses the challenges by proposing a globally stable numerical approach with the nodal position finite element method (NPFEM) and the implicit, symplectic, 2-stage and 4th order Gaussian-Legendre Runge-Kutta time integration. The NPFEM eliminates the numerical error accumulation by using the position instead of displacement of tether as the state variable, while the symplectic integration enforces the energy and momentum conservation of the discretized finite element model to ensure the global stability of numerical solution. The effectiveness and robustness of the proposed approach is assessed by an elastic pendulum problem, whose dynamic response resembles that of tethered spacecraft, in comparison with the commonly used time integrators such as the classical 4th order Runge-Kutta schemes and other families of non-symplectic Runge-Kutta schemes. Numerical results show that the proposed approach is accurate and the energy of the corresponding numerical model is conservative over the long-term numerical integration. Finally, the proposed approach is applied to the dynamic modeling of deorbiting process of tethered spacecraft over a long period.

  9. Development in the ISSP of Integrated-Optical Elements and Devices in LiNbO3

    NASA Astrophysics Data System (ADS)

    Kuneva, Mariana; Tonchev, Svetlen

    2010-01-01

    The article presented is a review of the main results on integrated-optical elements and devices developed in the Institute of Solid State Physics. Optical waveguiding structures were obtained by titanium in-diffusion and proton exchange using standard photolithography methods for device patterning. Electro-optical prism, electro-optical Bragg-modulator, electrically induced strip waveguides, integrated-optical Y-switches, total-internal-reflection modulator, Mach-Zehnder modulators of classic and new constructions etc. are discussed concerning their parameters and describing their fabrication as well. The emphasis is put on the novelties, advantages and disadvantages of each of them and on the specific problems of their fabrication.

  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. 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.

    1991-01-01

    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 used 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 a 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.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    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.

  14. Fast computational integral imaging reconstruction by combined use of spatial filtering and rearrangement of elemental image pixels

    NASA Astrophysics Data System (ADS)

    Jang, Jae-Young; Cho, Myungjin

    2015-12-01

    In this paper, we propose a new fast computational integral imaging reconstruction (CIIR) scheme without the deterioration of the spatial filtering effect by combined use of spatial filtering and rearrangement of elemental image pixels. In the proposed scheme, the elemental image array (EIA) recorded by lenslet array is spatially filtered through the convolution of depth-dependent delta function array for a given depth. Then, the spatially filtered EIA is reconstructed as the 3D slice image using pixels of the elemental image rearrangement technique. Our scheme provides both the fast calculation with the same properties of the conventional CIIR and the improved visual quality of the reconstructed 3D slice image. To verify our scheme, we perform preliminary experiments and compare other techniques.

  15. 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.

  16. 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. PMID:25974918

  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. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. Gene disruptions using P transposable elements: An integral component of the Drosophila genome project

    SciTech Connect

    Spradling, A.C.; Stern, D.M.; Kiss, I.

    1995-11-21

    Biologists require genetic as well as molecular tools to decipher genomic information and ultimately to understand gene function. The Berkeley Drosophila Genome Project is addressing these needs with a massive gene disruption project that uses individual, genetically engineered P transposable elements to target open reading frames throughout the Drosophila genome DNA flanking the insertions is sequenced thereby placing and extensive series of genetic markers on the physical genomic map and associating insertions with specific open reading frames and genes. Insertions from the collection now lie within or near most Drosophila genes, greatly reducing the time required to identify new mutations and analyze gene functions. Information revealed from these studies about P element site specificity is being used to target the remaining open reading frames. 38 refs., 5 figs., 1 tab.

  8. 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.

  9. 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…

  10. 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…

  11. 49 CFR 192.911 - What are the elements of an integrity management program?

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... operator must use the threat identification and risk assessment to prioritize covered segments for... § 192.923, and depending on the threat assessed, of §§ 192.925, 192.927, or 192.929. (e) Provisions...), by electronic or other means, a copy of the operator's risk analysis or integrity management...

  12. 49 CFR 192.911 - What are the elements of an integrity management program?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... operator must use the threat identification and risk assessment to prioritize covered segments for... § 192.923, and depending on the threat assessed, of §§ 192.925, 192.927, or 192.929. (e) Provisions...), by electronic or other means, a copy of the operator's risk analysis or integrity management...

  13. 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…

  14. Classroom Exercise That Incorporates Internet Discussion Groups as an Integral Element in a Communication Course.

    ERIC Educational Resources Information Center

    Bruning, Stephen D.

    Responding to the dramatic changes in the style and form of communication, a communication instructor integrated the Internet into his communication courses at a liberal arts college. Students are required to sign up for a discussion group (listserv) that focuses on the course offering as well as a discussion group in their area of interest. Every…

  15. 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

  16. The accuracy of the Gaussian-and-finite-element-Coulomb (GFC) method for the calculation of Coulomb integrals.

    PubMed

    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 (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

  17. 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.

  18. 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

  19. 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.

  20. Retrotransposons at Drosophila telomeres: host domestication of a selfish element for the maintenance of genome integrity

    PubMed Central

    Zhang, Liang; Rong, Yikang S.

    2012-01-01

    Telomere serves two essential functions for the cell. It prevents the recognition of natural chromosome ends as DNA breaks (the end capping function). It counteracts incomplete end replication by adding DNA to the ends of chromosomes (the end elongation function). In most organisms studied, telomerase fulfills the end elongation function. In Drosophila, however, telomere specific retrotransposons have been coerced into performing this essential function for the host. In this review, we focus our discussion on transposition mechanisms and transcriptional regulation of these transposable elements, and present provocative models for the purpose of spurring new interests in the field. PMID:22342531

  1. 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.

  2. 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.

  3. Simulations and first manufacturing steps of a fully integrated WDM-element in the visible spectrum

    NASA Astrophysics Data System (ADS)

    Höll, S.; Haupt, M.; Fischer, U. H. P.

    2013-09-01

    Due to their economical and easy-manageable advantages, POFs (polymer optical fiber) are going to replace traditional communication media such as copper and glass step by step within short distance communication systems. POFs are already used in various fields of optical communication, e.g. the automotive sector or in-house communication. Though single channel communication systems are state of the art technology, using of only one channel/wavelength for communication limits the bandwidth. For future scenarios this traditional technology is the bottleneck of bandwidth, particularly for HDTV with IP-TV. One solution to breakthrough this limitation is to use more than one wavelength over one single fiber, this is called WDM (wavelength division multiplexing) and is well-established for GOF communication. This technique will be adapted for the visible spectrum for POF. However this multiplexing technology requires two more key-elements: a multiplexer, which combines the multiple wavelengths signals into one fiber, and a demultiplexer at the end of the network to separate the colored signals. In this paper, the development of this key-element based on a Rowland spectrometer will be shown. It starts with the simulation, this is done by means of raytracing. Also the next process steps and solutions for injection molding are described.

  4. Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

    PubMed Central

    Wang, Zefeng; Burge, Christopher B.

    2008-01-01

    Alternative splicing of pre-mRNAs is a major contributor to both proteomic diversity and control of gene expression levels. Splicing is tightly regulated in different tissues and developmental stages, and its disruption can lead to a wide range of human diseases. An important long-term goal in the splicing field is to determine a set of rules or “code” for splicing that will enable prediction of the splicing pattern of any primary transcript from its sequence. Outside of the core splice site motifs, the bulk of the information required for splicing is thought to be contained in exonic and intronic cis-regulatory elements that function by recruitment of sequence-specific RNA-binding protein factors that either activate or repress the use of adjacent splice sites. Here, we summarize the current state of knowledge of splicing cis-regulatory elements and their context-dependent effects on splicing, emphasizing recent global/genome-wide studies and open questions. PMID:18369186

  5. 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.

  6. 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.

  7. Finite element analysis/hydroburst test data correlation for reverse dome integrated stage application

    NASA Astrophysics Data System (ADS)

    Burson, K. S.; Nowakowski, M.; Tiwari, S.

    1993-02-01

    The U.S. Army's Missile Integrated Stage ('MIST') program has undertaken the development of an advanced strategic interceptor booster's solid-fueled rocket motor. The primary structural components of this booster are a composite case with full-diameter aft closure opening, a titanium reverse dome, and a forced-deflection nozzle plug housing. Attention is presently given to the correlation between the analytical models used in this program and the hydroburst test data obtained for the MIST reverse dome. It is found that the reverse dome exceeded the minimum required burst pressure of 2300 psig.

  8. Finite element modeling and analysis of piezo-integrated composite structures under large applied electric fields

    NASA Astrophysics Data System (ADS)

    Rao, M. N.; Tarun, S.; Schmidt, R.; Schröder, K.-U.

    2016-05-01

    In this article, we focus on static finite element (FE) simulation of piezoelectric laminated composite plates and shells, considering the nonlinear constitutive behavior of piezoelectric materials under large applied electric fields. Under the assumptions of small strains and large electric fields, the second-order nonlinear constitutive equations are used in the variational principle approach, to develop a nonlinear FE model. Numerical simulations are performed to study the effect of material nonlinearity for piezoelectric bimorph and laminated composite plates as well as cylindrical shells. In comparison to the experimental investigations existing in the literature, the results predicted by the present model agree very well. The importance of the present nonlinear model is highlighted especially in large applied electric fields, and it is shown that the difference between the results simulated by linear and nonlinear constitutive FE models cannot be omitted.

  9. Finite element analysis for normal pressure hydrocephalus: The effects of the integration of sulci.

    PubMed

    Kim, Hakseung; Park, Dae-Hyeon; Yi, Seong; Jeong, Eun-Jin; Yoon, Byung C; Czosnyka, Marek; Sutcliffe, Michael P F; Kim, Dong-Joo

    2015-08-01

    Finite element analysis (FEA) is increasingly used to investigate the brain under various pathological changes. Although FEA has been used to study hydrocephalus for decades, previous studies have primarily focused on ventriculomegaly. The present study aimed to investigate the pathologic changes regarding sulcal deformation in normal pressure hydrocephalus (NPH). Two finite element (FE) models-an anatomical brain geometric (ABG) model and the conventional simplified brain geometric (SBG) model-of NPH were constructed. The models were constructed with identical boundary conditions but with different geometries. The ABG model contained details of the sulci geometry, whereas these details were omitted from the SBG model. The resulting pathologic changes were assessed via four biomechanical parameters: pore pressure, von Mises stress, pressure, and void ratio. NPH was induced by increasing the transmantle pressure gradient (TPG) from 0 to a maximum of 2.0 mmHg. Both models successfully simulated the major features of NPH (i.e., ventriculomegaly and periventricular lucency). The changes in the biomechanical parameters with increasing TPG were similar between the models. However, the SBG model underestimated the degree of stress across the cerebral mantle by 150% compared with the ABG model. The SBG model also overestimates the degree of ventriculomegaly (increases of 194.5% and 154.1% at TPG = 2.0 mmHg for the SBG and ABG models, respectively). Including the sulci geometry in a FEA for NPH clearly affects the overall results. The conventional SBG model is inferior to the ABG model, which accurately simulated sulcal deformation and the consequent effects on cortical or subcortical structures. The inclusion of sulci in future FEA for the brain is strongly advised, especially for models used to investigate space-occupying lesions.

  10. A new type of conjugative transposon encodes resistance to sulfamethoxazole, trimethoprim, and streptomycin in Vibrio cholerae O139.

    PubMed Central

    Waldor, M K; Tschäpe, H; Mekalanos, J J

    1996-01-01

    Vibrio cholerae O139 is the first non-O1 serogroup of V. cholerae to give rise to epidemic cholera. Apparently, this new serogroup arose from an El Tor O1 strain of V cholerae, but V. cholerae O139 is distinguishable from V. cholerae El Tor O1 by virtue of its novel antigenic structure and also its characteristic pattern of resistances to the antibiotics sulfamethoxazole, trimethoprim, streptomycin, and furazolidone. We found that the first three of these antibiotic resistances are carried on an approximately 62-kb self-transmissible, chromosomally integrating genetic element which we have termed the SXT element. This novel conjugative transposon-like element could be conjugally transferred from V. cholerae O139 to V cholerae O1 and Escherichia coli strains, where it integrated into the recipient chromosomes in a site-specific manner independent of recA. To study the potential virulence properties of the SXT element as well as to improve upon the live attenuated O139 vaccine strain Bengal-2, a large internal deletion in the SXT element was crossed on to the Bengal-2 chromosome. The resulting strain, Bengal-2.SXT(s), is sensitive to sulfamethoxazole and trimethoprim and colonizes the intestines of suckling mice as well as wild-type strains do, suggesting that the SXT element does not encode a colonization factor. Derivatives of Bengal-2.SXT(s) are predicted to be safe, antibiotic-sensitive, live attenuated vaccines for cholera due to the O139 serogroup. PMID:8763944

  11. Integration of liquid crystal elements for creating an infrared Lyot filter.

    PubMed

    Saito, Mitsunori; Hayashi, Keisuke

    2013-05-20

    An infrared Lyot filter was fabricated by integrating a polarization beam splitter and two retarders into a single device. A liquid crystal layer was constructed between two silicon pentaprisms that were designed suitably so that light was incident on this layer at 28°. At this angle, the liquid crystal transmitted p-polarized light (Brewster's angle) and reflected s-polarized light (total internal reflection). The p- or s-polarized light was directed to another liquid crystal layer (retarder) between the prism and a mirror, which induced a wavelength-dependent retardation in the reflection process. Consequently, the light that returned to the beam splitter was transmitted or reflected depending on wavelength. PMID:23736420

  12. Hybrid plasmon/dielectric waveguide for integrated silicon-on-insulator optical elements

    NASA Astrophysics Data System (ADS)

    Banks, Jonathan; Flammer, David; Durfee, Charles; Furtak, Tom; Collins, Reuben; Hollingsworth, Russell

    2009-10-01

    We present a hybrid plasmon/dielectric single-mode single-polarization waveguide on silicon-on-insulator wafers. The structure is fabricable using VLSI processing techniques and minimizes losses due to surface roughness and metallic losses. Because only a single mode and single polarization is admitted, birefringent effects are eliminated. Both simulations and experimental verification of the modes are presented. Simulations show the waveguide can be tuned for either very long propagation lengths or sub-wavelength confinement by changing a patterned metal line width and oxide thickness, which are easily done with VLSI methods. Simulations show sub-wavelength confinement modes with propagation lengths greater than 100 microns, and micron-scale confinement modes with 7mm propagation lengths. This structure naturally forms an MOS capacitor that may be used for active device integration.

  13. 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.

  14. 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

  15. 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

  16. 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

  17. Integrated survey of elemental stoichiometry (C, N, P) from the Western to Eastern Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Pujo-Pay, M.; Conan, P.; Oriol, L.; Cornet-Barthaux, V.; Falco, C.; Ghiglione, J.-F.; Goyet, C.; Moutin, T.; Prieur, L.

    2010-10-01

    This paper provides an extensive vertical and longitudinal description of the biogeochemistry in the whole Mediterranean Sea during the summer 2008. During this strong stratified period, the distribution of nutrients, particulate and dissolved organic carbon (DOC), nitrogen (DON) and phosphorus (DOP) were investigated along a 3000 km transect (BOUM cruise) crossing the Western and Eastern Mediterranean basins. The partitioning of chemical C, N and P species among all these mineral and organic pools has been analysed to produce a detailed spatial and vertical extended examination of the elemental stoichiometry. Surface Mediterranean waters were depleted in nutrients and the thickness of this depleted layer increased towards the East from about 10 m in the Gulf of Lion to more than 100 m in the Levantine basin, concomitantly to the gradual deepening of the thermocline and nutriclines. We used threshold in oxygen concentration to discriminate the water column in three layers; surface (Biogenic Layer BL), intermediate (Mineralization Layer ML), and deep layer (DL) and to propose a schematic representation of biogeochemical fluxes between the different compartments and to compare the functioning of the two basins. The stoichiometry revealed a clear longitudinal and vertical gradient in the mineral fraction with a P-depletion evidenced on both dimension. As a consequence of the severe deficiency in phosphorus, the C:N:P ratios in all pools within the BL largely exceed the Redfield ratios. Despite these gradients, the deep estimated fluxes in the mineral compartment tend towards the canonical Redfield values in both basins. A change in particulate matter composition has been evidenced by a C increase relative to N and P along the whole water column in the western basin and between BL and ML in the eastern one. More surprisingly, a decrease in N relative to P with depth was encountered in the whole Mediterranean Sea. We suggest that there was a more rapid recycling of N

  18. 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

  19. Synthetic vision as an integrated element of an enhanced vision system

    NASA Astrophysics Data System (ADS)

    Jennings, Chad W.; Alter, Keith W.; Barrows, Andrew K.; Bernier, Ken L.; Guell, Jeff J.

    2002-07-01

    Enhanced Vision Systems (EVS) and Synthetic Vision Systems (SVS) have the potential to allow vehicle operators to benefit from the best that various image sources have to offer. The ability to see in all directions, even in reduced visibility conditions, offers considerable benefits for operational effectiveness and safety. Nav3D and The Boeing Company are conducting development work on an Enhanced Vision System with an integrated Synthetic Vision System. The EVS consists of several imaging sensors that are digitally fused together to give a pilot a better view of the outside world even in challenging visual conditions. The EVS is limited however to provide imagery within the viewing frustum of the imaging sensors. The SVS can provide a rendered image of an a priori database in any direction that the pilot chooses to look and thus can provide information of terrain and flight path that are outside the purview of the EVS. Design concepts of the system will be discussed. In addition the ground and flight testing of the system will be described.

  20. Development of Path Integral Monte Carlo Simulations with Localized Nodal Surfaces for Second-Row Elements.

    PubMed

    Militzer, Burkhard; Driver, Kevin P

    2015-10-23

    We extend the applicability range of fermionic path integral Monte Carlo simulations to heavier elements and lower temperatures by introducing various localized nodal surfaces. Hartree-Fock nodes yield the most accurate prediction for pressure and internal energy, which we combine with the results from density functional molecular dynamics simulations to obtain a consistent equation of state for hot, dense silicon under plasma conditions and in the regime of warm dense matter (2.3-18.6  g cm(-3), 5.0×10(5)-1.3×10(8)  K). The shock Hugoniot curve is derived and the structure of the fluid is characterized with various pair correlation functions. PMID:26551129

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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)

  11. 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.

  12. 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

  13. An updated view of plasmid conjugation and mobilization in Staphylococcus.

    PubMed

    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

    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

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. Theoretical and methodological elements for integrating ethics as a foundation into the education of professional and design disciplines.

    PubMed

    d'Anjou, Philippe

    2004-04-01

    The paper addresses the integration of ethics into professional education related to the disciplines responsible for the conception and creation of the artificial (artefactual or technology). The ontological-epistemological paradigm of those disciplines is understood within the frame of the sciences of the artificial as established by Herbert Simon (1969). According to that paradigm, those sciences include disciplines not only related to the production of artefacts (technology), such as engineering, architecture, industrial design, etc, but also disciplines related to devised courses of action aimed at changing existing situations into preferred ones, like medicine, law, education, etc. They are centered on intentional action and at their core is the activity of design, which is their common foundation and attitude, or their common culture. The science of design becomes the broader foundational discipline for any professions engaged in the intentional transformation of the world. The main distinction between design disciplines and scientific ones rests on the object-project dichotomy. Indeed, contrary to Science that sees the world as an object to be observed, Design sees the world as a project and acts upon the world through projects, which are grounded in intentions, ends, and values. Design disciplines are meant to transform the world, or part of it, and are teleological. Being so, they are embodied in an act that is ethical and their ontology-epistemology must be addressed also through practical reason to resituate all professional disciplines according to their involved nature. The paper introduces theoretical, methodological, and ethical elements to establish a model that integrates ethics into the education of the professional disciplines, design-based disciplines, responsible for the creation of the artificial, artefactual or technological, world. The model is articulated around the notions of ethical engagement and responsibility through the act of design

  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. 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.

  2. 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.

  3. 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.

  4. 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

  5. Interchain vs. intrachain energy transfer in acceptor-capped conjugated polymers.

    PubMed

    Beljonne, D; Pourtois, G; Silva, C; Hennebicq, E; Herz, L M; Friend, R H; Scholes, G D; Setayesh, S; Mullen, K; Bredas, J L

    2002-08-20

    The energy-transfer processes taking place in conjugated polymers are investigated by means of ultrafast spectroscopy and correlated quantum-chemical calculations applied to polyindenofluorenes end-capped with a perylene derivative. Comparison between the time-integrated luminescence and transient absorption spectra measured in solution and in films allows disentangling of the contributions arising from intrachain and from interchain energy-migration phenomena. Intrachain processes dominate in solution where photoexcitation of the polyindenofluorene units induces a rather slow energy transfer to the perylene end moieties. In films, close contacts between chains favors interchain transport of the excited singlet species (from the conjugated bridge of one chain to the perylene unit of a neighboring one); this process is characterized by a 1-order-of-magnitude increase in transfer rate with respect to solution. This description is supported fully by the results of quantum-chemical calculations that go beyond the usual point-dipole model approximation and account for geometric relaxation phenomena in the excited state before energy migration. The calculations indicate a two-step mechanism for intrachain energy transfer with hopping along the conjugated chains as the rate-limiting step; the higher efficiency of the interchain transfer process is mainly due to larger electronic coupling matrix elements between closely lying chains.

  6. Conjugated polymer nanoparticles

    NASA Astrophysics Data System (ADS)

    Tuncel, Dönüs; Demir, Hilmi Volkan

    2010-04-01

    Conjugated polymer nanoparticles are highly versatile nano-structured materials that can potentially find applications in various areas such as optoelectronics, photonics, bio-imaging, bio-sensing and nanomedicine. Their straightforward synthesis in desired sizes and properties, biocompatibility and non-toxicity make these materials highly attractive for the aforementioned applications. This feature article reviews the recent developments in the synthesis, characterization, properties and application of these exciting nanostructured materials.

  7. Anti- (conjugate) linearity

    NASA Astrophysics Data System (ADS)

    Uhlmann, Armin

    2016-03-01

    This is an introduction to antilinear operators. In following Wigner the terminus antilinear is used as it is standard in Physics. Mathematicians prefer to say conjugate linear. By restricting to finite-dimensional complex-linear spaces, the exposition becomes elementary in the functional analytic sense. Nevertheless it shows the amazing differences to the linear case. Basics of antilinearity is explained in sects. 2, 3, 4, 7 and in sect. 1.2: Spectrum, canonical Hermitian form, antilinear rank one and two operators, the Hermitian adjoint, classification of antilinear normal operators, (skew) conjugations, involutions, and acq-lines, the antilinear counterparts of 1-parameter operator groups. Applications include the representation of the Lagrangian Grassmannian by conjugations, its covering by acq-lines. As well as results on equivalence relations. After remembering elementary Tomita-Takesaki theory, antilinear maps, associated to a vector of a two-partite quantum system, are defined. By allowing to write modular objects as twisted products of pairs of them, they open some new ways to express EPR and teleportation tasks. The appendix presents a look onto the rich structure of antilinear operator spaces.

  8. 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.

  9. 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

  10. Efficient transformation of Cellulomonas flavigena by electroporation and conjugation with Bacillus thuringiensis.

    PubMed

    Montes-Horcasitas, Carmen; Ruiz-Medrano, Roberto; Magaña-Plaza, Ignacio; Silva, Lidia Gómez; Herrera-Martínez, Aseneth; Hernández-Montalvo, Lourdes; Xoconostle-Cázares, Beatriz

    2004-12-01

    The conjugative self-transmissible plasmid pHT73, harbored in Bacillus thuringiensis var. kurstaki, was demonstrated to be transferred to Cellulomonas flavigena, a cellulolytic bacterium. Both conjugation and transformation procedures yielded resistant colonies; however, chromosomal integration was observed only when bacterial conjugation occurred. The efficiency of conjugation was 10% of recipient strain, which is considered a very efficient process. When the plasmid pHT73 was introduced by transformation, erythromycin-resistant cells contained the plasmid as an episome with no arrangements, as assayed by Southern blot analysis. In contrast, conjugated-resistant cells harbor the plasmid integrated into the chromosome. These data suggest a common mechanism of cell communication between nonrelated bacterial species with similar ecological habitats, and also that both electroporation and conjugation can be used to transform C. flavigena efficiently.

  11. Variations in SXT elements in epidemic Vibrio cholerae O1 El Tor strains in China.

    PubMed

    Wang, Ruibai; Yu, Dong; Yue, Junjie; Kan, Biao

    2016-01-01

    Vibrio cholerae O1 El Tor biotype strains are responsible for three multiyear epidemics of cholera in China during the seventh ongoing pandemic. The presence of the integrative conjugative element SXT is strongly correlated with resistance to nalidixic acid, tetracycline, and trimethoprim-sulfamethoxazole in these strains. Here, we sequenced the conserved genes of the SXT element, including eex, setR, and int, from 59 V. cholerae O1 El Tor strains and extracted and assembled the intact SXT sequences from the 11 genome sequenced strains. These elements had characteristics distinct from those of previously reported integrative conjugative elements (ICEs). They could be clearly divided into two types based on the clustering of conserved genes and gene structures of the elements, showing their possibly independent derivation and evolution. These two types were present before and after 2005, respectively, demonstrating the type substitution that occurred in 2005. Four to six antibiotic-resistant genes were found on the SXT elements, including genes resistant to tetracycline, trimethoprim-sulfamethoxazole, and multiple drugs. In summary, our findings demonstrated the roles of the SXT element in the emergence of multidrug resistance in epidemic O1 El Tor V. cholerae strains in China. PMID:26956038

  12. Variations in SXT elements in epidemic Vibrio cholerae O1 El Tor strains in China

    PubMed Central

    Wang, Ruibai; Yu, Dong; Yue, Junjie; Kan, Biao

    2016-01-01

    Vibrio cholerae O1 El Tor biotype strains are responsible for three multiyear epidemics of cholera in China during the seventh ongoing pandemic. The presence of the integrative conjugative element SXT is strongly correlated with resistance to nalidixic acid, tetracycline, and trimethoprim-sulfamethoxazole in these strains. Here, we sequenced the conserved genes of the SXT element, including eex, setR, and int, from 59 V. cholerae O1 El Tor strains and extracted and assembled the intact SXT sequences from the 11 genome sequenced strains. These elements had characteristics distinct from those of previously reported integrative conjugative elements (ICEs). They could be clearly divided into two types based on the clustering of conserved genes and gene structures of the elements, showing their possibly independent derivation and evolution. These two types were present before and after 2005, respectively, demonstrating the type substitution that occurred in 2005. Four to six antibiotic-resistant genes were found on the SXT elements, including genes resistant to tetracycline, trimethoprim-sulfamethoxazole, and multiple drugs. In summary, our findings demonstrated the roles of the SXT element in the emergence of multidrug resistance in epidemic O1 El Tor V. cholerae strains in China. PMID:26956038

  13. Variations in SXT elements in epidemic Vibrio cholerae O1 El Tor strains in China.

    PubMed

    Wang, Ruibai; Yu, Dong; Yue, Junjie; Kan, Biao

    2016-03-09

    Vibrio cholerae O1 El Tor biotype strains are responsible for three multiyear epidemics of cholera in China during the seventh ongoing pandemic. The presence of the integrative conjugative element SXT is strongly correlated with resistance to nalidixic acid, tetracycline, and trimethoprim-sulfamethoxazole in these strains. Here, we sequenced the conserved genes of the SXT element, including eex, setR, and int, from 59 V. cholerae O1 El Tor strains and extracted and assembled the intact SXT sequences from the 11 genome sequenced strains. These elements had characteristics distinct from those of previously reported integrative conjugative elements (ICEs). They could be clearly divided into two types based on the clustering of conserved genes and gene structures of the elements, showing their possibly independent derivation and evolution. These two types were present before and after 2005, respectively, demonstrating the type substitution that occurred in 2005. Four to six antibiotic-resistant genes were found on the SXT elements, including genes resistant to tetracycline, trimethoprim-sulfamethoxazole, and multiple drugs. In summary, our findings demonstrated the roles of the SXT element in the emergence of multidrug resistance in epidemic O1 El Tor V. cholerae strains in China.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. A two-dimensional flow sensor with integrated micro thermal sensing elements and a back propagation neural network.

    PubMed

    Que, Ruiyi; Zhu, Rong

    2013-01-01

    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°.

  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. Applications of condensed matter understanding to medical tissues and disease progression: Elemental analysis and structural integrity of tissue scaffolds

    NASA Astrophysics Data System (ADS)

    Bradley, D. A.; Farquharson, M. J.; Gundogdu, O.; Al-Ebraheem, Alia; Che Ismail, Elna; Kaabar, W.; Bunk, O.; Pfeiffer, F.; Falkenberg, G.; Bailey, M.

    2010-02-01

    The investigations reported herein link tissue structure and elemental presence with issues of environmental health and disease, exemplified by uptake and storage of potentially toxic elements in the body, the osteoarthritic condition and malignancy in the breast and other soft tissues. Focus is placed on application of state-of-the-art ionizing radiation techniques, including, micro-synchrotron X-ray fluorescence (μ-SXRF) and particle-induced X-ray emission/Rutherford backscattering mapping (μ-PIXE/RBS), coherent small-angle X-ray scattering (cSAXS) and X-ray phase-contrast imaging, providing information on elemental make-up, the large-scale organisation of collagen and anatomical features of moderate and low atomic number media. For the particular situations under investigation, use of such facilities is allowing information to be obtained at an unprecedented level of detail, yielding new understanding of the affected tissues and the progression of disease.

  1. 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.

  2. Non Linear Conjugate Gradient

    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, as well as point electric and magnetic dioples. The inversion process is carried out using a non-linear conjugate gradient optimization scheme, which minimizes the misfit between field data and model data using a least squares criteria.more » The software is an upgrade from the code NLCGCS_MP ver 1.0. The upgrade includes the following components: Incorporation of new 1 D field sourcing routines to more accurately simulate the 3D electromagnetic field for arbitrary geologic& media, treatment for generalized finite length transmitting antenna geometry (antennas with vertical and horizontal component directions). In addition, the software has been upgraded to treat transverse anisotropy in electrical conductivity.« less

  3. Generalized conjugate gradient squared

    SciTech Connect

    Fokkema, D.R.; Sleijpen, G.L.G.

