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Sample records for integrating conjugative element

  1. The dualistic nature of integrative and conjugative elements

    PubMed Central

    Carraro, Nicolas; Burrus, Vincent

    2015-01-01

    Integrative and conjugative elements (ICEs) are mobile genetic elements that play a key role in bacterial adaptation. Such elements are found in almost every bacterial genera and species, and often code for adaptive traits conferring selective advantages to their host. ICEs maintain by integrating into and replicating along with a replicon of the host genome. ICEs can propagate by conjugative transfer toward a recipient cell following excision from the replicon as a circular covalently-closed molecule. For a long time, the excised form of ICEs was assumed to be non-replicative. This assumption predicts that excised ICEs are sensitive to loss during cell division, unless they carry stabilization systems such as addiction modules or antibiotic resistance genes. Over the past few years, growing evidence have been presented that support conditional replication of the circular intermediate as an intrinsic feature of ICEs. We recently confirmed this feature in the large family of SXT/R391 ICEs, which thrive in several species of Enterobacteriaceae and Vibrionaceae. Furthermore, we demonstrated that SXT/R391 ICEs encode a functional plasmid-like type II partition system that enhances their stability, such systems being probably encoded by other ICEs. The lifecycle of ICEs is therefore much more complex than initially thought as many ICEs may use plasmid-like features to improve their stability and dissemination. PMID:26942046

  2. 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

  3. Identification of host genes that affect acquisition of an integrative and conjugative element in Bacillus subtilis

    PubMed Central

    Johnson, Christopher M.; Grossman, Alan D.

    2014-01-01

    Summary Conjugation, a major type of horizontal gene transfer in bacteria, involves transfer of DNA from a donor to a recipient using donor-encoded conjugation machinery. Using a high throughput screen (Tn-seq), we identified genes in recipients that contribute to acquisition of the integrative and conjugative element ICEBs1 by Bacillus subtilis. We found that null mutations in some genes caused an increase, and others a decrease in conjugation efficiency. Some mutations affected conjugation only when present in recipients. Other mutations affected conjugation when present in donors or recipients. Most of the genes identified are known or predicted to affect the cell envelope. Several encode enzymes involved in phospholipid biosynthesis and one encodes a homolog of penicillin binding proteins. Two of the genes identified also affected conjugation of Tn916, indicating that their roles in conjugation may be general. We did not identify any genes in recipients that were essential for ICEBs1 conjugation, indicating that if there are such genes, then these are either essential for cell growth or redundant. Our results indicate that acquisition of ICEBs1, and perhaps other conjugative elements, is robust and not easily avoided by mutation and that several membrane-related functions affect the efficiency of conjugation. PMID:25069588

  4. 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

  5. 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

  6. A conserved helicase processivity factor is needed for conjugation and replication of an integrative and conjugative element.

    PubMed

    Thomas, Jacob; Lee, Catherine A; Grossman, Alan D

    2013-01-01

    Integrative and conjugative elements (ICEs) are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits, including antibiotic resistances. ICEs are found integrated in a host chromosome and can excise and transfer to recipient bacteria via conjugation. Conjugation involves nicking of the ICE origin of transfer (oriT) by the ICE-encoded relaxase and transfer of the nicked single strand of ICE DNA. For ICEBs1 of Bacillus subtilis, nicking of oriT by the ICEBs1 relaxase NicK also initiates rolling circle replication. This autonomous replication of ICEBs1 is critical for stability of the excised element in growing cells. We found a conserved and previously uncharacterized ICE gene that is required for conjugation and replication of ICEBs1. Our results indicate that this gene, helP (formerly ydcP), encodes a helicase processivity factor that enables the host-encoded helicase PcrA to unwind the double-stranded ICEBs1 DNA. HelP was required for both conjugation and replication of ICEBs1, and HelP and NicK were the only ICEBs1 proteins needed for replication from ICEBs1 oriT. Using chromatin immunoprecipitation, we measured association of HelP, NicK, PcrA, and the host-encoded single-strand DNA binding protein Ssb with ICEBs1. We found that NicK was required for association of HelP and PcrA with ICEBs1 DNA. HelP was required for association of PcrA and Ssb with ICEBs1 regions distal, but not proximal, to oriT, indicating that PcrA needs HelP to progress beyond nicked oriT and unwind ICEBs1. In vitro, HelP directly stimulated the helicase activity of the PcrA homologue UvrD. Our findings demonstrate that HelP is a helicase processivity factor needed for efficient unwinding of ICEBs1 for conjugation and replication. Homologues of HelP and PcrA-type helicases are encoded on many known and putative ICEs. We propose that these factors are essential for ICE conjugation, replication, and genetic stability. PMID:23326247

  7. A Conserved Helicase Processivity Factor Is Needed for Conjugation and Replication of an Integrative and Conjugative Element

    PubMed Central

    Thomas, Jacob; Lee, Catherine A.; Grossman, Alan D.

    2013-01-01

    Integrative and conjugative elements (ICEs) are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits, including antibiotic resistances. ICEs are found integrated in a host chromosome and can excise and transfer to recipient bacteria via conjugation. Conjugation involves nicking of the ICE origin of transfer (oriT) by the ICE–encoded relaxase and transfer of the nicked single strand of ICE DNA. For ICEBs1 of Bacillus subtilis, nicking of oriT by the ICEBs1 relaxase NicK also initiates rolling circle replication. This autonomous replication of ICEBs1 is critical for stability of the excised element in growing cells. We found a conserved and previously uncharacterized ICE gene that is required for conjugation and replication of ICEBs1. Our results indicate that this gene, helP (formerly ydcP), encodes a helicase processivity factor that enables the host-encoded helicase PcrA to unwind the double-stranded ICEBs1 DNA. HelP was required for both conjugation and replication of ICEBs1, and HelP and NicK were the only ICEBs1 proteins needed for replication from ICEBs1 oriT. Using chromatin immunoprecipitation, we measured association of HelP, NicK, PcrA, and the host-encoded single-strand DNA binding protein Ssb with ICEBs1. We found that NicK was required for association of HelP and PcrA with ICEBs1 DNA. HelP was required for association of PcrA and Ssb with ICEBs1 regions distal, but not proximal, to oriT, indicating that PcrA needs HelP to progress beyond nicked oriT and unwind ICEBs1. In vitro, HelP directly stimulated the helicase activity of the PcrA homologue UvrD. Our findings demonstrate that HelP is a helicase processivity factor needed for efficient unwinding of ICEBs1 for conjugation and replication. Homologues of HelP and PcrA-type helicases are encoded on many known and putative ICEs. We propose that these factors are essential for ICE conjugation, replication, and genetic stability. PMID:23326247

  8. Selective pressures to maintain attachment site specificity of integrative and conjugative elements.

    PubMed

    Menard, Kayla L; Grossman, Alan D

    2013-01-01

    Integrative and conjugative elements (ICEs) are widespread mobile genetic elements that are usually found integrated in bacterial chromosomes. They are important agents of evolution and contribute to the acquisition of new traits, including antibiotic resistances. ICEs can excise from the chromosome and transfer to recipients by conjugation. Many ICEs are site-specific in that they integrate preferentially into a primary attachment site in the bacterial genome. Site-specific ICEs can also integrate into secondary locations, particularly if the primary site is absent. However, little is known about the consequences of integration of ICEs into alternative attachment sites or what drives the apparent maintenance and prevalence of the many ICEs that use a single attachment site. Using ICEBs1, a site-specific ICE from Bacillus subtilis that integrates into a tRNA gene, we found that integration into secondary sites was detrimental to both ICEBs1 and the host cell. Excision of ICEBs1 from secondary sites was impaired either partially or completely, limiting the spread of ICEBs1. Furthermore, induction of ICEBs1 gene expression caused a substantial drop in proliferation and cell viability within three hours. This drop was dependent on rolling circle replication of ICEBs1 that was unable to excise from the chromosome. Together, these detrimental effects provide selective pressure against the survival and dissemination of ICEs that have integrated into alternative sites and may explain the maintenance of site-specific integration for many ICEs. PMID:23874222

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. Identification of a Single Strand Origin of Replication in the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis

    PubMed Central

    Wright, Laurel D.; Johnson, Christopher M.; Grossman, Alan D.

    2015-01-01

    We identified a functional single strand origin of replication (sso) in the integrative and conjugative element ICEBs1 of Bacillus subtilis. Integrative and conjugative elements (ICEs, also known as conjugative transposons) are DNA elements typically found integrated into a bacterial chromosome where they are transmitted to daughter cells by chromosomal replication and cell division. Under certain conditions, ICEs become activated and excise from the host chromosome and can transfer to neighboring cells via the element-encoded conjugation machinery. Activated ICEBs1 undergoes autonomous rolling circle replication that is needed for the maintenance of the excised element in growing and dividing cells. Rolling circle replication, used by many plasmids and phages, generates single-stranded DNA (ssDNA). In many cases, the presence of an sso enhances the conversion of the ssDNA to double-stranded DNA (dsDNA) by enabling priming of synthesis of the second DNA strand. We initially identified sso1 in ICEBs1 based on sequence similarity to the sso of an RCR plasmid. Several functional assays confirmed Sso activity. Genetic analyses indicated that ICEBs1 uses sso1 and at least one other region for second strand DNA synthesis. We found that Sso activity was important for two key aspects of the ICEBs1 lifecycle: 1) maintenance of the plasmid form of ICEBs1 in cells after excision from the chromosome, and 2) stable acquisition of ICEBs1 following transfer to a new host. We identified sequences similar to known plasmid sso's in several other ICEs. Together, our results indicate that many other ICEs contain at least one single strand origin of replication, that these ICEs likely undergo autonomous replication, and that replication contributes to the stability and spread of these elements. PMID:26440206

  15. Conjugal Transfer of Polychlorinated Biphenyl/Biphenyl Degradation Genes in Acidovorax sp. Strain KKS102, Which Are Located on an Integrative and Conjugative Element

    PubMed Central

    Ishibashi, Yoko; Naganawa, Hideaki; Hirokawa, Satoshi; Atobe, Satomi; Nagata, Yuji; Tsuda, Masataka

    2012-01-01

    A polychlorinated biphenyl (PCB)/biphenyl degradation gene cluster in Acidovorax sp. strain KKS102, which is very similar to that in Tn4371 from Cupriavidus oxalaticus A5, was transferred to several proteobacterial strains by conjugation. The mobilized DNA fragment consisted of 61,807 bp and carried genes for mating-pair formation (mpf), DNA transfer (dtr), integrase (int), and replication-partition proteins (rep-parAB). In the transconjugants, transferred DNA was integrated at ATTGCATCAG or similar sequences. The circular-form integrative and conjugative element (ICE) was detected by PCR, and quantitative PCR analyses revealed that, in KKS102 cells, the ratio of the circular form to the integrated form was very low (approximately 10−5). The circular form was not detected in a mutant of the int gene, which was located at the extreme left and transcribed in the inward direction, and the level of int transcriptional activity was much higher in the circular form than in the integrated form. These findings clearly demonstrated that the genes for PCB/biphenyl degradation in KKS102 cells are located on an ICE, which was named ICEKKS1024677. Comparisons of similar ICE-like elements collected from the public database suggested that those of beta- and gammaproteobacteria were distinguishable from other ICE-like elements, including those in alphaproteobacteria, with respect to the gene composition and gene organization. PMID:22685277

  16. 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

  17. Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner.

    PubMed

    Carraro, Nicolas; Poulin, Dominique; Burrus, Vincent

    2015-06-01

    Integrative and Conjugative Elements (ICEs) of the SXT/R391 family disseminate multidrug resistance among pathogenic Gammaproteobacteria such as Vibrio cholerae. SXT/R391 ICEs are mobile genetic elements that reside in the chromosome of their host and eventually self-transfer to other bacteria by conjugation. Conjugative transfer of SXT/R391 ICEs involves a transient extrachromosomal circular plasmid-like form that is thought to be the substrate for single-stranded DNA translocation to the recipient cell through the mating pore. This plasmid-like form is thought to be non-replicative and is consequently expected to be highly unstable. We report here that the ICE R391 of Providencia rettgeri is impervious to loss upon cell division. We have investigated the genetic determinants contributing to R391 stability. First, we found that a hipAB-like toxin/antitoxin system improves R391 stability as its deletion resulted in a tenfold increase of R391 loss. Because hipAB is not a conserved feature of SXT/R391 ICEs, we sought for alternative and conserved stabilization mechanisms. We found that conjugation itself does not stabilize R391 as deletion of traG, which abolishes conjugative transfer, did not influence the frequency of loss. However, deletion of either the relaxase-encoding gene traI or the origin of transfer (oriT) led to a dramatic increase of R391 loss correlated with a copy number decrease of its plasmid-like form. This observation suggests that replication initiated at oriT by TraI is essential not only for conjugative transfer but also for stabilization of SXT/R391 ICEs. Finally, we uncovered srpMRC, a conserved locus coding for two proteins distantly related to the type II (actin-type ATPase) parMRC partitioning system of plasmid R1. R391 and plasmid stabilization assays demonstrate that srpMRC is active and contributes to reducing R391 loss. While partitioning systems usually stabilizes low-copy plasmids, srpMRC is the first to be reported that stabilizes a

  18. Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner

    PubMed Central

    Carraro, Nicolas; Poulin, Dominique; Burrus, Vincent

    2015-01-01

    Integrative and Conjugative Elements (ICEs) of the SXT/R391 family disseminate multidrug resistance among pathogenic Gammaproteobacteria such as Vibrio cholerae. SXT/R391 ICEs are mobile genetic elements that reside in the chromosome of their host and eventually self-transfer to other bacteria by conjugation. Conjugative transfer of SXT/R391 ICEs involves a transient extrachromosomal circular plasmid-like form that is thought to be the substrate for single-stranded DNA translocation to the recipient cell through the mating pore. This plasmid-like form is thought to be non-replicative and is consequently expected to be highly unstable. We report here that the ICE R391 of Providencia rettgeri is impervious to loss upon cell division. We have investigated the genetic determinants contributing to R391 stability. First, we found that a hipAB-like toxin/antitoxin system improves R391 stability as its deletion resulted in a tenfold increase of R391 loss. Because hipAB is not a conserved feature of SXT/R391 ICEs, we sought for alternative and conserved stabilization mechanisms. We found that conjugation itself does not stabilize R391 as deletion of traG, which abolishes conjugative transfer, did not influence the frequency of loss. However, deletion of either the relaxase-encoding gene traI or the origin of transfer (oriT) led to a dramatic increase of R391 loss correlated with a copy number decrease of its plasmid-like form. This observation suggests that replication initiated at oriT by TraI is essential not only for conjugative transfer but also for stabilization of SXT/R391 ICEs. Finally, we uncovered srpMRC, a conserved locus coding for two proteins distantly related to the type II (actin-type ATPase) parMRC partitioning system of plasmid R1. R391 and plasmid stabilization assays demonstrate that srpMRC is active and contributes to reducing R391 loss. While partitioning systems usually stabilizes low-copy plasmids, srpMRC is the first to be reported that stabilizes a

  19. 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.; Consortium, the BRaDP1T

    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

  20. Analysis of Streptococcus agalactiae pan-genome for prevalence, diversity and functionality of integrative and conjugative or mobilizable elements integrated in the tRNA(Lys CTT) gene.