    1994-12-31

    In order to solve non-symmetric linear systems of equations, the Conjugate Gradient Squared (CGS) is a well-known and widely used iterative method. In practice the method converges fast, often twice as fast as the Bi-Conjugate Gradient method. This is what you may expect, since CGS uses the square of the BiCG polynomial. However, CGS may suffer from its erratic convergence behavior. The method may diverge or the approximate solution may be inaccurate. BiCGSTAB uses the BiCG polynomial and a product of linear factors in an attempt to smoothen the convergence. In many cases, this has proven to be very effective. Unfortunately, the convergence of BiCGSTAB may stall when a linear factor (nearly) degenerates. BiCGstab({ell}) is designed to overcome this degeneration of linear factors. It generalizes BiCGSTAB and uses both the BiCG polynomial and a product of higher order factors. Still, CGS may converge faster than BiCGSTAB or BiCGstab({ell}). So instead of using a product of linear or higher order factors, it may be worthwhile to look for other polynomials. Since the BiCG polynomial is based on a three term recursion, a natural choice would be a polynomial based on another three term recursion. Possibly, a suitable choice of recursion coefficients would result in method that converges faster or as fast as CGS, but less erratic. It turns out that an algorithm for such a method can easily be formulated. One particular choice for the recursion coefficients leads to CGS. Therefore one could call this algorithm generalized CGS. Another choice for the recursion coefficients leads to BiCGSTAB. It is therefore possible to mix linear factors and some polynomial based on a three term recursion. This way one may get the best of both worlds. The authors will report on their findings.

  4. 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.

  5. Integration of experiments across diverse environments identifies the genetic determinants of variation in Sorghum bicolor seed element composition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. 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

  7. 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

  8. Targeting cancer using cholesterol conjugates

    PubMed Central

    Radwan, Awwad A.; Alanazi, Fares K.

    2013-01-01

    Conjugation of cholesterol moiety to active compounds for either cancer treatment or diagnosis is an attractive approach. Cholesterol derivatives are widely studied as cancer diagnostic agents and as anticancer derivatives either in vitro or in vivo using animal models. In largely growing studies, anticancer agents have been chemically conjugated to cholesterol molecules, to enhance their pharmacokinetic behavior, cellular uptake, target specificity, and safety. To efficiently deliver anticancer agents to the target cells and tissues, many different cholesterol–anticancer conjugates were synthesized and characterized, and their anticancer efficiencies were tested in vitro and in vivo. PMID:24493968

  9. 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.

  10. Extractability of trace elements in precipitated calcium carbonate (PCC) waste from an integrated pulp and paper mill complex.

    PubMed

    Nurmesniemi, Hannu; Pöykiö, Risto; Perämäki, Paavo; Kuokkanen, Toivo

    2008-01-01

    From the utilization point of view, it is notable that the total element concentrations in the precipitated calcium carbonate (PCC) waste were significantly lower than the maximal allowable heavy metal concentrations for fertilizers used in agriculture and in forestry, set on the basis of the EU and Finnish legislation. The easily soluble Ca concentration of 168.5g kg(-1) (d.w.) in PCC waste was 105 times higher than the typical value of 1.6g kg(-1) (d.w.) in the coarse mineral soil in Finland indicates that the PCC waste is a potential agent for soil remediation and for improving soil fertility if it is used as fertilizer. According to a five-stage sequential extraction procedure, the highest concentrations of most of the elements occurred either in HF+HNO3+HCl or H2O2+CH3COONH4 fraction. This means that the major part of the elements retained in the PCC waste are not easy to extract (leach) under conditions normally found in nature. This is beneficial since, if inorganic materials and by-products are utilized in earth construction, the content of harmful compounds must be low and the harmful components must be tightly bound to the matrix.

  11. Massively Parallel Boundary Integral Element Method Modeling of Particles in a Low Reynolds Number Mewtonian Fluid Flow

    SciTech Connect

    INGBER,M.S.; SUBIA,SAMUEL R.; MONDY,LISA ANN

    2000-01-18

    The analysis of many complex multiphase fluid flow systems is based on a scale decoupling procedure. At the macroscale continuum models are used to perform large-scale simulations. At the mesoscale statistical homogenization theory is used to derive continuum models based on representative volume elements (RVEs). At the microscale small-scale features, such as interfacial properties, are analyzed to be incorporated into mesoscale simulations. In this research mesoscopic simulations of hard particles suspended in a Newtonian fluid undergoing nonlinear shear flow are performed using a boundary element method. To obtain an RVE at higher concentrations, several hundred particles are included in the simulations, putting considerable demands on the computational resources both in terms of CPU and memory. Parallel computing provides a viable platform to study these large multiphase systems. The implementation of a portable, parallel computer code based on the boundary element method using a block-block data distribution is discussed in this paper. The code employs updated direct-solver technologies that make use of dual-processor compute nodes.

  12. 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.

  13. 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. PMID:25193457

  14. 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.

  15. Integrating Statistical and Clinical Research Elements in Intervention-Related Grant Applications: Summary from an NIMH Workshop

    ERIC Educational Resources Information Center

    Sherrill, Joel T.; Sommers, David I.; Nierenberg, Andrew A.; Leon, Andrew C.; Arndt, Stephan; Bandeen-Roche, Karen; Greenhouse, Joel; Guthrie, Donald; Normand, Sharon-Lise; Phillips, Katharine A.; Shear, M. Katherine; Woolson, Robert

    2009-01-01

    Objective: The authors summarize points for consideration generated in a National Institute of Mental Health (NIMH) workshop convened to provide an opportunity for reviewers from different disciplines--specifically clinical researchers and statisticians--to discuss how their differing and complementary expertise can be well integrated in the…

  16. A computer program for the 2-D magnetostatic problem based on integral equations for the field of the conductors and boundary elements

    SciTech Connect

    Morgan, G.H. )

    1992-01-01

    This paper reports on the iterative design of the 2-dimensional cross section of a beam transport magnet having infinitely permeable iron boundaries which requires a fast means of computing the field of the conductors. Solutions in the form of series expansions are used for rectangular iron boundaries, and programs based on the method of images are used to simulate circular iron boundaries. A single procedure or program for dealing with an arbitrary iron boundary would be useful. The present program has been tested with rectangular and circular iron boundaries and provision has been made for the use of other curves. It uses complex contour integral equations for the field of the constant-current density conductors and complex line integrals for the field of the piecewise-linear boundary elements.

  17. Metallocene-containing conjugated polymers.

    PubMed

    Vorotyntsev, Mikhail A; Vasilyeva, Svetlana V

    2008-06-22

    The paper gives a review of publications on polymers with conjugated matrices (PPy, PTh, PAni, hydrocarbon or mixed chains...) which incorporate metallocene complexes (Fe, Ru, Co; Ni, Ti, Zr, Ta) with two cyclopentadienyl ligands (Cp) and their derivatives, in particular with methylated cyclopentadienyl rings (Cp*), as well as hemi-metallocene complexes (Fe, Ru, Co, Mn), as pendant groups or inside the principal chain (part B). The information on related short-chain systems, monomers and oligomers, is also included. In part A, a brief overview of various conjugated polymer materials is presented, with their classification in accordance with the conductivity mechanism (ionic, electronic or mixed conductors) or with the structural type (linear-chain organic or mixed polymers, derivatization, metallopolymers, multi-dimensional structures, alternating and block copolymers with organic or mixed units, hybrid materials with a mixture of conjugated and inert polymers, polymers inside a solid matrix, conjugated polymers with incorporated nanoelements of transition metals, carbon, semiconductors etc.

  18. 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.

  19. Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database.

    PubMed

    Yadav, Chandra Bhan; Bonthala, Venkata Suresh; Muthamilarasan, Mehanathan; Pandey, Garima; Khan, Yusuf; Prasad, Manoj

    2015-02-01

    Transposable elements (TEs) are major components of plant genome and are reported to play significant roles in functional genome diversity and phenotypic variations. Several TEs are highly polymorphic for insert location in the genome and this facilitates development of TE-based markers for various genotyping purposes. Considering this, a genome-wide analysis was performed in the model plant foxtail millet. A total of 30,706 TEs were identified and classified as DNA transposons (24,386), full-length Copia type (1,038), partial or solo Copia type (10,118), full-length Gypsy type (1,570), partial or solo Gypsy type (23,293) and Long- and Short-Interspersed Nuclear Elements (3,659 and 53, respectively). Further, 20,278 TE-based markers were developed, namely Retrotransposon-Based Insertion Polymorphisms (4,801, ∼24%), Inter-Retrotransposon Amplified Polymorphisms (3,239, ∼16%), Repeat Junction Markers (4,451, ∼22%), Repeat Junction-Junction Markers (329, ∼2%), Insertion-Site-Based Polymorphisms (7,401, ∼36%) and Retrotransposon-Microsatellite Amplified Polymorphisms (57, 0.2%). A total of 134 Repeat Junction Markers were screened in 96 accessions of Setaria italica and 3 wild Setaria accessions of which 30 showed polymorphism. Moreover, an open access database for these developed resources was constructed (Foxtail millet Transposable Elements-based Marker Database; http://59.163.192.83/ltrdb/index.html). Taken together, this study would serve as a valuable resource for large-scale genotyping applications in foxtail millet and related grass species.

  20. Polymeric conjugates for drug delivery

    PubMed Central

    Larson, Nate; Ghandehari, Hamidreza

    2012-01-01

    The field of polymer therapeutics has evolved over the past decade and has resulted in the development of polymer-drug conjugates with a wide variety of architectures and chemical properties. Whereas traditional non-degradable polymeric carriers such as poly(ethylene glycol) (PEG) and N-(2-hydroxypropyl methacrylamide) (HPMA) copolymers have been translated to use in the clinic, functionalized polymer-drug conjugates are increasingly being utilized to obtain biodegradable, stimuli-sensitive, and targeted systems in an attempt to further enhance localized drug delivery and ease of elimination. In addition, the study of conjugates bearing both therapeutic and diagnostic agents has resulted in multifunctional carriers with the potential to both “see and treat” patients. In this paper, the rational design of polymer-drug conjugates will be discussed followed by a review of different classes of conjugates currently under investigation. The design and chemistry used for the synthesis of various conjugates will be presented with additional comments on their potential applications and current developmental status. PMID:22707853

  1. Protein carriers of conjugate vaccines

    PubMed Central

    Pichichero, Michael E

    2013-01-01

    The immunogenicity of polysaccharides as human vaccines was enhanced by coupling to protein carriers. Conjugation transformed the T cell-independent polysaccharide vaccines of the past to T cell-dependent antigenic vaccines that were much more immunogenic and launched a renaissance in vaccinology. This review discusses the conjugate vaccines for prevention of infections caused by Hemophilus influenzae type b, Streptococcus pneumoniae, and Neisseria meningitidis. Specifically, the characteristics of the proteins used in the construction of the vaccines including CRM, tetanus toxoid, diphtheria toxoid, Neisseria meningitidis outer membrane complex, and Hemophilus influenzae protein D are discussed. The studies that established differences among and key features of conjugate vaccines including immunologic memory induction, reduction of nasopharyngeal colonization and herd immunity, and antibody avidity and avidity maturation are presented. Studies of dose, schedule, response to boosters, of single protein carriers with single and multiple polysaccharides, of multiple protein carriers with multiple polysaccharides and conjugate vaccines administered concurrently with other vaccines are discussed along with undesirable consequences of conjugate vaccines. The clear benefits of conjugate vaccines in improving the protective responses of the immature immune systems of young infants and the senescent immune systems of the elderly have been made clear and opened the way to development of additional vaccines using this technology for future vaccine products. PMID:23955057

  2. Insights on the design and electron-acceptor properties of conjugated organophosphorus materials.

    PubMed

    Baumgartner, Thomas

    2014-05-20

    The development of conjugated organic materials has become a rapidly evolving field of research, particularly with a view toward practical applications in so-called organic electronics that encompass a variety of device types, such as OLEDs, OPVs, and OFETs. Almost all of these devices minimally require the presence of electron-donor and -acceptor components that act as p- and n-type semiconductors, respectively. Research over the past two decades has shown that while there is an abundant resource of organic p-type materials, suitable n-type species are few and far between. To overcome this severe bottleneck for the further development of organic electronics, researchers have identified organo-main-group avenues as valuable alternatives toward organic electron-acceptor materials that may ultimately be used as n-type components in practical devices. One particular element of interest in this context is phosphorus, which at first glance may not necessarily suggest such properties. In this Account, I provide detailed insights on the origin of the electron-acceptor properties of organophosphorus-based conjugated materials and include an overview of important molecular species that have been developed by my group and others. To this end, I explain that the electron-acceptor properties of conjugated organophosphorus materials originate from an interaction known as negative hyperconjugation. While this particular interaction creates a simply inductively withdrawing phosphoryl substituent for π-conjugated scaffolds, incorporation of a phosphorus atom as an integral part of a cyclic substructure within a π-conjugated system provides a much more complex, versatile, and consequently highly valuable tool for the tuning of the electron-acceptor properties of the materials. Notably, the degree of negative hyperconjugation can effectively be tailored in various ways via simple substitution at the phosphorus center. This is now well established for phosphole-based molecular

  3. Insights on the design and electron-acceptor properties of conjugated organophosphorus materials.

    PubMed

    Baumgartner, Thomas

    2014-05-20

    The development of conjugated organic materials has become a rapidly evolving field of research, particularly with a view toward practical applications in so-called organic electronics that encompass a variety of device types, such as OLEDs, OPVs, and OFETs. Almost all of these devices minimally require the presence of electron-donor and -acceptor components that act as p- and n-type semiconductors, respectively. Research over the past two decades has shown that while there is an abundant resource of organic p-type materials, suitable n-type species are few and far between. To overcome this severe bottleneck for the further development of organic electronics, researchers have identified organo-main-group avenues as valuable alternatives toward organic electron-acceptor materials that may ultimately be used as n-type components in practical devices. One particular element of interest in this context is phosphorus, which at first glance may not necessarily suggest such properties. In this Account, I provide detailed insights on the origin of the electron-acceptor properties of organophosphorus-based conjugated materials and include an overview of important molecular species that have been developed by my group and others. To this end, I explain that the electron-acceptor properties of conjugated organophosphorus materials originate from an interaction known as negative hyperconjugation. While this particular interaction creates a simply inductively withdrawing phosphoryl substituent for π-conjugated scaffolds, incorporation of a phosphorus atom as an integral part of a cyclic substructure within a π-conjugated system provides a much more complex, versatile, and consequently highly valuable tool for the tuning of the electron-acceptor properties of the materials. Notably, the degree of negative hyperconjugation can effectively be tailored in various ways via simple substitution at the phosphorus center. This is now well established for phosphole-based molecular

  4. [Lessons from health education for HIV/AIDS prevention: theoretical elements for the construction of a new integrated practice].

    PubMed

    Merchán-Hamman, E

    1999-11-01

    There is an evident contrast between health education practices and theoretical reflection concerning them as models. Health education practices have undergone considerable development in terms of strategies, methods, and modalities, while theoretical models have remained deficient, reductionist, fragmentary, and focused on behavior rather than social practices. Major problems include individualism, asymmetrical "teacher-student" relationships, students as passive objects of practices, lack of social and cultural contextualism, and excessive focus on factual behavior. We propose a praxis based on ten levels of integration regarding different human dimensions: 1) complexity requires interdisciplinarity; 2) holism; 3) combined perceptual and expressive dimensions in a integrated language; 4) framing of practices in real contexts; 5) realization of the continuity between the individual and collective realms; 6) symmetrical, dialogic and active educational practice; 7) integration of both intellectual-cognitive and affective-volitional processes; 8) risks as vulnerabilities of social groups that are capable of organization; 9) use of imagination in role-playing games; 10) recognition of others and diversity. Political aspects of education are emphasized as promoting citizenship and social change. PMID:10578080

  5. Aptamer-conjugated nanomaterials for bioanalysis and biotechnology applications

    NASA Astrophysics Data System (ADS)

    Chen, Tao; Shukoor, Mohammed Ibrahim; Chen, Yan; Yuan, Quan; Zhu, Zhi; Zhao, Zilong; Gulbakan, Basri; Tan, Weihong

    2011-02-01

    In recent years, nanomaterials have captured the attention of scientists from a wide spectrum of domains. With their unique properties, nanomaterials offer great promise for numerous applications, ranging from catalysis to energy harvesting and information technology. Functionalized with the desired biomolecules, nanomaterials can also be utilized for many biomedical applications. This paper summarizes recent achievements in the use of aptamer-conjugated nanomaterials for bioanalysis and biotechnology applications. First, we discuss the features and properties of aptamers and then illustrate the use of aptamer-conjugated nanomaterials as sensing platforms and delivery vehicles, emphasizing how such integration can result in enhanced sensitivity and selectivity.

  6. Biomechanical implications of intraspecific shape variation in chimpanzee crania: moving toward an integration of geometric morphometrics and finite element analysis.

    PubMed

    Smith, Amanda L; Benazzi, Stefano; Ledogar, Justin A; Tamvada, Kelli; Pryor Smith, Leslie C; Weber, Gerhard W; Spencer, Mark A; Dechow, Paul C; Grosse, Ian R; Ross, Callum F; Richmond, Brian G; Wright, Barth W; Wang, Qian; Byron, Craig; Slice, Dennis E; Strait, David S

    2015-01-01

    In a broad range of evolutionary studies, an understanding of intraspecific variation is needed in order to contextualize and interpret the meaning of variation between species. However, mechanical analyses of primate crania using experimental or modeling methods typically encounter logistical constraints that force them to rely on data gathered from only one or a few individuals. This results in a lack of knowledge concerning the mechanical significance of intraspecific shape variation that limits our ability to infer the significance of interspecific differences. This study uses geometric morphometric methods (GM) and finite element analysis (FEA) to examine the biomechanical implications of shape variation in chimpanzee crania, thereby providing a comparative context in which to interpret shape-related mechanical variation between hominin species. Six finite element models (FEMs) of chimpanzee crania were constructed from CT scans following shape-space Principal Component Analysis (PCA) of a matrix of 709 Procrustes coordinates (digitized onto 21 specimens) to identify the individuals at the extremes of the first three principal components. The FEMs were assigned the material properties of bone and were loaded and constrained to simulate maximal bites on the P(3) and M(2) . Resulting strains indicate that intraspecific cranial variation in morphology is associated with quantitatively high levels of variation in strain magnitudes, but qualitatively little variation in the distribution of strain concentrations. Thus, interspecific comparisons should include considerations of the spatial patterning of strains rather than focus only on their magnitudes.

  7. Biomechanical implications of intraspecific shape variation in chimpanzee crania: moving towards an integration of geometric morphometrics and finite element analysis

    PubMed Central

    Smith, Amanda L.; Benazzi, Stefano; Ledogar, Justin A.; Tamvada, Kelli; Smith, Leslie C. Pryor; Weber, Gerhard W.; Spencer, Mark A.; Dechow, Paul C.; Grosse, Ian R.; Ross, Callum F.; Richmond, Brian G.; Wright, Barth W.; Wang, Qian; Byron, Craig; Slice, Dennis E.; Strait, David S.

    2014-01-01

    In a broad range of evolutionary studies, an understanding of intraspecific variation is needed in order to contextualize and interpret the meaning of variation between species. However, mechanical analyses of primate crania using experimental or modeling methods typically encounter logistical constraints that force them to rely on data gathered from only one or a few individuals. This results in a lack of knowledge concerning the mechanical significance of intraspecific shape variation that limits our ability to infer the significance of interspecific differences. This study uses geometric morphometric methods (GM) and finite element analysis (FEA) to examine the biomechanical implications of shape variation in chimpanzee crania, thereby providing a comparative context in which to interpret shape-related mechanical variation between hominin species. Six finite element models (FEMs) of chimpanzee crania were constructed from CT scans following shape-space Principal Component Analysis (PCA) of a matrix of 709 Procrustes coordinates (digitized onto 21 specimens) to identify the individuals at the extremes of the first three principal components. The FEMs were assigned the material properties of bone and were loaded and constrained to simulate maximal bites on the P3 and M2. Resulting strains indicate that intraspecific cranial variation in morphology is associated with quantitatively high levels of variation in strain magnitudes, but qualitatively little variation in the distribution of strain concentrations. Thus, interspecific comparisons should include considerations of the spatial patterning of strains rather than focus only their magnitude. PMID:25529239

  8. The fractionation and geochemical characteristics of rare earth elements measured in ambient size-resolved PM in an integrated iron and steelmaking industry zone.

    PubMed

    Dai, Qili; Li, Liwei; Yang, Jiamei; Liu, Baoshuang; Bi, Xiaohui; Wu, Jianhui; Zhang, YuFen; Yao, Lin; Feng, Yinchang

    2016-09-01

    Improved understanding of the fractionation and geochemical characteristic of rare earth elements (REEs) from steel plant emissions is important due to the unclear atmospheric signature of these elements and their adverse impact on human health and the environment. In this study, ambient particulate matter of different sizes was collected from one site in an integrated iron and steelmaking industrial zone (HG) and one urban background site with no direct industrial emissions (ZWY) during a 1-year sampling campaign in China. The total concentrations of REEs for TSP, PM10, and PM2.5 were 27.248, 14.989, 3.542 ng/m(3) in HG and 6.326, 5.274, 1.731 ng/m(3), respectively, in ZWY, which revealed the local influence of the steelmaking activities to the air quality. With respect to ZWY, the REEs in HG site are obviously fractionated in the coarser fraction, and LREEs account for more than 80 % of the total REE burden in all of the samples. Additionally, the REEs in HG and ZWY show a homogeneous trend with successively increased LREE/HREE ratios from the coarse particles to the fine particles. In our samples, La, Ce, Nd, and Sm are the most enriched rare earth elements, especially in the HG site. Moreover, ternary diagrams of LaCeSm indicate that the REEs in HG are potentially contributed by steelworks, carrier vehicles, coal combustion, and road dust re-suspension.

  9. On the exploitation of Armstrong-Frederik type nonlinear kinematic hardening in the numerical integration and finite-element implementation of pressure dependent plasticity models

    NASA Astrophysics Data System (ADS)

    Metzger, Mario; Seifert, Thomas

    2013-09-01

    In this paper, an unconditionally stable algorithm for the numerical integration and finite-element implementation of a class of pressure dependent plasticity models with nonlinear isotropic and kinematic hardening is presented. Existing algorithms are improved in the sense that the number of equations to be solved iteratively is significantly reduced. This is achieved by exploitation of the structure of Armstrong-Frederik-type kinematic hardening laws. The consistent material tangent is derived analytically and compared to the numerically computed tangent in order to validate the implementation. The performance of the new algorithm is compared to an existing one that does not consider the possibility of reducing the number of unknowns to be iterated. The algorithm is used to implement a time and temperature dependent cast iron plasticity model, which is based on the pressure dependent Gurson model, in the finite-element program ABAQUS. The implementation is applied to compute stresses and strains in a large-scale finite-element model of a three cylinder engine block. This computation proofs the applicability of the algorithm in industrial practice that is of interest in applied sciences.

  10. A hybrid finite element-boundary integral for the analysis of cavity-backed antennas of arbitrary shape

    NASA Technical Reports Server (NTRS)

    Gong, Jian; Volakis, John L.; Woo, A. C.; Wang, H. T. G.

    1993-01-01

    This is the final report on this project which was concerned with the analysis of cavity-backed antennas and more specifically spiral antennas. The project was a continuation of a previous analysis, which employed rectangular brick elements, and was, thus, restricted to planar rectangular patch antennas. A total of five reports were submitted under this project and we expect that at least four journal papers will result from the research described in these reports. The abstracts of the four previous reports are included. The first of the reports (028918-1-T) is over 75 pages and describes the general formulation using tetrahedral elements and the computer program. Report 028918-2-T was written after the completion of the computer program and reviews the capability of the analysis and associated software for planar circular rectangular patches and for a rectangular planar spiral. Measurements were also done at the University of Michigan and at Mission Research Corp. for the purpose of validating the software. We are pleased to acknowledge a partial support from Mission Research Corp. in carrying out the work described in this report. The third report (028918-3-T) describes the formulation and partial validation (using 2D data) for patch antennas on a circular platform. The 3D validation and development of the formulation for patch antennas on circular platforms is still in progress. The fourth report (028918-4-T) is basically an invited journal paper which will appear in the 'J. Electromagnetic Waves and Applications' in early 1994. It describes the application of the finite element method in electromagnetics and is primarily based on our work here at U-M. This final report describes the culmination of our efforts in characterizing complex cavity-backed antennas on planar platforms. The report describes for the first time the analysis of non-planar spirals and non-rectangular slot antennas as well as traditional planar patch antennas. The comparisons between

  11. 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)

    Otte, Neil E.; Lyles, Garry; Reuter, James L.; Davis, Daniel J.

    2008-01-01

    Fielding an integrated launch vehicle system entails many challenges, not the least of which is the fact that it has been over 30 years since the United States has developed a human-rated vehicle - the venerable Space Shuttle. Over time, whole generations of rocket scientists have passed through the aerospace community without the opportunity to perform such exacting, demanding, and rewarding work. However, with almost 50 years of experience leading the design, development, and end-to-end systems engineering and integration of complex launch vehicles, the National Aeronautics and Space Administration's (NASA's) Marshall Space Flight Center offers the in-house talent - both junior- and senior-level personnel - to shape a new national asset to meet the requirements for safe, reliable, and affordable space exploration solutions. The technical personnel are housed primarily in Marshall's Engineering Directorate and are matrixed into the programs and projects that reside at the rocket center. Fortunately, many Apollo-era and Shuttle engineers, as well as those who gained valuable hands-on experience in the 1990s by conducting technology demonstrator projects such as the Delta-Clipper Experimental Advanced, X-33, X-34, and X-37, as well as the short-lived Orbital Space Plane, work closely with industry partners to advance the nation's strategic capability for human access to space. The Ares Projects Office, resident at Marshall, is managing the design and development of America's new space fleet, including the Ares I, which will loft the Orion crew capsule for its first test flight in the 2013 timeframe, as well as the heavy-lift Ares V, which will round out the capability to leave low-Earth orbit once again, when it delivers the Altair lunar lander to orbit late next decade. This paper provides information about the approach to integrating the Ares I stack and designing the upper stage in house, using unique facilities and an expert workforce to revitalize the nation

  12. A Scintilla of Unified Field Mechanics Revealed by a Conceptual Integration of New Fundamental Elements Associated With Wavepacket Dispersion

    NASA Astrophysics Data System (ADS)

    Amoroso, Richard L.; Dunning-Davies, Jeremy

    2013-09-01

    A third regime is proposed in the natural progression of the description of the physical world - Classical to Quantum to Unified Field (UF) Mechanics. We describe the new conceptual panoply and propose an experimental method to falsify the new UF hypotheses. Like Penzias & Wilson wondering if bird droppings affected their antenna we describe a serendipitous insight into wavepacket dispersion of 1800 MHz telecommunication em-waves in the arena where signal strength attenuates periodically by factors attributed to perceived properties that we postulate can only be mediated by UF mechanics. Salient suggested elements include extended geometrodynamics (duality of Newton's instantaneous and Einstein's relativistic models), Solar dynamo activity, geomagnetic phenomena, seasonal precession of the Earth's axis, near - far field: geomagnetic core dynamo - solar scale-invariant wavepacket dispersion coupling and longitudinal em components. This UF model putatively also provides an indirect measure of photon mass.

  13. Towards an integrated numerical simulator for crack-seal vein microstructure: Coupling phase-field with the Discrete Element Method

    NASA Astrophysics Data System (ADS)

    Virgo, Simon; Ankit, Kumar; Nestler, Britta; Urai, Janos L.

    2016-04-01

    Crack-seal veins form in a complex interplay of coupled thermal, hydraulic, mechanical and chemical processes. Their formation and cyclic growth involves brittle fracturing and dilatancy, phases of increased fluid flow and the growth of crystals that fill the voids and reestablish the mechanical strength. Existing numerical models of vein formation focus on selected aspects of the coupled process. Until today, no model exists that is able to use a realistic representation of the fracturing AND sealing processes, simultaneously. To address this challenge, we propose the bidirectional coupling of two numerical methods that have proven themselves as very powerful to model the fundamental processes acting in crack-seal systems: Phase-field and the Discrete Element Method (DEM). The phase-field Method was recently successfully extended to model the precipitation of quartz crystals from an aqueous solution and applied to model the sealing of a vein over multiple opening events (Ankit et al., 2013; Ankit et al., 2015a; Ankit et al., 2015b). The advantage over former, purely kinematic approaches is that in phase-field, the crystal growth is modeled based on thermodynamic and kinetic principles. Different driving forces for microstructure evolution, such as chemical bulk free energy, interfacial energy, elastic strain energy and different transport processes, such as mass diffusion and advection, can be coupled and the effect on the evolution process can be studied in 3D. The Discrete Element Method was already used in several studies to model the fracturing of rocks and the incremental growth of veins by repeated fracturing (Virgo et al., 2013; Virgo et al., 2014). Materials in DEM are represented by volumes of packed spherical particles and the response to the material to stress is modeled by interaction of the particles with their nearest neighbours. For rocks, in 3D, the method provides a realistic brittle failure behaviour. Exchange Routines are being developed that

  14. Estimating contemporary early life-history dispersal in an estuarine fish: integrating molecular and otolith elemental approaches.

    PubMed

    Bradbury, I R; Campana, S E; Bentzen, P

    2008-03-01

    Dispersal during the early life history of the anadromous rainbow smelt, Osmerus mordax, was examined using assignment testing and mixture analysis of multilocus genotypes and otolith elemental composition. Six spawning areas and associated estuarine nurseries were sampled throughout southeastern Newfoundland. Samples of adults and juveniles isolated by > 25 km displayed moderate genetic differentiation (F(ST) ~ 0.05), whereas nearby (< 25 km) spawning and nursery samples displayed low differentiation (F(ST) < 0.01). Self-assignment and mixture analysis of adult spawning samples supported the hypothesis of independence of isolated spawning locations (> 80% self-assignment) with nearby runs self-assigning at rates between 50 % and 70%. Assignment and mixture analysis of juveniles using adult baselines indicated high local recruitment at several locations (70-90%). Nearby (< 25 km) estuaries at the head of St Mary's Bay showed mixtures of individuals (i.e. 20-40% assignment to adjacent spawning location). Laser ablation inductively coupled mass spectrometry transects across otoliths of spawning adults of unknown dispersal history were used to estimate dispersal among estuaries across the first year of life. Single-element trends and multivariate discriminant function analysis (Sr:Ca and Ba:Ca) classified the majority of samples as estuarine suggesting limited movement between estuaries (< 0.5%). The mixtures of juveniles evident in the genetic data at nearby sites and a lack of evidence of straying in the otolith data support a hypothesis of selective mortality of immigrants. If indeed selective mortality of immigrants reduces the survivorship of dispersers, estimates of dispersal in marine environments that neglect survival may significantly overestimate gene flow.

  15. Integrated non-destructive assessment of relevant structural elements of an Italian heritage site: the Carthusian monastery of Trisulti

    NASA Astrophysics Data System (ADS)

    Rainieri, C.; Marra, A.; Rainieri, G. M.; Gargaro, D.; Pepe, M.; Fabbrocino, G.

    2015-07-01

    The analysis of historical structures in need of preservation and restoration interventions is a very complex task due to the large uncertainties in the characterization of structural properties and detailing in view of the structural response. Moreover, the predictive performance of numerical analyses and simulations depend on the availability of information about the constructional properties of the architectural complex, crack patterns and active degradation phenomena. In particular, local changes in material properties or damage due to past events (such as earthquakes) can affect individual structural elements. They can be hardly detected as a result of the maintenance interventions carried out over the centuries and the possibility to carry out limited or even no destructive investigations due to the historical relevance of the structure. Thus, non-destructive investigations play a fundamental role in the assessment of historical structures minimizing, at the same time, the invasiveness of interventions. The present paper deals with an explanatory case study concerning the structural investigations carried out in view of the seismic assessment of an Italian historical monument, the Carthusian monastery of Trisulti in Collepardo, erected in 1204 under Pope Innocenzo HI. The relevance of the case study is due to the application, in combination, of different NDT methods, such as sonic tests, and active and passive infrared thermography, in order to characterize relevant masonry elements. Moreover, an advanced system for the in-situ nondestructive vibration-based estimation of the tensile loads in ancient tie-rods is described and the main results obtained from its application for the characterization of the tie-rods of the cloister are presented.

  16. Mapping Synapses by Conjugate Light-Electron Array Tomography

    PubMed Central

    Buchanan, JoAnn; Phend, Kristen D.; Micheva, Kristina D.; Weinberg, Richard J.; Smith, Stephen J

    2015-01-01

    Synapses of the mammalian CNS are diverse in size, structure, molecular composition, and function. Synapses in their myriad variations are fundamental to neural circuit development, homeostasis, plasticity, and memory storage. Unfortunately, quantitative analysis and mapping of the brain's heterogeneous synapse populations has been limited by the lack of adequate single-synapse measurement methods. Electron microscopy (EM) is the definitive means to recognize and measure individual synaptic contacts, but EM has only limited abilities to measure the molecular composition of synapses. This report describes conjugate array tomography (AT), a volumetric imaging method that integrates immunofluorescence and EM imaging modalities in voxel-conjugate fashion. We illustrate the use of conjugate AT to advance the proteometric measurement of EM-validated single-synapse analysis in a study of mouse cortex. PMID:25855189

  17. KOALA, a wide-field 1000 element integral-field unit for the Anglo-Australian Telescope: assembly and commissioning

    NASA Astrophysics Data System (ADS)

    Zhelem, Ross; Brzeski, Jurek; Case, Scott; Churilov, Vladimir; Ellis, Simon; Farrell, Tony; Green, Andrew; Heng, Anthony; Horton, Anthony; Ireland, Michael; Jones, Damien; Klauser, Urs; Lawrence, Jon; Miziarski, Stan; Orr, David; Pai, Naveen; Staszak, Nick; Tims, Julia; Vuong, Minh; Waller, Lew; Xavier, Pascal

    2014-07-01

    The KOALA optical fibre feed for the AAOmega spectrograph has been commissioned at the Anglo-Australian Telescope. The instrument samples the reimaged telescope focal plane at two scales: 1.23 arcsec and 0.70 arcsec per image slicing hexagonal lenslet over a 49x27 and 28x15 arcsec field of view respectively. The integral field unit consists of 2D hexagonal and circular lenslet arrays coupling light into 1000 fibres with 100 micron core diameter. The fibre run is over 35m long connecting the telescope Cassegrain focus with the bench mounted spectrograph room where all fibres are reformatted into a one-dimensional slit. Design and assembly of the KOALA components, engineering challenges encountered, and commissioning results are discussed.

  18. KOALA: a wide-field 1000 element integral-field unit for the Anglo-Australian Telescope

    NASA Astrophysics Data System (ADS)

    Ellis, S. C.; Ireland, M.; Lawrence, J. S.; Tims, J.; Staszak, N.; Brzeski, J.; Parker, Q. A.; Sharp, R.; Bland-Hawthorn, J.; Case, S.; Colless, M.; Croom, S.; Couch, W.; De Marco, O.; Glazebrook, K.; Saunders, W.; Webster, R.; Zucker, D. B.

    2012-09-01

    KOALA, the Kilofibre Optimised Astronomical Lenslet Array, is a wide-field, high efficiency integral field unit being designed for use with the bench mounted AAOmega spectrograph on the AAT. KOALA will have 1000 fibres in a rectangular array with a selectable field of view of either 1390 or 430 sq. arcseconds with a spatial sampling of 1.25" or 0.7" respectively. To achieve this KOALA will use a telecentric double lenslet array with interchangeable fore-optics. The IFU will feed AAOmega via a 31m fibre run. The efficiency of KOALA is expected to be ≍ 52% at 3700A and ≍ 66% at 6563°Å with a throughput of > 52% over the entire wavelength range.

  19. Light-emitting conjugated polymers with microporous network architecture: interweaving scaffold promotes electronic conjugation, facilitates exciton migration, and improves luminescence.

    PubMed

    Xu, Yanhong; Chen, Long; Guo, Zhaoqi; Nagai, Atsushi; Jiang, Donglin

    2011-11-01

    Herein we report a strategy for the design of highly luminescent conjugated polymers by restricting rotation of the polymer building blocks through a microporous network architecture. We demonstrate this concept using tetraphenylethene (TPE) as a building block to construct a light-emitting conjugated microporous polymer. The interlocked network successfully restricted the rotation of the phenyl units, which are the major cause of fluorescence deactivation in TPE, thus providing intrinsic luminescence activity for the polymers. We show positive "CMP effects" that the network promotes π-conjugation, facilitates exciton migration, and improves luminescence activity. Although the monomer and linear polymer analogue in solvents are nonemissive, the network polymers are highly luminescent in various solvents and the solid state. Because emission losses due to rotation are ubiquitous among small chromophores, this strategy can be generalized for the de novo design of light-emitting materials by integrating the chromophores into an interlocked network architecture.

  20. Creep Life Prediction of Ceramic Components Using the Finite Element Based Integrated Design Program (CARES/Creep)

    NASA Technical Reports Server (NTRS)

    Jadaan, Osama M.; Powers, Lynn M.; Gyekenyesi, John P.

    1997-01-01

    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. Such long life requirements necessitate 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 work is to present a design methodology for predicting the lifetimes of structural components subjected to multiaxial creep loading. This methodology utilizes commercially available finite element packages and takes into account the time varying creep stress distributions (stress relaxation). In this methodology, the creep life of a component is divided into short time steps, during which, the stress and strain distributions are assumed constant. The damage, D, is calculated for each time step based on a modified Monkman-Grant creep rupture criterion. For components subjected to predominantly tensile loading, failure is assumed to occur when the normalized accumulated damage at any point in the component is greater than or equal to unity.

  1. Innovative low cost procedure for nutrient removal as an integrated element of a decentralised water management concept for rural areas.

    PubMed

    Burde, M; Rolf, F; Grabowski, F

    2001-01-01

    The absence of large rivers with rather high niveau of self purifying effect in parts of east Germany leads to a discharging of the effluent of wastewater treatment plants into the groundwater in many cases. One useful consequence is the idea of realisation of decentralised measures and concepts in urban water resources management concerning municipal wastewater as well as rainfall, precipitation. At the same time, only the upper soil zone--a few decimetres--is water--saturated and thus discharge effective, even when extreme rainfall takes place. Underneath, however, there generally exists an unsaturated soil zone, which is up to now a rather unexplored retardation element of the hydrologic- and substrate-cycle. Nutrient removal in small wastewater treatment plants that are emptying into ground waters is often beneficial. The presented studies optimised an inexpensive method of subsequent enhanced wastewater treatment. The developed reactor is similar to a concentrated subsoil passage. The fixed bed reactor is divided in two sections to achieve aerobic and anoxic conditions for nitrification/denitrification processes. To enhance phosphorus removal, ferrous particles are put into the aerobic zone. Two series of column tests were carried out and a technical pilot plant was built to verify the efficiency of the process. The results show that this method can be implemented successfully.

  2. Variation on a theme; an overview of the Tn916/Tn1545 family of mobile genetic elements in the oral and nasopharyngeal streptococci

    PubMed Central

    Santoro, Francesco; Vianna, Morgana E.; Roberts, Adam P.

    2014-01-01

    The oral and nasopharyngeal streptococci are a major part of the normal microbiota in humans. Most human associated streptococci are considered commensals, however, a small number of them are pathogenic, causing a wide range of diseases including oral infections such as dental caries and periodontitis and diseases at other body sites including sinusitis and endocarditis, and in the case of Streptococcus pneumoniae, meningitis. Both phenotypic and sequence based studies have shown that the human associated streptococci from the mouth and nasopharynx harbor a large number of antibiotic resistance genes and these are often located on mobile genetic elements (MGEs) known as conjugative transposons or integrative and conjugative elements of the Tn916/Tn1545 family. These MGEs are responsible for the spread of the resistance genes between streptococci and also between streptococci and other bacteria. In this review we describe the resistances conferred by, and the genetic variations between the many different Tn916-like elements found in recent studies of oral and nasopharyngeal streptococci and show that Tn916-like elements are important mediators of antibiotic resistance genes within this genus. We will also discuss the role of the oral environment and how this is conducive to the transfer of these elements and discuss the contribution of both transformation and conjugation on the transfer and evolution of these elements in different streptococci. PMID:25368607

  3. Development of pVCR94ΔX from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids

    PubMed Central

    Carraro, Nicolas; Sauvé, Maxime; Matteau, Dominick; Lauzon, Guillaume; Rodrigue, Sébastien; Burrus, Vincent

    2013-01-01

    Antibiotic resistance has grown steadily in Vibrio cholerae over the last few decades to become a major threat in countries affected by cholera. Multi-drug resistance (MDR) spreads among clinical and environmental V. cholerae strains by lateral gene transfer often mediated by integrative and conjugative elements (ICEs) of the SXT/R391 family. However, in a few reported but seemingly isolated cases, MDR in V. cholerae was shown to be associated with other self-transmissible genetic elements such as conjugative plasmids. IncA/C conjugative plasmids are often found associated with MDR in isolates of Enterobacteriaceae. To date, IncA/C plasmids have not been commonly found in V. cholerae or other species of Vibrio. Here we present a detailed analysis of pVCR94ΔX derived from pVCR94, a novel IncA/C conjugative plasmid identified in a V. cholerae clinical strain isolated during the 1994 Rwandan cholera outbreak. pVCR94 was found to confer resistance to sulfamethoxazole, trimethoprim, ampicillin, streptomycin, tetracycline, and chloramphenicol and to transfer at very high frequency. Sequence analysis revealed its mosaic nature as well as high similarity of the core genes responsible for transfer and maintenance with other IncA/C plasmids and ICEs of the SXT/R391 family. Although IncA/C plasmids are considered a major threat in antibiotics resistance, their basic biology has received little attention, mostly because of the difficulty to genetically manipulate these MDR conferring elements. Therefore, we developed a convenient derivative from pVCR94, pVCR94Δ X, a 120.5-kb conjugative plasmid which only codes for sulfamethoxazole resistance. Using pVCR94Δ X, we identified the origin of transfer (oriT) and discovered an essential gene for transfer, both located within the shared backbone, allowing for an annotation update of all IncA/C plasmids. pVCR94Δ X may be a useful model that will provide new insights on the basic biology of IncA/C conjugative plasmids. PMID

  4. An Integrated Musculoskeletal-Finite-Element Model to Evaluate Effects of Load Carriage on the Tibia During Walking.

    PubMed

    Xu, Chun; Silder, Amy; Zhang, Ju; Hughes, Julie; Unnikrishnan, Ginu; Reifman, Jaques; Rakesh, Vineet

    2016-10-01

    Prior studies have assessed the effects of load carriage on the tibia. Here, we expand on these studies and investigate the effects of load carriage on joint reaction forces (JRFs) and the resulting spatiotemporal stress/strain distributions in the tibia. Using full-body motion and ground reaction forces from a female subject, we computed joint and muscle forces during walking for four load carriage conditions. We applied these forces as physiological loading conditions in a finite-element (FE) analysis to compute strain and stress. We derived material properties from computed tomography (CT) images of a sex-, age-, and body mass index-matched subject using a mesh morphing and mapping algorithm, and used them within the FE model. Compared to walking with no load, the knee JRFs were the most sensitive to load carriage, increasing by as much as 26.2% when carrying a 30% of body weight (BW) load (ankle: 16.4% and hip: 19.0%). Moreover, our model revealed disproportionate increases in internal JRFs with increases in load carriage, suggesting a coordinated adjustment in the musculature functions in the lower extremity. FE results reflected the complex effects of spatially varying material properties distribution and muscular engagement on tibial biomechanics during walking. We observed high stresses on the anterior crest and the medial surface of the tibia at pushoff, whereas high cumulative stress during one walking cycle was more prominent in the medioposterior aspect of the tibia. Our findings reinforce the need to include: (1) physiologically accurate loading conditions when modeling healthy subjects undergoing short-term exercise training and (2) the duration of stress exposure when evaluating stress-fracture injury risk. As a fundamental step toward understanding the instantaneous effect of external loading, our study presents a means to assess the relationship between load carriage and bone biomechanics. PMID:27437640

  5. Purified mariner (Mos1) transposase catalyzes the integration of marked elements into the germ-line of the yellow fever mosquito, Aedes aegypti.

    PubMed

    Coates, C J; Jasinskiene, N; Morgan, D; Tosi, L R; Beverley, S M; James, A A

    2000-11-01

    Derivatives of the mariner transposable element, Mos1, from Drosophila mauritiana, can integrate into the germ-line of the yellow fever mosquito, Aedes aegypti. Previously, the transposase required to mobilize Mos1 was provided in trans by a helper plasmid expressing the enzyme under the control of the D. psuedoobscura heat-shock protein 82 promoter. Here we tested whether purified recombinant Mos1 transposase could increase the recovery of Ae. aegypti transformants. Mos1 transposase was injected into white-eyed, kh(w)/kh(w), Ae. aegypti embryos with a Mos1 donor plasmid containing a copy of the wild-type allele of the D. melanogaster cinnabar gene. Transformed mosquitoes were recognized by partial restoration of eye color in the G(1) animals and confirmed by Southern analyses of genomic DNA. At Mos1 transposase concentrations approaching 100 nM, the rate of germ-line transformants arising from independent insertions in G(0) animals was elevated 2-fold compared to that seen in experiments with helper plasmids. Furthermore, the recovery of total G(1) transformants was increased 7.5-fold over the frequency seen with co-injected helper plasmid. Southern blot analyses and gene amplification experiments confirmed the integration of the transposons into the mosquito genome, although not all integrations were of the expected cut-and-paste type transposition. The increased frequency of germ-line integrations obtained with purified transposase will facilitate the generation of Mos1 transgenic mosquitoes and the application of transgenic approaches to the biology of this important vector of multiple pathogens. PMID:10989286

  6. Phase conjugation with CO 2 lasers

    NASA Astrophysics Data System (ADS)

    Klingenberg, H. H.; Riede, W.; Hall, Th.

    1995-01-01

    A TEA CO 2 laser was used for the investigation of four-wave mixing (4WM) processes in sulfur hexafluoride (SF 6), an organic solvent (toluene), and III/V semiconductor wafers (InSb, InAs). The relevant involved grating mechanisms were probed by the 4WM technique. It was found that the decay times of the corresponding built-up transient gratings in the various nonlinear media differ by approximately six orders of magnitude. Furthermore, simulations of a phase conjugates mirror (PCM) were carried out by solving the Kirchhoff-Fresnel integral equations by complex conjugating the spatial field distribution at the PCM. Applying this technique an efficient production of low divergence high energy CO 2 laser pulses generated from a 4WM master oscillator/power amplifier (MOPA) scheme was predictable. For the modelling a large volume e-beam controlled CO 2 amplifier was placed along the signal beam. The optical homogeneity of the laser gas was disturbed by shock waves and by the laser-induced medium perturbation (LIMP) effect. The disturbing influence of both effects on the optical quality of the output radiation will be shown.

  7. An integrated framework for finite-element modeling of mitral valve biomechanics from medical images: application to MitralClip intervention planning.

    PubMed

    Mansi, Tommaso; Voigt, Ingmar; Georgescu, Bogdan; Zheng, Xudong; Mengue, Etienne Assoumou; Hackl, Michael; Ionasec, Razvan I; Noack, Thilo; Seeburger, Joerg; Comaniciu, Dorin

    2012-10-01

    Treatment of mitral valve (MV) diseases requires comprehensive clinical evaluation and therapy personalization to optimize outcomes. Finite-element models (FEMs) of MV physiology have been proposed to study the biomechanical impact of MV repair, but their translation into the clinics remains challenging. As a step towards this goal, we present an integrated framework for finite-element modeling of the MV closure based on patient-specific anatomies and boundary conditions. Starting from temporal medical images, we estimate a comprehensive model of the MV apparatus dynamics, including papillary tips, using a machine-learning approach. A detailed model of the open MV at end-diastole is then computed, which is finally closed according to a FEM of MV biomechanics. The motion of the mitral annulus and papillary tips are constrained from the image data for increased accuracy. A sensitivity analysis of our system shows that chordae rest length and boundary conditions have a significant influence upon the simulation results. We quantitatively test the generalization of our framework on 25 consecutive patients. Comparisons between the simulated closed valve and ground truth show encouraging results (average point-to-mesh distance: 1.49 ± 0.62 mm) but also the need for personalization of tissue properties, as illustrated in three patients. Finally, the predictive power of our model is tested on one patient who underwent MitralClip by comparing the simulated intervention with the real outcome in terms of MV closure, yielding promising prediction. By providing an integrated way to perform MV simulation, our framework may constitute a surrogate tool for model validation and therapy planning.

  8. Fine-tuning key parameters of an integrated reactor system for the simultaneous removal of COD, sulfate and ammonium and elemental sulfur reclamation.

    PubMed

    Yuan, Ye; Chen, Chuan; Liang, Bin; Huang, Cong; Zhao, Youkang; Xu, Xijun; Tan, Wenbo; Zhou, Xu; Gao, Shuang; Sun, Dezhi; Lee, Duujong; Zhou, Jizhong; Wang, Aijie

    2014-03-30

    In this paper, we proposed an integrated reactor system for simultaneous removal of COD, sulfate and ammonium (integrated C-S-N removal system) and investigated the key parameters of the system for a high level of elemental sulfur (S(0)) production. The system consisted of 4 main units: sulfate reduction and organic carbon removal (SR-CR), autotrophic and heterotrophic denitrifying sulfide removal (A&H-DSR), sulfur reclamation (SR), and aerated filter for aerobic nitrification (AN). In the system, the effects of key operational parameters on production of elemental sulfur were investigated, including hydraulic retention time (HRT) of each unit, sulfide/nitrate (S(2-)-S/NO3(-)-N) ratios, reflux ratios between the A&H-DSR and AN units, and loading rates of chemical oxygen demand (COD), sulfate and ammonium. Physico-chemical characteristics of biosulfur were studied for acquiring efficient S(0) recovery. The experiments successfully explored the optimum parameters for each unit and demonstrated 98% COD, 98% sulfate and 78% nitrogen removal efficiency. The optimum HRTs for SR-CR, A&H-DSR and AN were 12h, 3h and 3h, respectively. The reflux ratio of 3 could provide adequate S(2-)-S/NO3(-)-N ratio (approximately 1:1) to the A&H-DSR unit for obtaining maximum sulfur production. In this system, the maximum production of S(0) reached 90%, but only 60% S(0) was reclaimed from effluent. The S(0) that adhered to the outer layer of granules was deposited in the bottom of the A&H-DSR unit. Finally, the microbial community structure of the corresponding unit at different operational stage were analyzed by 16S rRNA gene based high throughput Illumina MiSeq sequencing and the potential function of dominant species were discussed.

  9. An integrated framework for finite-element modeling of mitral valve biomechanics from medical images: application to MitralClip intervention planning.

    PubMed

    Mansi, Tommaso; Voigt, Ingmar; Georgescu, Bogdan; Zheng, Xudong; Mengue, Etienne Assoumou; Hackl, Michael; Ionasec, Razvan I; Noack, Thilo; Seeburger, Joerg; Comaniciu, Dorin

    2012-10-01

    Treatment of mitral valve (MV) diseases requires comprehensive clinical evaluation and therapy personalization to optimize outcomes. Finite-element models (FEMs) of MV physiology have been proposed to study the biomechanical impact of MV repair, but their translation into the clinics remains challenging. As a step towards this goal, we present an integrated framework for finite-element modeling of the MV closure based on patient-specific anatomies and boundary conditions. Starting from temporal medical images, we estimate a comprehensive model of the MV apparatus dynamics, including papillary tips, using a machine-learning approach. A detailed model of the open MV at end-diastole is then computed, which is finally closed according to a FEM of MV biomechanics. The motion of the mitral annulus and papillary tips are constrained from the image data for increased accuracy. A sensitivity analysis of our system shows that chordae rest length and boundary conditions have a significant influence upon the simulation results. We quantitatively test the generalization of our framework on 25 consecutive patients. Comparisons between the simulated closed valve and ground truth show encouraging results (average point-to-mesh distance: 1.49 ± 0.62 mm) but also the need for personalization of tissue properties, as illustrated in three patients. Finally, the predictive power of our model is tested on one patient who underwent MitralClip by comparing the simulated intervention with the real outcome in terms of MV closure, yielding promising prediction. By providing an integrated way to perform MV simulation, our framework may constitute a surrogate tool for model validation and therapy planning. PMID:22766456

  10. Boundary element methods in elastography: a first explorative study

    NASA Astrophysics Data System (ADS)

    Berger, Hans-Uwe; Hann, Chris E.; Chase, J. Geoffrey; Broughton, Robert L.; Van Houten, Elijah

    2007-03-01

    Next to Magnet Resonance Elastography and Ultrasound Elastography, Digital Image Elasto-Tomography (DIET) is a new imaging-technique, using only motion data available on the boundary, to reconstruct mechanical material parameters, i.e. the interior sti.ness of a domain, in order to diagnose tissue related disease such as breast cancer. Where classically Finite Element Methods have been employed to solve this inverse problem, this paper explores a new approach to the reconstruction of mechanical material properties of tissue and tissue defects by the use of Boundary Element Methods (BEM). Using the Boundary Integral Equations for Linear Elasticity in two dimensions within a Conjugate Gradients based inverse solver, material properties of healthy and malicious tissue could be determined from displacement data on the boundary. First simulation results are presented.

  11. Phase conjugation method and apparatus for an active retrodirective antenna array

    NASA Technical Reports Server (NTRS)

    Tausworthe, R. C.; Chernoff, R. C. (Inventor)

    1979-01-01

    An active retrodirective antenna array wherein a reference array element is used to generate a phase reference which is replicated at succeeding elements of the array. Each element of the array is associated with a phase regeneration circuit and the phase conjugation circuitry of an adjacent element. In one implementation, the phase reference circuit operates on the input signal at the reference element, a voltage controlled oscillator (VCO) output signal and the input pilot signal at the next array element received from a transmission line. By proper filtering and mixing, a phase component may be produced to which the VCO may be locked to produce the phase conjugate of the pilot signal at the next array element plus a transmission line delay. In another implementation, particularly suited for large arrays in space, two different input pilot frequencies are employed.

  12. Integrated optoelectronic model for organic solar cells based on the finite element method including the effect of oblique sunlight incidence and a non-ohmic electrode contact

    NASA Astrophysics Data System (ADS)

    Lee, Yongjeong; Kang, Kyungnam; Lee, Sanghwa; Kim, Hyeong Pil; Jang, Jin; Kim, Jungho

    2016-10-01

    We present an integrated optoelectronic model for organic solar cells (OSCs) based on the finite element method, which can numerically simulate the optical and electrical properties in the same calculation domain. In the optical model, the spatial distribution of optical absorption is calculated with respect to the incidence angle and light polarization. A glass factor is introduced to include the incoherent light interaction inside the thick glass substrate. In the electrical model, the current density-voltage (J-V) characteristics can be calculated by self-consistently solving the combined equations based on the Onsager-Braun charge-transfer exciton dissociation, drift-diffusion carrier transport, and non-ohmic contact models. The calculation results of the carrier density, the electric potential, and the electric field in the active layer are compared between the ohmic and non-ohmic contact models at the electrode-organic interface. We numerically calculate the angular and polarization dependences of the short-circuit current density, the open-circuit voltage, and the output electric power density at the spectral irradiance of the AM 1.5 spectrum. The calculation results are well matched with the experimental results at various incidence angles and light polarizations. The application of the proposed integrated optoelectronic model to OSCs will not be restricted to one-dimensional planar structures and can be extended to nonplanar or surface-textured structures.

  13. Orderings for conjugate gradient preconditionings

    NASA Technical Reports Server (NTRS)

    Ortega, James M.

    1991-01-01

    The effect of orderings on the rate of convergence of the conjugate gradient method with SSOR or incomplete Cholesky preconditioning is examined. Some results also are presented that help to explain why red/black ordering gives an inferior rate of convergence.

  14. Enhanced photophysics of conjugated polymers

    DOEpatents

    Chen, Liaohai

    2007-06-12

    A particulate fluorescent conjugated polymer surfactant complex and method of making and using same. The particles are between about 15 and about 50 nm and when formed from a lipsome surfactant have a charge density similar to DNA and are strongly absorbed by cancer cells.

  15. Precision measurement of the top quark mass in the lepton + jets channel using a matrix element method with Quasi-Monte Carlo integration

    SciTech Connect

    Lujan, Paul Joseph

    2009-12-01

    This thesis presents a measurement of the top quark mass obtained from p$\\bar{p}$ collisions at √s = 1.96 TeV at the Fermilab Tevatron using the CDF II detector. The measurement uses a matrix element integration method to calculate a t$\\bar{t}$ likelihood, employing a Quasi-Monte Carlo integration, which enables us to take into account effects due to finite detector angular resolution and quark mass effects. We calculate a t$\\bar{t}$ likelihood as a 2-D function of the top pole mass mt and ΔJES, where ΔJES parameterizes the uncertainty in our knowledge of the jet energy scale; it is a shift applied to all jet energies in units of the jet-dependent systematic error. By introducing ΔJES into the likelihood, we can use the information contained in W boson decays to constrain ΔJES and reduce error due to this uncertainty. We use a neural network discriminant to identify events likely to be background, and apply a cut on the peak value of individual event likelihoods to reduce the effect of badly reconstructed events. This measurement uses a total of 4.3 fb-1 of integrated luminosity, requiring events with a lepton, large ET, and exactly four high-energy jets in the pseudorapidity range |η| < 2.0, of which at least one must be tagged as coming from a b quark. In total, we observe 738 events before and 630 events after applying the likelihood cut, and measure mt = 172.6 ± 0.9 (stat.) ± 0.7 (JES) ± 1.1 (syst.) GeV/c2, or mt = 172.6 ± 1.6 (tot.) GeV/c2.

  16. FUEL ELEMENT

    DOEpatents

    Fortescue, P.; Zumwalt, L.R.

    1961-11-28

    A fuel element was developed for a gas cooled nuclear reactor. The element is constructed in the form of a compacted fuel slug including carbides of fissionable material in some cases with a breeder material carbide and a moderator which slug is disposed in a canning jacket of relatively impermeable moderator material. Such canned fuel slugs are disposed in an elongated shell of moderator having greater gas permeability than the canning material wherefore application of reduced pressure to the space therebetween causes gas diffusing through the exterior shell to sweep fission products from the system. Integral fission product traps and/or exterior traps as well as a fission product monitoring system may be employed therewith. (AEC)

  17. Bacteriophytochromes control conjugation in Agrobacterium fabrum.

    PubMed

    Bai, Yingnan; Rottwinkel, Gregor; Feng, Juan; Liu, Yiyao; Lamparter, Tilman

    2016-08-01

    Bacterial conjugation, the transfer of single stranded plasmid DNA from donor to recipient cell, is mediated through the type IV secretion system. We performed conjugation assays using a transmissible artificial plasmid as reporter. With this assay, conjugation in Agrobacterium fabrum was modulated by the phytochromes Agp1 and Agp2, photoreceptors that are most sensitive in the red region of visible light. In conjugation studies with wild-type donor cells carrying a pBIN-GUSINT plasmid as reporter that lacked the Ti (tumor inducing) plasmid, no conjugation was observed. When either agp1(-) or agp2(-) knockout donor strains were used, plasmid DNA was delivered to the recipient, indicating that both phytochromes suppress conjugation in the wild type donor. In the recipient strains, the loss of Agp1 or Agp2 led to diminished conjugation. When wild type cells with Ti plasmid and pBIN-GUS reporter plasmid were used as donor, a high rate of conjugation was observed. The DNA transfer was down regulated by red or far-red light by a factor of 3.5. With agp1(-) or agp2(-) knockout donor cells, conjugation in the dark was about 10 times lower than with the wild type donor, and with the double knockout donor no conjugation was observed. These results imply that the phytochrome system has evolved to inhibit conjugation in the light. The decrease of conjugation under different temperature correlated with the decrease of phytochrome autophosphorylation. PMID:27261700

  18. Designer diatom episomes delivered by bacterial conjugation.

    PubMed

    Karas, Bogumil J; Diner, Rachel E; Lefebvre, Stephane C; McQuaid, Jeff; Phillips, Alex P R; Noddings, Chari M; Brunson, John K; Valas, Ruben E; Deerinck, Thomas J; Jablanovic, Jelena; Gillard, Jeroen T F; Beeri, Karen; Ellisman, Mark H; Glass, John I; Hutchison, Clyde A; Smith, Hamilton O; Venter, J Craig; Allen, Andrew E; Dupont, Christopher L; Weyman, Philip D

    2015-01-01

    Eukaryotic microalgae hold great promise for the bioproduction of fuels and higher value chemicals. However, compared with model genetic organisms such as Escherichia coli and Saccharomyces cerevisiae, characterization of the complex biology and biochemistry of algae and strain improvement has been hampered by the inefficient genetic tools. To date, many algal species are transformable only via particle bombardment, and the introduced DNA is integrated randomly into the nuclear genome. Here we describe the first nuclear episomal vector for diatoms and a plasmid delivery method via conjugation from Escherichia coli to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. We identify a yeast-derived sequence that enables stable episome replication in these diatoms even in the absence of antibiotic selection and show that episomes are maintained as closed circles at copy number equivalent to native chromosomes. This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research. PMID:25897682

  19. Designer diatom episomes delivered by bacterial conjugation

    PubMed Central

    Karas, Bogumil J.; Diner, Rachel E.; Lefebvre, Stephane C.; McQuaid, Jeff; Phillips, Alex P.R.; Noddings, Chari M.; Brunson, John K.; Valas, Ruben E.; Deerinck, Thomas J.; Jablanovic, Jelena; Gillard, Jeroen T.F.; Beeri, Karen; Ellisman, Mark H.; Glass, John I.; Hutchison III, Clyde A.; Smith, Hamilton O.; Venter, J. Craig; Allen, Andrew E.; Dupont, Christopher L.; Weyman, Philip D.