    PubMed

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

    2015-10-01

    Streptococcus agalactiae is the first cause of invasive infections in human neonates and is also a major bovine and fish pathogen. High genomic diversity was observed in this species that hosts numerous mobile genetic elements, in particular elements transferable by conjugation. This works aims to evaluate the contribution of these elements to GBS genome diversity. Focusing on genomic islands integrated in the tRNA(Lys) (CTT) gene, a known hotspot of recombination, an extensive in silico search was performed on the sequenced genome of 303 strains of S. agalactiae isolated from different hosts. In all the isolates (except 9), whatever their origin (human, bovine, camel, dog, gray seal, dolphin, fish species or bullfrog), this locus carries highly diverse genomic islands transferable by conjugation such as integrative and conjugative elements (ICEs), integrative and mobilizable elements (IMEs), CIs-mobilizable elements (CIMEs) or composite elements. Transfer of an ICE from an ST67 bovine strain to a phylogenetically distant ST23 human isolate was obtained experimentally indicating that there was no barrier to ICE transfer between strains from different hosts. Interestingly, a novel family of putative IMEs that site-specifically integrate in the nic site of oriT of ICEs belonging to Tn916/ICESt3 superfamily was detected in silico. These elements carry an antibiotic resistance gene (lsa(C)) already described to confer cross-resistance to lincosamides, streptogramins A and pleuromutilins. Further work is needed to evaluate the impact of these IMEs on the transfer of targeted ICEs and the mobility and the dissemination of these IMEs. PMID:25832353

  1. 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

  2. Comparison of SXT and R391, two conjugative integrating elements: definition of a genetic backbone for the mobilization of resistance determinants.

    PubMed

    Beaber, J W; Burrus, V; Hochhut, B; Waldor, M K

    2002-12-01

    The SXT element (SXT) is becoming an increasingly prevalent vector for the dissemination of antibiotic resistances in Vibrio cholerae. SXT is a member of a larger family of elements, formerly defined as IncJ plasmids, that are self-transmissible by conjugation and integrate site-specifically into the host chromosome. Comparison of the DNA sequences of SXT and R391, an IncJ element from Providencia rettgeri, indicate that these elements consist of a conserved backbone that mediates the regulation, excision/integration and conjugative transfer of the elements. Both elements have insertions into this backbone that either confer the element-specific properties or are of unknown function. Interestingly, the conserved SXT and R391 backbone apparently contains hotspots for insertion of additional DNA sequences. This backbone represents a scaffold for the mobilization of genetic material between a wide range of gram-negative bacteria, allowing for rapid adaptation to changing environments. PMID:12568332

  3. A new large-DNA-fragment delivery system based on integrase activity from an integrative and conjugative element.

    PubMed

    Miyazaki, Ryo; van der Meer, Jan Roelof

    2013-07-01

    During the past few decades, numerous plasmid vectors have been developed for cloning, gene expression analysis, and genetic engineering. Cloning procedures typically rely on PCR amplification, DNA fragment restriction digestion, recovery, and ligation, but increasingly, procedures are being developed to assemble large synthetic DNAs. In this study, we developed a new gene delivery system using the integrase activity of an integrative and conjugative element (ICE). The advantage of the integrase-based delivery is that it can stably introduce a large DNA fragment (at least 75 kb) into one or more specific sites (the gene for glycine-accepting tRNA) on a target chromosome. Integrase recombination activity in Escherichia coli is kept low by using a synthetic hybrid promoter, which, however, is unleashed in the final target host, forcing the integration of the construct. Upon integration, the system is again silenced. Two variants with different genetic features were produced, one in the form of a cloning vector in E. coli and the other as a mini-transposable element by which large DNA constructs assembled in E. coli can be tagged with the integrase gene. We confirmed that the system could successfully introduce cosmid and bacterial artificial chromosome (BAC) DNAs from E. coli into the chromosome of Pseudomonas putida in a site-specific manner. The integrase delivery system works in concert with existing vector systems and could thus be a powerful tool for synthetic constructions of new metabolic pathways in a variety of host bacteria. PMID:23686268

  4. 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

  5. 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

    2016-03-01

    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 sequences of

  6. Antigen I/II encoded by integrative and conjugative elements of Streptococcus agalactiae and role in biofilm formation.

    PubMed

    Chuzeville, Sarah; Dramsi, Shaynoor; Madec, Jean-Yves; Haenni, Marisa; Payot, Sophie

    2015-11-01

    Streptococcus agalactiae (i.e. Group B streptococcus, GBS) is a major human and animal pathogen. Genes encoding putative surface proteins and in particular an antigen I/II have been identified on Integrative and Conjugative Elements (ICEs) found in GBS. Antigens I/II are multimodal adhesins promoting colonization of the oral cavity by streptococci such as Streptococcus gordonii and Streptococcus mutans. The prevalence and diversity of antigens I/II in GBS were studied by a bioinformatic analysis. It revealed that antigens I/II, which are acquired by horizontal transfer via ICEs, exhibit diversity and are widespread in GBS, in particular in the serotype Ia/ST23 invasive strains. This study aimed at characterizing the impact on GBS biology of proteins encoded by a previously characterized ICE of S. agalactiae (ICE_515_tRNA(Lys)). The production and surface exposition of the antigen I/II encoded by this ICE was examined using RT-PCR and immunoblotting experiments. Surface proteins of ICE_515_tRNA(Lys) were found to contribute to GBS biofilm formation and to fibrinogen binding. Contribution of antigen I/II encoded by SAL_2056 to biofilm formation was also demonstrated. These results highlight the potential for ICEs to spread microbial adhesins between species. PMID:26232503

  7. 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

  8. 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

  9. 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

  10. Diverse regulatory circuits for transfer of conjugative elements.

    PubMed

    Singh, Praveen K; Meijer, Wilfried J J

    2014-09-01

    Conjugation systems are present on many plasmids as well as on chromosomally integrated elements. Conjugation, which is a major route by which bacteria exchange genetic material, is a complex and energy-consuming process. Hence, a shared feature of conjugation systems is that expression of the genes involved is strictly controlled in such a way that conjugation is kept in a default 'OFF' state and that the process is switched on only under conditions that favor the transfer of the conjugative element into a recipient cell. However, there is a remarkable diversity in the way by which conjugation genes present on different transferable elements are regulated. Here, we review these diverse regulatory circuits on the basis of several prototypes with a special focus on the recently discovered regulation of the conjugation genes present on the native Bacillus subtilis plasmid pLS20. PMID:24995588

  11. Characterization of the Integration and Modular Excision of the Integrative Conjugative Element PAISt in Streptomyces turgidiscabies Car8

    PubMed Central

    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

  12. 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

  13. 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. PMID:26522159

  14. 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.

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

    PubMed

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

    2013-01-01

    In this study, we characterize 18 cultivable bacteria associated within the mucus of the coral Fungia echinata from Andaman Sea, India. 16S rRNA gene sequence analysis showed that all the 18 strains isolated in this study from the coral mucus belong to the group Gammaproteobacteria and majority of them were identified as Vibrio core group. Our objective was to investigate the presence of the SXT/R391 integrating conjugative elements (ICEs) targeting integrase int(SXT) and SXT Hotspot IV genetic elements in these isolates. SXT/ICE initially reported in Vibrio cholerae contains many antibiotic and heavy metal resistance genes and acts as an effective tool for the horizontal transfer of resistance genes in other bacterial populations. Two of our strains, AN44 and AN60, were resistant to sulfamethoxazole, trimethoprim, chloramphenicol, and streptomycin, in addition to other antibiotics such as neomycin, ampicillin, rifampicin, and tetracycline. Using PCR followed by sequencing, we detected the SXT/ICE in these strains. The SXT integrase genes of AN44 and AN60 had a 99% and 100% identity with V. cholerae serogroup O139 strain SG24. This study provides the first evidence of the presence of SXT/R391 ICEs in Marinomonas sp. strain AN44 (JCM 18476(T) ) and Vibrio fortis strain AN60 (DSM 26067(T) ) isolated from the mucus of the coral F. echinata. PMID:23083057

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

    PubMed Central

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

    2014-01-01

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

  17. An Operon of Three Transcriptional Regulators Controls Horizontal Gene Transfer of the Integrative and Conjugative Element ICEclc in Pseudomonas knackmussii B13

    PubMed Central

    Pradervand, Nicolas; Sulser, Sandra; Delavat, François; Miyazaki, Ryo; Lamas, Iker; van der Meer, Jan Roelof

    2014-01-01

    The integrative and conjugative element ICEclc is a mobile genetic element in Pseudomonas knackmussii B13, and an experimental model for a widely distributed group of elements in Proteobacteria. ICEclc is transferred from specialized transfer competent cells, which arise at a frequency of 3-5% in a population at stationary phase. Very little is known about the different factors that control the transfer frequency of this ICE family. Here we report the discovery of a three-gene operon encoded by ICEclc, which exerts global control on transfer initiation. The operon consists of three consecutive regulatory genes, encoding a TetR-type repressor MfsR, a MarR-type regulator and a LysR-type activator TciR. We show that MfsR autoregulates expression of the operon, whereas TciR is a global activator of ICEclc gene expression, but no clear role was yet found for MarR. Deletion of mfsR increases expression of tciR and marR, causing the proportion of transfer competent cells to reach almost 100% and transfer frequencies to approach 1 per donor. mfsR deletion also caused a two orders of magnitude loss in population viability, individual cell growth arrest and loss of ICEclc. This indicates that autoregulation is an important feature maintaining ICE transfer but avoiding fitness loss. Bioinformatic analysis showed that the mfsR-marR-tciR operon is unique for ICEclc and a few highly related ICE, whereas tciR orthologues occur more widely in a large variety of suspected ICE among Proteobacteria. PMID:24945944

  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. PMID:27215217

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

    PubMed

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

    2016-01-01

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

  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. Ordering the bestiary of genetic elements transmissible by conjugation

    PubMed Central

    Garcillán-Barcia, Maria Pilar; de la Cruz, Fernando

    2013-01-01

    Phylogenetic reconstruction of three highly conserved proteins involved in bacterial conjugation (relaxase, coupling protein and a type IV secretion system ATPase) allowed the classification of transmissible elements in relaxase MOB families and mating pair formation MPF groups. These evolutionary studies point to the existence of a limited number of module combinations in transmissible elements, preferentially associated with specific genetic or environmental backgrounds. A practical protocol based on the MOB classification was implemented to detect and assort transmissible plasmids and integrative elements from γ-Proteobacteria. It was called “Degenerate Primer MOB Typing” or DPMT. It resulted in a powerful technique that discovers not only backbones related to previously classified elements (typically by PCR-based replicon typing or PBRT), but also distant new members sharing a common evolutionary ancestor. The DPMT method, conjointly with PBRT, promises to be useful to gain information on plasmid backbones and helpful to investigate the dissemination routes of transmissible elements in microbial ecosystems. PMID:23734300

  3. 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.

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

    PubMed Central

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

    2013-01-01

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

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. Characterization of a novel integrative element, ICESt1, in the lactic acid bacterium Streptococcus thermophilus.

    PubMed

    Burrus, V; Roussel, Y; Decaris, B; Guédon, G

    2000-04-01

    The 35.5-kb ICESt1 element of Streptococcus thermophilus CNRZ368 is bordered by a 27-bp repeat and integrated into the 3' end of a gene encoding a putative fructose-1,6-biphosphate aldolase. This element encodes site-specific integrase and excisionase enzymes related to those of conjugative transposons Tn5276 and Tn5252. The integrase was found to be involved in a site-specific excision of a circular form. ICESt1 also encodes putative conjugative transfer proteins related to those of the conjugative transposon Tn916. Therefore, ICESt1 could be or could be derived from an integrative conjugative element. PMID:10742276

  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. PMID:22607168

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

    PubMed

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

    2016-07-01

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

  12. 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.

  13. 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.

  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. The presence of conjugative transposon Tn916 in the recipient strain does not impede transfer of a second copy of the element.

    PubMed Central

    Norgren, M; Scott, J R

    1991-01-01

    Transfer of the conjugative transposon Tn916 from the chromosome of Bacillus subtilis to a transposon-free Streptococcus pyogenes strain occurs at the same frequency as transfer to a Tn916-containing recipient. This rules out a model for conjugal transfer of Tn916 in which a copy of the element in the recipient represses transposition of a copy introduced by conjugation. Homology-directed integration of the incoming transposon into the resident one is less frequent than insertion elsewhere in the chromosome. This shows that after conjugation, transposition occurs more frequently than homologous recombination. However, because transconjugants arising from homologous recombination can be selected, it is possible to use Tn916 as a shuttle for gram-positive organisms for which there is no easy means of introducing DNA. Images PMID:1846138

  16. 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

  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. Microfluidic bioassay system based on microarrays of hydrogel sensing elements entrapping quantum dot-enzyme conjugates.