    2015-01-01

    Eukaryotic microalgae hold great promise for the bioproduction of fuels and higher value chemicals. However, compared with model genetic organisms such as Escherichia coli and Saccharomyces cerevisiae, characterization of the complex biology and biochemistry of algae and strain improvement has been hampered by the inefficient genetic tools. To date, many algal species are transformable only via particle bombardment, and the introduced DNA is integrated randomly into the nuclear genome. Here we describe the first nuclear episomal vector for diatoms and a plasmid delivery method via conjugation from Escherichia coli to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. We identify a yeast-derived sequence that enables stable episome replication in these diatoms even in the absence of antibiotic selection and show that episomes are maintained as closed circles at copy number equivalent to native chromosomes. This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research. PMID:25897682

  20. Transfer of pRD1 to Pseudomonas syringae and evidence for its integration into the chromosome.

    PubMed Central

    Vincent, J R; Fulbright, D W

    1983-01-01

    Plasmid pRD1 was conjugatively transferred from Escherichia coli to Pseudomonas syringae. Subculturing the transconjugate on a medium that selected for pRD1-determined His+ Kmr resulted in the loss of pRD1 as an extrachromosomal element as detected by agarose gel electrophoresis. DNA hybridization provided evidence for the integration of pRD1 into the P. syringae chromosome. Images PMID:6358197

  1. Gender and conjugal differences in happiness.

    PubMed

    Lu, L

    2000-02-01

    The author examined conjugal congruence on 4 role experiences--spousal, parental, filial, worker--and on subjective well-being (SWB). According to purposive sampling strategy, 222 community adults (111 married couples) in Taiwan completed a research questionnaire. Conjugal congruence on role experiences was linked to conjugal congruence on SWB as well as personal well-being. Analyses showed that conjugal congruence on role experiences (except the worker role) and SWB was generally high. However, some conjugal discrepancies persisted: The husbands were more committed to the worker role, whereas the wives were more committed to the parental role. Furthermore, conjugal discrepancies in role experiences were related to conjugal discrepancies in SWB as well as to husbands' happiness.

  2. Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

    PubMed Central

    Brown, Christopher D.; Mangravite, Lara M.; Engelhardt, Barbara E.

    2013-01-01

    Genetic variants in cis-regulatory elements or trans-acting regulators frequently influence the quantity and spatiotemporal distribution of gene transcription. Recent interest in expression quantitative trait locus (eQTL) mapping has paralleled the adoption of genome-wide association studies (GWAS) for the analysis of complex traits and disease in humans. Under the hypothesis that many GWAS associations tag non-coding SNPs with small effects, and that these SNPs exert phenotypic control by modifying gene expression, it has become common to interpret GWAS associations using eQTL data. To fully exploit the mechanistic interpretability of eQTL-GWAS comparisons, an improved understanding of the genetic architecture and causal mechanisms of cell type specificity of eQTLs is required. We address this need by performing an eQTL analysis in three parts: first we identified eQTLs from eleven studies on seven cell types; then we integrated eQTL data with cis-regulatory element (CRE) data from the ENCODE project; finally we built a set of classifiers to predict the cell type specificity of eQTLs. The cell type specificity of eQTLs is associated with eQTL SNP overlap with hundreds of cell type specific CRE classes, including enhancer, promoter, and repressive chromatin marks, regions of open chromatin, and many classes of DNA binding proteins. These associations provide insight into the molecular mechanisms generating the cell type specificity of eQTLs and the mode of regulation of corresponding eQTLs. Using a random forest classifier with cell specific CRE-SNP overlap as features, we demonstrate the feasibility of predicting the cell type specificity of eQTLs. We then demonstrate that CREs from a trait-associated cell type can be used to annotate GWAS associations in the absence of eQTL data for that cell type. We anticipate that such integrative, predictive modeling of cell specificity will improve our ability to understand the mechanistic basis of human complex phenotypic

  3. GLOBULAR CLUSTER ABUNDANCES FROM HIGH-RESOLUTION, INTEGRATED-LIGHT SPECTROSCOPY. IV. THE LARGE MAGELLANIC CLOUD: {alpha}, Fe-PEAK, LIGHT, AND HEAVY ELEMENTS

    SciTech Connect

    Colucci, Janet E.; Bernstein, Rebecca A.; McWilliam, Andrew E-mail: rab@ucolick.org E-mail: andy@ociw.edu

    2012-02-10

    We present detailed chemical abundances in eight clusters in the Large Magellanic Cloud (LMC). We measure abundances of 22 elements for clusters spanning a range in age of 0.05-12 Gyr, providing a comprehensive picture of the chemical enrichment and star formation history of the LMC. The abundances were obtained from individual absorption lines using a new method for analysis of high-resolution (R {approx} 25,000), integrated-light (IL) spectra of star clusters. This method was developed and presented in Papers I, II, and III of this series. In this paper, we develop an additional IL {chi}{sup 2}-minimization spectral synthesis technique to facilitate measurement of weak ({approx}15 mA) spectral lines and abundances in low signal-to-noise ratio data (S/N {approx} 30). Additionally, we supplement the IL abundance measurements with detailed abundances that we measure for individual stars in the youngest clusters (age < 2 Gyr) in our sample. In both the IL and stellar abundances we find evolution of [{alpha}/Fe] with [Fe/H] and age. Fe-peak abundance ratios are similar to those in the Milky Way (MW), with the exception of [Cu/Fe] and [Mn/Fe], which are sub-solar at high metallicities. The heavy elements Ba, La, Nd, Sm, and Eu are significantly enhanced in the youngest clusters. Also, the heavy to light s-process ratio is elevated relative to the MW ([Ba/Y] >+0.5) and increases with decreasing age, indicating a strong contribution of low-metallicity asymptotic giant branch star ejecta to the interstellar medium throughout the later history of the LMC. We also find a correlation of IL Na and Al abundances with cluster mass in the sense that more massive, older clusters are enriched in the light elements Na and Al with respect to Fe, which implies that these clusters harbor star-to-star abundance variations as is common in the MW. Lower mass, intermediate-age, and young clusters have Na and Al abundances that are lower and more consistent with LMC field stars. Our

  4. The ISG15 conjugation system.

    PubMed

    Durfee, Larissa A; Huibregtse, Jon M

    2012-01-01

    ISG15 is a ubiquitin-like modifier that is expressed in response to type 1 interferon signaling (IFN-α/β) and plays a role in antiviral responses. The core E1, E2, and E3 enzymes for ISG15 are Ube1L, UbcH8, and Herc5, respectively, and these are all also induced at the transcriptional level by IFN-α/β. We recently showed that Herc5 associates with polysomes and modifies target proteins in a cotranslational manner. Here, we describe the expression of the core conjugating enzymes in human cells, the detection of ISG15 conjugates, and the methods for fractionation of Herc5 with polysomes. PMID:22350882

  5. Enhanced photophysics of conjugated polymers

    DOEpatents

    Chen, Liaohai; Xu, Su; McBranch, Duncan; Whitten, David

    2003-05-27

    The addition of oppositely charged surfactant to fluorescent ionic conjugated polymer forms a polymer-surfactant complex that exhibits at least one improved photophysical property. The conjugated polymer is a fluorescent ionic polymer that typically has at least one ionic side chain or moiety that interacts with the specific surfactant selected. The photophysical property improvements may include increased fluorescence quantum efficiency, wavelength-independent emission and absorption spectra, and more stable fluorescence decay kinetics. The complexation typically occurs in a solution of a polar solvent in which the polymer and surfactant are soluble, but it may also occur in a mixture of solvents. The solution is commonly prepared with a surfactant molecule:monomer repeat unit of polymer ratio ranging from about 1:100 to about 1:1. A polymer-surfactant complex precipitate is formed as the ratio approaches 1:1. This precipitate is recoverable and usable in many forms.

  6. Incorporating distant sequence features and radial basis function networks to identify ubiquitin conjugation sites.

    PubMed

    Lee, Tzong-Yi; Chen, Shu-An; Hung, Hsin-Yi; Ou, Yu-Yen

    2011-03-09

    Ubiquitin (Ub) is a small protein that consists of 76 amino acids about 8.5 kDa. In ubiquitin conjugation, the ubiquitin is majorly conjugated on the lysine residue of protein by Ub-ligating (E3) enzymes. Three major enzymes participate in ubiquitin conjugation. They are E1, E2 and E3 which are responsible for activating, conjugating and ligating ubiquitin, respectively. Ubiquitin conjugation in eukaryotes is an important mechanism of the proteasome-mediated degradation of a protein and regulating the activity of transcription factors. Motivated by the importance of ubiquitin conjugation in biological processes, this investigation develops a method, UbSite, which uses utilizes an efficient radial basis function (RBF) network to identify protein ubiquitin conjugation (ubiquitylation) sites. This work not only investigates the amino acid composition but also the structural characteristics, physicochemical properties, and evolutionary information of amino acids around ubiquitylation (Ub) sites. With reference to the pathway of ubiquitin conjugation, the substrate sites for E3 recognition, which are distant from ubiquitylation sites, are investigated. The measurement of F-score in a large window size (-20∼+20) revealed a statistically significant amino acid composition and position-specific scoring matrix (evolutionary information), which are mainly located distant from Ub sites. The distant information can be used effectively to differentiate Ub sites from non-Ub sites. As determined by five-fold cross-validation, the model that was trained using the combination of amino acid composition and evolutionary information performs best in identifying ubiquitin conjugation sites. The prediction sensitivity, specificity, and accuracy are 65.5%, 74.8%, and 74.5%, respectively. Although the amino acid sequences around the ubiquitin conjugation sites do not contain conserved motifs, the cross-validation result indicates that the integration of distant sequence features of Ub

  7. Incorporating Distant Sequence Features and Radial Basis Function Networks to Identify Ubiquitin Conjugation Sites

    PubMed Central

    Hung, Hsin-Yi; Ou, Yu-Yen

    2011-01-01

    Ubiquitin (Ub) is a small protein that consists of 76 amino acids about 8.5 kDa. In ubiquitin conjugation, the ubiquitin is majorly conjugated on the lysine residue of protein by Ub-ligating (E3) enzymes. Three major enzymes participate in ubiquitin conjugation. They are – E1, E2 and E3 which are responsible for activating, conjugating and ligating ubiquitin, respectively. Ubiquitin conjugation in eukaryotes is an important mechanism of the proteasome-mediated degradation of a protein and regulating the activity of transcription factors. Motivated by the importance of ubiquitin conjugation in biological processes, this investigation develops a method, UbSite, which uses utilizes an efficient radial basis function (RBF) network to identify protein ubiquitin conjugation (ubiquitylation) sites. This work not only investigates the amino acid composition but also the structural characteristics, physicochemical properties, and evolutionary information of amino acids around ubiquitylation (Ub) sites. With reference to the pathway of ubiquitin conjugation, the substrate sites for E3 recognition, which are distant from ubiquitylation sites, are investigated. The measurement of F-score in a large window size (−20∼+20) revealed a statistically significant amino acid composition and position-specific scoring matrix (evolutionary information), which are mainly located distant from Ub sites. The distant information can be used effectively to differentiate Ub sites from non-Ub sites. As determined by five-fold cross-validation, the model that was trained using the combination of amino acid composition and evolutionary information performs best in identifying ubiquitin conjugation sites. The prediction sensitivity, specificity, and accuracy are 65.5%, 74.8%, and 74.5%, respectively. Although the amino acid sequences around the ubiquitin conjugation sites do not contain conserved motifs, the cross-validation result indicates that the integration of distant sequence features

  8. Variable metric conjugate gradient methods

    SciTech Connect

    Barth, T.; Manteuffel, T.

    1994-07-01

    1.1 Motivation. In this paper we present a framework that includes many well known iterative methods for the solution of nonsymmetric linear systems of equations, Ax = b. Section 2 begins with a brief review of the conjugate gradient method. Next, we describe a broader class of methods, known as projection methods, to which the conjugate gradient (CG) method and most conjugate gradient-like methods belong. The concept of a method having either a fixed or a variable metric is introduced. Methods that have a metric are referred to as either fixed or variable metric methods. Some relationships between projection methods and fixed (variable) metric methods are discussed. The main emphasis of the remainder of this paper is on variable metric methods. In Section 3 we show how the biconjugate gradient (BCG), and the quasi-minimal residual (QMR) methods fit into this framework as variable metric methods. By modifying the underlying Lanczos biorthogonalization process used in the implementation of BCG and QMR, we obtain other variable metric methods. These, we refer to as generalizations of BCG and QMR.

  9. Augmented weak forms and element-by-element preconditioners: Efficient iterative strategies for structural finite elements. A preliminary study

    NASA Technical Reports Server (NTRS)

    Muller, A.; Hughes, T. J. R.

    1984-01-01

    A weak formulation in structural analysis that provides well conditioned matrices suitable for iterative solutions is presented. A mixed formulation ensures the proper representation of the problem and the constitutive relations are added in a penalized form. The problem is solved by a double conjugate gradient algorithm combined with an element by element approximate factorization procedure. The double conjugate gradient strategy resembles Uzawa's variable-length type algorithms the main difference is the presence of quadratic terms in the mixed variables. In the case of shear deformable beams these terms ensure that the proper finite thickness solution is obtained.

  10. Separate elements of the TERMINAL FLOWER 1 cis-regulatory region integrate pathways to control flowering time and shoot meristem identity.

    PubMed

    Serrano-Mislata, Antonio; Fernández-Nohales, Pedro; Doménech, María J; Hanzawa, Yoshie; Bradley, Desmond; Madueño, Francisco

    2016-09-15

    TERMINAL FLOWER 1 (TFL1) is a key regulator of Arabidopsis plant architecture that responds to developmental and environmental signals to control flowering time and the fate of shoot meristems. TFL1 expression is dynamic, being found in all shoot meristems, but not in floral meristems, with the level and distribution changing throughout development. Using a variety of experimental approaches we have analysed the TFL1 promoter to elucidate its functional structure. TFL1 expression is based on distinct cis-regulatory regions, the most important being located 3' of the coding sequence. Our results indicate that TFL1 expression in the shoot apical versus lateral inflorescence meristems is controlled through distinct cis-regulatory elements, suggesting that different signals control expression in these meristem types. Moreover, we identified a cis-regulatory region necessary for TFL1 expression in the vegetative shoot and required for a wild-type flowering time, supporting that TFL1 expression in the vegetative meristem controls flowering time. Our study provides a model for the functional organisation of TFL1 cis-regulatory regions, contributing to our understanding of how developmental pathways are integrated at the genomic level of a key regulator to control plant architecture. PMID:27385013

  11. ICEG2D: An Integrated Software Package for Automated Prediction of Flow Fields for Single-Element Airfoils with Ice Accretion

    NASA Technical Reports Server (NTRS)

    Thompson, David S.; Soni, Bharat K.

    2000-01-01

    An integrated software package, ICEG2D, was developed to automate computational fluid dynamics (CFD) simulations for single-element airfoils with ice accretion. ICEG2D is designed to automatically perform three primary functions: (1) generating a grid-ready, surface definition based on the geometrical characteristics of the iced airfoil surface, (2) generating a high-quality grid using the generated surface point distribution, and (3) generating the input and restart files needed to run the general purpose CFD solver NPARC. ICEG2D can be executed in batch mode using a script file or in an interactive mode by entering directives from a command line. This report summarizes activities completed in the first year of a three-year research and development program to address issues related to CFD simulations for aircraft components with ice accretion. Specifically, this document describes the technology employed in the software, the installation procedure, and a description of the operation of the software package. Validation of the geometry and grid generation modules of ICEG2D is also discussed.

  12. ICEG2D (v2.0) - An Integrated Software Package for Automated Prediction of Flow Fields for Single-Element Airfoils With Ice Accretion

    NASA Technical Reports Server (NTRS)

    Thompson David S.; Soni, Bharat K.

    2001-01-01

    An integrated geometry/grid/simulation software package, ICEG2D, is being developed to automate computational fluid dynamics (CFD) simulations for single- and multi-element airfoils with ice accretions. The current version, ICEG213 (v2.0), was designed to automatically perform four primary functions: (1) generate a grid-ready surface definition based on the geometrical characteristics of the iced airfoil surface, (2) generate high-quality structured and generalized grids starting from a defined surface definition, (3) generate the input and restart files needed to run the structured grid CFD solver NPARC or the generalized grid CFD solver HYBFL2D, and (4) using the flow solutions, generate solution-adaptive grids. ICEG2D (v2.0) can be operated in either a batch mode using a script file or in an interactive mode by entering directives from a command line within a Unix shell. This report summarizes activities completed in the first two years of a three-year research and development program to address automation issues related to CFD simulations for airfoils with ice accretions. As well as describing the technology employed in the software, this document serves as a users manual providing installation and operating instructions. An evaluation of the software is also presented.

  13. First steps of integrated spatial modeling of titanium, zirconium, and rare earth element resources within the Coastal Plain sediments of the southeastern United States

    USGS Publications Warehouse

    Ellefsen, Karl J.; Van Gosen, Bradley S.; Fey, David L.; Budahn, James R.; Smith, Steven M.; Shah, Anjana K.

    2015-01-01

    The Coastal Plain of the southeastern United States has extensive, unconsolidated sedimentary deposits that are enriched in heavy minerals containing titanium, zirconium, and rare earth element resources. Areas favorable for exploration and development of these resources are being identified by geochemical data, which are supplemented with geological, geophysical, hydrological, and geographical data. The first steps of this analysis have been completed. The concentrations of lanthanum, yttrium, and titanium tend to decrease as distance from the Piedmont (which is the likely source of these resources) increases and are moderately correlated with airborne measurements of equivalent thorium concentration. The concentrations of lanthanum, yttrium, and titanium are relatively high in those watersheds that adjoin the Piedmont, south of the Cape Fear Arch. Although this relation suggests that the concentrations are related to the watersheds, it may be simply an independent regional trend. The concentration of zirconium is unrelated to the distance from the Piedmont, the equivalent thorium concentration, and the watershed. These findings establish a foundation for more sophisticated analyses using integrated spatial modeling.

  14. Separate elements of the TERMINAL FLOWER 1 cis-regulatory region integrate pathways to control flowering time and shoot meristem identity.

    PubMed

    Serrano-Mislata, Antonio; Fernández-Nohales, Pedro; Doménech, María J; Hanzawa, Yoshie; Bradley, Desmond; Madueño, Francisco

    2016-09-15

    TERMINAL FLOWER 1 (TFL1) is a key regulator of Arabidopsis plant architecture that responds to developmental and environmental signals to control flowering time and the fate of shoot meristems. TFL1 expression is dynamic, being found in all shoot meristems, but not in floral meristems, with the level and distribution changing throughout development. Using a variety of experimental approaches we have analysed the TFL1 promoter to elucidate its functional structure. TFL1 expression is based on distinct cis-regulatory regions, the most important being located 3' of the coding sequence. Our results indicate that TFL1 expression in the shoot apical versus lateral inflorescence meristems is controlled through distinct cis-regulatory elements, suggesting that different signals control expression in these meristem types. Moreover, we identified a cis-regulatory region necessary for TFL1 expression in the vegetative shoot and required for a wild-type flowering time, supporting that TFL1 expression in the vegetative meristem controls flowering time. Our study provides a model for the functional organisation of TFL1 cis-regulatory regions, contributing to our understanding of how developmental pathways are integrated at the genomic level of a key regulator to control plant architecture.

  15. Application of Conjugate Gradient methods to tidal simulation

    USGS Publications Warehouse

    Barragy, E.; Carey, G.F.; Walters, R.A.

    1993-01-01

    A harmonic decomposition technique is applied to the shallow water equations to yield a complex, nonsymmetric, nonlinear, Helmholtz type problem for the sea surface and an accompanying complex, nonlinear diagonal problem for the velocities. The equation for the sea surface is linearized using successive approximation and then discretized with linear, triangular finite elements. The study focuses on applying iterative methods to solve the resulting complex linear systems. The comparative evaluation includes both standard iterative methods for the real subsystems and complex versions of the well known Bi-Conjugate Gradient and Bi-Conjugate Gradient Squared methods. Several Incomplete LU type preconditioners are discussed, and the effects of node ordering, rejection strategy, domain geometry and Coriolis parameter (affecting asymmetry) are investigated. Implementation details for the complex case are discussed. Performance studies are presented and comparisons made with a frontal solver. ?? 1993.

  16. Identification of potent orally active factor Xa inhibitors based on conjugation strategy and application of predictable fragment recommender system.

    PubMed

    Ishihara, Tsukasa; Koga, Yuji; Iwatsuki, Yoshiyuki; Hirayama, Fukushi

    2015-01-15

    Anticoagulant agents have emerged as a promising class of therapeutic drugs for the treatment and prevention of arterial and venous thrombosis. We investigated a series of novel orally active factor Xa inhibitors designed using our previously reported conjugation strategy to boost oral anticoagulant effect. Structural optimization of anthranilamide derivative 3 as a lead compound with installation of phenolic hydroxyl group and extensive exploration of the P1 binding element led to the identification of 5-chloro-N-(5-chloro-2-pyridyl)-3-hydroxy-2-{[4-(4-methyl-1,4-diazepan-1-yl)benzoyl]amino}benzamide (33, AS1468240) as a potent factor Xa inhibitor with significant oral anticoagulant activity. We also reported a newly developed Free-Wilson-like fragment recommender system based on the integration of R-group decomposition with collaborative filtering for the structural optimization process.

  17. Active retrodirective arrays for SPS beam pointing. [phase conjugation

    NASA Technical Reports Server (NTRS)

    Chernoff, R.

    1980-01-01

    The basic requirement of the SPS beam pointing system is that it deliver a certain amount of S-band (lambda = 12.5 cm) power to a 9.6 km diameter receiving rectenna on the ground. The power is transmitted from a 1.0 km diameter antenna array on the SPS, which is, for a rectenna at about plus or minus 40 deg. latitude, some 37.5x10 to the 6th power km distant. At the present time ARA's appear to be the best bet to realize this very stringent beam pointing requirement. An active retrodirective array (ARA) transmits a beam towards the apparent source of an illuminating signal called the pilot. The array produces, not merely reflects, RF power. Retrodirectivity is achieved by retransmitting from each element of the array a signal whose phase is the "conjugate" of that received by the element. Phase conjugate circuits and pointing errors in ARA's are described. Results obtained using a 2-element X-band ARA and an 8-element S-band ARA are included.

  18. Synthesis and Characterization of Fatty Acid Conjugates of Niacin and Salicylic Acid.

    PubMed

    Vu, Chi B; Bemis, Jean E; Benson, Ericka; Bista, Pradeep; Carney, David; Fahrner, Richard; Lee, Diana; Liu, Feng; Lonkar, Pallavi; Milne, Jill C; Nichols, Andrew J; Picarella, Dominic; Shoelson, Adam; Smith, Jesse; Ting, Amal; Wensley, Allison; Yeager, Maisy; Zimmer, Michael; Jirousek, Michael R

    2016-02-11

    This report describes the synthesis and preliminary biological characterization of novel fatty acid niacin conjugates and fatty acid salicylate conjugates. These molecular entities were created by covalently linking two bioactive molecules, either niacin or salicylic acid, to an omega-3 fatty acid. This methodology allows the simultaneous intracellular delivery of two bioactives in order to elicit a pharmacological response that could not be replicated by administering the bioactives individually or in combination. The fatty acid niacin conjugate 5 has been shown to be an inhibitor of the sterol regulatory element binding protein (SREBP), a key regulator of cholesterol metabolism proteins such as PCSK9, HMG-CoA reductase, ATP citrate lyase, and NPC1L1. On the other hand, the fatty acid salicylate conjugate 11 has been shown to have a unique anti-inflammatory profile based on its ability to modulate the NF-κB pathway through the intracellular release of the two bioactives.

  19. Teaching Integrity

    ERIC Educational Resources Information Center

    Saunders, Sue; Butts, Jennifer Lease

    2011-01-01

    Integrity is one of those essential yet highly ambiguous concepts. For the purpose of this chapter, integrity is defined as that combination of both attributes and actions that makes entities appear to be whole and ethical, as well as consistent. Like the concepts of leadership or wisdom or community or collaboration, integrity is a key element of…

  20. Phononic Phase Conjugation in an Optomechanical System

    NASA Astrophysics Data System (ADS)

    Buchmann, Lukas; Wright, Ewan; Meystre, Pierre

    2013-05-01

    We study theoretically the phase conjugation of a phononic field in an optomechanical system with two mechanical modes coupled to a common optical field. Phase conjugation becomes the dominant process for an appropriate choice of driving field parameters, and he effective coupling coefficients between phonon modes can result in amplification and entanglement, phase-conjugation or a mixture thereof. We discuss surprising consequences of mechanical phase-conjugation that could lead to the preparation of mechanical states with negative temperature, the improvement of quantum memories and the study of the quantum-classical transition. Supported by DARPA ORCHID program.

  1. Frequency translating phase conjugation circuit for active retrodirective antenna array. [microwave transmission

    NASA Technical Reports Server (NTRS)

    Chernoff, R. (Inventor)

    1980-01-01

    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.

  2. Phospholipid-detergent conjugates as novel tools for siRNA delivery.

    PubMed

    Pierrat, Philippe; Laverny, Gilles; Creusat, Gaëlle; Wehrung, Patrick; Strub, Jean-Marc; VanDorsselaer, Alain; Pons, Françoise; Zuber, Guy; Lebeau, Luc

    2013-02-11

    One of the potential benefits of drug delivery systems in medicine is the creation of nanoparticle-based vectors that deliver a therapeutic cargo in sufficient quantity to a target site to enable a selective effect, width of the therapeutic window depending on the toxicity of the vector and the cargo. In this work, we intended to improve the siRNA delivery efficiency of a new kind of nucleic acid carrier, which is the result of the conjugation of the membrane phospholipid 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) to the membrane-active species Triton X-100 (TX100). We hypothesized that by improving the biodegradability the cytotoxicity of the conjugate might by reduced, whereas its original transfection potential would be tentatively preserved. DOPC was conjugated to Triton X-100 through spacers displaying various resistance to chemical hydrolysis and enzyme degradation. The results obtained through in vitro siRNA delivery experiments showed that the initial phosphoester bond can be replaced with a phospho(alkyl)enecarbonate group with no loss in the transfection activity, whereas the associated cytotoxicity was significantly decreased, as assessed by metabolic activity and membrane integrity measurements. The toxicity of the conjugates incorporating a phospho(alkyl)enesuccinnate moiety proved even lower but was clearly balanced with a reduction of the siRNA delivery efficiency. Hydrolytic stability and intracellular degradation of the conjugates were investigated by NMR spectroscopy and mass spectrometry. A general trend was that the more readily degraded conjugates were those with the lower toxicity. Otherwise, the phospho(alkyl)enecarbonate conjugates revealed some hemolytic activity, whereas the parent phosphoester did not. The reason why these conjugates behave differently with respect to hemolysis might be a consequence of unusual fusogenic properties and probably reflects the difference in the stability of the conjugates in the intracellular

  3. Element-topology-independent preconditioners for parallel finite element computations

    NASA Technical Reports Server (NTRS)

    Park, K. C.; Alexander, Scott

    1992-01-01

    A family of preconditioners for the solution of finite element equations are presented, which are element-topology independent and thus can be applicable to element order-free parallel computations. A key feature of the present preconditioners is the repeated use of element connectivity matrices and their left and right inverses. The properties and performance of the present preconditioners are demonstrated via beam and two-dimensional finite element matrices for implicit time integration computations.

  4. Genomic signatures of distributive conjugal transfer among mycobacteria.

    PubMed

    Mortimer, Tatum D; Pepperell, Caitlin S

    2014-08-30

    Distributive conjugal transfer (DCT) is a newly described mechanism of lateral gene transfer (LGT) that results in a mosaic transconjugant structure, similar to the products of meiosis. We have tested popular LGT detection methods on whole-genome sequence data from experimental DCT transconjugants and used the best performing methods to compare genomic signatures of DCT with those of LGT through natural transformation, conjugative plasmids, and mobile genetic elements (MGE). We found that DCT results in transfer of larger chromosomal segments, that these segments are distributed more broadly around the chromosome, and that a greater proportion of the chromosome is affected by DCT than by other mechanisms of LGT. We used the best performing methods to characterize LGT in Mycobacterium canettii, the mycobacterial species most closely related to Mycobacterium tuberculosis. Patterns of LGT among M. canettii were highly distinctive. Gene flow appeared unidirectional, from lineages with minimal evidence of LGT to isolates with a substantial proportion (6-13%) of sites identified as recombinant. Among M. canettii isolates with evidence of LGT, recombinant fragments were larger and more evenly distributed relative to bacteria that undergo LGT through natural transformation, conjugative plasmids, and MGE. Spatial bias in M. canettii was also unusual in that patterns of recombinant fragment sharing mirrored overall phylogenetic structure. Based on the proportion of recombinant sites, the size of recombinant fragments, their spatial distribution and lack of association with MGE, as well as unidirectionality of DNA transfer, we conclude that DCT is the predominant mechanism of LGT among M. canettii.

  5. Improved method for conjugative transfer by filter mating of Streptococcus pneumoniae

    SciTech Connect

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

    1980-10-01

    The frequency of conjugation during filter mating of pneumococcus was increased to 10- to 100-fold when the filter was embedded in agar during incubation instead of being on the surface. The major effect was not due to protection from oxygen. The factor of increase was similar for transfer of plasmids and of chromosomal insertions of drug resistance elements.

  6. An M-step preconditioned conjugate gradient method for parallel computation

    NASA Technical Reports Server (NTRS)

    Adams, L.

    1983-01-01

    This paper describes a preconditioned conjugate gradient method that can be effectively implemented on both vector machines and parallel arrays to solve sparse symmetric and positive definite systems of linear equations. The implementation on the CYBER 203/205 and on the Finite Element Machine is discussed and results obtained using the method on these machines are given.

  7. The diversity of prokaryotic DDE transposases of the mutator superfamily, insertion specificity, and association with conjugation machineries.

    PubMed

    Guérillot, Romain; Siguier, Patricia; Gourbeyre, Edith; Chandler, Michael; Glaser, Philippe

    2014-02-01

    Transposable elements (TEs) are major components of both prokaryotic and eukaryotic genomes and play a significant role in their evolution. In this study, we have identified new prokaryotic DDE transposase families related to the eukaryotic Mutator-like transposases. These genes were retrieved by cascade PSI-Blast using as initial query the transposase of the streptococcal integrative and conjugative element (ICE) TnGBS2. By combining secondary structure predictions and protein sequence alignments, we predicted the DDE catalytic triad and the DNA-binding domain recognizing the terminal inverted repeats. Furthermore, we systematically characterized the organization and the insertion specificity of the TEs relying on these prokaryotic Mutator-like transposases (p-MULT) for their mobility. Strikingly, two distant TE families target their integration upstream σA dependent promoters. This allowed us to identify a transposase sequence signature associated with this unique insertion specificity and to show that the dissymmetry between the two inverted repeats is responsible for the orientation of the insertion. Surprisingly, while DDE transposases are generally associated with small and simple transposons such as insertion sequences (ISs), p-MULT encoding TEs show an unprecedented diversity with several families of IS, transposons, and ICEs ranging in size from 1.1 to 52 kb.

  8. Kinetic models of conjugated metabolic cycles

    NASA Astrophysics Data System (ADS)

    Ershov, Yu. A.

    2016-01-01

    A general method is developed for the quantitative kinetic analysis of conjugated metabolic cycles in the human organism. This method is used as a basis for constructing a kinetic graph and model of the conjugated citric acid and ureapoiesis cycles. The results from a kinetic analysis of the model for these cycles are given.

  9. Description of charge conjugation from first principles

    SciTech Connect

    Lujan-Peschard, C.; Napsuciale, M.

    2006-09-25

    We construct the charge conjugation operator as a unitary automorphism in the spinor space ((1/2), 0) + (0 (1/2)) from first principles. We calculate its eigenspinors and derive the equation of motion they satisfy. The mapping associated to charge conjugation is constructed from parity eigenstates which are considered as particle and antiparticle.

  10. The Conjugate Acid-Base Chart.

    ERIC Educational Resources Information Center

    Treptow, Richard S.

    1986-01-01

    Discusses the difficulties that beginning chemistry students have in understanding acid-base chemistry. Describes the use of conjugate acid-base charts in helping students visualize the conjugate relationship. Addresses chart construction, metal ions, buffers and pH titrations, and the organic functional groups and nonaqueous solvents. (TW)

  11. Approximate error conjugation gradient minimization methods

    DOEpatents

    Kallman, Jeffrey S

    2013-05-21

    In one embodiment, a method includes selecting a subset of rays from a set of all rays to use in an error calculation for a constrained conjugate gradient minimization problem, calculating an approximate error using the subset of rays, and calculating a minimum in a conjugate gradient direction based on the approximate error. In another embodiment, a system includes a processor for executing logic, logic for selecting a subset of rays from a set of all rays to use in an error calculation for a constrained conjugate gradient minimization problem, logic for calculating an approximate error using the subset of rays, and logic for calculating a minimum in a conjugate gradient direction based on the approximate error. In other embodiments, computer program products, methods, and systems are described capable of using approximate error in constrained conjugate gradient minimization problems.

  12. Immunization of newborns with bacterial conjugate vaccines.

    PubMed

    van den Biggelaar, Anita H J; Pomat, William S

    2013-05-17

    Bacterial conjugate vaccines are based on the principle of coupling immunogenic bacterial capsular polysaccharides to a carrier protein to facilitate the induction of memory T-cell responses. Following the success of Haemophilus influenzae type b conjugate vaccines in the 1980s, conjugate vaccines for Streptococcus pneumoniae and Neisseria meningitidis infections were developed and proven to be effective in protecting children against invasive disease. In this review, the use of conjugate vaccines in human newborns is discussed. Neonatal Haemophilus influenzae type b and pneumococcal conjugate vaccination schedules have been trialed and proven to be safe, with the majority of studies demonstrating no evidence for the induction of immune tolerance. Whether their neonatal administration also results in an earlier induction of clinical protection in the first 2-3 critical months of life is still to be demonstrated. PMID:22728221

  13. Conjugated Polymer Surfaces and Interfaces

    NASA Astrophysics Data System (ADS)

    Salaneck, W. R.; Stafstrom, S.; Brédas, J. L.

    2003-10-01

    The authors illustrate the basic physics and materials science of conjugated polymers and their interfaces, particularly, but not exclusively, as they are applied to polymer-based light emitting diodes. The approach is to describe the basic physical and associated chemical principles that apply to these materials, which in many instances are different from those that apply to their inorganic counterparts. The main aim of the authors is to highlight specific issues and properties of polymer surfaces and interfaces that are relevant in the context of the emerging field of polymer-based electronics in general, and polymer-based light emitting diodes in particular. Both theoretical and experimental methods used in the study of these systems are discussed. This book will be of interest to graduate students and research workers in departments of physics, chemistry, electrical engineering and materials sciences studying polymer surfaces and interfaces and their application in polymer-based electronics.

  14. The partitioning behavior of trace element and its distribution in the surrounding soil of a cement plant integrated utilization of hazardous wastes.

    PubMed

    Yang, Zhenzhou; Chen, Yan; Sun, Yongqi; Liu, Lili; Zhang, Zuotai; Ge, Xinlei

    2016-07-01

    In the present study, the trace elements partitioning behavior during cement manufacture process were systemically investigated as well as their distribution behaviors in the soil surrounding a cement plant using hazardous waste as raw materials. In addition to the experimental analysis, the thermodynamic equilibrium calculations were simultaneously conducted. The results demonstrate that in the industrial-scale cement manufacture process, the trace elements can be classified into three groups according to their releasing behaviors. Hg is recognized as a highly volatile element, which almost totally partitions into the vapor phase. Co, Cu, Mn, V, and Cr are considered to be non-volatile elements, which are largely incorporated into the clinker. Meanwhile, Cd, Ba, As, Ni, Pb, and Zn can be classified into semi-volatile elements, as they are trapped into clinker to various degrees. Furthermore, the trace elements emitted into the flue gas can be adsorbed onto the fine particles, transport and deposit in the soil, and it is clarified here that the soil around the cement plant is moderately polluted by Cd, slightly polluted by As, Cr, Ba, Zn, yet rarely influenced by Co, Mn, Ni, Cu, Hg, and V elements. It was also estimated that the addition of wastes can efficiently reduce the consumption of raw materials and energy. The deciphered results can thus provide important insights for estimating the environmental impacts of the cement plant on its surroundings by utilizing wastes as raw materials. PMID:27040541

  15. Development and Integration of Single-Asperity Nanotribology Experiments & Nanoscale Interface Finite Element Modeling for Prediction and Control of Friction and Damage in Micro- and Nano-mechnical Systems

    SciTech Connect

    R.W. Carpick; M.E. Plesha

    2007-03-03

    This report describes the accomplishments of the DOE BES grant entitled "Development and Integration of Single-Asperity Nanotribology Experiments & Nanoscale Interface Finite Element Modeling for Prediction and Control of Friction and Damage in Micro- and Nano-mechnical Systems". Key results are: the determination of nanoscale frictional properties of MEMS surfaces, self-assembled monolayers, and novel carbon-based films, as well as the development of models to describe this behavior.

  16. It's elemental

    NASA Astrophysics Data System (ADS)

    The Periodic Table of the elements will now have to be updated. An international team of researchers has added element 110 to the Earth's armory of elements. Though short-lived—of the order of microseconds, element 110 bottoms out the list as the heaviest known element on the planet. Scientists at the Heavy Ion Research Center in Darmstadt, Germany, made the 110-proton element by colliding a lead isotope with nickel atoms. The element, which is yet to be named, has an atomic mass of 269.

  17. TAT Peptide and Its Conjugates: Proteolytic Stability

    PubMed Central

    Grunwald, Jacob; Rejtar, Tomas; Sawant, Rupa; Wang, Zhouxi; Torchilin, Vladimir P.

    2009-01-01

    The proteolytic cleavage of TATp, TATp-PEG1000-PE conjugate (TATp-conjugate), and TATp as TATp-conjugate in mixed micelles made of TATp-conjugate and PEG5000-PE (2.5% mol of TATp-conjugate, TATp-Mic) were studied by HPLC with fluorescent detection using fluorenylmethyl chloroformate (FMOC) labeling and by MALDI-TOF MS analysis. The cleavage kinetics were analyzed in human blood plasma and in trypsin-containing phosphate buffered saline (PBS), pH 7.4, to simulate the proteolytic activity of human plasma. The trypsinolysis of free TATp, TATp-conjugate, and TATp-Mic revealed that the main initial fragmentation is an endocleavage at the carboxyl terminus resulting in an Arg-Arg (RR) dimer. The trypsinolysis followed pseudo-first-order kinetics. The cleavage of the free TATp was relatively fast with a half-life of a few minutes (t1/2 ∼ 3.5 min). The TATp-conjugate showed more stability with about a 3-fold increase in half-life (t1/2 ∼ 10 min). TATp in TATp-Mic was highly protected against proteolysis with an over 100-fold increase in half-life (t1/2 ∼ 430 min). The shielding of TATp by PEG moieties in the proposed TATp-Mic is of great importance for its potential use as a cell-penetrating moiety for multifunctional “smart” drug delivery systems with detachable PEG. PMID:19601640

  18. Substance of Presentation on The J-Coefficient and Job-Element Procedure as a Means of Integrating All Evidences of Ability to Meet Educational or Job Requirements.

    ERIC Educational Resources Information Center

    Primoff, Ernest S.

    This paper concerns two features of a project on the assessment of job potential: the J-Coefficient, and the J-Scale. The J-Coefficient is a means of determining the validity of a test for a position on the basis of (1) the Beta Weights for predicting test scores from a set of elements and (2) estimates of importance of each element in the…

  19. Multipath-enabled super-resolution for rf and microwave communication using phase-conjugate arrays.

    PubMed

    Henty, Benjamin E; Stancil, Daniel D

    2004-12-10

    We demonstrate experimentally that phase-conjugate techniques can be used to achieve super-resolution focusing of electromagnetic waves in a multipath indoor environment at 2.45 GHz. The focusing phenomena was used to direct independent signals to two locations separated by approximately one-half wavelength, thereby creating two simultaneous channels at the same frequency. An increase in channel capacity is shown to be achievable by an experimental transmission of a 1 Mbps signal over two channels created using a four element phase-conjugate array.

  20. The Zinc Finger Protein Zfr1p Is Localized Specifically to Conjugation Junction and Required for Sexual Development in Tetrahymena thermophila

    PubMed Central

    Xu, Jing; Tian, Huaru; Wang, Wei; Liang, Aihua

    2012-01-01

    Conjugation in Tetrahymena thermophila involves a developmental program consisting of three prezygotic nuclear divisions, pronuclear exchange and fusion, and postzygotic and exconjugant stages. The conjugation junction structure appears during the initiation of conjugation development, and disappears during the exconjugant stage. Many structural and functional proteins are involved in the establishment and maintenance of the junction structure in T. thermophila. In the present study, a zinc finger protein-encoding gene ZFR1 was found to be expressed specifically during conjugation and to localize specifically to the conjugation junction region. Truncated Zfr1p localized at the plasma membrane in ordered arrays and decorated Golgi apparatus located adjacent to basal body. The N-terminal zinc finger and C-terminal hydrophobic domains of Zfr1p were found to be required for its specific conjugation junction localization. Conjugation development of ZFR1 somatic knockout cells was aborted at the pronuclear exchange and fusion conjugation stages. Furthermore, Zfr1p was found to be important for conjugation junction stability during the prezygotic nuclear division stage. Taken together, our data reveal that Zfr1p is required for the stability and integrity of the conjugation junction structure and essential for the sexual life cycle of the Tetrahymena cell. PMID:23251712

  1. Synthesis of C-5, C-2' and C-4'-neomycin-conjugated triplex forming oligonucleotides and their affinity to DNA-duplexes.

    PubMed

    Tähtinen, Ville; Granqvist, Lotta; Virta, Pasi

    2015-08-01

    Neomycin-conjugated homopyrimidine oligo 2'-deoxyribonucleotides have been synthesized on a solid phase and their potential as triplex forming oligonucleotides (TFOs) with DNA-duplexes has been studied. For the synthesis of the conjugates, C-5, C-2' and C-4'-tethered alkyne-modified nucleoside derivatives were used as an integral part of the standard automated oligonucleotide chain elongation. An azide-derived neomycin was then conjugated to the incorporated terminal alkynes by Cu(I)-catalyzed 1,3-dipolar cycloaddition (the click chemistry). Concentrated ammonia released the desired conjugates in acceptable purity and yields. The site of conjugation was expectedly important for the Hoogsteen-face recognition: C-5-conjugation showed a notable positive effect, whereas the influence of the C-2' and C-4'-modification remained marginal. In addition to conventional characterization methods (UV- and CD-spectroscopy), (19)F NMR spectroscopy was applied for the monitoring of triplex/duplex/single strand-conversions.

  2. Ultraviolet phase conjugation and its practical implications

    SciTech Connect

    Shapiro, S.L.; Fisher, R.A.; Feldman, B.J.

    1981-01-01

    We report the first demonstration of uv phase conjugation. Using a 15 psec, 2660 A pulse, 0.1% conjugate reflectivities were obtained via degenerate four-wave mixing in 1-mm samples of CS/sub 2/ mixtures. While pure CS/sub 2/ did not exhibit the effect, dilution in several uv transmitting solvents opened up a concentration-tunable (2450 A - 2850 A) spectral window, allowing the optical Kerr effect to be utilized. Weaker phase conjugation at 2660 A was also observed in other Kerr media and in saturable absorber media.

  3. Scattering and radiation analysis of three-dimensional cavity arrays via a hybrid finite element method

    NASA Technical Reports Server (NTRS)

    Jin, Jian-Ming; Volakis, John L.

    1992-01-01

    A hybrid numerical technique is presented for a characterization of the scattering and radiation properties of three-dimensional cavity arrays recessed in a ground plane. The technique combines the finite element and boundary integral methods and invokes Floquet's representation to formulate a system of equations for the fields at the apertures and those inside the cavities. The system is solved via the conjugate gradient method in conjunction with the Fast Fourier Transform (FFT) thus achieving an O(N) storage requirement. By virtue of the finite element method, the proposed technique is applicable to periodic arrays comprised of cavities having arbitrary shape and filled with inhomogeneous dielectrics. Several numerical results are presented, along with new measured data, which demonstrate the validity, efficiency, and capability of the technique.

  4. MHOST: An efficient finite element program for inelastic analysis of solids and structures

    NASA Technical Reports Server (NTRS)

    Nakazawa, S.

    1988-01-01

    An efficient finite element program for 3-D inelastic analysis of gas turbine hot section components was constructed and validated. A novel mixed iterative solution strategy is derived from the augmented Hu-Washizu variational principle in order to nodally interpolate coordinates, displacements, deformation, strains, stresses and material properties. A series of increasingly sophisticated material models incorporated in MHOST include elasticity, secant plasticity, infinitesimal and finite deformation plasticity, creep and unified viscoplastic constitutive model proposed by Walker. A library of high performance elements is built into this computer program utilizing the concepts of selective reduced integrations and independent strain interpolations. A family of efficient solution algorithms is implemented in MHOST for linear and nonlinear equation solution including the classical Newton-Raphson, modified, quasi and secant Newton methods with optional line search and the conjugate gradient method.

  5. Construction of minimum energy high-order Helmholtz bases for structured elements

    NASA Astrophysics Data System (ADS)

    Rodrigues, Caio F.; Suzuki, Jorge L.; Bittencourt, Marco L.

    2016-02-01

    We present a construction procedure for high-order expansion bases for structured finite elements specific for the operator under consideration. The procedure aims to obtain bases in such way that the condition numbers for the element matrices are almost constant or have a moderate increase in terms of the polynomial order. The internal modes of the mass and stiffness matrices are made simultaneously diagonal and the minimum energy concept is used to make the boundary modes orthogonal to the internal modes. The performance of the proposed bases is compared to the standard basis using Jacobi polynomials. This is performed through numerical examples for Helmholtz problem and transient linear elasticity employing explicit and implicit time integration algorithms and the conjugate gradient method with diagonal, SSOR and Gauss-Seidel pre-conditioners. The sparsity patterns, conditioning and solution costs are investigated. A significant speedup and reduction in the number of iterations are obtained when compared to the standard basis.

  6. Trace element emissions

    SciTech Connect

    Benson, S.A.; Erickson, T.A.; Steadman, E.N.; Zygarlicke, C.J.; Hauserman, W.B.; Hassett, D.J.

    1994-10-01

    The Energy & Environmental Research Center (EERC) is carrying out an investigation that will provide methods to predict the fate of selected trace elements in integrated gasification combined cycle (IGCC) and integrated gasification fuel cell (IGFC) systems to aid in the development of methods to control the emission of trace elements determined to be air toxics. The goal of this project is to identify the effects of critical chemical and physical transformations associated with trace element behavior in IGCC and IGFC systems. The trace elements included in this project are arsenic, chromium, cadmium, mercury, nickel, selenium, and lead. The research seeks to identify and fill, experimentally and/or theoretically, data gaps that currently exist on the fate and composition of trace elements. The specific objectives are to (1) review the existing literature to identify the type and quantity of trace elements from coal gasification systems, (2) perform laboratory-scale experimentation and computer modeling to enable prediction of trace element emissions, and (3) identify methods to control trace element emissions.

  7. Conjugated amplifying polymers for optical sensing applications.

    PubMed

    Rochat, Sébastien; Swager, Timothy M

    2013-06-12

    Thanks to their unique optical and electrochemical properties, conjugated polymers have attracted considerable attention over the last two decades and resulted in numerous technological innovations. In particular, their implementation in sensing schemes and devices was widely investigated and produced a multitude of sensory systems and transduction mechanisms. Conjugated polymers possess numerous attractive features that make them particularly suitable for a broad variety of sensing tasks. They display sensory signal amplification (compared to their small-molecule counterparts) and their structures can easily be tailored to adjust solubility, absorption/emission wavelengths, energy offsets for excited state electron transfer, and/or for use in solution or in the solid state. This versatility has made conjugated polymers a fluorescence sensory platform of choice in the recent years. In this review, we highlight a variety of conjugated polymer-based sensory mechanisms together with selected examples from the recent literature.

  8. Design and Application of Antimicrobial Peptide Conjugates

    PubMed Central

    Reinhardt, Andre; Neundorf, Ines

    2016-01-01

    Antimicrobial peptides (AMPs) are an interesting class of antibiotics characterized by their unique antibiotic activity and lower propensity for developing resistance compared to common antibiotics. They belong to the class of membrane-active peptides and usually act selectively against bacteria, fungi and protozoans. AMPs, but also peptide conjugates containing AMPs, have come more and more into the focus of research during the last few years. Within this article, recent work on AMP conjugates is reviewed. Different aspects will be highlighted as a combination of AMPs with antibiotics or organometallic compounds aiming to increase antibacterial activity or target selectivity, conjugation with photosensitizers for improving photodynamic therapy (PDT) or the attachment to particles, to name only a few. Owing to the enormous resonance of antimicrobial conjugates in the literature so far, this research topic seems to be very attractive to different scientific fields, like medicine, biology, biochemistry or chemistry. PMID:27187357

  9. Fluorescent and photochemical properties of a single zinc finger conjugated to a fluorescent DNA-binding probe.

    PubMed

    Thompson, M; Woodbury, N W

    2000-04-18

    A single zinc finger derived from the DNA-binding domain of the glucocorticoid receptor (GR) has been tethered to the intercalating fluorophore thiazole orange, and the DNA recognition characteristics of the conjugate have been examined. DNA sequence specificity for the peptide-dye conjugate, determined by steady-state fluorescence measurements and photoactivated DNA cleavage experiments, reproduce the binding features of response element recognition found in the native GR. The thiazole orange is able to intercalate and fluoresce when the conjugate binds, at concentrations where little fluorescence is observed from either the conjugate alone or the conjugate mixed with DNA lacking the zinc finger target sequence. The conjugate preferentially targets a 5'-TGTTCT-3' sequence (the native glucocorticoid receptor element) with a dissociation constant of about 25 nM. Lower binding affinities (up to 10-fold) are observed for single site variants of this sequence, and much lower affinity (40-50-fold) is observed for binding to the estrogen response element (which differs from the glucocorticoid receptor element at two positions) as well as to nonspecific DNA. Footprinting reactions show a 4-6 base pair region that is protected by the zinc finger moiety. Photocleavage assays reveal a several base pair region flanking the recognition sequence where the tethered thiazole orange moiety is able to intercalate and subsequently cleave DNA upon visible light exposure. Thiazole orange is also shown to oxidize the 5'-G of remote GG sequences, depending on the details of the intervening DNA sequence. Small synthetic protein-dye conjugates such as this one are potentially useful for a variety of purposes including sequence-specific probes that work under physiological conditions (without melting and hybridization of DNA), sequence-specific photocleavage agents, and self-assembling components in electron and energy transfer systems that utilize DNA as a scaffold and/or photochemical

  10. A novel near-infrared indocyanine dye-polyethylenimine conjugate allows DNA delivery imaging in vivo.

    PubMed

    Masotti, Andrea; Vicennati, Paola; Boschi, Federico; Calderan, Laura; Sbarbati, Andrea; Ortaggi, Giancarlo

    2008-05-01

    Near-infrared (NIR) fluorescence light has been applied to monitor several biological events in vivo since it penetrates tissues more efficiently than visible light. Dyes exhibiting NIR fluorescence and having large Stokes shift are key elements for this promising optical imaging technology. Here, we report the synthesis of a novel conjugate between a near-infrared indocyanine dye and an organic polyamine polymer (polyethylenimine, PEI) (IR820-PEI) with high chemical stability and good optical properties. IR820-PEI absorbs at 665 nm, emits at 780 nm, and displays a large Stokes shift (115 nm). Moreover, the reported conjugate is able to bind DNA, and the delivery process can be monitored in vivo with noninvasive optical imaging techniques. These characteristics make IR820-PEI one of the most effective and versatile indocyanine dye polymeric-conjugate reported so far.

  11. Elemental ZOO

    NASA Astrophysics Data System (ADS)

    Helser, Terry L.

    2003-04-01

    This puzzle uses the symbols of 39 elements to spell the names of 25 animals found in zoos. Underlined spaces and the names of the elements serve as clues. To solve the puzzle, students must find the symbols that correspond to the elemental names and rearrange them into the animals' names.

  12. Photonics-on-a-chip: recent advances in integrated waveguides as enabling detection elements for real-world, lab-on-a-chip biosensing applications.

    PubMed

    Washburn, Adam L; Bailey, Ryan C

    2011-01-21

    By leveraging advances in semiconductor microfabrication technologies, chip-integrated optical biosensors are poised to make an impact as scalable and multiplexable bioanalytical measurement tools for lab-on-a-chip applications. In particular, waveguide-based optical sensing technology appears to be exceptionally amenable to chip integration and miniaturization, and, as a result, the recent literature is replete with examples of chip-integrated waveguide sensing platforms developed to address a wide range of contemporary analytical challenges. As an overview of the most recent advances within this dynamic field, this review highlights work from the last 2-3 years in the areas of grating-coupled, interferometric, photonic crystal, and microresonator waveguide sensors. With a focus towards device integration, particular emphasis is placed on demonstrations of biosensing using these technologies within microfluidically controlled environments. In addition, examples of multiplexed detection and sensing within complex matrices--important features for real-world applicability--are given special attention.

  13. Conjugated microporous polymers: design, synthesis and application.

    PubMed

    Xu, Yanhong; Jin, Shangbin; Xu, Hong; Nagai, Atsushi; Jiang, Donglin

    2013-10-21

    Conjugated microporous polymers (CMPs) are a class of organic porous polymers that combine π-conjugated skeletons with permanent nanopores, in sharp contrast to other porous materials that are not π-conjugated and with conventional conjugated polymers that are nonporous. As an emerging material platform, CMPs offer a high flexibility for the molecular design of conjugated skeletons and nanopores. Various chemical reactions, building blocks and synthetic methods have been developed and a broad variety of CMPs with different structures and specific properties have been synthesized, driving the rapid growth of the field. CMPs are unique in that they allow the complementary utilization of π-conjugated skeletons and nanopores for functional exploration; they have shown great potential for challenging energy and environmental issues, as exemplified by their excellent performance in gas adsorption, heterogeneous catalysis, light emitting, light harvesting and electrical energy storage. This review describes the molecular design principles of CMPs, advancements in synthetic and structural studies and the frontiers of functional exploration and potential applications.

  14. Self-assembly of conjugated oligomers and polymers at the interface: structure and properties.

    PubMed

    Xu, Lirong; Yang, Liu; Lei, Shengbin

    2012-08-01

    conjugated oligomers and polymers. The information obtained could benefit the understanding of the elements affecting the film morphology and helps the optimization of device performance.

  15. Elements of discovery.

    PubMed

    Toledo-Pereyra, Luis H

    2008-01-01

    I understand discovery as the essence of thinking man, or to paraphrase the notable French philosopher René Descartes, "I think, therefore I discover." In this study, I introduce discovery as the foundation of modern science. Discovery consists of six stages or elements, including: concept, belief, ability, support, proof, and protection. Each element is discussed within the context of the whole discovery enterprise. Fundamental tenets for understanding discovery are given throughout the paper, and a few examples illustrate the significance of some of the most important elements. I invite clinicians, researchers, and/or clinical researchers to integrate themselves into the active process of discovery. Remember--I think, therefore I discover.

  16. Design and characterization of nanomaterial-biomolecule conjugates

    NASA Astrophysics Data System (ADS)

    Yim, Tae-Jin

    In the field of nanobiotechnology, nanoscale dimensions result in physical properties that differ from more conventional bulk material state. The integration of nanomaterials with biomolecules has begun to be used for unique physical properties, and for biological specific recognition, thereby leading to novel nanomaterial-biomolecule conjugates. The direction of this dissertation is to develop biocatalytic nanomaterial-biomolecule conjugates and to characterize them. For this, biological catalysts are employed to combine with nanomaterials. Two large parts include functional ization of nanomaterials with biomolecules and assembly of nanomaterials using a biological catalyst. First part of this thesis work is the exploration of the biocatalytic properties of nanomaterial-biomolecule conjugates. Si nanocolumns have higher surface area which leads more amount of biocatalytis immobilization than flat Si wafer with the same projected area. The enhanced activity of soybean peroxidase (SBP) immobilized onto Si nanocolumns as novel nanostructured supports is focused. Next, the catalytic activity of immobilized DNAzyme onto multiwalled carbon nanotubes (MWNTs) is compared to that in solution phase, and multiple turnovers are examined. The relationship between hybridization efficiency and activity is investigated as a function of surface density of DNAzyme on MWNTs. Then, cellular delivery of silica nanoparticle-protein conjugates is visually confirmed and therefore the intracellular function of a protein delivered by silica nanoparticle-protein conjugates is proved. For one example of the intracellular function, stable SBP immobilized onto silica nanoparticles to activate a prodrug is demonstrated. Second part of this thesis work is the formation of nanostructured materials through the enzymatic assembly of single-walled carbon nanotubes (SWNTs). Enzymatic polymerization of a phenol compound is applied to the bridging of two or more SWNTs functionalized with phenol

  17. Continuous-variable quantum cloning of coherent states with phase-conjugate input modes using linear optics

    SciTech Connect

    Chen, Haixia; Zhang, Jing

    2007-02-15

    We propose a scheme for continuous-variable quantum cloning of coherent states with phase-conjugate input modes using linear optics. The quantum cloning machine yields M identical optimal clones from N replicas of a coherent state and N replicas of its phase conjugate. This scheme can be straightforwardly implemented with the setups accessible at present since its optical implementation only employs simple linear optical elements and homodyne detection. Compared with the original scheme for continuous-variable quantum cloning with phase-conjugate input modes proposed by Cerf and Iblisdir [Phys. Rev. Lett. 87, 247903 (2001)], which utilized a nondegenerate optical parametric amplifier, our scheme loses the output of phase-conjugate clones and is regarded as irreversible quantum cloning.

  18. Two-dimensional finite element neutron diffusion analysis using hierarchic shape functions

    SciTech Connect

    Carpenter, D.C.

    1997-04-01

    Recent advances have been made in the use of p-type finite element method (FEM) for structural and fluid dynamics problems that hold promise for reactor physics problems. These advances include using hierarchic shape functions, element-by-element iterative solvers and more powerful mapping techniques. Use of the hierarchic shape functions allows greater flexibility and efficiency in implementing energy-dependent flux expansions and incorporating localized refinement of the solution space. The irregular matrices generated by the p-type FEM can be solved efficiently using element-by-element conjugate gradient iterative solvers. These solvers do not require storage of either the global or local stiffness matrices and can be highly vectorized. Mapping techniques based on blending function interpolation allow exact representation of curved boundaries using coarse element grids. These features were implemented in a developmental two-dimensional neutron diffusion program based on the use of hierarchic shape functions (FEM2DH). Several aspects in the effective use of p-type analysis were explored. Two choices of elemental preconditioning were examined--the proper selection of the polynomial shape functions and the proper number of functions to use. Of the five shape function polynomials tested, the integral Legendre functions were the most effective. The serendipity set of functions is preferable over the full tensor product set. Two global preconditioners were also examined--simple diagonal and incomplete Cholesky. The full effectiveness of the finite element methodology was demonstrated on a two-region, two-group cylindrical problem but solved in the x-y coordinate space, using a non-structured element grid. The exact, analytic eigenvalue solution was achieved with FEM2DH using various combinations of element grids and flux expansions.