    PubMed

    Jang, Eunji; Kim, Sinyoung; Koh, Won-Gun

    2012-01-15

    This paper presents a simple method to fabricate a microfluidic biosensor that is able to detect substrates for H(2)O(2)-generating oxidase. The biosensor consists of three components (quantum dot-enzyme conjugates, hydrogel microstructures, and a set of microchannels) that were hierarchically integrated into a microfluidic device. The quantum dot (QD)-enzyme conjugates were entrapped within the poly(ethylene glycol) (PEG)-based hydrogel microstructures that were fabricated within the microchannels by a photopatterning process. Glucose oxidase (GOX) and alcohol oxidase (AOX) were chosen as the model oxidase enzymes, conjugated to carboxyl-terminated CdSe/ZnS QDs, and entrapped within the hydrogel microstructures, which resulted in a fluorescent hydrogel microarray that was responsive to glucose or alcohol. The hydrogel-entrapped GOX and AOX were able to perform enzyme-catalyzed oxidation of glucose and alcohol, respectively, to produce H(2)O(2), which subsequently quenched the fluorescence of the conjugated QDs. The fluorescence intensity of the hydrogel microstructures decreased as the glucose and alcohol concentrations increased, and the detection limits of this system were found to be 50 μM of glucose and 70 μM of alcohol. Because each microchannel was able to carry out different assays independently, the simultaneous detection of glucose and alcohol was possible using our novel microfluidic device composed of multiple microchannels. PMID:22177543

  19. 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

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

    PubMed

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

    2015-11-01

    Bacitracins are mixtures of structurally related cyclic polypeptides with antibiotic properties. They act by interfering with the biosynthesis of the bacterial cell wall. In this study, we analyzed an avian necrotic enteritis strain of Clostridium perfringens that was resistant to bacitracin and produced NetB toxin. We identified a bacitracin resistance locus that resembled a bacitracin resistance determinant from Enterococcus faecalis. It contained the structural genes bcrABD and a putative regulatory gene, bcrR. Mutagenesis studies provided evidence that both bcrA and bcrB are essential for bacitracin resistance, and that evidence was supported by the results of experiments in which the introduction of both the bcrA and bcrB genes into a bacitracin-susceptible C. perfringens strain was required to confer bacitracin resistance. The wild-type strain was shown to contain at least three large, putatively conjugative plasmids, and the bcrRABD locus was localized to an 89.7-kb plasmid, pJIR4150. This plasmid was experimentally shown to be conjugative and was sequenced. The sequence revealed that it also carries a tpeL toxin gene and is related to the pCW3 family of conjugative antibiotic resistance and toxin plasmids from C. perfringens. The bcr genes were located on a genetic element, ICECp1, which is related to the Tn916 family of integrative conjugative elements (ICEs). ICECp1 appears to be the first Tn916-like element shown to confer bacitracin resistance. In summary, we identified in a toxin-producing C. perfringens strain a novel mobile bacitracin resistance element which was experimentally shown to be essential for bacitracin resistance and is carried by a putative ICE located on a conjugative plasmid. PMID:26282424

  1. 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.

  2. Improving performance of optical phase conjugation by splitting the nonlinear element.

    PubMed

    Morshed, Monir; Lowery, Arthur J; Du, Liang B

    2013-02-25

    We show that optical phase conjugation (OPC) based on third order nonlinear effects for mid-span spectral inversion (MSSI) can be improved by splitting the nonlinear element into two parts and adding an optical filter between them. This band-stop filter suppresses the cross-phase-modulation products that are generated around the pump, which, if not removed, will be shifted to fall around the output OPC signal band. Numerical simulations show that this method reduces the fundamental limitations introduced by OPC by 3 dB, which results in improvement of the maximum signal quality, Qmax, by 1 dB in a 10 × 80-km 4-QAM 224-Gb/s CO-OFDM system with MSSI. PMID:23481990

  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. 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.

  5. Integrated finite element model of composite materials

    NASA Astrophysics Data System (ADS)

    Teply, Jan L.; Herbein, William C.

    1989-05-01

    Two problems traditionally addressed in the area of micromechanics of composite materials can be briefly summarized as follows: (1) for a macroscopically uniform volume of composite material, which is subjected to macroscopically uniform boundary tractions, displacements or heat influx, find overall thermomechanical properties in terms of the thermomechanical properties of the individual constituents; and (2) for the same material volume and boundary conditions as above, find the local stress, strain, and temperature fields in the constituents and on the interfaces. Two different types of micromechanical models are usually applied to the solutions of these two types of problems. For linear elastic materials, the micromechanical models to solve problem (1) offer simple solutions of overall thermomechanical properties either in terms of bound which are derived from periodic or random microstructures, or in terms of single estimates, which are derived from a solution of an isolated inclusion. The finite element variational approaches are applied to integrate the solutions of problems (1) and (2) into one model. The application of displacement and equilibrium variational approaches to the calculation of overall elastic-plastic properties, are extended to the solution of the second problem. The integrated model is then applied to calculate the overall properties and local stress and strain fields of boron-aluminum composites subjected to transverse tension, in-plane shear and bending.

  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. International Space Station Multi-Element Integrated Test

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

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

  8. 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

  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 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.

  10. 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

  11. 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.

  12. Treatment of domain integrals in boundary element methods

    SciTech Connect

    Nintcheu Fata, Sylvain

    2012-01-01

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

  13. 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.

  14. 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

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

    PubMed Central

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

    2007-01-01

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

  16. Fundamental Studies on Donor-acceptor Conjugated Polymers Containing 'Heavy' Group 14 and Group 16 Elements

    NASA Astrophysics Data System (ADS)

    Gibson, Gregory Laird

    One advantage of conjugated polymers as organic materials is that their properties may be readily tuned through covalent modifications. This thesis presents studies on the structure-property relationships resulting from single- and double-atom substitutions on an alternating donor-acceptor conjugated polymer. Specifically, single selenium and tellurium atoms have been incorporated into the acceptor monomer in place of sulfur; silicon and germanium atoms have been substituted in place of carbon at the donor monomer bridge position. The carbon-donor/ tellurium-acceptor polymer was synthesized by a post-polymerization reaction sequence and demonstrated the utility of heavy group 16 atoms to red shift a polymer absorption spectrum. Density functional theory calculations point to a new explanation for this result invoking the lower heavy atom ionization energy and reduced aromaticity of acceptor monomers containing selenium and tellurium compared to sulfur. Absorption and emission experiments demonstrate that both silicon and germanium substitutions in the donor slightly blue shift the polymer absorption spectrum. Polymers containing sulfur in the acceptor are the strongest light absorbers of all polymers studied here. Molecular weight and phenyl end capping studies show that molecular weight appears to affect polymer absorption to the greatest degree in a medium molecular weight regime and that these effects have a significant aggregation component. Solar cell devices containing either the silicon- or germanium-donor/selenium-acceptor polymer display improved red light harvesting or hole mobility relative to their structural analogues. Overall, these results clarify the effects of single atom substitution on donor-acceptor polymers and aid in the future design of polymers containing heavy atoms.

  17. The finite element method: Is weighted volume integration essential?

    NASA Astrophysics Data System (ADS)

    Narasimhan, T. N.

    In developing finite element equations for steady state and transient diffusion-type processes, weighted volume integration is generally assumed to be an intrinsic requirement. It is shown that such finite element equations can be developed directly and with ease on the basis of the elementary notion of a surface integral. Although weighted volume integration is mathematically correct, the algebraic equations stemming from it are no more informative than those derived directly on the basis of a surface integral. An interesting upshot is that the derivation based on surface integration does not require knowledge of a partial differential equation but yet is logically rigorous. It is commonly stated that weighted volume integration of the differential equation helps one carry out analyses of errors, convergence and existence, and therefore, weighted volume integration is preferable. It is suggested that because the direct derivation is logically consistent, numerical solutions emanating from it must be testable for accuracy and internal consistency in ways that the style of which may differ from the classical procedures of error- and convergence-analysis. In addition to simplifying the teaching of the finite element method, the thoughts presented in this paper may lead to establishing the finite element method independently in its own right, rather than it being a surrogate of the differential equation. The purpose of this paper is not to espouse any one particular way of formulating the finite element equations. Rather, it is one of introspection. The desire is to critically examine our traditional way of doing things and inquire whether alternate approaches may reveal to us new and interesting insights.

  18. 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.

  19. 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.

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

    NASA Technical Reports Server (NTRS)

    Janin, G.; Bond, V. R.

    1981-01-01

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

  1. Elements of an advanced integrated operator control station

    SciTech Connect

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

    1984-01-01

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

  2. Elements of an advanced integrated operator control station

    SciTech Connect

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

    1984-01-01

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

  3. 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

  4. Integration of narrow-host-range vectors from Escherichia coli into the genomes of amino acid-producing corynebacteria after intergeneric conjugation.

    PubMed Central

    Mateos, L M; Schäfer, A; Kalinowski, J; Martin, J F; Pühler, A

    1996-01-01

    Conjugative transfer of mobilizable derivatives of the Escherichia coli narrow-host-range plasmids pBR322, pBR325, pACYC177, and pACYC184 from E. coli to species of the gram-positive genera Corynebacterium and Brevibacterium resulted in the integration of the plasmids into the genomes of the recipient bacteria. Transconjugants appeared at low frequencies and reproducibly with a delay of 2 to 3 days compared with matings with replicative vectors. Southern analysis of corynebacterial transconjugants and nucleotide sequences from insertion sites revealed that integration occurs at different locations and that different parts of the vector are involved in the process. Integration is not dependent on indigenous insertion sequence elements but results from recombination between very short homologous DNA segments (8 to 12 bp) present in the vector and in the host DNA. In the majority of the cases (90%), integration led to cointegrate formation, and in some cases, deletions or rearrangements occurred during the recombination event. Insertions were found to be quite stable even in the absence of selective pressure. PMID:8824624

  5. Optimal low-order fully integrated solid-shell elements

    NASA Astrophysics Data System (ADS)

    Rah, K.; Paepegem, W. Van; Habraken, A. M.; Degrieck, J.; de Sousa, R. J. Alves; Valente, R. A. F.

    2013-03-01

    This paper presents three optimal low-order fully integrated geometrically nonlinear solid-shell elements based on the enhanced assumed strain (EAS) method and the assumed natural strain method for different types of structural analyses, e.g. analysis of thin homogeneous isotropic and multilayer anisotropic composite shell-like structures and the analysis of (near) incompressible materials. The proposed solid-shell elements possess eight nodes with only displacement degrees of freedom and a few internal EAS parameters. Due to the 3D geometric description of the proposed elements, 3D constitutive laws can directly be employed in these formulations. The present formulations are based on the well-known Fraeijs de Veubeke-Hu-Washizu multifield variational principle. In terms of accuracy as well as efficiency point of view, the choice of the optimal EAS parameters plays a very critical role in the EAS method, therefore a systematic numerical study has been carried out to find out the optimal EAS parameters to alleviate different locking phenomena for the proposed solid-shell formulations. To assess the accuracy of the proposed solid-shell elements, a variety of popular numerical benchmark examples related to element convergence, mesh distortions, element aspect ratios and different locking phenomena are investigated and the results are compared with the well-known solid-shell formulations available in the literature. The results of our numerical assessment show that the proposed solid-shell formulations provide very accurate results, without showing any numerical problems, for a variety of geometrically linear and nonlinear structural problems.

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 49 CFR 192.1007 - What are the required elements of an integrity management plan?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 3 2010-10-01 2010-10-01 false What are the required elements of an integrity... 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...

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

    NASA Technical Reports Server (NTRS)

    Abdul-Aziz, Ali; Baaklini, George Y.

    2001-01-01

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

  12. An integrated approach for enhanced protein conjugation and capture with viral nanotemplates and hydrogel microparticle platforms via rapid bioorthogonal reactions.

    PubMed

    Jung, Sukwon; Yi, Hyunmin

    2014-07-01

    We demonstrate significantly enhanced protein conjugation and target protein capture capacity by exploiting tobacco mosaic virus (TMV) templates assembled with hydrogel microparticles. Protein conjugation results with a red fluorescent protein R-Phycoerythrin (R-PE) show significantly enhanced protein conjugation capacity of TMV-assembled particles (TMV-particles) compared to planar substrates or hydrogel microparticles. In-depth examination of protein conjugation kinetics via tetrazine (Tz)-trans-cyclooctene (TCO) cycloaddition and strain-promoted alkyne-azide cycloaddition (SPAAC) reaction demonstrates that TMV-particles provide a less hindered environment for protein conjugation. Target protein capture results using an anti-R-PE antibody (R-Ab)-R-PE pair also show substantially improved capture capacity of R-Ab conjugated TMV-particles over R-Ab conjugated hydrogel microparticles. We further demonstrate readily controlled protein and antibody conjugation capacity by simply varying TMV concentrations, which show negligible negative impact of densely assembled TMVs on protein conjugation and capture capacity. Combined, these results illustrate a facile postfabrication protein conjugation approach with TMV templates assembled onto hydrogel microparticles for improved and controlled protein conjugation and sensing platforms. We anticipate that our approach can be readily applied to various protein sensing applications. PMID:24937661

  13. A CAD Approach to Integrating NDE With Finite Element

    NASA Technical Reports Server (NTRS)

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

    2004-01-01

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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 49 CFR 192.1007 - What are the required elements of an integrity management plan?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 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...

  1. 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. PMID:22955616

  2. 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

  3. 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.