  19. Multiplexed protein detection using antibody-conjugated microbead arrays in a microfabricated electrophoretic device

    PubMed Central

    Barbee, Kristopher D.; Hsiao, Alexander P.; Roller, Eric E.; Huang, Xiaohua

    2011-01-01

    We report the development of a microfabricated electrophoretic device for assembling high-density arrays of antibody-conjugated microbeads for chip-based protein detection. The device consists of a flow cell formed between a gold-coated silicon chip with an array of microwells etched in a silicon dioxide film and a glass coverslip with a series of thin gold counter electrode lines. We have demonstrated that 0.4 and 1 μm beads conjugated with antibodies can be rapidly assembled into the microwells by applying a pulsed electric field across the chamber. By assembling step-wise a mixture of fluorescently labeled antibody-conjugated microbeads, we incorporated both spatial and fluorescence encoding strategies to demonstrate significant multiplexing capabilities. We have shown that these antibody-conjugated microbead arrays can be used to perform on-chip sandwich immunoassays to detect test antigens at concentrations as low as 40 pM (6 ng/mL). A finite element model was also developed to examine the electric field distribution within the device for different counter electrode configurations over a range of line pitches and chamber heights. This device will be useful for assembling high-density, encoded antibody arrays for multiplexed detection of proteins and other types of protein-conjugated microbeads for applications such as the analysis of protein-protein interactions. PMID:20820631

  20. Conjugative DNA Transfer Induces the Bacterial SOS Response and Promotes Antibiotic Resistance Development through Integron Activation

    PubMed Central

    Baharoglu, Zeynep; Bikard, David; Mazel, Didier

    2010-01-01

    Conjugation is one mechanism for intra- and inter-species horizontal gene transfer among bacteria. Conjugative elements have been instrumental in many bacterial species to face the threat of antibiotics, by allowing them to evolve and adapt to these hostile conditions. Conjugative plasmids are transferred to plasmidless recipient cells as single-stranded DNA. We used lacZ and gfp fusions to address whether conjugation induces the SOS response and the integron integrase. The SOS response controls a series of genes responsible for DNA damage repair, which can lead to recombination and mutagenesis. In this manuscript, we show that conjugative transfer of ssDNA induces the bacterial SOS stress response, unless an anti-SOS factor is present to alleviate this response. We also show that integron integrases are up-regulated during this process, resulting in increased cassette rearrangements. Moreover, the data we obtained using broad and narrow host range plasmids strongly suggests that plasmid transfer, even abortive, can trigger chromosomal gene rearrangements and transcriptional switches in the recipient cell. Our results highlight the importance of environments concentrating disparate bacterial communities as reactors for extensive genetic adaptation of bacteria. PMID:20975940

  1. A new method integrating high-precision U-Pb geochronology with zircon trace element analysis (U-Pb TIMS-TEA)

    NASA Astrophysics Data System (ADS)

    Schoene, B.; Latkoczy, C.; Schaltegger, U.; Günther, D.

    2010-12-01

    Increased precision in isotope-dilution thermal ionization mass spectrometry (ID-TIMS) U-Pb geochronology has revealed age complexities in zircon populations that require new tools for understanding how the growth of zircon is related to geologic processes. U and Pb are routinely separated from other elements in dated minerals by ion exchange separation prior to TIMS isotope measurement. We develop a method in which trace elements in the exact same volume of zircon are redissolved and analyzed using solution nebulization inductively coupled plasma sector-field mass spectrometry with matrix-matched external liquid calibration. Using <0.5 ml solution, resulting concentrations are between <1 ppt for elements such as Ti, Nb and Ta and tens of ppb for Zr. By analyzing a series of standard solutions, zircons and procedural blanks, we show that accurate measurements are performed on Zr, Hf, Y, Sc, and the HREE while low-concentration elements can be measured accurately to <5 ppt. We performed combined U-Pb ID-TIMS geochronology with trace element analysis (here called U-Pb TIMS-TEA) on zircons from eight volcanic rocks comprising several volcanic systems and one metamorphic sample. Similar to previous in situ trace element analyses, zircon geochemistry is distinct between different samples and records petrogenetic processes such as fractional crystallization, assimilation and/or magma mixing. Unique from in situ analysis, U-Pb TIMS-TEA can trace geochemical evolution in accessory minerals with adequate age precision to resolve magmatic processes in rocks at least 200 million years old. This provides a means to identify auto-, ante- and xenocrystic zircon and lead to more robust age interpretations in ID-TIMS U-Pb geochronology. One suite of Cretaceous andesitic zircons shows correlations in geochemistry and absolute time that record evolution of a magmatic system over ˜250 ka prior to eruption. Future work will combine U-Pb TIMS-TEA with solution isotopic analysis of Nd

  2. Formation of the Thiol Conjugates and Active Metabolite of Clopidogrel by Human Liver Microsomes

    PubMed Central

    Lau, Wei C.; Hollenberg, Paul F.

    2012-01-01

    We reported previously the formation of a glutathionyl conjugate of the active metabolite (AM) of clopidogrel and the covalent modification of a cysteinyl residue of human cytochrome P450 2B6 in a reconstituted system (Mol Pharmacol 80:839–847, 2011). In this work, we extended our studies of the metabolism of clopidogrel to human liver microsomes in the presence of four reductants, namely, GSH, l-Cys, N-acetyl-l-cysteine (NAC), and ascorbic acid. Our results demonstrated that formation of the AM was greatly affected by the reductant used and the relative amounts of the AM formed were increased in the following order: NAC (17%) < l-Cys (53%) < ascorbic acid (61%) < GSH (100%). AM-thiol conjugates were observed in the presence of NAC, l-Cys, and GSH. In the case of GSH, the formation of both the AM and the glutathionyl conjugate was dependent on the GSH concentrations, with similar Km values of ∼0.5 mM, which indicates that formation of the thiol conjugates constitutes an integral part of the bioactivation processes for clopidogrel. It was observed that the AM was slowly converted to the thiol conjugate, with a half-life of ∼10 h. Addition of dithiothreitol to the reaction mixture reversed the conversion, which resulted in a decrease in AM-thiol conjugate levels and a concomitant increase in AM levels, whereas addition of NAC led to the formation of AM-NAC and a concomitant decrease in AM-GSH levels. These results not only confirm that the AM is formed through oxidative opening of the thiolactone ring but also suggest the existence of an equilibrium between the AM, the thiol conjugates, and the reductants. These factors may affect the effective concentrations of the AM in vivo. PMID:22584220

  3. Refinement of the Diatom Episome Maintenance Sequence and Improvement of Conjugation-Based DNA Delivery Methods

    PubMed Central

    Diner, Rachel E.; Bielinski, Vincent A.; Dupont, Christopher L.; Allen, Andrew E.; Weyman, Philip D.

    2016-01-01

    Conjugation of episomal plasmids from bacteria to diatoms advances diatom genetic manipulation by simplifying transgene delivery and providing a stable and consistent gene expression platform. To reach its full potential, this nascent technology requires new optimized expression vectors and a deeper understanding of episome maintenance. Here, we present the development of an additional diatom vector (pPtPBR1), based on the parent plasmid pBR322, to add a plasmid maintained at medium copy number in Escherichia coli to the diatom genetic toolkit. Using this new vector, we evaluated the contribution of individual yeast DNA elements comprising the 1.4-kb tripartite CEN6-ARSH4-HIS3 sequence that enables episome maintenance in Phaeodactylum tricornutum. While various combinations of these individual elements enable efficient conjugation and high exconjugant yield in P. tricornutum, individual elements alone do not. Conjugation of episomes containing CEN6-ARSH4 and a small sequence from the low GC content 3′ end of HIS3 produced the highest number of diatom exconjugant colonies, resulting in a smaller and more efficient vector design. Our findings suggest that the CEN6 and ARSH4 sequences function differently in yeast and diatoms, and that low GC content regions of greater than ~500 bp are a potential indicator of a functional diatom episome maintenance sequence. Additionally, we have developed improvements to the conjugation protocol including a high-throughput option utilizing 12-well plates and plating methods that improve exconjugant yield and reduce time and materials required for the conjugation protocol. The data presented offer additional information regarding the mechanism by which the yeast-derived sequence enables diatom episome maintenance and demonstrate options for flexible vector design. PMID:27551676

  4. Refinement of the Diatom Episome Maintenance Sequence and Improvement of Conjugation-Based DNA Delivery Methods.

    PubMed

    Diner, Rachel E; Bielinski, Vincent A; Dupont, Christopher L; Allen, Andrew E; Weyman, Philip D

    2016-01-01

    Conjugation of episomal plasmids from bacteria to diatoms advances diatom genetic manipulation by simplifying transgene delivery and providing a stable and consistent gene expression platform. To reach its full potential, this nascent technology requires new optimized expression vectors and a deeper understanding of episome maintenance. Here, we present the development of an additional diatom vector (pPtPBR1), based on the parent plasmid pBR322, to add a plasmid maintained at medium copy number in Escherichia coli to the diatom genetic toolkit. Using this new vector, we evaluated the contribution of individual yeast DNA elements comprising the 1.4-kb tripartite CEN6-ARSH4-HIS3 sequence that enables episome maintenance in Phaeodactylum tricornutum. While various combinations of these individual elements enable efficient conjugation and high exconjugant yield in P. tricornutum, individual elements alone do not. Conjugation of episomes containing CEN6-ARSH4 and a small sequence from the low GC content 3' end of HIS3 produced the highest number of diatom exconjugant colonies, resulting in a smaller and more efficient vector design. Our findings suggest that the CEN6 and ARSH4 sequences function differently in yeast and diatoms, and that low GC content regions of greater than ~500 bp are a potential indicator of a functional diatom episome maintenance sequence. Additionally, we have developed improvements to the conjugation protocol including a high-throughput option utilizing 12-well plates and plating methods that improve exconjugant yield and reduce time and materials required for the conjugation protocol. The data presented offer additional information regarding the mechanism by which the yeast-derived sequence enables diatom episome maintenance and demonstrate options for flexible vector design. PMID:27551676

  5. Dynamics of photorefractive self-pumped phase-conjugate mirrors with a linear resonator

    SciTech Connect

    Vakhdani, M Mekhran; Rudenko, K V; Shuvalov, V V

    2008-04-30

    The phase-conjugation dynamics in a self-pumped phase-conjugate mirror (SP PCM) based on a BaTiO{sub 3} photorefractive crystal (PRC) with a linear resonator is simulated numerically. It is shown that a phased array of dynamic holograms is formed in such a SP PCM under optimal conditions, and the interference of the waves scattered by this array provides the very high stationary phase-conjugation efficiency (the nonlinear reflection coefficient and overlap integral exceeding 80% and 95%, respectively). It is found that the development of instabilities is caused both by the violation of phase relations in this array and the formation of additional dynamic holograms in the PRC in the geometry typical of a SP PCM with a semi-linear resonator and by the self-bending effect typical of PRCs. (nonlinear optical phenomena)

  6. A complete implementation of the conjugate gradient algorithm on a reconfigurable supercomputer

    SciTech Connect

    Dubois, David H; Dubois, Andrew J; Connor, Carolyn M; Boorman, Thomas M; Poole, Stephen W

    2008-01-01

    The conjugate gradient is a prominent iterative method for solving systems of sparse linear equations. Large-scale scientific applications often utilize a conjugate gradient solver at their computational core. In this paper we present a field programmable gate array (FPGA) based implementation of a double precision, non-preconditioned, conjugate gradient solver for fmite-element or finite-difference methods. OUf work utilizes the SRC Computers, Inc. MAPStation hardware platform along with the 'Carte' software programming environment to ease the programming workload when working with the hybrid (CPUIFPGA) environment. The implementation is designed to handle large sparse matrices of up to order N x N where N <= 116,394, with up to 7 non-zero, 64-bit elements per sparse row. This implementation utilizes an optimized sparse matrix-vector multiply operation which is critical for obtaining high performance. Direct parallel implementations of loop unrolling and loop fusion are utilized to extract performance from the various vector/matrix operations. Rather than utilize the FPGA devices as function off-load accelerators, our implementation uses the FPGAs to implement the core conjugate gradient algorithm. Measured run-time performance data is presented comparing the FPGA implementation to a software-only version showing that the FPGA can outperform processors running up to 30x the clock rate. In conclusion we take a look at the new SRC-7 system and estimate the performance of this algorithm on that architecture.

  7. Development of an integrated BEM approach for hot fluid structure interaction: BEST-FSI: Boundary Element Solution Technique for Fluid Structure Interaction

    NASA Technical Reports Server (NTRS)

    Dargush, G. F.; Banerjee, P. K.; Shi, Y.

    1992-01-01

    As part of the continuing effort at NASA LeRC to improve both the durability and reliability of hot section Earth-to-orbit engine components, significant enhancements must be made in existing finite element and finite difference methods, and advanced techniques, such as the boundary element method (BEM), must be explored. The BEM was chosen as the basic analysis tool because the critical variables (temperature, flux, displacement, and traction) can be very precisely determined with a boundary-based discretization scheme. Additionally, model preparation is considerably simplified compared to the more familiar domain-based methods. Furthermore, the hyperbolic character of high speed flow is captured through the use of an analytical fundamental solution, eliminating the dependence of the solution on the discretization pattern. The price that must be paid in order to realize these advantages is that any BEM formulation requires a considerable amount of analytical work, which is typically absent in the other numerical methods. All of the research accomplishments of a multi-year program aimed toward the development of a boundary element formulation for the study of hot fluid-structure interaction in Earth-to-orbit engine hot section components are detailed. Most of the effort was directed toward the examination of fluid flow, since BEM's for fluids are at a much less developed state. However, significant strides were made, not only in the analysis of thermoviscous fluids, but also in the solution of the fluid-structure interaction problem.

  8. A pass planning method for multi-hit stretching of heavy forgings by integration of a semi-analytical technique and degrees-reduced finite element

    NASA Astrophysics Data System (ADS)

    Cui, Zhenshan; Chen, Wen; Sui, Dashan; Liu, Juan

    2013-05-01

    A pass planning method for multi-pass and multi-hit stretching of heavy forgings is proposed, which composes of a semi-analytical procedure and a degrees-reduced finite element code. The semi-analytical procedure is based on a kinematically admissible velocity and Markov variational principle, and can be applied to roughly calculate the deformed shape and working force for stretch forging process for work-piece which has vertical and lateral symmetrical lines in cross-section. Meanwhile, in order to obtain the distributions of metal flow, temperature, strain and stress in detail, a degrees-reduced thermo-mechanical coupled rigid finite element code is developed. In this code, the instantaneous deformation zone is specially extracted from the total domain and simulated for metal flow, while the total domain is used to simulate the evolution of thermal field. Taking the semi-analytical method as a solver, the pass planning procedure for stretch forging is developed, and the degrees-reduced finite element code is used as a supplement to check the rationality of the planed pass schedule. An example is implemented to demonstrate the application of the proposed technique.

  9. Effects of antenatal care and HIV treatment integration on elements of the PMTCT cascade: Results from the SHAIP cluster-randomized controlled trial in Kenya

    PubMed Central

    Turan, Janet M.; Onono, Maricianah; Steinfeld, Rachel L.; Shade, Starley B.; Owuor, Kevin; Washington, Sierra; Bukusi, Elizabeth A.; Ackers, Marta L.; Kioko, Jackson; Interis, Evelyn C.; Cohen, Craig R.

    2015-01-01

    Background Integrating antenatal care (ANC) and HIV care may improve uptake and retention in services along the prevention of mother-to-child transmission (PMTCT) cascade. The current study aimed to determine if integration of HIV services into ANC settings improves PMTCT service utilization outcomes. Methods ANC clinics in rural Kenya were randomized to integrated (6 clinics, 569 women) or non-integrated (6 clinics, 603 women) services. Intervention clinics provided all HIV services, including highly active antiretroviral therapy (HAART), while control clinics provided PMTCT services but referred women to HIV care clinics within the same facility. PMTCT utilization outcomes among HIV-infected women (maternal HIV care enrollment, HAART initiation, and 3-month infant HIV testing uptake) were compared using generalized estimating equations and Cox regression. Results HIV care enrollment was higher in intervention compared to control clinics (69% versus 36%, Odds Ratio (OR)=3.94, 95% Confidence Interval (CI): 1.14–13.63). Median time to enrollment was significantly shorter among intervention arm women (0 versus 8 days, Hazard Ratio (HR)=2.20, 95% CI: 1.62–3.01). Eligible women in the intervention arm were more likely to initiate HAART (40% versus 17%, OR=3.22, 95% CI: 1.81–5.72). Infant testing was more common in the intervention arm (25% versus 18%), however not statistically different. No significant differences were detected in postnatal service uptake or maternal retention. Conclusions Service integration increased maternal HIV care enrollment and HAART uptake. However, PMTCT utilization outcomes were still suboptimal, and postnatal service utilization remained poor in both study arms. Further improvements in the PMTCT cascade will require additional research and interventions. PMID:25967269

  10. A complex genetic switch involving overlapping divergent promoters and DNA looping regulates expression of conjugation genes of a gram-positive plasmid.

    PubMed

    Ramachandran, Gayetri; Singh, Praveen K; Luque-Ortega, Juan Roman; Yuste, Luis; Alfonso, Carlos; Rojo, Fernando; Wu, Ling J; Meijer, Wilfried J J

    2014-10-01

    Plasmid conjugation plays a significant role in the dissemination of antibiotic resistance and pathogenicity determinants. Understanding how conjugation is regulated is important to gain insights into these features. Little is known about regulation of conjugation systems present on plasmids from Gram-positive bacteria. pLS20 is a native conjugative plasmid from the Gram-positive bacterium Bacillus subtilis. Recently the key players that repress and activate pLS20 conjugation have been identified. Here we studied in detail the molecular mechanism regulating the pLS20 conjugation genes using both in vivo and in vitro approaches. Our results show that conjugation is subject to the control of a complex genetic switch where at least three levels of regulation are integrated. The first of the three layers involves overlapping divergent promoters of different strengths regulating expression of the conjugation genes and the key transcriptional regulator RcoLS20. The second layer involves a triple function of RcoLS20 being a repressor of the main conjugation promoter and an activator and repressor of its own promoter at low and high concentrations, respectively. The third level of regulation concerns formation of a DNA loop mediated by simultaneous binding of tetrameric RcoLS20 to two operators, one of which overlaps with the divergent promoters. The combination of these three layers of regulation in the same switch allows the main conjugation promoter to be tightly repressed during conditions unfavorable to conjugation while maintaining the sensitivity to accurately switch on the conjugation genes when appropriate conditions occur. The implications of the regulatory switch and comparison with other genetic switches involving DNA looping are discussed. PMID:25340403

  11. Synthesis and characterization of new ferrocene peptide conjugates.

    PubMed

    Drexler, Cailin; Milne, Mark; Morgan, Erin; Jennings, Michael; Kraatz, H-B

    2009-06-14

    Three classes of diamine linked ferrocene (Fc)-conjugates were prepared and their properties were investigates in solution and the solid state: (a) acyclic diamine-linked 1,n'-Fc conjugates, (b) acyclic diamine-linked 1,n'-Fc peptide conjugates, and (c) cyclic 1,n'-Fc-peptide diamine conjugates. In all cases, the synthetic procedure started from 1,1'-ferrocenecarboxylic acid methyl ester or 1,1'-ferrocene dicarboxylic acid or their amino acid conjugates followed by coupling with diaminoalkanes. The resulting conjugates exhibit H-bonding as is evident by temperature and, in some cases, concentration-dependent NMR shifts and in the solid-state structure of one of the conjugates. Our studies show that the structural properties of Fc-diamine-linked systems are different from those of the related cystamine conjugates, presumably due to the enhanced flexibility of the conjugates.

  12. Studies on conjugation of Spirogyra using monoclonal culture.

    PubMed

    Ikegaya, Hisato; Nakase, Takuto; Iwata, Kazuyoshi; Tsuchida, Hideaki; Sonobe, Seiji; Shimmen, Teruo

    2012-05-01

    We succeeded in inducing conjugation of Spirogyra castanacea by incubating algal filaments on agar plate. Conjugation could be induced using clone culture. The scalariform conjugation was generally observed, while lateral conjugation was rarely. When two filaments formed scalariform conjugation, all cells of one filament behaved as male and those of other filament did as female. Very rarely, however, zygospores were formed in both of pair filaments. The surface of conjugation tube was stained with fluorescently labeled-lectins, such as Bandeiraea (Griffonia) simplicifolia lectin (BSL-I) and jacalin. BSL-I strongly stained the conjugation tubes, while weakly did the cell surface of female gamete first and then that of male gamete. Jacalin stained mainly the conjugation tubes. Addition of jacalin inhibited the formation of papilla, suggesting some important role of jacalin-binding material at the initial step of formation of the conjugation tubes.

  13. Synthesis, characterization and the release kinetics of antiproliferative agents from polyamidoamine conjugates.

    PubMed

    Aderibigbe, B A; Sadiku, E R; Ray, S S; Mbianda, X Y; Fotsing, M C; Jayaramudu, J; Owonubi, S J

    2015-01-01

    Polyamidoamine conjugates containing curcumin and bisphosphonate were synthesized via a one-pot aqueous phase Michael addition reaction. In the design of the conjugate, bisphosphonate formed an integral part of the polymer carrier backbone. Curcumin was incorporated onto the polyamidoamine backbone via piperazine linker. The conjugates were characterized by Fourier transform spectroscopy, energy-dispersive X-ray analysis, atomic force spectroscopy and nuclear magnetic resonance spectroscopy and it confirmed the successful incorporation of the antiproliferative agents onto the carriers. The weight percentage incorporation of bisphosphonate to the carriers was found to be between 2.56% and 3.34%. The in vitro release studies of curcumin from the polyamidoamine conjugate were performed in dialysis bag at selected pH values. The release of curcumin was significantly slower at pH 7.4 when compared to pH 5.8. The release profiles indicate that the conjugates are more stable at pH 7.4 and are potential sustained drug-delivery systems for combination therapy.

  14. Crustal-scale architecture and segmentation of the Argentine margin and its conjugate off South Africa

    NASA Astrophysics Data System (ADS)

    Blaich, Olav A.; Faleide, Jan Inge; Tsikalas, Filippos; Franke, Dieter; León, Enric

    2009-07-01

    Integration of regional seismic reflection and refraction profiles and potential field data across the Argentine margin and its conjugate off South Africa, complemented by crustal-scale gravity modelling, is used to reveal and illustrate the whole-crust architecture, onshore-offshore crustal structure correlations, the character of the continent-ocean boundary/transition and the relationship of crustal structure to regional variation of potential field anomalies. The study reveals, within these two provinces, distinct along-margin structural and magmatic changes that are spatially related to a number of conjugate transfer systems governing the margin segmentation and evolution, clearly implying structural inheritance. In particular, the Colorado transfer system on the Argentina margin, marks a distinct along-margin boundary in the distribution and volume of breakup-related magmatism. Similarly, the Hope transfer system on the conjugate South Africa margin also marks a distinct along-margin transition from a zone of relative magnetic quiescence to a zone of prominent magnetic anomalies. Furthermore, the study indicates that the `G-magnetic anomaly' along the South Africa margin probably defines the eastern limit of the continent-ocean transition (COT) rather than a discrete continent-ocean boundary (COB). Potential field plate reconstructions of the South Atlantic suggest conjugate margin asymmetry, characterized by a rather broad Argentine margin conjugate to a narrow South Africa margin. In detail, the Argentine margin is characterized by a sharp and relatively constant COT, whereas the COT along the conjugate South Africa margin is considerably wider. An along-strike tectonomagmatic asymmetry variation is also observed and is expressed by the northward increase in width of the COT on the South African margin. The study clearly shows that integration of regional seismic reflection and refraction profiles, potential field data and gravity modelling provide a

  15. Elemental health

    SciTech Connect

    Tonneson, L.C.

    1997-01-01

    Trace elements used in nutritional supplements and vitamins are discussed in the article. Relevant studies are briefly cited regarding the health effects of selenium, chromium, germanium, silicon, zinc, magnesium, silver, manganese, ruthenium, lithium, and vanadium. The toxicity and food sources are listed for some of the elements. A brief summary is also provided of the nutritional supplements market.

  16. Conjugate gradient algorithms using multiple recursions

    SciTech Connect

    Barth, T.; Manteuffel, T.

    1996-12-31

    Much is already known about when a conjugate gradient method can be implemented with short recursions for the direction vectors. The work done in 1984 by Faber and Manteuffel gave necessary and sufficient conditions on the iteration matrix A, in order for a conjugate gradient method to be implemented with a single recursion of a certain form. However, this form does not take into account all possible recursions. This became evident when Jagels and Reichel used an algorithm of Gragg for unitary matrices to demonstrate that the class of matrices for which a practical conjugate gradient algorithm exists can be extended to include unitary and shifted unitary matrices. The implementation uses short double recursions for the direction vectors. This motivates the study of multiple recursion algorithms.

  17. Squeezing in phase-conjugated resonance fluorescence

    NASA Technical Reports Server (NTRS)

    Arnoldus, Henk F.

    1993-01-01

    Emission of resonance fluorescence by an atom near the surface of a four-wave mixing phase conjugator is considered. The dipole radiation field, regarded as a Heisenberg-operator field, is decomposed into plane waves with the aid of Weyl's representation of the Green's function for the wave equation. Each plane-wave component which is incident on the surface of the nonlinear medium, is reflected as its phase-conjugate image. Summation of all reflected plane waves then yields the phase conjugate replica of the incident dipole radiation. This field adds to the radiation which is emitted by the atom into the direction away from the medium. The condition under which squeezing occurs in the emitted resonance fluorescence is investigated.

  18. Biomedical Applications of Organometal-Peptide Conjugates

    NASA Astrophysics Data System (ADS)

    Metzler-Nolte, Nils

    Peptides are well suited as targeting vectors for the directed delivery of metal-based drugs or probes for biomedical investigations. This chapter describes synthetic strategies for the preparation of conjugates of medically interesting peptides with covalently bound metal complexes. Peptides that were used include neuropeptides (enkephalin, neuropeptide Y, neurotensin), uptake peptides (TAT and poly-Arg), and intracellular localization sequences. To these peptides, a whole variety of transition metal complexes has been attached in recent years by solid-phase peptide synthesis (SPPS) techniques. The metal complex can be attached to the peptide on the resin as part of the SPPS scheme. Alternatively, the metal complex may be attached to the peptide as a postsynthetic modification. Advantages as well as disadvantages for either strategy are discussed. Biomedical applications include radiopharmaceutical applications, anticancer and antibacterial activity, metal-peptide conjugates as targeted CO-releasing molecules, and metal-peptide conjugates in biosensor applications.

  19. Serogroup A meningococcal conjugate vaccines in Africa.

    PubMed

    Kristiansen, Paul A; Jørgensen, Hannah J; Caugant, Dominique A

    2015-01-01

    Serogroup A meningococcal epidemics have been a recurrent public health problem, especially in resource-poor countries of Africa. Recently, the administration in mass vaccination campaigns of a single dose of the monovalent meningococcal conjugate vaccine, MenAfriVac, to the 1-29 year-old population of sub-Saharan Africa has prevented epidemics of meningitis caused by serogroup A Neisseria meningitidis. This strategy has also been shown to provide herd protection of the non-vaccinated population. Development of meningococcal conjugate vaccines covering other serogroups and enhanced use of the pneumococcal and Haemophilus influenzae type b conjugate vaccines must be pursued to fully control bacterial meningitis in sub-Saharan Africa. PMID:26358167

  20. Serogroup A meningococcal conjugate vaccines in Africa.

    PubMed

    Kristiansen, Paul A; Jørgensen, Hannah J; Caugant, Dominique A

    2015-01-01

    Serogroup A meningococcal epidemics have been a recurrent public health problem, especially in resource-poor countries of Africa. Recently, the administration in mass vaccination campaigns of a single dose of the monovalent meningococcal conjugate vaccine, MenAfriVac, to the 1-29 year-old population of sub-Saharan Africa has prevented epidemics of meningitis caused by serogroup A Neisseria meningitidis. This strategy has also been shown to provide herd protection of the non-vaccinated population. Development of meningococcal conjugate vaccines covering other serogroups and enhanced use of the pneumococcal and Haemophilus influenzae type b conjugate vaccines must be pursued to fully control bacterial meningitis in sub-Saharan Africa.

  1. Hydrochromic conjugated polymers for human sweat pore mapping.

    PubMed

    Lee, Joosub; Pyo, Minkyeong; Lee, Sang-hwa; Kim, Jaeyong; Ra, Moonsoo; Kim, Whoi-Yul; Park, Bum Jun; Lee, Chan Woo; Kim, Jong-Man

    2014-04-29

    Hydrochromic materials have been actively investigated in the context of humidity sensing and measuring water contents in organic solvents. Here we report a sensor system that undergoes a brilliant blue-to-red colour transition as well as 'Turn-On' fluorescence upon exposure to water. Introduction of a hygroscopic element into a supramolecularly assembled polydiacetylene results in a hydrochromic conjugated polymer that is rapidly responsive (<20 μs), spin-coatable and inkjet-compatible. Importantly, the hydrochromic sensor is found to be suitable for mapping human sweat pores. The exceedingly small quantities (sub-nanolitre) of water secreted from sweat pores are sufficient to promote an instantaneous colorimetric transition of the polymer. As a result, the sensor can be used to construct a precise map of active sweat pores on fingertips. The sensor technology, developed in this study, has the potential of serving as new method for fingerprint analysis and for the clinical diagnosis of malfunctioning sweat pores.