  4. Finite element methodology for integrated flow-thermal-structural analysis

    NASA Technical Reports Server (NTRS)

    Thornton, Earl A.; Ramakrishnan, R.; Vemaganti, G. R.

    1988-01-01

    Papers entitled, An Adaptive Finite Element Procedure for Compressible Flows and Strong Viscous-Inviscid Interactions, and An Adaptive Remeshing Method for Finite Element Thermal Analysis, were presented at the June 27 to 29, 1988, meeting of the AIAA Thermophysics, Plasma Dynamics and Lasers Conference, San Antonio, Texas. The papers describe research work supported under NASA/Langley Research Grant NsG-1321, and are submitted in fulfillment of the progress report requirement on the grant for the period ending February 29, 1988.

  5. 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

  6. 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.

  7. 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.

  8. Multiple Roles for Enterococcus faecalis Glycosyltransferases in Biofilm-Associated Antibiotic Resistance, Cell Envelope Integrity, and Conjugative Transfer

    PubMed Central

    Dale, Jennifer L.; Cagnazzo, Julian; Phan, Chi Q.; Barnes, Aaron M. T.

    2015-01-01

    The emergence of multidrug-resistant bacteria and the limited availability of new antibiotics are of increasing clinical concern. A compounding factor is the ability of microorganisms to form biofilms (communities of cells encased in a protective extracellular matrix) that are intrinsically resistant to antibiotics. Enterococcus faecalis is an opportunistic pathogen that readily forms biofilms and also has the propensity to acquire resistance determinants via horizontal gene transfer. There is intense interest in the genetic basis for intrinsic and acquired antibiotic resistance in E. faecalis, since clinical isolates exhibiting resistance to multiple antibiotics are not uncommon. We performed a genetic screen using a library of transposon (Tn) mutants to identify E. faecalis biofilm-associated antibiotic resistance determinants. Five Tn mutants formed wild-type biofilms in the absence of antibiotics but produced decreased biofilm biomass in the presence of antibiotic concentrations that were subinhibitory to the parent strain. Genetic determinants responsible for biofilm-associated antibiotic resistance include components of the quorum-sensing system (fsrA, fsrC, and gelE) and two glycosyltransferase (GTF) genes (epaI and epaOX). We also found that the GTFs play additional roles in E. faecalis resistance to detergent and bile salts, maintenance of cell envelope integrity, determination of cell shape, polysaccharide composition, and conjugative transfer of the pheromone-inducible plasmid pCF10. The epaOX gene is located in a variable extended region of the enterococcal polysaccharide antigen (epa) locus. These data illustrate the importance of GTFs in E. faecalis adaptation to diverse growth conditions and suggest new targets for antimicrobial design. PMID:25918141

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

  11. 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.

  12. 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.

  13. An Imbricate Finite Element Method (I-FEM) using full, reduced, and smoothed integration

    NASA Astrophysics Data System (ADS)

    Cazes, Fabien; Meschke, Günther

    2013-11-01

    A method to design finite elements that imbricate with each other while being assembled, denoted as imbricate finite element method, is proposed to improve the smoothness and the accuracy of the approximation based upon low order elements. Although these imbricate elements rely on triangular meshes, the approximation stems from the shape functions of bilinear quadrilateral elements. These elements satisfy the standard requirements of the finite element method: continuity, delta function property, and partition of unity. The convergence of the proposed approximation is investigated by means of two numerical benchmark problems comparing three different schemes for the numerical integration including a cell-based smoothed FEM based on a quadratic shape of the elements edges. The method is compared to related existing methods.

  14. 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).

  15. 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.

  16. Computer-integrated finite element modeling of human middle ear.

    PubMed

    Sun, Q; Gan, R Z; Chang, K-H; Dormer, K J

    2002-10-01

    The objective of this study was to produce an improved finite element (FE) model of the human middle ear and to compare the model with human data. We began with a systematic and accurate geometric modeling technique for reconstructing the middle ear from serial sections of a freshly frozen temporal bone. A geometric model of a human middle ear was constructed in a computer-aided design (CAD) environment with particular attention to geometry and microanatomy. Using the geometric model, a working FE model of the human middle ear was created using previously published material properties of middle ear components. This working FE model was finalized by a cross-calibration technique, comparing its predicted stapes footplate displacements with laser Doppler interferometry measurements from fresh temporal bones. The final FE model was shown to be reasonable in predicting the ossicular mechanics of the human middle ear. PMID:14595544

  17. Analysis of sequences flanking the vap regions of Dichelobacter nodosus: evidence for multiple integration events, a killer system, and a new genetic element.

    PubMed

    Bloomfield, G A; Whittle, G; McDonagh, M B; Katz, M E; Cheetham, B F

    1997-02-01

    Dichelobacter nodosus is the causative agent of ovine footrot. The vap regions of the D. nodosus genome may have arisen by the integration of a genetic element and may have a role in virulence. The virulent D. nodosus strain A198 has multiple copies of the vap regions. In the present study, sequences to the left and right of vap regions 1, 2 and 3 of strain A198 were analysed by Southern blotting and DNa sequencing. The results suggest that vap regions 1 and 2 rose by independent integration events into different tRNA genes. The discovery of a second integrase gene (intB), a gene with similarity to bacteriophage repressor proteins (regA), and a gene similar to an ORF from a conjugative transposon (gepA), suggests that a second genetic element, either a bacteriophage or a conjugative transposon, is integrated next to vap region 3 in the D. nodosus genome. The arrangement of intB and the vap regions in three other virulent strains and one benign strain was determined using using Southern blotting and PCR. One strain, H1215, contained vapE' and not vapE, and thus resembles vap region 3, suggesting that vap region 3 also may have arisen by an independent integration event. In all strains, a copy of intB was found next to the vap regions. The vap regions contain two genes, vapA and toxA, with similarity to the hig genes of the killer plasmid Rts1. Evidence is presented that vapA and toxA have a similar function in D. nodosus. PMID:9043132

  18. Polybutylcyanoacrylate nanoparticles for delivering hormone response element-conjugated neurotrophin-3 to the brain of intracerebral hemorrhagic rats.

    PubMed

    Chung, Chiu-Yen; Yang, Jen-Tsung; Kuo, Yung-Chih

    2013-12-01

    Hypertensive intracerebral hemorrhage (ICH) is a rapidly evolutional pathology, inducing necrotic cell death followed by apoptosis, and alters gene expression levels in surrounding tissue of an injured brain. For ICH therapy by controlled gene release, the development of intravenously administrable delivery vectors to promote the penetration across the blood-brain barrier (BBB) is a critical challenge. To enhance transfer efficiency of genetic materials under hypoxic conditions, polybutylcyanoacrylate (PBCA) nanoparticles (NPs) were used to mediate the intracellular transport of plasmid neurotrophin-3 (NT-3) containing hormone response element (HRE) with a cytomegalovirus (cmv) promoter and to differentiate induced pluripotent stem cells (iPSCs). The differentiation ability of iPSCs to neurons was justified by various immunological stains for protein fluorescence. The effect of PBCA NP/cmvNT-3-HRE complexes on treating ICH rats was studied by immunostaining, western blotting and Nissl staining. We found that the treatments with PBCA NP/cmvNT-3-HRE complexes increased the capability of differentiating iPSCs to express NT-3, TrkC and MAP-2. Moreover, PBCA NPs could protect cmvNT-3-HRE against degradation with EcoRI/PstI and DNase I in vitro and raise the delivery across the BBB in vivo. The administration of PBCA NP/cmvNT-3-HRE complexes increased the expression of NT-3, inhibited the expression of apoptosis-inducing factor, cleaved caspase-3 and DNA fragmentation, and reduced the cell death rate after ICH in vivo. PBCA NPs are demonstrated as an appropriate delivery system for carrying cmvNT-3-HRE to the brain for ICH therapy. PMID:24034503

  19. 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.

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

    PubMed

    Kurashige, Yuki; Nakajima, Takahito; Hirao, Kimihiko

    2007-04-14

    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 alpha-helix chains and three-dimensional diamond pieces. PMID:17444700

  1. 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.

  2. Effect of cis-9,trans-11 and trans-10,cis-12 isomers of conjugated linoleic acid on the integrity and functionality of cryopreserved bovine spermatozoa.

    PubMed

    Soares, Marcio Pereira; Brandelli, Adriano; Celeghini, Eneiva Carla Carvalho; de Arruda, Rubens Paes; Rodriguez, Shirley Andrea Florez

    2013-08-01

    Plasma membranes of sperm subjected to low temperatures undergo changes in their structure and permeability. The addition of fatty acids in semen cryopreservation media may influence the sperm motility after thawing, possibly by maintaining the membrane fluidity due to their incorporation in lipid bilayers. In this work, different concentrations of the isomers cis-9,trans-11 and trans-10,cis-12 of conjugated linoleic acid (CLA) were added in the cryopreservation medium of bovine sperm. Four Jersey bulls were used, and the ejaculates were processed as a pool. The Tris-based extender (Dilutris®) was supplemented with 20% egg yolk (MB). The treatments with CLA (Luta-CLA®), which had oily presentation, were prepared from MB with addition of 1% sodium lauryl sulfate, and denominated MBL. The concentrations of CLA tested were 50, 100, and 150 μM. The motility characteristics of the post-thaw semen were analyzed by computerized analysis system (CASA), and plasma membrane integrity and acrosomal and mitochondrial function assessed by the association of the fluorescent probes propidium iodide, fluorescein isothiocyanate-conjugated Pisum sativum agglutinin (FITC-PSA), JC-1 and Hoechst 33342. No significant differences were observed among treatments, excepting for a decreased mitochondrial potential of cells treated with 150 μM CLA. The addition of CLA, at the concentrations used, showed no advantages on the integrity and functionality of bovine sperm submitted to cryopreservation. PMID:23721967

  3. 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.

  4. 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'.

  5. 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.

  6. 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.

  7. 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.

  8. Temporally and spatially integrated elemental analysis algorithm for low-pressure micro-LIBS measurements

    SciTech Connect

    Mungas, Greg

    2007-07-01

    Microscopic laser-induced breakdown spectroscopy (micro-LIBS) is a promising measurement technique for determining the relative elemental abundances of microscopic spots. Currently, the predominant source of measurement accuracy errors for micro-LIBS is shown to be based on a constant plasma temperature assumption. To reduce these measurement errors particularly in low-pressure applications (i.e.,extraterrestrial environments), a mathematical data analysis algorithm is presented that utilizes the many linear independent emission lines per element to estimate the time-integrated state of the plasma in the form of a plasma state matrix coupled with a vector of relative elemental abundances in the observed emission.

  9. 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.

  10. 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.

  11. Viewing angle enhancement of an integral imaging display using Bragg mismatched reconstruction of holographic optical elements.

    PubMed

    Lee, Seungjae; Jang, Changwon; Cho, Jaebum; Yeom, Jiwoon; Jeong, Jinsoo; Lee, Byoungho

    2016-01-20

    Holographic-optical-element (HOE)-based integral imaging display can be applied to augmented reality. However, a narrow viewing angle is a bottleneck for commercialization. Here, we propose a method to enhance the viewing angle of the integral imaging display using Bragg mismatched reconstruction of HOEs. The viewing angle of the integral imaging display can be enlarged with two probe waves, which form two different viewing zones. The effect of Bragg mismatched reconstruction is analyzed with simulation and experiment. In order to show feasibility of the proposed method, a display experiment is demonstrated. PMID:26835963

  12. 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.

  13. 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.

  14. Fully Integrated EAS-Based Solid-Shell Finite Elements in Implicit Sheet Metal Forming Simulations

    SciTech Connect

    Valente, R.A. Fontes; Cardoso, R.P.R.; Alves de Sousa, R.J.; Parente, M.P.L.; Jorge, R.M. Natal

    2005-08-05

    In this communication sheet metal forming problems are analyzed with the Finite Element Method and a fully-integrated solid-shell element, based on the Enhanced Assumed Strain (EAS) method. Among the solid-shell element's distinguish features, it should be mentioned the solely use of the EAS approach in dealing with either transverse and volumetric-based locking pathologies, thus avoiding the inclusion of other mixed methods into the formulation. The adopted methodology is then able to successfully deal with small thickness shell problems within the incompressible range, aspects commonly appearing in sheet metal forming modeling with solid elements.Simulations of this type of forming processes are mainly solved resorting to membrane and shell-type finite elements, included in explicit commercial programs. Nevertheless, the presented solid-shell formulation, within a fully implicit approach, provides reliable solutions when compared to experimental results. It is also worth mentioning that the present solid-shell formulation encompasses a minimum set of enhancing strain variables, if compared to other fully integrated hexahedral finite elements in the literature.In order to assess the performance of the presented formulation, the S-Rail Forming problem of an aluminum alloy is described and analyzed, with the results being compared to experimental and numerical simulation data.

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  16. 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.

  17. 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.

  18. piggyBac-based insertional mutagenesis in the presence of stably integrated P elements in Drosophila.

    PubMed

    Hacker, Udo; Nystedt, Sverker; Barmchi, Mojgan Padash; Horn, Carsten; Wimmer, Ernst A

    2003-06-24

    P element-mediated mutagenesis has been used to disrupt an estimated 25% of genes essential for Drosophila adult viability. Mutation of all genes in the fly genome, however, poses a problem, because P elements show significant hotspots of integration. In addition, advanced screening scenarios often require the use of P element-based tools like the generation of germ-line mosaics using FLP recombinase-mediated recombination or gene misexpression using the UAS/Gal4 system. These techniques are P element-based and can therefore not be combined with the use of P elements as mutagenic agents. To circumvent these limitations, we have developed an insertional mutagenesis system using non-P element transposons. An enhanced yellow fluorescent protein-marked piggyBac-based mutator element was mobilized by a piggyBac specific transposase source expressed from a Hermes-based jump-starter transposon marked with enhanced cyan fluorescent protein. In a pilot screen, we have generated 798 piggyBac insertions on FRT bearing third chromosomes of which 9% have sustained a putatively piggyBac-related lethal hit. The FRTs present on the target chromosome remained stably integrated during the screen and could subsequently be used to generate germ-line clones associated with maternal and zygotic phenotypes. PCR-based analysis of insertion loci shows that 57% of the insertions are in genes for which no P element insertions have been reported. Our data demonstrate the potential of this technique to facilitate the quest for saturation mutagenesis of the Drosophila genome. The system is Drosophila nonspecific and potentially applicable in a broad spectrum of nonmodel organisms. PMID:12802016

  19. Finite Element Analysis Of An Axially Moving Beam, Part I: Time Integration

    NASA Astrophysics Data System (ADS)

    Stylianou, M.; Tabarrok, B.