  2. Hydrochromic conjugated polymers for human sweat pore mapping

    NASA Astrophysics Data System (ADS)

    Lee, Joosub; Pyo, Minkyeong; Lee, Sang-Hwa; Kim, Jaeyong; Ra, Moonsoo; Kim, Whoi-Yul; Park, Bum Jun; Lee, Chan Woo; Kim, Jong-Man

    2014-04-01

    Hydrochromic materials have been actively investigated in the context of humidity sensing and measuring water contents in organic solvents. Here we report a sensor system that undergoes a brilliant blue-to-red colour transition as well as ‘Turn-On’ fluorescence upon exposure to water. Introduction of a hygroscopic element into a supramolecularly assembled polydiacetylene results in a hydrochromic conjugated polymer that is rapidly responsive (<20 μs), spin-coatable and inkjet-compatible. Importantly, the hydrochromic sensor is found to be suitable for mapping human sweat pores. The exceedingly small quantities (sub-nanolitre) of water secreted from sweat pores are sufficient to promote an instantaneous colorimetric transition of the polymer. As a result, the sensor can be used to construct a precise map of active sweat pores on fingertips. The sensor technology, developed in this study, has the potential of serving as new method for fingerprint analysis and for the clinical diagnosis of malfunctioning sweat pores.

  3. Solvent immersion nanoimprint lithography of fluorescent conjugated polymers

    SciTech Connect

    Whitworth, G. L.; Zhang, S.; Stevenson, J. R. Y.; Ebenhoch, B.; Samuel, I. D. W.; Turnbull, G. A.

    2015-10-19

    Solvent immersion imprint lithography (SIIL) was used to directly nanostructure conjugated polymer films. The technique was used to create light-emitting diffractive optical elements and organic semiconductor lasers. Gratings with lateral features as small as 70 nm and depths of ∼25 nm were achieved in poly(9,9-dioctylfluorenyl-2,7-diyl). The angular emission from the patterned films was studied, comparing measurement to theoretical predictions. Organic distributed feedback lasers fabricated with SIIL exhibited thresholds for lasing of ∼40 kW/cm{sup 2}, similar to those made with established nanoimprint processes. The results show that SIIL is a quick, convenient and practical technique for nanopatterning of polymer photonic devices.

  4. Preconditioned conjugate residual methods for the solution of spectral equations

    NASA Technical Reports Server (NTRS)

    Wong, Y. S.; Zang, T. A.; Hussaini, M. Y.

    1986-01-01

    Conjugate residual methods for the solution of spectral equations are described. An inexact finite-difference operator is introduced as a preconditioner in the iterative procedures. Application of these techniques is limited to problems for which the symmetric part of the coefficient matrix is positive definite. Although the spectral equation is a very ill-conditioned and full matrix problem, the computational effort of the present iterative methods for solving such a system is comparable to that for the sparse matrix equations obtained from the application of either finite-difference or finite-element methods to the same problems. Numerical experiments are shown for a self-adjoint elliptic partial differential equation with Dirichlet boundary conditions, and comparison with other solution procedures for spectral equations is presented.

  5. Phase conjugation of high energy lasers.

    SciTech Connect

    Bliss, David E; Valley, Michael T.; Atherton, Briggs W.; Bigman, Verle Howard; Boye, Lydia Ann; Broyles, Robin Scott; Kimmel, Mark W.; Law, Ryan J.; Yoder, James R.

    2013-01-01

    In this report we explore claims that phase conjugation of high energy lasers by stimulated Brillouin scattering (SBS) can compensate optical aberrations associated with severely distorted laser amplifier media and aberrations induced by the atmosphere. The SBS media tested was a gas cell pressurized up to 300 psi with SF6 or Xe or both. The laser was a 10 Hz, 3J, Q-switched Nd:YAG with 25 ns wide pulses. Atmospheric aberrations were created with space heaters, helium jets and phase plates designed with a Kolmogorov turbulence spectrum characterized by a Fried parameter, ro , ranging from 0.6 6.0 mm. Phase conjugate tests in the laboratory were conducted without amplification. For the strongest aberrations, D/ro ~ 20, created by combining the space heaters with the phase plate, the Strehl ratio was degraded by a factor of ~50. Phase conjugation in SF6 restored the peak focusable intensity to about 30% of the original laser. Phase conjugate tests at the outdoor laser range were conducted with laser amplifiers providing gain in combination with the SBS cell. A large 600,000 BTU kerosene space heater was used to create turbulence along the beam path. An atmospheric structure factor of Cn2 = 5x10-13 m2/3 caused the illumination beam to expand to a diameter 250mm and overfill the receiver. The phase conjugate amplified return could successfully be targeted back onto glints 5mm in diameter. Use of a lenslet arrays to lower the peak focusable intensity in the SBS cell failed to produce a useful phase conjugate beam; The Strehl ratio was degraded with multiple random lobes instead of a single focus. I will review literature results which show how multiple beams can be coherently combined by SBS when a confocal reflecting geometry is used to focus the laser in the SBS cell.

  6. Dynamics of photogenerated polarons in conjugated polymers.

    PubMed

    An, Z; Wu, C Q; Sun, X

    2004-11-19

    Within a tight-binding electron-phonon interacting model, we investigate the dynamics of photoexcitations to address the generation mechanism of charged polarons in conjugated polymers by using a nonadiabatic evolution method. Besides the neutral polaron exciton which is well known, we identify a novel product of lattice dynamic relaxation from the photoexcited states in a few hundreds of femtoseconds, which is a mixed state composed of both charged polarons and neutral excitons. Our results show that the charged polarons are generated directly with a yield of about 25%, which is independent of the excitation energies, in good agreement with results from experiments. Effects of the conjugation length are also discussed.

  7. Dynamics of Photogenerated Polarons in Conjugated Polymers

    NASA Astrophysics Data System (ADS)

    An, Z.; Wu, C. Q.; Sun, X.

    2004-11-01

    Within a tight-binding electron-phonon interacting model, we investigate the dynamics of photoexcitations to address the generation mechanism of charged polarons in conjugated polymers by using a nonadiabatic evolution method. Besides the neutral polaron exciton which is well known, we identify a novel product of lattice dynamic relaxation from the photoexcited states in a few hundreds of femtoseconds, which is a mixed state composed of both charged polarons and neutral excitons. Our results show that the charged polarons are generated directly with a yield of about 25%, which is independent of the excitation energies, in good agreement with results from experiments. Effects of the conjugation length are also discussed.

  8. Synthesis of cyanopyridine based conjugated polymer.

    PubMed

    Hemavathi, B; Ahipa, T N; Pillai, Saju; Pai, Ranjith Krishna

    2016-06-01

    This data file contains the detailed synthetic procedure for the synthesis of two new cyanopyridine based conjugated polymer P1 and P2 along with the synthesis of its monomers. The synthesised polymers can be used for electroluminescence and photovoltaic (PV) application. The physical data of the polymers are provided in this data file along with the morphological data of the polymer thin films. The data provided here are in association with the research article entitled 'Cyanopyridine based conjugated polymer-synthesis and characterisation' (Hemavathi et al., 2015) [3]. PMID:27158642

  9. Slave finite elements: The temporal element approach to nonlinear analysis

    NASA Technical Reports Server (NTRS)

    Gellin, S.

    1984-01-01

    A formulation method for finite elements in space and time incorporating nonlinear geometric and material behavior is presented. The method uses interpolation polynomials for approximating the behavior of various quantities over the element domain, and only explicit integration over space and time. While applications are general, the plate and shell elements that are currently being programmed are appropriate to model turbine blades, vanes, and combustor liners.

  10. Conjugate Points in the Gravitational n-Body Problem

    NASA Astrophysics Data System (ADS)

    Mingarelli, Angelo B.; Mingarelli, Chiara M. F.

    2005-03-01

    In an effort to understand the nature of almost periodic orbits in the n-body problem (for all time t) we look first to the more basic question of the oscillatory nature of solutions of this problem (on a half-line, usually taken as R +). Intimately related to this is the notion of a conjugate point(due to A. Wintner) of a solution. Specifically, by rewriting the mass unrestricted general problem of n-bodies in a symmetric form we prove that in the gravitational Newtonian n-body problem with collisionless motions there exists arbitrarily large conjugate points in the case of arbitrary (positive) masses whenever the cube of the reciprocal of at least one of the mutual distances is not integrable at infinity. The implication of this result is that there are possibly many Wintner oscillatorysolutions in these cases (some of which may or may not be almost periodic). As a consequence, we obtain sufficient conditions for all continuable solutions (to infinity) to be either unbounded or to allow for near misses (at infinity). The results also apply to potentials other than Newtonian ones. Our techniques are drawn from results in systems oscillation theory and are applicable to more general situations.

  11. Solving the forward problem in electrical impedance tomography for the human head using IDEAS (integrated design engineering analysis software), a finite element modelling tool.

    PubMed

    Bayford, R H; Gibson, A; Tizzard, A; Tidswell, T; Holder, D S

    2001-02-01

    If electrical impedance tomography is to be used as a clinical tool, the image reconstruction algorithms must yield accurate images of impedance changes. One of the keys to producing an accurate reconstructed image is the inclusion of prior information regarding the physical geometry of the object. To achieve this, many researchers have created tools for solving the forward problem by means of finite element methods (FEMs). These tools are limited, allowing only a set number of meshes to be produced from the geometric information of the object. There is a clear need for geometrical accurate FEM models to improve the quality of the reconstructed images. We present a commercial tool called IDEAS, which can be used to create FEM meshes for these models. The application of this tool is demonstrated by using segmented data from the human head to model impedance changes inside the head.

  12. Intelligent Elements for ISHM

    NASA Technical Reports Server (NTRS)

    Schmalzel, John L.; Morris, Jon; Turowski, Mark; Figueroa, Fernando; Oostdyk, Rebecca

    2008-01-01

    There are a number of architecture models for implementing Integrated Systems Health Management (ISHM) capabilities. For example, approaches based on the OSA-CBM and OSA-EAI models, or specific architectures developed in response to local needs. NASA s John C. Stennis Space Center (SSC) has developed one such version of an extensible architecture in support of rocket engine testing that integrates a palette of functions in order to achieve an ISHM capability. Among the functional capabilities that are supported by the framework are: prognostic models, anomaly detection, a data base of supporting health information, root cause analysis, intelligent elements, and integrated awareness. This paper focuses on the role that intelligent elements can play in ISHM architectures. We define an intelligent element as a smart element with sufficient computing capacity to support anomaly detection or other algorithms in support of ISHM functions. A smart element has the capabilities of supporting networked implementations of IEEE 1451.x smart sensor and actuator protocols. The ISHM group at SSC has been actively developing intelligent elements in conjunction with several partners at other Centers, universities, and companies as part of our ISHM approach for better supporting rocket engine testing. We have developed several implementations. Among the key features for these intelligent sensors is support for IEEE 1451.1 and incorporation of a suite of algorithms for determination of sensor health. Regardless of the potential advantages that can be achieved using intelligent sensors, existing large-scale systems are still based on conventional sensors and data acquisition systems. In order to bring the benefits of intelligent sensors to these environments, we have also developed virtual implementations of intelligent sensors.

  13. Superheavy Elements

    ERIC Educational Resources Information Center

    Tsang, Chin Fu

    1975-01-01

    Discusses the possibility of creating elements with an atomic number of around 114. Describes the underlying physics responsible for the limited extent of the periodic table and enumerates problems that must be overcome in creating a superheavy nucleus. (GS)

  14. Identification of the rctA gene, which is required for repression of conjugative transfer of rhizobial symbiotic megaplasmids.

    PubMed

    Pérez-Mendoza, Daniel; Sepúlveda, Edgardo; Pando, Victoria; Muñoz, Socorro; Nogales, Joaquina; Olivares, José; Soto, Maria J; Herrera-Cervera, José A; Romero, David; Brom, Susana; Sanjuán, Juan

    2005-11-01

    An analysis of the conjugative transfer of pRetCFN42d, the symbiotic plasmid (pSym) of Rhizobium etli, has revealed a novel gene, rctA, as an essential element of a regulatory system for silencing the conjugative transfer of R. etli pSym by repressing the transcription of conjugal transfer genes in standard laboratory media. The rctA gene product lacks sequence conservation with other proteins of known function but may belong to the winged-helix DNA-binding subfamily of transcriptional regulators. Similar to that of many transcriptional repressors, rctA transcription seems to be positively autoregulated. rctA expression is greatly reduced upon overexpression of another gene, rctB, previously identified as a putative activator of R. etli pSym conjugal transfer. Thus, rctB seems to counteract the repressive action of rctA. rctA homologs are present in at least three other bacterial genomes within the order Rhizobiales, where they are invariably located adjacent to and divergently transcribed from putative virB-like operons. We show that similar to that of R. etli pSym, conjugative transfer of the 1.35-Mb symbiotic megaplasmid A of Sinorhizobium meliloti is also subjected to the inhibitory action of rctA. Our data provide strong evidence that the R. etli and S. meliloti pSym plasmids are indeed self-conjugative plasmids and that this property would only be expressed under optimal, as yet unknown conditions that entail inactivation of the rctA function. The rctA gene seems to represent novel but probably widespread regulatory systems controlling the transfer of conjugative elements within the order Rhizobiales.

  15. Isolation of Discrete Nanoparticle-DNA Conjugates for Plasmonic Applications

    SciTech Connect

    Alivisatos, Paul; Claridge, Shelley A.; Liang, Huiyang W.; Basu, Sourav Roger; Frechet, Jean M.J.; Alivisatos, A. Paul

    2008-04-11

    Discrete DNA-gold nanoparticle conjugates with DNA lengths as short as 15 bases for both 5 nm and 20 nm gold particles have been purified by anion-exchange HPLC. Conjugates comprising short DNA (<40 bases) and large gold particles (>_ 20 nm) are difficult to purify by other means, and are potential substrates for plasmon coupling experiments. Conjugate purity is demonstrated by hybridizing complementary conjugates to form discrete structures, which are visualized by TEM.

  16. Continuous flow synthesis of conjugated polymers.

    PubMed

    Seyler, Helga; Jones, David J; Holmes, Andrew B; Wong, Wallace W H

    2012-02-01

    A selection of conjugated polymers, widely studied in organic electronics, was synthesised using continuous flow methodology. As a result of superior heat transfer and reagent control, excellent polymer molecular mass distributions were achieved in significantly reduced reaction times compared to conventional batch reactions.

  17. Bacillus thuringiensis Conjugation in Simulated Microgravity

    NASA Astrophysics Data System (ADS)

    Beuls, Elise; van Houdt, Rob; Leys, Natalie; Dijkstra, Camelia; Larkin, Oliver; Mahillon, Jacques

    2009-10-01

    Spaceflight experiments have suggested a possible effect of microgravity on the plasmid transfer among strains of the Gram-positive Bacillus thuringiensis, as opposed to no effect recorded for Gram-negative conjugation. To investigate these potential effects in a more affordable experimental setup, three ground-based microgravity simulators were tested: the Rotating Wall Vessel (RWV), the Random Positioning Machine (RPM), and a superconducting magnet. The bacterial conjugative system consisted in biparental matings between two B. thuringiensis strains, where the transfer frequencies of the conjugative plasmid pAW63 and its ability to mobilize the nonconjugative plasmid pUB110 were assessed. Specifically, potential plasmid transfers in a 0-g position (simulated microgravity) were compared to those obtained under 1-g (normal gravity) condition in each device. Statistical analyses revealed no significant difference in the conjugative and mobilizable transfer frequencies between the three different simulated microgravitational conditions and our standard laboratory condition. These important ground-based observations emphasize the fact that, though no stimulation of plasmid transfer was observed, no inhibition was observed either. In the case of Gram-positive bacteria, this ability to exchange plasmids in weightlessness, as occurs under Earth's conditions, should be seen as particularly relevant in the scope of spread of antibiotic resistances and bacterial virulence.

  18. Antibody-drug conjugates: Intellectual property considerations

    PubMed Central

    Storz, Ulrich

    2015-01-01

    Antibody-drug conjugates are highly complex entities that combine an antibody, a linker and a toxin. This complexity makes them demanding both technically and from a regulatory point of view, and difficult to deal with in their patent aspects. This article discusses different issues of patent protection and freedom to operate with regard to this promising new class of drugs. PMID:26292154

  19. Conjugal Succession and the American Kinship System.

    ERIC Educational Resources Information Center

    Furstenberg, Frank F., Jr.

    Although not the preferred type of family formation, conjugal succession is now an accepted, if not expected, alternative to continuous marriage in the United States. This new trend appears to be related to a shift in the meaning of matrimony. Previously, marriage was part of a cultural pattern of transitions and as such was closely timed to…

  20. Antibody-drug conjugates: Intellectual property considerations.

    PubMed

    Storz, Ulrich

    2015-01-01

    Antibody-drug conjugates are highly complex entities that combine an antibody, a linker and a toxin. This complexity makes them demanding both technically and from a regulatory point of view, and difficult to deal with in their patent aspects. This article discusses different issues of patent protection and freedom to operate with regard to this promising new class of drugs. PMID:26292154

  1. Predicting the optical gap of conjugated systems

    NASA Astrophysics Data System (ADS)

    Botelho, Andre Leitao

    The adapted Su-Schrieffer-Heeger model is developed in this work as a tool for in silico prediction of the optical gap of pi-conjugated systems for photovoltaic applications. Full transferability of the model ensures reliable predictive power - excellent agreement with 180 independent experimental data points covering virtually all existing conjugated system types with an accuracy exceeding the time-dependent density functional theory, one of the most accurate first-principles methods. Insights on the structure-property relation of conjugated systems obtained from the model lead to guiding rules for optical gap design: 1) fusing aromatic rings parallel to the conjugated path does not significantly lower the optical gap, 2) fusing rings perpendicularly lowers the optical gap of the monomer, but has a reduced benefit from polymerization, and 3) copolymers take advantage of the lower optical gap of perpendicular fused rings and benefit from further optical gap reduction through added parallel fused rings as electronic communicators. A copolymer of parallel and perpendicular benzodithiophenes, differing only in sulfur atom locations, is proposed as a candidate to achieve the optimal 1.2 eV donor optical gap for organic photovoltaics. For small-molecule organic photovoltaics, substituting the end pairs of carbon atoms on pentacene with sulfur atoms is predicted to lower the optical gap from 1.8 eV to 1.1 eV. Furthermore, the model offers an improvement of orders of magnitude in the computational efficiency over commonly used first-principles tools.

  2. Compositions for directed alignment of conjugated polymers

    DOEpatents

    Kim, Jinsang; Kim, Bong-Gi; Jeong, Eun Jeong

    2016-04-19

    Conjugated polymers (CPs) achieve directed alignment along an applied flow field and a dichroic ratio of as high as 16.67 in emission from well-aligned thin films and fully realized anisotropic optoelectronic properties of CPs in field-effect transistor (FET).

  3. DELAYED HYPERSENSITIVITY TO HAPTEN-PROTEIN CONJUGATES

    PubMed Central

    Cell, P. G. H.; Silverstein, Arthur M.

    1962-01-01

    Further data have been presented showing that the specificity of the delayed hypersensitivity reaction in the guinea pig to hapten-protein conjugates involves to a considerable degree a contribution by the protein carrier. The carrier contribution is such that sensitization to guinea pig albumin-m-azobenzenesulfonate, for example, does not result in cross-reaction with conjugates of the same hapten with unrelated proteins such as ovalbumin or human gamma globulin, nor were cross-reactions observed between conjugates prepared with the same hapten, coupled to the same protein, but by two different chemical routes, such that the point of attachment of the hapten to the protein differed. It thus appears that in this system both hapten and carrier protein are necessary, but that neither alone is in general sufficient to stimulate the delayed sensitive cell. Desensitization experiments with cross-reacting hapten-protein conjugates have suggested the presence of a multiplicity of antigenic determinants participating in the elicitation of the delayed lesion, and of a concomitant development of a heterogeneity of specificities in the population of delayed sensitive cells in the sensitized animal. The data are discussed in terms of the apparent requirement of the delayed sensitivity mechanism for a larger functional antigenic determinant than that required for interaction with circulating antibodies. Some possible explanations for this difference, and some of its consequences, are discussed. PMID:13897619

  4. Hyperbranched: a universal conjugated polymer platform.

    PubMed

    Tolosa, Juan; Kub, Chris; Bunz, Uwe H F

    2009-01-01

    Out on a limb: Sonogashira coupling of a suitable AB(2) monomer containing two iodine and one alkyne group forms a hyperbranched conjugated polymer that is studded with iodine end groups (see picture: I purple). These iodine groups are a perfect handle for convenient, efficient, and high-yielding post-functionalization to access hyperbranched, fluorescent poly(phenyleneethynylene)s. PMID:19373821

  5. Improved conjugation and purification strategies for the preparation of protein-polysaccharide conjugates.

    PubMed

    Suárez, N; Massaldi, H; Franco Fraguas, L; Ferreira, F

    2008-12-12

    A glycoconjugate constituted by the Streptococcus pneumoniae serotype 14 capsular polysaccharide (CPS14) and bovine serum albumin (BSA) was prepared, and the unique properties of Sephadex LH-20 were used to separate the conjugate from the unconjugated material. The strength of this approach consists in its capacity to produce pure polysaccharide-protein conjugate in good yield and free from unconjugated material, a common residual contaminant of this type of immunobiologicals. The CPS14-BSA conjugate prepared via an improved 1-cyano-4-dimethylaminopyridinium tetrafluoroborate (CDAP)-activation technique was characterized chemically and its immunogenicity was evaluated in mice. The purified conjugate, unlike the corresponding polysaccharide, produced a T-cell-dependent response in this species. PMID:18992885

  6. Improved conjugation and purification strategies for the preparation of protein-polysaccharide conjugates.

    PubMed

    Suárez, N; Massaldi, H; Franco Fraguas, L; Ferreira, F

    2008-12-12

    A glycoconjugate constituted by the Streptococcus pneumoniae serotype 14 capsular polysaccharide (CPS14) and bovine serum albumin (BSA) was prepared, and the unique properties of Sephadex LH-20 were used to separate the conjugate from the unconjugated material. The strength of this approach consists in its capacity to produce pure polysaccharide-protein conjugate in good yield and free from unconjugated material, a common residual contaminant of this type of immunobiologicals. The CPS14-BSA conjugate prepared via an improved 1-cyano-4-dimethylaminopyridinium tetrafluoroborate (CDAP)-activation technique was characterized chemically and its immunogenicity was evaluated in mice. The purified conjugate, unlike the corresponding polysaccharide, produced a T-cell-dependent response in this species.

  7. Finite element model of surface acoustic wave method for mechanical characterization of patterned thin films of the ultra-large scaled integrated interconnect.

    PubMed

    Xiao, Xia; Shan, Xingmeng; Tao, Ye; Sun, Yuan; Kikkawa, Takamaro

    2013-02-01

    Surface acoustic waves (SAWs) technique is a promising method to determine the mechanical properties of thin low dielectric constant (low-k) dielectrics by matching the experimental dispersion curve with the theoretical dispersion curves. However, it is difficult to calculate the dispersion curves when SAWs propagate along patterned structure. In this paper, finite element method (FEM) is applied to obtain the numerical dispersion results of SAWs propagating on patterned film. Periodic boundary condition and plane-strain model is used to improve the computation speed. Four structures of bulk silicon, single layered low-k film, two layered Cu and SiO2 film, and patterned film, are simulated in this paper. The dispersion curves of single low-k films derived from the FEM simulation agree very well with those calculated by traditional method, which verifies the correct employment of the FEM approach. Dispersion curves of two patterned film structure of Cu and SiO2 with difference metal wire width are obtained. Effective Young's moduli are achieved by fitting the FEM simulated results with those of traditional theoretical calculation through least square error method.

  8. Static analysis of Timoshenko beam resting on elastic half-plane based on the coupling of locking-free finite elements and boundary integral

    NASA Astrophysics Data System (ADS)

    Tullini, Nerio; Tralli, Antonio

    2010-01-01

    Making use of a mixed variational formulation including the Green function of the soil and assuming as independent fields both the structure displacements and the contact pressure, a finite element (FE) model is derived for the static analysis of a foundation beam resting on elastic half-plane. Timoshenko beam model is adopted to describe structural foundations with low slenderness and to impose displacement compatibility between beam and half-plane without requiring the continuity of the first order derivative of the surface displacements enforced by Euler-Bernoulli beam. Numerical results are obtained by using locking-free Hermite polynomials for the Timoshenko beam and constant reaction over the soil. Foundation beams loaded by many load configurations illustrate accuracy and convergence properties of the proposed formulation. Moreover, the different behaviour of the Euler-Bernoulli and Timoshenko beam models is thoroughly discussed. Rectangular pipe loaded by a force in the upper beam exemplifies the straightforward coupling of the foundation FE with a structure described by usual FEs.

  9. Phase transition in conjugated oligomers suspended in chloroform

    NASA Astrophysics Data System (ADS)

    Dwivedi, Shikha; Kumar, Anupam; Yadav, S. N. S.; Mishra, Pankaj

    2015-08-01

    Density functional theory (DFT) has been used to investigate the isotropic-nematic (I-N) phase transition in a system of high aspect ratio conjugated oligomers suspended in chloroform. The interaction between the oligomers is modeled using Gay-Berne potential in which effect of solvent is implicit. Percus-Yevick integral equation theory has been used to evaluate the pair correlation functions of the fluid phase at several temperatures and densities. These pair correlation function has been used in the DFT to evaluate the I-N freezing parameters. Highly oriented nematic is found to stabilize at low density. The results obtained are in qualitative agreement with the simulation and are verifiable.

  10. Merging thiophene with boron: new building blocks for conjugated materials.

    PubMed

    Ren, Yi; Jäkle, Frieder

    2016-09-28

    This perspective highlights recent progress on the design, synthesis and applications of thienylboranes as building blocks for new functional materials. Well-controlled synthetic protocols, such as boron-tin and boron-silicon exchange reactions, hydroboration of alkynyl groups, and electrophilic borylations provide opportunities to access thiophene-boranes that are chemically robust and display desirable photophysical properties, redox characteristics, and solid-state assembly behavior. Diverse protocols for further functionalization allow for facile integration into larger conjugated structures and even polymeric systems. Moreover, the strong Lewis acid character that is characteristic of trivalent boranes facilitates intra- and intermolecular Lewis acid-base interactions that can further enrich the chemical and electronic properties of thiophene-borane materials. Recent advances with respect to applications in sensing, organic electronics, and the development of molecular switches are also discussed.

  11. Novel magnetic fibrin hydrogel scaffolds containing thrombin and growth factors conjugated iron oxide nanoparticles for tissue engineering

    PubMed Central

    Ziv-Polat, Ofra; Skaat, Hadas; Shahar, Abraham; Margel, Shlomo

    2012-01-01

    Novel tissue-engineered magnetic fibrin hydrogel scaffolds were prepared by the interaction of thrombin-conjugated iron oxide magnetic nanoparticles with fibrinogen. In addition, stabilization of basal fibroblast growth factor (bFGF) was achieved by the covalent and physical conjugation of the growth factor to the magnetic nanoparticles. Adult nasal olfactory mucosa (NOM) cells were seeded in the transparent fibrin scaffolds in the absence or presence of the free or conjugated bFGF-iron oxide nanoparticles. The conjugated bFGF enhanced significantly the growth and differentiation of the NOM cells in the fibrin scaffolds, compared to the same or even five times higher concentration of the free bFGF. In the presence of the bFGF-conjugated magnetic nanoparticles, the cultured NOM cells proliferated and formed a three-dimensional interconnected network composed mainly of tapered bipolar cells. The magnetic properties of these matrices are due to the integration of the thrombin- and bFGF-conjugated magnetic nanoparticles within the scaffolds. The magnetic properties of these scaffolds may be used in future work for various applications, such as magnetic resonance visualization of the scaffolds after implantation and reloading the scaffolds via magnetic forces with bioactive agents, eg, growth factors bound to the iron oxide magnetic nanoparticles. PMID:22419873

  12. Matrix Elements for Hylleraas CI

    NASA Astrophysics Data System (ADS)

    Harris, Frank E.

    The limitation to at most a single interelectron distance in individual configurations of a Hylleraas-type multiconfiguration wave function restricts significantly the types of integrals occurring in matrix elements for energy calculations, but even then if the formulation is not handled efficiently the angular parts of these integrals escalate to create expressions of great complexity. This presentation reviews ways in which the angular-momentum calculus can be employed to systematize and simplify the matrix element formulas, particularly those for the kinetic-energy matrix elements.

  13. Identification and characterization of novel Salmonella mobile elements involved in the dissemination of genes linked to virulence and transmission.

    PubMed

    Moreno Switt, Andrea I; den Bakker, Henk C; Cummings, Craig A; Rodriguez-Rivera, Lorraine D; Govoni, Gregory; Raneiri, Matthew L; Degoricija, Lovorka; Brown, Stephanie; Hoelzer, Karin; Peters, Joseph E; Bolchacova, Elena; Furtado, Manohar R; Wiedmann, Martin

    2012-01-01

    The genetic diversity represented by >2,500 different Salmonella serovars provides a yet largely uncharacterized reservoir of mobile elements that can contribute to the frequent emergence of new pathogenic strains of this important zoonotic pathogen. Currently, our understanding of Salmonella mobile elements is skewed by the fact that most studies have focused on highly virulent or common serovars. To gain a more global picture of mobile elements in Salmonella, we used prediction algorithms to screen for mobile elements in 16 sequenced Salmonella genomes representing serovars for which no prior genome scale mobile element data were available. From these results, selected mobile elements underwent further analyses in the form of validation studies, comparative analyses, and PCR-based population screens. Through this analysis we identified a novel plasmid that has two cointegrated replicons (IncI1-IncFIB); this plasmid type was found in four genomes representing different Salmonella serovars and contained a virulence gene array that had not been previously identified. A Salmonella Montevideo isolate contained an IncHI and an IncN2 plasmid, which both encoded antimicrobial resistance genes. We also identified two novel genomic islands (SGI2 and SGI3), and 42 prophages with mosaic architecture, seven of them harboring known virulence genes. Finally, we identified a novel integrative conjugative element (ICE) encoding a type IVb pilus operon in three non-typhoidal Salmonella serovars. Our analyses not only identified a considerable number of mobile elements that have not been previously reported in Salmonella, but also found evidence that these elements facilitate transfer of genes that were previously thought to be limited in their distribution among Salmonella serovars. The abundance of mobile elements encoding pathogenic properties may facilitate the emergence of strains with novel combinations of pathogenic traits.