    1994-12-01

    Axially moving materials arise in problems associated with spacecraft antennas, pipes conveying fluid and telescopic robotic manipulators. Axially moving beams are a special class of axially moving materials, in which the axially moving material is modelled as a slender beam and the mechanism of elastic deformation is transverse bending. The mass of this system is not constant and the general analytical solution to the equation of motion is not known. In this study, numerical solutions are obtained using finite element analysis. However, instead of following the obvious (but cumbersome) approach of using fixed-size elements and increasing their number, in a step-wise fashion, as mass elements enter the domain of interest, a more elegant approach is followed wherein the number of elements is fixed, while the sizes of the elements change with time. To this end, a variable-domain beam finite element the size of which is a prescribed function of time is formulated in Part I. The accuracy of this variable-domain beam element is demonstrated through the time-integration of equations of motion using various extrusion profiles. The effects of wall flexibility, tip mass, and high frequency axial motion perturbations to the transverse response of the flexible extendible beam are also examined.

  20. Autonomous plasmid-like replication of a conjugative transposon

    PubMed Central

    Lee, Catherine A.; Babic, Ana; Grossman, Alan D.

    2010-01-01

    Summary Integrative and conjugative elements (ICEs), a.k.a. conjugative transposons, are mobile genetic elements involved in many biological processes, including pathogenesis, symbiosis, and the spread of antibiotic resistance. Unlike conjugative plasmids that are extra-chromosomal and replicate autonomously, ICEs are integrated in the chromosome and replicate passively during chromosomal replication. It is generally thought that ICEs do not replicate autonomously. We found that when induced, Bacillus subtilis ICEBs1 undergoes autonomous plasmid-like replication. Replication was unidirectional, initiated from the ICEBs1 origin of transfer, oriT, and required the ICEBs1-encoded relaxase NicK. Replication also required several host proteins needed for chromosomal replication, but did not require the replicative helicase DnaC or the helicase loader protein DnaB. Rather, replication of ICEBs1 required the helicase PcrA that is required for rolling circle replication of many plasmids. Transfer of ICEBs1 from the donor required PcrA, but did not require replication, indicating that PcrA, and not DNA replication, facilitates unwinding of ICEBs1 DNA for horizontal transfer. Although not needed for horizontal transfer, replication of ICEBs1 was needed for stability of the element. We propose that autonomous plasmid-like replication is a common property of ICEs and contributes to the stability and maintenance of these mobile genetic elements in bacterial populations. PMID:19943900

  1. 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

  2. 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

  3. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

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

  5. Optimization of acoustic liners by the hybrid finite element-integral approach

    NASA Technical Reports Server (NTRS)

    Sigman, R. K.; Horowitz, S. J.; Zinn, B. T.

    1983-01-01

    An iterative solution technique for predicting the sound field radiated from a turbofan inlet is used to predict the optimum inlet acoustic liner. The analytical approach divides the sound field 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. A continuous solution is obtained by matching the finite element and integral solutions at the interface between the two regions. Using a trial and error scheme, this analytical procedure is used to calculate the impedance value of the duct liner which will produce a minimum sound pressure level in the far field. Several examples of straight and non-uniform ducts with and without flow are presented.

  6. Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces.

    PubMed

    Bardhan, Jaydeep P; Altman, Michael D; Willis, David J; Lippow, Shaun M; Tidor, Bruce; White, Jacob K

    2007-07-01

    Surface formulations of biophysical modeling problems offer attractive theoretical and computational properties. Numerical simulations based on these formulations usually begin with discretization of the surface under consideration; often, the surface is curved, possessing complicated structure and possibly singularities. Numerical simulations commonly are based on approximate, rather than exact, discretizations of these surfaces. To assess the strength of the dependence of simulation accuracy on the fidelity of surface representation, here methods were developed to model several important surface formulations using exact surface discretizations. Following and refining Zauhar's work [J. Comput.-Aided Mol. Des. 9, 149 (1995)], two classes of curved elements were defined that can exactly discretize the van der Waals, solvent-accessible, and solvent-excluded (molecular) surfaces. Numerical integration techniques are presented that can accurately evaluate nonsingular and singular integrals over these curved surfaces. After validating the exactness of the surface discretizations and demonstrating the correctness of the presented integration methods, a set of calculations are presented that compare the accuracy of approximate, planar-triangle-based discretizations and exact, curved-element-based simulations of surface-generalized-Born (sGB), surface-continuum van der Waals (scvdW), and boundary-element method (BEM) electrostatics problems. Results demonstrate that continuum electrostatic calculations with BEM using curved elements, piecewise-constant basis functions, and centroid collocation are nearly ten times more accurate than planar-triangle BEM for basis sets of comparable size. The sGB and scvdW calculations give exceptional accuracy even for the coarsest obtainable discretized surfaces. The extra accuracy is attributed to the exact representation of the solute-solvent interface; in contrast, commonly used planar-triangle discretizations can only offer improved

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

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

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

  8. 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.

  9. Finite element numerical integration for first order approximations on multi- and many-core architectures

    NASA Astrophysics Data System (ADS)

    Banaś, Krzysztof; Krużel, Filip; Bielański, Jan

    2016-06-01

    The paper presents investigations on the implementation and performance of the finite element numerical integration algorithm for first order approximations and three processor architectures, popular in scientific computing, classical CPU, Intel Xeon Phi and NVIDIA Kepler GPU. A unifying programming model and portable OpenCL implementation is considered for all architectures. Variations of the algorithm due to different problems solved and different element types are investigated and several optimizations aimed at proper optimization and mapping of the algorithm to computer architectures are demonstrated. Performance models of execution are developed for different processors and tested in practical experiments. The results show the varying levels of performance for different architectures, but indicate that the algorithm can be effectively ported to all of them. The general conclusion is that the finite element numerical integration can achieve sufficient performance on different multi- and many-core architectures and should not become a performance bottleneck for finite element simulation codes. Specific observations lead to practical advises on how to optimize the kernels and what performance can be expected for the tested architectures.

  10. The Bacteroides mobilizable transposon Tn4555 integrates by a site-specific recombination mechanism similar to that of the gram-positive bacterial element Tn916.

    PubMed Central

    Tribble, G D; Parker, A C; Smith, C J

    1997-01-01

    The Bacteroides mobilizable transposon Tn4555 is a 12.2-kb molecule that encodes resistance to cefoxitin. Conjugal transposition is hypothesized to occur via a circular intermediate and is stimulated by coresident tetracycline resistance elements and low levels of tetracycline. In this work, the ends of the transposon were identified and found to consist of 12-bp imperfect inverted repeats, with an extra base at one end. In the circular form, the ends were separated by a 6-bp "coupling sequence" which was associated with either the left or the right transposon terminus when the transposon was inserted into the chromosome. Tn4555 does not duplicate its target site upon insertion. Using a conjugation-based transposition assay, we showed that the coupling sequence originated from 6 bases of genomic DNA flanking either side of the transposon prior to excision. Tn4555 preferentially transposed into a 589-bp genomic locus containing a 207-bp direct repeat. Integration occurred before or after the repeated sequence, with one integration site between the two repeats. These observations are consistent with a transposition model based on site-specific recombination. In the bacteriophage lambda model for site-specific recombination, the bacteriophage recombines with the Escherichia coli chromosome via a 7-bp "crossover" region. We propose that the coupling sequence of Tn4555 is analogous in function to the crossover region of lambda but that unlike the situation in lambda, recombination occurs between regions of nonhomologous DNA. This ability to recombine into divergent target sites is also a feature of the gram-positive bacterial transposon Tn916. PMID:9098073

  11. 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

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

    PubMed

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

    2014-01-01

    This study examined the reliability and validity of the structural section of the Ayres Sensory Integration® Fidelity Measure© (ASIFM), which provides a method for monitoring the extent to which an intervention was implemented as conceptualized in studies of occupational therapy using sensory integration intervention methods (OT-SI). We examined the structural elements of the measure, including content of assessment reports, availability of specific equipment and adequate space, safety monitoring, and integration of communication with parents and other team members, such as collaborative goal setting with parents or family and teacher education, into the intervention program. Analysis of self-report ratings by 259 occupational therapists from 185 different facilities indicated that the structural section of the ASIFM has acceptable interrater reliability (r ≥ .82) and significantly differentiates between settings in which therapists reportedly do and do not practice OT-SI (p < .001). PMID:25184462

  13. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Tantrabandit, Manop

    2014-06-01

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

  16. 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

  17. Fabrication of an integrated holographic imaging element for a three-dimensional eye-gaze detection system.

    PubMed

    Zhou, Minniu; Matoba, Osamu; Kitagawa, Yoichi; Takizawa, Yukako; Matsumoto, Tetsuya; Ueda, Hideaki; Mizuno, Akio; Kosaka, Nobuyuki

    2010-07-01

    We evaluate the imaging characteristics of an integrated optical imaging element that is used to obtain images from opposite directions in one imaging sensor for a three-dimensional eye-gaze detection system. The element consists of a transmission-type holographic imaging element, a reflection-type holographic imaging element, and a noise reduction filter. In the evaluation of the imaging characteristics, modulation transfer functions of both the reflection-type and the transmission-type holographic imaging elements are evaluated. Results indicate that both holographic imaging elements have enough resolution, even under white-light illumination conditions, for eye-gaze detection. We also demonstrate the simultaneous detection of images by an artificial eye and objects by using the integrated element under white light or sunlight. PMID:20648147

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

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

    PubMed

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

    2016-08-20

    The α-glucosidase inhibitor acarbose is used for treatment of diabetes mellitus type II, and is manufactured industrially with overproducing derivatives of Actinoplanes sp. SE50/110, reportedly obtained by conventional mutagenesis. Despite of high industrial significance, only limited information exists regarding acarbose metabolism, function and regulation of these processes, due to the absence of proper genetic engineering methods and tools developed for this strain. Here, a basic toolkit for genetic engineering of Actinoplanes sp. SE50/110 was developed, comprising a standardized protocol for a DNA transfer through Escherichia coli-Actinoplanes intergeneric conjugation and applied for the transfer of ϕC31, ϕBT1 and VWB actinophage-based integrative vectors. Integration sites, occurring once per genome for all vectors, were sequenced and characterized for the first time in Actinoplanes sp. SE50/110. Notably, in case of ϕC31 based vector pSET152, the integration site is highly conserved, while for ϕBT1 and the VWB based vectors pRT801 and pSOK804, respectively, no sequence similarities to those in other bacteria were detected. The studied plasmids were proven to be stable and neutral with respect to strain morphology and acarbose production, enabling future use for genetic manipulations of Actinoplanes sp. SE50/110. To further broaden the spectrum of available tools, a GUS reporter system, based on the pSET152 derived vector, was also established in Actinoplanes sp. SE50/110. PMID:27181842

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

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2016-01-01

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

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

    PubMed

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

    2012-01-01

    Computational modeling offers versatility, scalability, and cost advantages to researchers in the trauma and injury biomechanics communities. The Global Human Body Models Consortium (GHBMC) is a group of government, industry, and academic researchers developing human body models (HBMs) that aim to become the standard tool to meet this growing research need. The objective of this study is to present the methods used to develop the average seated male occupant model (M50, weight = 78 kg, height = 175 cm) from five separately validated body region models (BRMs). BRMs include the head, neck, thorax, abdomen, and a combined pelvis and lower extremity model. Modeling domains were split at the atlanto-occipital joint, C7-T1 boundary, diaphragm, abdominal cavity (peritoneum/retroperitoneum), and the acetabulum respectively. BRM meshes are based on a custom CAD model of the seated male built from a multi-modality imaging protocol of a volunteer subject found in literature.[1] Various meshing techniques were used to integrate the full body model (FBM) including 1-D beam and discrete element connections (e.g. ligamentous structures), 2D shell nodal connections (e.g. inferior vena cava to right atrium), 3D hexahedral nodal connections (e.g. soft tissue envelope connections between regions), and contact definitions varying from tied (muscle insertions) to sliding (liver and diaphragm contact). The model was developed in a general-purpose finite element code, LS-Dyna (LTSC, Livermore, CA) R4.2.1., and consists of 1.95 million elements and 1.3 million nodes. The element breakdown by type is 41% hexahedral, 33.7% tetrahedral, 19.5% quad shells and 5% tria shell. The integration methodology presented highlights the viability of using a collaborative development paradigm for the construction of HBMs, and will be used as template for expanding the suite of GHBMC models. PMID:22846315

  9. 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

  10. Time-resolved and time-integrated radiography of fast reactor fuel elements

    SciTech Connect

    De Volpi, A.

    1981-01-01

    The fast-reactor safety program has some unusual requirements in radiography. Applications may be divided into two areas: time-resolved or time-integrated radiography. The fast-neutron hodoscope has supplied all recent time-resolved cineradiographic in-pile fuel-motion data, and various x-ray and photographic techniques have been used for out-of-pile experiments. Thick containers and the large number of radioactive fuel pins involved in safety research have been responsible for some nonconventional applications of time-integrated radiography of stationary objects. Hodoscopes record fuel-motion during transient experiments at the TREAT reactor in the United States and CABRI in France. Other special techniques have been under development for out-of-pile nondestructive radiography of fuel element subassemblies, including fast-neutron and gamma-ray tomographic methods.

  11. 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

  12. Seamless integration of global Dirichlet-to-Neumann boundary condition and spectral elements for transformation electromagnetics

    NASA Astrophysics Data System (ADS)

    Yang, Zhiguo; Wang, Li-Lian; Rong, Zhijian; Wang, Bo; Zhang, Baile

    2016-04-01

    In this paper, we present an efficient spectral-element method (SEM) for solving general two-dimensional Helmholtz equations in anisotropic media, with particular applications in accurate simulation of polygonal invisibility cloaks, concentrators and circular rotators arisen from the field of transformation electromagnetics (TE). In practice, we adopt a transparent boundary condition (TBC) characterized by the Dirichlet-to-Neumann (DtN) map to reduce wave propagation in an unbounded domain to a bounded domain. We then introduce a semi-analytic technique to integrate the global TBC with local curvilinear elements seamlessly, which is accomplished by using a novel elemental mapping and analytic formulas for evaluating global Fourier coefficients on spectral-element grids exactly. From the perspective of TE, an invisibility cloak is devised by a singular coordinate transformation of Maxwell's equations that leads to anisotropic materials coating the cloaked region to render any object inside invisible to observers outside. An important issue resides in the imposition of appropriate conditions at the outer boundary of the cloaked region, i.e., cloaking boundary conditions (CBCs), in order to achieve perfect invisibility. Following the spirit of [48], we propose new CBCs for polygonal invisibility cloaks from the essential "pole" conditions related to singular transformations. This allows for the decoupling of the governing equations of inside and outside the cloaked regions. With this efficient spectral-element solver at our disposal, we can study the interesting phenomena when some defects and lossy or dispersive media are placed in the cloaking layer of an ideal polygonal cloak.

  13. The role of size constancy for the integration of local elements into a global shape

    PubMed Central

    Rennig, Johannes; Karnath, Hans-Otto; Huberle, Elisabeth

    2013-01-01

    Visual perception depends on the visual context and is likely to be influenced by size constancy, which predicts a size and distance invariant perception of objects. However, size constancy can also result in optical illusions that allow the manipulation of the perceived size. We thus asked whether the integration of local elements into a global object can be influenced by manipulations of the visual context and size constancy? A set of stimuli was applied in healthy individuals that took advantage of the “Kanizsa” illusion, in which three circles with open wedges oriented toward a center point are placed to form an illusionary perception of a triangle. In addition, a 3D-perspective view was implemented in which the global target (“Kanizsa” triangle) was placed in combination with several distractor circles either in a close or a distant position. Subjects were engaged in a global recognition task on the location of the “Kanizsa” triangle. Global recognition of “Kanizsa” triangles improved with a decreasing length of the illusory contour. Interestingly, recognition of “Kanizsa” triangles decreased when they were perceived as if they were located further away. We conclude that the integration of local elements into a global object is dependent on the visual context and dominated by size constancy. PMID:23840187

  14. Femtosecond laser fabrication of hybrid micro-optical elements and their integration on the fiber tip

    NASA Astrophysics Data System (ADS)

    Malinauskas, Mangirdas; Gilbergs, Holger; Zukauskas, Albertas; Belazaras, Kastytis; Purlys, Vytautas; Rutkauskas, Marius; Bickauskaite, Gabija; Momot, Andrej; Paipulas, Domas; Gadonas, Roaldas; Juodkazis, Saulius; Piskarskas, Algis

    2010-05-01

    Femtosecond laser photo-polymerization of zirconium-silicon based sol-gel photopolymer SZ2080 is used to fabricate micro-optical elements with a single and hybrid optical functions. We demonstrate photo-polymerization of the solid immersion and Fresnel lenses. Gratings can be added onto the surface of lenses. The effective refractive index of polymerized structures can be controlled via the volume fraction of polymer. We used woodpile structure with volume fraction of 0.65-0.8. Tailoring of dispersion properties of micro-optical elements by changing filling ratio of polymer are discussed. Direct write approach is used to form such structures on a cover glass and on the tip of an optical fiber. Close matching of refractive indices between the polymer and substrate in visible and near infra red spectral regions (nSZ2080 = 1.504, nglass = 1.52) is favorable for such integration. The surface roughness of laser-polymerized resits was ~30 nm (min-max value), which is acceptable for optical applications in the visible range. For the bulk micro-optical elements the efficiency of 3D laser polymerization is increased by a factor ~ (2 - 4) × 102 times (depends on the design) by the shell-formation polymerization: (i) contour scanning for definition of shell-surface, (ii) development for removal of nonfunctional resist, and (iii) UV exposure for the final volumetric polymerization of an enclosed volume.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. Integrative network-based approach identifies key genetic elements in breast invasive carcinoma

    PubMed Central

    2015-01-01

    Background Breast cancer is a genetically heterogeneous type of cancer that belongs to the most prevalent types with a high mortality rate. Treatment and prognosis of breast cancer would profit largely from a correct classification and identification of genetic key drivers and major determinants driving the tumorigenesis process. In the light of the availability of tumor genomic and epigenomic data from different sources and experiments, new integrative approaches are needed to boost the probability of identifying such genetic key drivers. We present here an integrative network-based approach that is able to associate regulatory network interactions with the development of breast carcinoma by integrating information from gene expression, DNA methylation, miRNA expression, and somatic mutation datasets. Results Our results showed strong association between regulatory elements from different data sources in terms of the mutual regulatory influence and genomic proximity. By analyzing different types of regulatory interactions, TF-gene, miRNA-mRNA, and proximity analysis of somatic variants, we identified 106 genes, 68 miRNAs, and 9 mutations that are candidate drivers of oncogenic processes in breast cancer. Moreover, we unraveled regulatory interactions among these key drivers and the other elements in the breast cancer network. Intriguingly, about one third of the identified driver genes are targeted by known anti-cancer drugs and the majority of the identified key miRNAs are implicated in cancerogenesis of multiple organs. Also, the identified driver mutations likely cause damaging effects on protein functions. The constructed gene network and the identified key drivers were compared to well-established network-based methods. Conclusion The integrated molecular analysis enabled by the presented network-based approach substantially expands our knowledge base of prospective genomic drivers of genes, miRNAs, and mutations. For a good part of the identified key drivers

  20. 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

  1. 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.

  2. 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

  3. 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. PMID:25836836

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

    PubMed

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

    2014-01-01

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

  5. Finite-element blunt-crack propagation: a modified J-integral approach. [LMFBR

    SciTech Connect

    Pan, Y.C.; Marchertas, A.H.; Kennedy, J.M.

    1983-01-01

    In assessing the safety of a liquid metal fast breeder reactor (LMFBR), a major concern is the behavior of concrete structures subjected to high temperatures. The potential of concrete cracking is an important parameter which could significantly influence the safety assessment of thermally attacked concrete. A new modified J-integral approach for the blunt crack model has been derived to provide a general procedure to accurately predict the direction of crack growth. This formulation has been incorporated into the coupled heat transfer-stress analysis finite element code TEMP-STRESS. A description of the formulation is presented in this paper. Results for the problems of a Mode I and mixed mode crack in a plate using regular and slanted meshes subjected to uniaxial and shear loading are presented.

  6. A process chain for integrating microfluidic interconnection elements by micro-overmoulding of thermoplastic elastomers

    NASA Astrophysics Data System (ADS)

    Attia, U. M.; Alcock, J. R.

    2010-05-01

    This paper presents a process chain for in-line integration of microfluidic interconnection elements by a variant of micro-injection moulding (µIM). A SEBS-based thermoplastic elastomer (TPE) was moulded over polymethylmethacrylate (PMMA) to produce a hybrid microfluidic structure with an aspect ratio of 2. The process chain implemented micro-milling for fabricating micro-structured tool inserts, and µIM and micro-overmoulding was used for replication. A two-plate mould was used for moulding the substrate, whilst a three-plate mould with a replaceable insert was used for TPE overmoulding. The presented application was an interconnect system for a microfluidic device, which enabled direct fitting of standard tubes into microfluidic substrates. A leakage test showed that the interconnection was leak-proof within a range of flow rates between 0.32 and 0.62 ml min-1.

  7. 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.

  8. Design of multilayered grating couplers as key elements of a fully integrated IR-absorption sensor

    NASA Astrophysics Data System (ADS)

    Kasberger, Juergen; Jakoby, Bernhard

    2008-08-01

    For the online characterization of fluids regarding their chemical composition, the miniaturization of an IR-absorption sensor at application-specific distinguished wavelengths for the mid-IR-region promises outstanding features. Utilizing micromachining technology facilitates the integration of all required components (including thermal emitter and detector) into a complete sensor system. The absorption is sensed in the evanescent field of an appropriately designed slab mono-mode waveguide (ZnSe, n=2.42) residing on a BaF2-substrate (n=1.44), which represents the central element of the system. A typical application for such a system is, e.g., the characterization of engine oil oxidation in terms of the absorption at 5.85 μm as an indicator for deterioration. The thermal generation and detection of mid-IR-radiation is preferred over expensive and sophisticated quantum well devices. However, the spatial and non-coherent character of thermally generated IR-radiation requires an extension of the numerical methods established for coherent light sources for a proper design of the system's grating couplers, which act as key elements determining the system performance. These couplers yield efficient coupling into and out of the sensing waveguide and provide the required spectral filtering at the same time. In the actually projected implementation, a multilayer waveguide Si/BaF2/ZnSe is used, where the silicon substrate practically represents a rear-reflector in the grating region featuring several advantages compared to simpler grating couplers. In this contribution we discuss the modelling of the coupling of non-coherent, thermally generated and detected IR-radiation by means of these multilayer grating couplers in the context of a fully integrated IR-absorption sensor system.

  9. Femtosecond laser polymerization of hybrid/integrated micro-optical elements and their characterization

    NASA Astrophysics Data System (ADS)

    Malinauskas, Mangirdas; Žukauskas, Albertas; Purlys, Vytautas; Belazaras, Kastytis; Momot, Andrej; Paipulas, Domas; Gadonas, Roaldas; Piskarskas, Algis; Gilbergs, Holger; Gaidukevičiūtė, Arunė; Sakellari, Ioanna; Farsari, Maria; Juodkazis, Saulius

    2010-12-01

    The femtosecond laser-induced multi-photon polymerization of a zirconium-silicon based sol-gel photopolymer was employed for the fabrication of a series of micro-optical elements with single and combined optical functions: convex and Fresnel lenses, gratings, solid immersion lenses on a glass slide and on the tip of an optical fiber. The microlenses were produced as polymer caps of varying radii from 10 to 90 µm. The matching of refractive indices between the polymer and substrate was exploited for the creation of composite glass-resist structures which functioned as single lenses. Using this principle, solid immersion lenses were fabricated and their performance demonstrated. The magnification of the composite solid immersion lenses corresponded to the calculated values. The surface roughness of the lenses was below ~ 30 nm, acceptable for optical applications in the visible range. In addition, the integration of micro-optical elements onto the tip of an optical fiber was demonstrated. To increase the efficiency of the 3D laser polymerization, the lenses were formed by scanning only the outer shell and polymerizing the interior by exposure to UV light.

  10. 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.

  11. 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.

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

    SciTech Connect

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

    2011-05-04

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

  13. A time-domain finite element boundary integration method for ultrasonic nondestructive evaluation.

    PubMed

    Shi, Fan; Choi, Wonjae; Skelton, Elizabeth A; Lowe, Michael J S; Craster, Richard V

    2014-12-01

    A 2-D and 3-D numerical modeling approach for calculating the elastic wave scattering signals from complex stress-free defects is evaluated. In this method, efficient boundary integration across the complex boundary of the defect is coupled with a time-domain finite element (FE) solver. The model is designed to simulate time-domain ultrasonic nondestructive evaluation in bulk media. This approach makes use of the hybrid concept of linking a local numerical model to compute the near-field scattering behavior and theoretical mathematical formulas for postprocessing to calculate the received signals. It minimizes the number of monitoring signals from the FE calculation so that the computation effort in postprocessing decreases significantly. In addition, by neglecting the conventional regular monitoring box, the region for FE calculation can be made smaller. In this paper, the boundary integral method is implemented in a commercial FE code, and it is validated by comparing the scattering signals with results from corresponding full FE models. The coupled method is then implemented in real inspection scenarios in both 2-D and 3-D, and the accuracy and the efficiency are demonstrated. The limitations of the proposed model and future works are also discussed. PMID:25474780

  14. 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.

  15. 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

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

    NASA Astrophysics Data System (ADS)

    Chang, Ruinan

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

  17. 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.

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

    NASA Technical Reports Server (NTRS)

    Kim, Sang-Wook

    1988-01-01

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

  19. 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.

  20. 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.

  1. 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.