  14. Two grid iteration with a conjugate gradient fine grid smoother applied to a groundwater flow model

    SciTech Connect

    Hagger, M.J.; Spence, A.; Cliffe, K.A.

    1994-12-31

    This talk is concerned with the efficient solution of Ax=b, where A is a large, sparse, symmetric positive definite matrix arising from a standard finite element discretisation of the groundwater flow problem {triangledown}{sm_bullet}(k{triangledown}p)=0. Here k is the coefficient of rock permeability in applications and is highly discontinuous. The discretisation is carried out using the Harwell NAMMU finite element package, using, for 2D, 9 node biquadratic rectangular elements, and 27 node biquadratics for 3D. The aim is to develop a robust technique for iterative solutions of 3D problems based on a regional groundwater flow model of a geological area with sharply varying hydrogeological properties. Numerical experiments with polynomial preconditioned conjugate gradient methods on a 2D groundwater flow model were found to yield very poor results, converging very slowly. In order to utilise the fact that A comes from the discretisation of a PDE the authors try the two grid method as is well analysed from studies of multigrid methods, see for example {open_quotes}Multi-Grid Methods and Applications{close_quotes} by W. Hackbusch. Specifically they consider two discretisations resulting in stiffness matrices A{sub N} and A{sub n}, of size N and n respectively, where N > n, for both a model problem and the geological model. They perform a number of conjugate gradient steps on the fine grid, ie using A{sub N}, followed by an exact coarse grid solve, using A{sub n}, and then update the fine grid solution, the exact coarse grid solve being done using a frontal method factorisation of A{sub n}. Note that in the context of the standard two grid method this is equivalent to using conjugate gradients as a fine grid smoothing step. Experimental results are presented to show the superiority of the two grid iteration method over the polynomial preconditioned conjugate gradient method.

  15. FUEL ELEMENT

    DOEpatents

    Bean, R.W.

    1963-11-19

    A ceramic fuel element for a nuclear reactor that has improved structural stability as well as improved cooling and fission product retention characteristics is presented. The fuel element includes a plurality of stacked hollow ceramic moderator blocks arranged along a tubular raetallic shroud that encloses a series of axially apertured moderator cylinders spaced inwardly of the shroud. A plurality of ceramic nuclear fuel rods are arranged in the annular space between the shroud and cylinders of moderator and appropriate support means and means for directing gas coolant through the annular space are also provided. (AEC)

  16. Digital optical phase conjugation of fluorescence in turbid tissue

    SciTech Connect

    Vellekoop, Ivo M.; Cui Meng; Yang Changhuei

    2012-08-20

    We demonstrate a method for phase conjugating fluorescence. Our method, called reference free digital optical phase conjugation, can conjugate extremely weak, incoherent optical signals. It was used to phase conjugate fluorescent light originating from a bead covered with 0.5 mm of light-scattering tissue. The phase conjugated beam refocuses onto the bead and causes a local increase of over two orders of magnitude in the light intensity. Potential applications are in imaging, optical trapping, and targeted photochemical activation inside turbid tissue.

  17. Minimizing inter-channel cross-phase modulation with optical phase conjugation in asymmetric fibre links.

    PubMed

    Hesketh, Graham D; Petropoulos, Periklis

    2016-09-01

    Using analytic and numerical modelling of fibre transmission systems that employ optical phase conjugation (OPC), we show inter-channel cross-phase modulation depends on the integrated square error between nonlinear profiles before and after OPC and that arranging amplifiers and tuning power levels is crucial to minimizing noise. We derive modulation transparent formulas for phase noise and optimal power settings. Examples are shown for 16 and 64 quadrature amplitude modulation. PMID:27607633

  18. Elemental analysis in biotechnology.

    PubMed

    Hann, Stephan; Dernovics, Mihaly; Koellensperger, Gunda

    2015-02-01

    This article focuses on analytical strategies integrating atomic spectroscopy in biotechnology. The rationale behind developing such methods is inherently linked to unique features of the key technique in elemental analysis, which is inductively coupled plasma mass spectrometry: (1) the high sensitivity and selectivity of state of the art instrumentation, (2) the possibility of accurate absolute quantification even in complex matrices, (3) the capability of combining elemental detectors with chromatographic separation methods and the versatility of the latter approach, (4) the complementarity of inorganic and organic mass spectrometry, (5) the multi-element capability and finally (6) the capability of isotopic analysis. The article highlights the most recent bio-analytical developments exploiting these methodological advantages and shows the potential in biotechnological applications.

  19. Functional Integration

    NASA Astrophysics Data System (ADS)

    Cartier, Pierre; DeWitt-Morette, Cecile

    2010-06-01

    Acknowledgements; List symbols, conventions, and formulary; Part I. The Physical and Mathematical Environment: 1. The physical and mathematical environment; Part II. Quantum Mechanics: 2. First lesson: gaussian integrals; 3. Selected examples; 4. Semiclassical expansion: WKB; 5. Semiclassical expansion: beyond WKB; 6. Quantum dynamics: path integrals and operator formalism; Part III. Methods from Differential Geometry: 7. Symmetries; 8. Homotopy; 9. Grassmann analysis: basics; 10. Grassmann analysis: applications; 11. Volume elements, divergences, gradients; Part IV. Non-Gaussian Applications: 12. Poisson processes in physics; 13. A mathematical theory of Poisson processes; 14. First exit time: energy problems; Part V. Problems in Quantum Field Theory: 15. Renormalization 1: an introduction; 16. Renormalization 2: scaling; 17. Renormalization 3: combinatorics; 18. Volume elements in quantum field theory Bryce DeWitt; Part VI. Projects: 19. Projects; Appendix A. Forward and backward integrals: spaces of pointed paths; Appendix B. Product integrals; Appendix C. A compendium of gaussian integrals; Appendix D. Wick calculus Alexander Wurm; Appendix E. The Jacobi operator; Appendix F. Change of variables of integration; Appendix G. Analytic properties of covariances; Appendix H. Feynman's checkerboard; Bibliography; Index.

  20. Functional Integration

    NASA Astrophysics Data System (ADS)

    Cartier, Pierre; DeWitt-Morette, Cecile

    2006-11-01

    Acknowledgements; List symbols, conventions, and formulary; Part I. The Physical and Mathematical Environment: 1. The physical and mathematical environment; Part II. Quantum Mechanics: 2. First lesson: gaussian integrals; 3. Selected examples; 4. Semiclassical expansion: WKB; 5. Semiclassical expansion: beyond WKB; 6. Quantum dynamics: path integrals and operator formalism; Part III. Methods from Differential Geometry: 7. Symmetries; 8. Homotopy; 9. Grassmann analysis: basics; 10. Grassmann analysis: applications; 11. Volume elements, divergences, gradients; Part IV. Non-Gaussian Applications: 12. Poisson processes in physics; 13. A mathematical theory of Poisson processes; 14. First exit time: energy problems; Part V. Problems in Quantum Field Theory: 15. Renormalization 1: an introduction; 16. Renormalization 2: scaling; 17. Renormalization 3: combinatorics; 18. Volume elements in quantum field theory Bryce DeWitt; Part VI. Projects: 19. Projects; Appendix A. Forward and backward integrals: spaces of pointed paths; Appendix B. Product integrals; Appendix C. A compendium of gaussian integrals; Appendix D. Wick calculus Alexander Wurm; Appendix E. The Jacobi operator; Appendix F. Change of variables of integration; Appendix G. Analytic properties of covariances; Appendix H. Feynman's checkerboard; Bibliography; Index.

  1. Element Research.

    ERIC Educational Resources Information Center

    Herald, Christine

    2001-01-01

    Describes a research assignment for 8th grade students on the elements of the periodic table. Students use web-based resources and a chemistry handbook to gather information, construct concept maps, and present the findings to the full class using the mode of their choice: a humorous story, a slideshow or gameboard, a brochure, a song, or skit.…

  2. Mercury, elemental

    Integrated Risk Information System (IRIS)

    Mercury , elemental ; CASRN 7439 - 97 - 6 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinoge

  3. Impact of conjugation chemistry on the immunogenicity of S. Typhimurium conjugate vaccines.

    PubMed

    Stefanetti, G; Rondini, S; Lanzilao, L; Saul, A; MacLennan, C A; Micoli, F

    2014-10-21

    Salmonella Typhimurium is major cause of invasive nontyphoidal Salmonella disease in Africa. Conjugation of S. Typhimurium O-antigen to an appropriate carrier protein constitutes a possible strategy for the development of a vaccine against this disease, for which no vaccines are currently available. The conjugation chemistry used is one of the parameters that can affect the immunogenicity of glycoconjugate vaccines. Herein different glycoconjugates were synthesized to investigate the impact of this variable on the immunogenicity of S. Typhimurium conjugate vaccines in mice, all with CRM₁₉₇ as carrier protein. Random derivatization along the O-antigen chain was compared with site-directed activation of the terminal KDO sugar residue of the core oligosaccharide. In particular, two different random approaches were used, based on the oxidation of the polysaccharide, which differently impact the structure and conformation of the O-antigen chain. For the selective conjugation methods, linkers of two different lengths were compared. When tested in mice, all conjugates induced anti-O-antigen IgG antibodies with serum bactericidal activity. Similar anti-O-antigen antibody levels were elicited independent of the chemistry used and a higher degree of saccharide derivatization did not impact negatively on the anti-O-antigen IgG response. Bactericidal activity of serum antibodies induced by selective conjugates was similar independent of the length of the spacer used. Random conjugates elicited antibodies with greater bactericidal activity than selective ones, and an inverse correlation was found between degree of O-antigen modification and antibody functional activity.

  4. Impact of conjugation chemistry on the immunogenicity of S. Typhimurium conjugate vaccines.

    PubMed

    Stefanetti, G; Rondini, S; Lanzilao, L; Saul, A; MacLennan, C A; Micoli, F

    2014-10-21

    Salmonella Typhimurium is major cause of invasive nontyphoidal Salmonella disease in Africa. Conjugation of S. Typhimurium O-antigen to an appropriate carrier protein constitutes a possible strategy for the development of a vaccine against this disease, for which no vaccines are currently available. The conjugation chemistry used is one of the parameters that can affect the immunogenicity of glycoconjugate vaccines. Herein different glycoconjugates were synthesized to investigate the impact of this variable on the immunogenicity of S. Typhimurium conjugate vaccines in mice, all with CRM₁₉₇ as carrier protein. Random derivatization along the O-antigen chain was compared with site-directed activation of the terminal KDO sugar residue of the core oligosaccharide. In particular, two different random approaches were used, based on the oxidation of the polysaccharide, which differently impact the structure and conformation of the O-antigen chain. For the selective conjugation methods, linkers of two different lengths were compared. When tested in mice, all conjugates induced anti-O-antigen IgG antibodies with serum bactericidal activity. Similar anti-O-antigen antibody levels were elicited independent of the chemistry used and a higher degree of saccharide derivatization did not impact negatively on the anti-O-antigen IgG response. Bactericidal activity of serum antibodies induced by selective conjugates was similar independent of the length of the spacer used. Random conjugates elicited antibodies with greater bactericidal activity than selective ones, and an inverse correlation was found between degree of O-antigen modification and antibody functional activity. PMID:25192974

  5. Canonical orbital elements in terms of an arbitrary independent variable

    NASA Technical Reports Server (NTRS)

    Bond, V. R.; Janin, G.

    1981-01-01

    Within the framework of the Hamiltonian mechanics in the extended phase space, a set of canonical elements of the Delaunay type is developed in terms of an arbitary independent angular variable. Application to the four classical anomalies - eccentric, true, elliptic, and mean - is presented. Particular attention is given to the generalized time equation and its conjugate energy equation.

  6. Superheavy Elements

    NASA Astrophysics Data System (ADS)

    Hofmann, S.

    The nuclear shell model predicts that the next doubly magic shell closure beyond 208Pb is at a proton number Z=114, 120, or 126 and at a neutron number N=172 or 184. The outstanding aim of experimental investigations is the exploration of this region of spherical `SuperHeavy Elements' (SHEs). Experimental methods have been developed which allowed for the identification of new elements at production rates of one atom per month. Using cold fusion reactions which are based on lead and bismuth targets, relatively neutron-deficient isotopes of the elements from 107 to 113 were synthesized at GSI in Darmstadt, Germany, and/or at RIKEN in Wako, Japan. In hot fusion reactions of 48Ca projectiles with actinide targets more neutron-rich isotopes of the elements from 112 to 116 and even 118 were produced at the Flerov Laboratory of Nuclear Reactions (FLNR) at the Joint Institute for Nuclear Research (JINR) in Dubna, Russia. Recently, part of these data which represent the first identification of nuclei located on the predicted island of SHEs were confirmed in two independent experiments. The decay data reveal that for the heaviest elements, the dominant decay mode is α emission rather than fission. Decay properties as well as reaction cross-sections are compared with results of theoretical studies. Finally, plans are presented for the further development of the experimental set-up and the application of new techniques. At a higher sensitivity, the detailed exploration of the region of spherical SHEs will be in the center of interest of future experimental work. New data will certainly challenge theoretical studies on the mechanism of the synthesis, on the nuclear decay properties, and on the chemical behavior of these heaviest atoms at the limit of stability.

  7. Optimization of the conjugation method for a serogroup B/C meningococcal vaccine.

    PubMed

    Fukasawa, Lucila O; Schenkman, Rocilda P F; Perciani, Catia T; Carneiro, Sylvia M; Dias, Waldely O; Tanizaki, Martha M

    2006-11-01

    A conjugate meningococcal vaccine against serogroup B/C consisting of capsular PS (polysaccharide) from serogroup C conjugated to OMV (outer membrane vesicle) from serogroup B would be a very useful vaccine in regions where there is a prevalence of both serogroups, for example in Brazil. For this purpose, the conjugation method that uses ADHy (adipic acid dihydrazide) as spacer and a carbodi-imide derivative, EDAC [1-ethyl-3-(3-dimethylaminopropyl)carbodi-imide], as catalyser was optimized looking for synthesis yield and maintenance of the antigenicity of both components. The best synthesis conditions preserving the vaccine immunogenicity resulted in a final yield of approx. 17%. Immunogenicity of the vaccine was highest when 10% of the sialic acid residues of the PS were occupied by the ADHy spacer. Sterilization of the conjugate by filtration through a 0.22-microm-pore-size membrane resulted in a low recovery of protein and PS (approximately 50%), although the vaccine immunogenicity was maintained. Using gamma irradiation on freeze-dried sample, it was possible to maintain the integrity of OMV structure and, consequently, its ability to induce bactericidal antibodies. PMID:16776648

  8. Membrane protein crystallization in micelles conjugated by nucleoside base-pairing: A different concept.

    PubMed

    Hosamani, Basavaprabhu; Kale, Raju R; Sharma, Hemlata; Wachtel, Ellen; Kesselman, Ellina; Danino, Dganit; Friedman, Noga; Sheves, Mordechai; Namboothiri, Irishi N N; Patchornik, Guy

    2016-09-01

    The dearth of high quality, three dimensional crystals of membrane proteins, suitable for X-ray diffraction analysis, constitutes a serious barrier to progress in structural biology. To address this challenge, we have developed a new crystallization medium that relies on the conjugation of surfactant micelles via base-pairing of complementary hydrophobic nucleosides. Base-pairs formed at the interface between micelles bring them into proximity with each other; and when the conjugated micelles contain a membrane protein, crystal nucleation centers can be stabilized, thereby promoting crystal growth. Accordingly, two hydrophobic nucleoside derivatives - deoxyguanosine (G) and deoxycytidine (C), each covalently bonded to a 10 carbon chain were synthesized and added to an aqueous solution containing octyl β-d-thioglucopyranoside micelles. These hydrophobic nucleosides induced the formation of oil-rich globules after 2days incubation at 19°C or after a few hours in the presence of ammonium sulfate; however, phase separation was inhibited by 100mM GMP. The presence of the membrane protein bacteriorhodopsin in the conjugated - micellar dispersion resulted in the growth within the colorless globules of a variety of purple crystals, the color indicating a functional protein. On this basis, we suggest that conjugation of micelles via base-pair complementarity may provide significant assistance to the structural determination of integral membrane proteins. PMID:27368128

  9. A comparison between finite element modeling and various thermographic non-destructive testing techniques for the quantification of the thermal integrity of macro-brush plasma facing components used in a tokamak.

    PubMed

    Pandya, Santosh P; Pandya, Shwetang N; Patil, Yashashri V; Krishnan, Deepu S; Murugesan, Menaka; Sharath, D; Singh, K Premjit; Khan, Md Shoaib; Arafat, M; Biju, N; Khirwadkar, Samir S; Govidarajan, Jagannathan; Venkatraman, B; Balasubramaniam, Krishnan

    2016-02-01

    The plasma facing components (PFCs) inside a tokamak are typically exposed to extremely high heat flux of the order of MW/m(2). The brazing quality between the plasma facing materials (PFMs) and the heat sink will determine the structural integrity and hence the effective service life of these PFCs. Suitable non-destructive testing (NDT) techniques for the pre-qualification of these components are thus essential to evaluate their structural integrity at various stages of their service life. Macro-brush type mockups of prototype PFCs with graphite as PFM have been inspected for their brazing quality using different active Infrared (IR)-thermographic NDT techniques. The results obtained from these techniques are compared and discussed. The brazing quality was quantified by establishing a comparison between the experimental results and the results from Finite Element Analysis (FEA). The percentage of contact between the PFM and the substrate was varied in FEA. FEA results when compared with experiments shows that tiles have different amounts of contact with the substrate ranging between 10% and 80%. PMID:26931878

  10. A comparison between finite element modeling and various thermographic non-destructive testing techniques for the quantification of the thermal integrity of macro-brush plasma facing components used in a tokamak

    NASA Astrophysics Data System (ADS)

    Pandya, Santosh P.; Pandya, Shwetang N.; Patil, Yashashri V.; Krishnan, Deepu S.; Murugesan, Menaka; Sharath, D.; Singh, K. Premjit; Khan, Md. Shoaib; Arafat, M.; Biju, N.; Khirwadkar, Samir S.; Govidarajan, Jagannathan; Venkatraman, B.; Balasubramaniam, Krishnan

    2016-02-01

    The plasma facing components (PFCs) inside a tokamak are typically exposed to extremely high heat flux of the order of MW/m2. The brazing quality between the plasma facing materials (PFMs) and the heat sink will determine the structural integrity and hence the effective service life of these PFCs. Suitable non-destructive testing (NDT) techniques for the pre-qualification of these components are thus essential to evaluate their structural integrity at various stages of their service life. Macro-brush type mockups of prototype PFCs with graphite as PFM have been inspected for their brazing quality using different active Infrared (IR)-thermographic NDT techniques. The results obtained from these techniques are compared and discussed. The brazing quality was quantified by establishing a comparison between the experimental results and the results from Finite Element Analysis (FEA). The percentage of contact between the PFM and the substrate was varied in FEA. FEA results when compared with experiments shows that tiles have different amounts of contact with the substrate ranging between 10% and 80%.

  11. A comparison between finite element modeling and various thermographic non-destructive testing techniques for the quantification of the thermal integrity of macro-brush plasma facing components used in a tokamak.

    PubMed

    Pandya, Santosh P; Pandya, Shwetang N; Patil, Yashashri V; Krishnan, Deepu S; Murugesan, Menaka; Sharath, D; Singh, K Premjit; Khan, Md Shoaib; Arafat, M; Biju, N; Khirwadkar, Samir S; Govidarajan, Jagannathan; Venkatraman, B; Balasubramaniam, Krishnan

    2016-02-01

    The plasma facing components (PFCs) inside a tokamak are typically exposed to extremely high heat flux of the order of MW/m(2). The brazing quality between the plasma facing materials (PFMs) and the heat sink will determine the structural integrity and hence the effective service life of these PFCs. Suitable non-destructive testing (NDT) techniques for the pre-qualification of these components are thus essential to evaluate their structural integrity at various stages of their service life. Macro-brush type mockups of prototype PFCs with graphite as PFM have been inspected for their brazing quality using different active Infrared (IR)-thermographic NDT techniques. The results obtained from these techniques are compared and discussed. The brazing quality was quantified by establishing a comparison between the experimental results and the results from Finite Element Analysis (FEA). The percentage of contact between the PFM and the substrate was varied in FEA. FEA results when compared with experiments shows that tiles have different amounts of contact with the substrate ranging between 10% and 80%.

  12. High power phase conjugated solid state lasers

    SciTech Connect

    Hackel, L.A.; Dane, C.B.; Zapata, L.E.; Hermann, M.R.

    1994-07-01

    Three laser systems that are being developed for use in x-ray generation which incorporate SBS phase conjugate mirrors are described. A 25J/pulse Nd:glass laser is being developed for commercial proximity print x-ray lithography; a 0.5J/pulse, 1.3 kHz pulse repetition frequency laser is being built for soft x-ray projection lithography; and a 1 kJ/pulse laser driver for a table top x-ray laser has been designed. The results of prototypical experimental investigations are presented and the basic design principles for high average power phase conjugated laser systems shared by each of these lasers are discussed.

  13. [Pneumococcal vaccines. New conjugate vaccines for adults].

    PubMed

    Campins Martí, Magda

    2015-11-01

    Pneumococcal infections are a significant cause of morbidity and mortality, and are one of the 10 leading causes of death worldwide. Children under 2 years have a higher incidence rate, followed by adults over 64 years. The main risk group are individuals with immunodeficiency, and those with anatomical or functional asplenia, but can also affect immunocompetent persons with certain chronic diseases. Significant progress has been made in the last 10 years in the prevention of these infections. Until a few years ago, only the 23-valent non-conjugate pneumococcal vaccine was available. Its results were controversial in terms of efficacy and effectiveness, and with serious limitations on the type of immune response induced. The current possibility of using the 13-valent conjugate vaccine in adults has led to greater expectations in improving the prevention of pneumococcal disease in these age groups.

  14. An immunosuppressive antibody-drug conjugate.

    PubMed

    Wang, Rongsheng E; Liu, Tao; Wang, Ying; Cao, Yu; Du, Jintang; Luo, Xiaozhou; Deshmukh, Vishal; Kim, Chan Hyuk; Lawson, Brian R; Tremblay, Matthew S; Young, Travis S; Kazane, Stephanie A; Wang, Feng; Schultz, Peter G

    2015-03-11

    We have developed a novel antibody-drug conjugate (ADC) that can selectively deliver the Lck inhibitor dasatinib to human T lymphocytes. This ADC is based on a humanized antibody that selectively binds with high affinity to CXCR4, an antigen that is selectively expressed on hematopoietic cells. The resulting dasatinib-antibody conjugate suppresses T-cell-receptor (TCR)-mediated T-cell activation and cytokine expression with low nM EC50 and has minimal effects on cell viability. This ADC may lead to a new class of selective immunosuppressive drugs with improved safety and extend the ADC strategy to the targeted delivery of kinase inhibitors for indications beyond oncology.

  15. STX-liposome conjugates as candidate vaccines.

    PubMed

    Uchida, Tetsuya

    2003-09-01

    Infection with Shiga toxin-producing (Stx) Escherichia coli (STEC) currently represents a serious public health problem due to its life-threatening complications: hemorrhagic colitis and hemolytic uremic syndrome. An inability to induce neutralizing antibody in response to primary STEC infection has been reported in STEC-infected humans. Therefore, active immunization with detoxified Stx to induce the production of neutralizing antibodies against Stx is currently an attractive option. Although this would not prevent the spread of infection, it would protect against death caused by cytotoxin-producing E. coli infection. Stx coupled with liposomes effectively induced protection against challenge with lethal doses of Stx in mice and in monkeys. Unique characteristics of antigen-liposome conjugates found in our investigations are reviewed, and the possible application of Stx-liposome conjugates in vaccines for the prevention of life-threatening systemic complications caused by STEC infection is discussed.

  16. Stereoselective Synthesis of Conjugated Fluoro Enynes

    PubMed Central

    Kumar, Rakesh; Zajc, Barbara

    2013-01-01

    Metalation-electrophilic fluorination of TMS- and TIPS-protected 1,3-benzothiazol-2-yl (BT) propargyl sulfones gave corresponding BT fluoropropargyl sulfones, Julia-Kocienski reagents for the synthesis of fluoro enynes. Both reagents reacted with aldehydes under mild DBU, or LHMDS-mediated conditions, giving high yields of conjugated fluoro enynes with E- stereoselectivity. In comparison to DBU-mediated reactions, stereoselectivity was higher in low-temperature LHMDS-mediated reactions. Two ketones were shown to react as well, using LHMDS as base. In situ removal of the TMS group gave terminal conjugated 2-fluoro 1,3-enynes. Synthetic utility of the fluoro enynes was demonstrated by conversion to internal alkynes and to stereoisomeric fluoro dienes via Sonogashira and Heck couplings. PMID:23005035

  17. Peptide conjugation: before or after nanoparticle formation?

    PubMed

    Valetti, Sabrina; Mura, Simona; Noiray, Magali; Arpicco, Silvia; Dosio, Franco; Vergnaud, Juliette; Desmaële, Didier; Stella, Barbara; Couvreur, Patrick

    2014-11-19

    We report herein a detailed study concerning the impact of different bioconjugation and nanoformulation strategies on the in vitro targeting ability of peptide-decorated squalenoyl gemcitabine (SQdFdC) nanoparticles (NPs). NPs have been functionalized with the CKAAKN peptide, previously identified as an efficient homing device within the pancreatic pathological microenvironment. Two approaches have been followed: (i) either the CKAAKN peptide was directly conjugated at the surface of preformed SQdFdC nanoparticles (conjugation after NP formation) or (ii) it was first reacted with a maleimide squalenoyl derivative before the resulting bioconjugate was co-nanoprecipitated with SQdFdC to form the peptide-decorated NPs (conjugation before NP formation). NPs were characterized with respect to mean diameter, zeta potential, and stability over time. Then, their specific interaction with the sFRP-4 protein was evaluated by surface plasmon resonance. Although both synthetic strategies allowed us to formulate NPs able to interact with the corresponding receptor, enhanced target binding and better specific avidity were observed with CKAAKN-NPs functionalized before NP formation. These NPs displayed the highest cell uptake and cytotoxicity in an in vitro model of human MIA Paca-2 pancreatic cancer cells.

  18. Oligonucleotide conjugates - Candidates for gene silencing therapeutics.

    PubMed

    Gooding, Matt; Malhotra, Meenakshi; Evans, James C; Darcy, Raphael; O'Driscoll, Caitriona M

    2016-10-01

    The potential therapeutic and diagnostic applications of oligonucleotides (ONs) have attracted great attention in recent years. The capability of ONs to selectively inhibit target genes through antisense and RNA interference mechanisms, without causing un-intended sideeffects has led them to be investigated for various biomedical applications, especially for the treatment of viral diseases and cancer. In recent years, many researchers have focused on enhancing the stability and target specificity of ONs by encapsulating/complexing them with polymers or lipid chains to formulate nanoparticles/nanocomplexes/micelles. Also, chemical modification of nucleic acids has emerged as an alternative to impart stability to ONs against nucleases and other degrading enzymes and proteins found in blood. In addition to chemically modifying the nucleic acids directly, another strategy that has emerged, involves conjugating polymers/peptide/aptamers/antibodies/proteins, preferably to the sense strand (3'end) of siRNAs. Conjugation to the siRNA not only enhances the stability and targeting specificity of the siRNA, but also allows for the development of self-administering siRNA formulations, with a much smaller size than what is usually observed for nanoparticle (∼200nm). This review concentrates mainly on approaches and studies involving ON-conjugates for biomedical applications. PMID:27521696

  19. RGD-Xyloside Conjugates Prime Glycosaminoglycans

    PubMed Central

    Tran, Vy M.; Victor, Xylophone V.; Yockman, James W.; Kuberan, Balagurunathan

    2010-01-01

    Glycosaminoglycans (GAG) play decisive roles in various cardio-vascular & cancer-associated processes. Changes in the expression of GAG fine structures, attributed to deregulation of their biosynthetic and catabolic enzymes, are hallmarks of vascular dysfunction and tumor progression. Wide spread role of GAG chains in blood clotting, wound healing and tumor biology has led to the development of modified GAG chains, GAG binding peptides and GAG based enzyme inhibitors as therapeutic agents. Xylosides, carrying hydrophobic aglycone, are known to induce GAG biosynthesis in various systems. Given the important roles of GAG chains in vascular and tumor biology, we envision that RGD-conjugated xylosides could be targeted to activated endothelial and cancer cells, which are known to express αvβ3 integrin, and thereby, modulate the pathological processes. To accomplish this vision, xylose residue was conjugated to linear and cyclic RGD containing peptides using click chemistry. Our results demonstrate that RGD-conjugated xylosides are able to prime GAG chains in various cell types, and future studies are aimed toward evaluating potential utility of such xylosides in treating myocardial infarction as well as cancer-associated thrombotic complications. PMID:20717719

  20. Oligonucleotide conjugates - Candidates for gene silencing therapeutics.

    PubMed

    Gooding, Matt; Malhotra, Meenakshi; Evans, James C; Darcy, Raphael; O'Driscoll, Caitriona M

    2016-10-01

    The potential therapeutic and diagnostic applications of oligonucleotides (ONs) have attracted great attention in recent years. The capability of ONs to selectively inhibit target genes through antisense and RNA interference mechanisms, without causing un-intended sideeffects has led them to be investigated for various biomedical applications, especially for the treatment of viral diseases and cancer. In recent years, many researchers have focused on enhancing the stability and target specificity of ONs by encapsulating/complexing them with polymers or lipid chains to formulate nanoparticles/nanocomplexes/micelles. Also, chemical modification of nucleic acids has emerged as an alternative to impart stability to ONs against nucleases and other degrading enzymes and proteins found in blood. In addition to chemically modifying the nucleic acids directly, another strategy that has emerged, involves conjugating polymers/peptide/aptamers/antibodies/proteins, preferably to the sense strand (3'end) of siRNAs. Conjugation to the siRNA not only enhances the stability and targeting specificity of the siRNA, but also allows for the development of self-administering siRNA formulations, with a much smaller size than what is usually observed for nanoparticle (∼200nm). This review concentrates mainly on approaches and studies involving ON-conjugates for biomedical applications.