  2. 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)

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

    PubMed Central

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

    2014-01-01

    Contour integration (CI) combines appropriately aligned and oriented elements into continuous boundaries. Collinear facilitation (CF) occurs when a low-contrast oriented element becomes more visible when flanked by collinear high-contrast elements. Both processes rely at least partly on long-range horizontal connections in early visual cortex, and thus both have been extensively studied to understand visual cortical functioning in aging, development, and clinical disorders. Here, we ask: Can acuity differences within the normal range predict CI or CF? To consider this question, we measured binocular visual acuity and compared subjects with 20/20 vision to those with better-than-20/20 vision (SharpPerceivers) on two tasks. In the CI task, subjects located an integrated shape embedded in varying amounts of noise; in the CF task, subjects detected a low-contrast element flanked by collinear or orthogonal high-contrast elements. In each case, displays were scaled in size to modulate element visibility and spatial frequency (4-12 cycles/deg). SharpPerceivers could integrate contours under noisier conditions than the 20/20 group (p=.0002) especially for high spatial frequency displays. Moreover, although the two groups exhibited similar collinear facilitation, SharpPerceivers could detect the central target with lower contrast at high spatial frequencies (p<.05). These results suggest that small acuity differences within the normal range—corresponding to about a one line difference on a vision chart—strongly predict element detection and integration. Furthermore, simply ensuring that subjects have normal or corrected-to-normal vision is not sufficient when comparing groups on contour tasks; visual acuity confounds also need to be ruled out. PMID:24845876

  4. Integration of growth factor signals at the c-fos serum response element.

    PubMed

    Price, M A; Hill, C; Treisman, R

    1996-04-29

    A transcription factor ternary complex composed of serum response factor (SRF) and a second factor, ternary complex factor (TCF), mediates the response of the c-fos Serum Response Element to growth factors and mitogens. In NIH3T3 fibroblasts, TCF binding is required for transcriptional activation by the SRE in response to activation of the Ras-Raf-ERK pathway. We compared the properties of three members of the TCF family, Elk-1, SAP-1 and SAP-2 (ERP/NET). Although all the proteins contain sequences required for ternary complex formation with SRF, only Elk-1 and SAP-1 appear to interact with the c-fos SRE efficiently in vivo. Each TCF contains a C-terminal activation domain capable of transcriptional activation in response to activation of the Ras-Raf-ERK pathway, and this is dependent on the integrity of S/T-P motifs conserved between all the TCF family members. In contrast, activation of the SRE by whole serum and the mitogenic phospholipid LPA requires SRF binding alone. Constitutively activated members of the Rho subfamily of Ras-like GTPases are also capable of inducing activation of the SRE in the absence of TCF; unlike activated Ras itself, these proteins do not activate the TCFs in NIH3T3 cells. At the SRE, SRF- and TCF-linked signalling pathways act synergistically to potentiate transcription. PMID:8735278

  5. 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.

  6. Phase conjugation in short pulse megajoule class lasers

    SciTech Connect

    Eimerl, D.; Chernyak, V.M.; Pergament, M.I.; Smirnov, R.V.; Sokolov, V.I.

    1995-12-31

    The main goal of this report is to analyze the feasibility to use phase conjugation (PC) in Megajoule class lasers for Inertial Confinement Fusion (ICF). Phase conjugation has the potential for relieving the fabrication requirements to any optical elements and for compensation of residual thermooptical distortions. The key problems for phase conjugation are the dynamic range over which phase conjugation operates efficiently, the reflected energy limit, the effect of the laser light bandwidth, and the possibility to mount PC subsystem into a real megajoule laser. Analytical results of possibility of use of classical stimulated Brillouin scattering (SBS) mirror and based on nonlinear crystal phase conjugator in ICF laser are presented.

  7. Comparison of finite element J-integral evaluations for the blunt crack model and the sharp crack model

    SciTech Connect

    Pan, Y.C.; Kennedy, J.M.

    1983-01-01

    In assessing the safety of a liquid metal fast breeder reactor (LMFBR), a major concern is that of hot sodium coming into contact with either unprotected concrete or steel-lined concrete equipment cells and containment structures. An aspect of this is the potential of concrete cracking which would significantly influence the safety assessment. Concrete cracking in finite element analysis can be modeled as a blunt crack in which the crack is assumed to be uniformly distributed throughout the area of the element. A blunt crack model based on the energy release rate and the effective strength concepts which was insensitive to the element size was presented by Bazant and Cedolin. Some difficulties were encountered in incorporating their approach into a general purpose finite element code. An approach based on the J-integral to circumvent some of the difficulties was proposed by Pan, Marchertas, and Kennedy. Alternatively, cracking can also be modeled as a sharp crack where the crack surface is treated as the boundary of the finite element mesh. The sharp crack model is adopted by most researchers and its J-integral has been well established. It is desirable to establish the correlation between the J-integrals, or the energy release rates, for the blunt crack model and the sharp crack model so that data obtained from one model can be used on the other.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Fiber bundle phase conjugate mirror

    SciTech Connect

    Ward, Benjamin G.

    2012-05-01

    An improved method and apparatus for passively conjugating the phases of a distorted wavefronts resulting from optical phase mismatch between elements of a fiber laser array are disclosed. A method for passively conjugating a distorted wavefront comprises the steps of: multiplexing a plurality of probe fibers and a bundle pump fiber in a fiber bundle array; passing the multiplexed output from the fiber bundle array through a collimating lens and into one portion of a non-linear medium; passing the output from a pump collection fiber through a focusing lens and into another portion of the non-linear medium so that the output from the pump collection fiber mixes with the multiplexed output from the fiber bundle; adjusting one or more degrees of freedom of one or more of the fiber bundle array, the collimating lens, the focusing lens, the non-linear medium, or the pump collection fiber to produce a standing wave in the non-linear medium.

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

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

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

  20. 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.

  1. An iterative finite element-integral technique for predicting sound radiation from turbofan inlets in steady flight

    NASA Technical Reports Server (NTRS)

    Horowitz, S. J.; Sigman, R. K.; Zinn, B. T.

    1982-01-01

    A new iterative solution technique for predicting the sound field radiated from a turbofan inlet in steady flight is presented. 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. A continuous solution is obtained by matching the finite element and integral solutions at the interface between the two regions. The applicability of the iterative technique is demonstrated by comparison of experimental results with the theoretical results for several different inlet configurations with and without flow. These examples show that good agreement between experiment and theory is obtained within five iterations.

  2. Compensation of reflector surface distortions using conjugate field matching

    NASA Technical Reports Server (NTRS)

    Acosta, R. J.

    1986-01-01

    The feasibility of compensating for reflector surface distortions has been investigated. The performance characteristics (gain, sidelobe level, null location, beamwidth, etc.) of space communication reflector antenna systems degrade as the reflector surface distorts due to thermal effects from a varying solar flux. The technique reported here will maintain the design radiation performance independently of thermal effects on the reflector surface. With the advent of monolithic microwave integrated circuits (MMIC), a greater flexibility in array-fed reflector system design can be achieved. MMIC arrays provides independent control of amplitude and phase for each of many radiating elements of the feed array. The conjugate field matching technique provide a basis for obtaining the required element excitations under surface distortion for maintaining the design radiation performance. It is assumed that the surface characteristics (x, y, z, first derivatives, and second derivatives) under distortion are known.

  3. A combined finite element-boundary element formulation for solution of two-dimensional problems via CGFFT

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

    A method for the computation of electromagnetic scattering from arbitrary two-dimensional bodies is presented. The method combines the finite element and boundary element methods leading to a system for solution via the conjugate gradient Fast Fourier Transform (FFT) algorithm. Two forms of boundaries aimed at reducing the storage requirement of the boundary integral are investigated. It is shown that the boundary integral becomes convolutional when a circular enclosure is chosen, resulting in reduced storage requirement when the system is solved via the conjugate gradient FFT method. The same holds for the ogival enclosure, except that some of the boundary integrals are not convolutional and must be carefully treated to maintain O(N) memory requirement. Results for several circular and ogival structures are presented and shown to be in excellent agreement with those obtained by traditional methods.

  4. Occurrence, transport, and fate of trace elements, Blue River Basin, Summit County, Colorado: an integrated approach

    USGS Publications Warehouse

    Apodaca, L.E.; Driver, N.E.; Bails, J.B.

    2000-01-01

    Mining activities in the Blue River Basin, Summit County, Colorado, have affected the trace-element chemistry and biota along French Gulch and the Blue River. Elevated concentrations of As, Cd, Cu, Pb, and Zn were present in the bed and suspended sediments. Bed sediment trace-element concentrations were high in the streams in and near mining activities in the basin and remained high as water flowed into Dillon Reservoir about 3.5 km downstream. Bed-sediment (< 63 μm) data were useful in assessing the distribution of trace elements in the basin. Suspended-sediment measurements provided information as to the transport of the trace elements. Filtered (< 0.45 μm) water-column trace-element concentrations were orders of magnitude less than the sediment concentrations. Concentrations of Cd and Zn in the water column at some sites exceeded stream water-quality standards. Elevated trace-element concentrations in the sediment and water column are a source of contamination and must be considered in water-quality management of the Blue River Basin.

  5. 49 CFR 192.911 - What are the elements of an integrity management program?

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...), by electronic or other means, a copy of the operator's risk analysis or integrity management program... threats to each covered pipeline segment, which must include data integration and a risk assessment. An operator must use the threat identification and risk assessment to prioritize covered segments...

  6. Analysis of Thermal Field on Integrated LED Light Source Based on COMSOL Multi-physics Finite Element Simulation

    NASA Astrophysics Data System (ADS)

    Li, Jingsong; Yang, Qingxin; Niu, Pingjuan; Jin, Liang; Meng, Bo; Li, Yang; Xiao, Zhaoxia; Zhang, Xian

    This paper obtained the average integrated heat transfer coefficient for the thermal resistance of a classic of integrated LED light source and its cooling fin-root on the basis of thermal circuit method. Simulation analysis on its steady-state temperature field distribution using COMSOL Multi-physics finite element method was carried out. This method has high precision and intuitive simulation results. The iteration method of the Numerical Analysis is introduced into method for the first time. The results have significant promotion on the LED cast light structure optimization and the affection of reduced heat coupling on the light temperature distribution. The comparison between thermocouple experimental data and calculation results proved the correctness and validity of the proposed method. This experimental study plays a guiding role to thermal analysis and design of other integrated lights.

  7. Interrater Reliability and Discriminative Validity of the Structural Elements of the Ayres Sensory Integration® Fidelity Measure©

    PubMed Central

    Roley, Susanne Smith; Mailloux, Zoe; Parham, L. Diane; Koomar, Jane; Schaaf, Roseann C.; Van Jaarsveld, Annamarie; Cohn, Ellen

    2014-01-01

    This study examined the reliability and validity of the structural section of the Ayres Sensory Integration® Fidelity Measure© (ASIFM), which provides a method for monitoring the extent to which an intervention was implemented as conceptualized in studies of occupational therapy using sensory integration intervention methods (OT–SI). We examined the structural elements of the measure, including content of assessment reports, availability of specific equipment and adequate space, safety monitoring, and integration of communication with parents and other team members, such as collaborative goal setting with parents or family and teacher education, into the intervention program. Analysis of self-report ratings by 259 occupational therapists from 185 different facilities indicated that the structural section of the ASIFM has acceptable interrater reliability (r ≥ .82) and significantly differentiates between settings in which therapists reportedly do and do not practice OT–SI (p < .001). PMID:25184462

  8. Retroposons do jump: a B2 element recently integrated in an 18S rDNA gene.

    PubMed Central

    Oberbäumer, I

    1992-01-01

    Several cDNA clones were isolated from cDNA libraries constructed with mRNA longer than 28S RNA from the murine cell line PYS-2/12. The plasmids have inserts containing 1-1.2 kb of the ribosomal 5' external transcribed spacer followed by nearly 700 nt of sequence for 18S rRNA and ending with a B2 element (retroposon). The cloned sequence differed in a few positions from published ribosomal sequences. The 3' adjacent genomic sequence was obtained by polymerase chain reaction (PCR) and showed that the B2 element has a poly(A) tail of about 50 nt and is surrounded by perfect direct repeats of 15 nt. Analysis of genomic DNA from several murine cell lines revealed that PYS cells contain at least one copy of 18S RNA with the B2 element which is not present in the genome of other murine cell lines derived from the same teratocarcinoma. Similarly, rRNA transcripts containing the B2 element were only detected in PYS cells. According to the publication dates of the different cell lines, the B2 element must have been integrated into an rRNA transcription unit during the years 1970 through 1974 thus proving that retroposons (SINEs) can still be inserted into the genome in our times. Images PMID:1311830

  9. Thermomechanical stability and integrability of an embedded ceramic antenna with an integrated sensor element for wireless reading in harsh environments

    NASA Astrophysics Data System (ADS)

    Sturesson, P.; Khaji, Z.; Knaust, S.; Sundqvist, J.; Klintberg, L.; Thornell, G.

    2013-12-01

    This paper reports on the design, manufacturing and evaluation of a small, wirelessly powered and read resonating antenna circuit with an integrated pressure sensor. The work aims at developing miniature devices suitable for harsh environments, where high temperature prevents the use of conventional, silicon-based microdevices. Here, the device is made of alumina with platinum as conducting material. Ceramic green tapes were structured using high-precision milling, metallized using screen printing, and subsequently laminated to form stacks before they were sintered. The device's frequency shift as a function of temperature was studied up to 900°C. The contributions to the shift both from the thermomechanical deformation of the device at large, and from the integrated and, so far, self-pressurized sensor were sorted out. A total frequency shift of 3200 ppm was observed for the pressure sensor for heating over the whole range. Negligible levels of thermally induced radius of curvature were observed. With three-point bending, a frequency shift of 180 ppm was possible to induce with a curvature of radius of 220 m at a 10 N load. The results indicate that a robust pressure sensor node, which can register pressure changes of a few bars at 900°C and wirelessly transmit the signal, is viable.

  10. 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

  11. A DNA-Fullerene Conjugate as a Template for Supramolecular Chromophore Assemblies: Towards DNA-Based Solar Cells.

    PubMed

    Ensslen, Philipp; Gärtner, Stefan; Glaser, Konstantin; Colsmann, Alexander; Wagenknecht, Hans-Achim

    2016-01-26

    A fullerene was covalently attached to a (dA)20 template that serves as structural scaffold to self-assemble an ordered and mixed array of ethynyl-pyrene- and ethynyl-Nile-red-nucleoside conjugates. Fluorescence spectroscopy revealed evidence for energy transfer between the two different chromophores. Moreover, fluorescence quenching is significantly enhanced by the attached fullerene in mixed assemblies of different chromophore ratios. This indicates exciton dissociation by electron transfer from the photo-generated exciton on the chromophore stack to the fullerene. The fullerene-DNA-conjugate was integrated as a photo-active layer in solar cells that showed charge-carrier generation in the spectral regime of all three components of the conjugate. This work clearly demonstrates that DNA is suitable as structural element for chromophore assemblies in future organic optoelectronic devices, such as solar cells. PMID:26689149

  12. The master regulator of IncA/C plasmids is recognized by the Salmonella Genomic island SGI1 as a signal for excision and conjugal transfer.

    PubMed

    Kiss, János; Papp, Péter Pál; Szabó, Mónika; Farkas, Tibor; Murányi, Gábor; Szakállas, Erik; Olasz, Ferenc

    2015-10-15

    The genomic island SGI1 and its variants, the important vehicles of multi-resistance in Salmonella strains, are integrative elements mobilized exclusively by the conjugative IncA/C plasmids. Integration and excision of the island are carried out by the SGI1-encoded site-specific recombinase Int and the recombination directionality factor Xis. Chromosomal integration ensures the stable maintenance and vertical transmission of SGI1, while excision is the initial step of horizontal transfer, followed by conjugation and integration into the recipient. We report here that SGI1 not only exploits the conjugal apparatus of the IncA/C plasmids but also utilizes the regulatory mechanisms of the conjugation system for the exact timing and activation of excision to ensure efficient horizontal transfer. This study demonstrates that the FlhDC-family activator AcaCD, which regulates the conjugation machinery of the IncA/C plasmids, serves as a signal of helper entry through binding to SGI1 xis promoter and activating SGI1 excision. Promoters of int and xis genes have been identified and the binding site of the activator has been located by footprinting and deletion analyses. We prove that expression of xis is activator-dependent while int is constitutively expressed, and this regulatory mechanism is presumably responsible for the efficient transfer and stable maintenance of SGI1. PMID:26209134

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. Integration of finite element modeling with solid modeling through a dynamic interface

    NASA Technical Reports Server (NTRS)

    Shephard, Mark S.

    1987-01-01

    Finite element modeling is dominated by geometric modeling type operations. Therefore, an effective interface to geometric modeling requires access to both the model and the modeling functionality used to create it. The use of a dynamic interface that addresses these needs through the use of boundary data structures and geometric operators is discussed.

  18. Gene therapy for hemophilia B with liver-specific element mediated by Rep-RBE site-specific integration system.

    PubMed

    Xu, Zhengxin; Ye, Juan; Zhang, Amin; Xie, Linjun; Shen, Qi; Xue, Jinglun; Chen, Jinzhong

    2015-02-01

    Adeno-associated virus (AAV) is a nonpathogenic virus capable of targeting human chromosome 19 for integration at AAVS1 site, and a 16 bp Rep binding element (RBE) sequence of AAV was sufficient for mediating this specific integration in the presence of AAV regulation proteins (Rep). Previously, we cotransduced 2 plasmids, pRBE-CMV-hFIX and pRC, into the AAVS1 transgenic mice by hydrodynamic injection, and a long-term expression of human coagulation Factor IX (hFIX) was observed. The corresponding AAVS1 locus site-specific integrations were verified by nested polymerase chain reaction. In this study, we established a novel hFIX expression plasmid, pRBE-HCR-hAAT-hFIX, driven by a liver-specific promoter by replacing the CMV promoter of pRBE-CMV-hFIX with a humanized promoter consisting of HCR-hAAT. The expression of hFIX in vitro was almost the same in transient transfection of pRBE-CMV-hFIX or pRBE-HCR-hAAT-hFIX. AAVS1-specific integrations were identified both in mice transfected with pRC/pRBE-CMV-hFIX cocktail and pRC/pRBE-HCR-hAAT-hFIX cocktail. However, the expression of hFIX of pRBE-HCR-hAAT-hFIX mice was higher and persisted longer. It achieved more than 1% of normal plasma hFIX concentration and maintained for 240 days. The result suggested that RBE-HCR-hAAT element could improve the expression of hFIX and present potential usage of Rep-RBE site-specific integration in gene therapy for hemophilia B. PMID:25295466

  19. An efficient formulation of the coupled finite element-integral equation technique for solving large 3D scattering problems

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

    It is often desirable to calculate the electromagnetic fields inside and about a complicated system of scattering bodies, as well as in their far-field region. The finite element method (FE) is well suited to solving the interior problem, but the domain has to be limited to a manageable size. At the truncation of the FE mesh one can either impose approximate (absorbing) boundary conditions or set up an integral equation (IE) for the fields scattered from the bodies. The latter approach is preferable since it results in higher accuracy. Hence, the two techniques can be successfully combined by introducing a surface that encloses the scatterers, applying a FE model to the inner volume and setting up an IE for the tangential fields components on the surface. Here the continuity of the tangential fields is used bo obtain a consistent solution. A few coupled FE-IE methods have recently appeared in the literature. The approach presented here has the advantage of using edge-based finite elements, a type of finite elements with degrees of freedom associated with edges of the mesh. Because of their properties, they are better suited than the conventional node based elements to represent electromagnetic fields, particularly when inhomogeneous regions are modeled, since the node based elements impose an unnatural continuity of all field components across boundaries of mesh elements. Additionally, our approach is well suited to handle large size problems and lends itself to code parallelization. We will discuss the salient features that make our approach very efficient from the standpoint of numerical computation, and the fields and RCS of a few objects are illustrated as examples.

  20. Integrating the human element into the systems engineering process and MBSE methodology.

    SciTech Connect

    Tadros, Michael Samir.

    2013-12-01

    In response to the challenges related to the increasing size and complexity of systems, organizations have recognized the need to integrate human considerations in the beginning stages of systems development. Human Systems Integration (HSI) seeks to accomplish this objective by incorporating human factors within systems engineering (SE) processes and methodologies, which is the focus of this paper. A representative set of HSI methods from multiple sources are organized, analyzed, and mapped to the systems engineering Vee-model. These methods are then consolidated and evaluated against the SE process and Models-Based Systems Engineering (MBSE) methodology to determine where and how they could integrate within systems development activities in the form of specific enhancements. Overall conclusions based on these evaluations are presented and future research areas are proposed.

  1. 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.

  2. Integrated Nondestructive Evaluation and Finite Element Analysis Predicts Crack Location and Shape

    NASA Technical Reports Server (NTRS)

    Abdul-Azia, Ali; Baaklini, George Y.; Trudell, Jeffrey J.

    2002-01-01

    This study describes the finite-element analyses and the NDE modality undertaken on two flywheel rotors that were spun to burst speed. Computed tomography and dimensional measurements were used to nondestructively evaluate the rotors before and/or after they were spun to the first crack detection. Computed tomography data findings of two- and three-dimensional crack formation were used to conduct finite-element (FEA) and fracture mechanics analyses. A procedure to extend these analyses to estimate the life of these components is also outlined. NDE-FEA results for one of the rotors are presented in the figures. The stress results, which represent the radial stresses in the rim, clearly indicate that the maximum stress region is within the section defined by the computed tomography scan. Furthermore, the NDE data correlate well with the FEA results. In addition, the measurements reported show that the NDE and FEA data are in parallel.

  3. From high-resolution CT data to finite element models: development of an integrated modular framework.

    PubMed

    Pahr, Dieter H; Zysset, Philippe K

    2009-02-01

    This work introduces a novel method of automating the process of patient-specific finite element (FE) model development using a mapped mesh technique. The objective is to map a predefined mesh (template) of high quality directly onto a new bony surface (target) definition, thereby yielding a similar mesh with minimal user interaction. To bring the template mesh into correspondence with the target surface, a deformable registration technique based on the FE method has been adopted. The procedure has been made hierarchical allowing several levels of mesh refinement to be used, thus reducing the time required to achieve a solution. Our initial efforts have focused on the phalanx bones of the human hand. Mesh quality metrics, such as element volume and distortion were evaluated. Furthermore, the distance between the target surface and the final mapped mesh were measured. The results have satisfactorily proven the applicability of the proposed method. PMID:18839383

  4. 49 CFR 192.911 - What are the elements of an integrity management program?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 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...

  5. 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...

  6. 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...

  7. 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…

  8. 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…

  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. Progress in system design using integrated multi-element interferometric switches

    NASA Astrophysics Data System (ADS)

    Kehayas, E.; Kanellos, G. T.; Stampoulidis, L.; Theophilopoulos, G.; Avramopoulos, H.

    2007-11-01

    In the present communication we discuss recent advances in the development of Semiconductor optical amplifier (SOA)-based interferometric optical gates and their use through the implementation of functional high-speed optical systems. SOA Mach-Zehnder interferometers (SOA-MZI) show great potential for being used as fundamental building blocks in developing intelligent high speed all-optical sub-systems. In this context we discuss the development of optical systems that perform diverse and non-trivial network functionalities that find application in Optical Packet/Burst Switching networks (OPS/OBS). The use of generic building blocks to develop a variety of optical sub-systems is essential, as this avoids the requirement for custom-made technological solutions and allows for a common fabrication procedure for all subsystems. In this context, we discuss latest research on integration of arrays of such optical switches onto the same photonic chip using hybrid integration technology. The development of such arrays reduces the cost of photonic devices by sharing the packaging and pigtailing costs. By using an integrated quadruple array of SOA-MZI switches we demonstrate the front-end unit of an All-optical Label Switched node that performs clock recovery, data recovery and label/payload separation, and a scalable Time Slot Interchanger (TSI), proving the multi-functionality and processing power of such device. Both functional systems exhibit comparable performance compared to implementations using single switches with significantly lower device costs. The cost reduction offered by the integration of multiple switches on the same chip is also evident in high-speed WDM networks, where multi-wavelength regeneration can be achieved with the use of several integrated switch arrays.

  12. 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

  13. 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

  14. J-integral patch for finite element analysis of dynamic fracture due to impact of pressure vessels

    NASA Astrophysics Data System (ADS)

    Kunin, Boris I.

    1993-11-01

    Prediction of whether a pressurized cylinder will fail catastrophically when impacted by a projectile has important applications ranging from perforation of an airplane's skin by a failed turbine blade to meteorite impact of a space station habitation module. This report summarizes the accomplishment of one task for a project whose aim is to simulate numerically the outcome of a high velocity impact of pressure vessels. A finite element patch covering the vicinity of a growing crack has been constructed to estimate the J-integral (crack driving force) during the impact. Explicit expressions for the J-integral through the nodal values of displacement, strain, and stress have been written. The patch is to be used repeatedly to estimate the amount of crack growth during the time of the impact. The resulting crack size is to be compared to an estimated critical crack size for the pressurized cylinder.

  15. 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.

  16. Using WordNet to improve the mapping of data elements to UMLS for data sources integration.

    PubMed

    Mougin, Fleur; Burgun, Anita; Bodenreider, Olivier

    2006-01-01

    Each biomedical system has its own way of naming the pieces of information it contains, i.e., of defining its data elements (DEs). Integrating DEs facilitates the integration of biomedical resources. However, the mapping of DEs to the UMLS is ambiguous in many cases, when any correspondence is found at all. We propose to evaluate the potential contribution of a more general terminology: WordNet. Our method is based on synonyms, definitions, and structural properties of the terminologies. We applied it to a set of 474 DEs extracted from eleven biomedical sources. We show that WordNet can improve the direct mapping of DEs to UMLS when used to validate and disambiguate UMLS direct mappings. WordNet can also help identify indirect mappings of DEs to the UMLS. PMID:17238406

  17. The Role of Heterologous Chloroplast Sequence Elements in Transgene Integration and Expression1[W][OA

    PubMed Central

    Ruhlman, Tracey; Verma, Dheeraj; Samson, Nalapalli; Daniell, Henry

    2010-01-01

    Heterologous regulatory elements and flanking sequences have been used in chloroplast transformation of several crop species, but their roles and mechanisms have not yet been investigated. Nucleotide sequence identity in the photosystem II protein D1 (psbA) upstream region is 59% across all taxa; similar variation was consistent across all genes and taxa examined. Secondary structure and predicted Gibbs free energy values of the psbA 5′ untranslated region (UTR) among different families reflected this variation. Therefore, chloroplast transformation vectors were made for tobacco (Nicotiana tabacum) and lettuce (Lactuca sativa), with endogenous (Nt-Nt, Ls-Ls) or heterologous (Nt-Ls, Ls-Nt) psbA promoter, 5′ UTR and 3′ UTR, regulating expression of the anthrax protective antigen (PA) or human proinsulin (Pins) fused with the cholera toxin B-subunit (CTB). Unique lettuce flanking sequences were completely eliminated during homologous recombination in the transplastomic tobacco genomes but not unique tobacco sequences. Nt-Ls or Ls-Nt transplastomic lines showed reduction of 80% PA and 97% CTB-Pins expression when compared with endogenous psbA regulatory elements, which accumulated up to 29.6% total soluble protein PA and 72.0% total leaf protein CTB-Pins, 2-fold higher than Rubisco. Transgene transcripts were reduced by 84% in Ls-Nt-CTB-Pins and by 72% in Nt-Ls-PA lines. Transcripts containing endogenous 5′ UTR were stabilized in nonpolysomal fractions. Stromal RNA-binding proteins were preferentially associated with endogenous psbA 5′ UTR. A rapid and reproducible regeneration system was developed for lettuce commercial cultivars by optimizing plant growth regulators. These findings underscore the need for sequencing complete crop chloroplast genomes, utilization of endogenous regulatory elements and flanking sequences, as well as optimization of plant growth regulators for efficient chloroplast transformation. PMID:20130101

  18. 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.

  19. 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

  20. Inter- and intraspecies transfer of a Clostridium difficile conjugative transposon conferring resistance to MLSB.

    PubMed

    Wasels, François; Monot, Marc; Spigaglia, Patrizia; Barbanti, Fabrizio; Ma, Laurence; Bouchier, Christiane; Dupuy, Bruno; Mastrantonio, Paola

    2014-12-01

    Resistance to the macrolide-lincosamide-streptogramin B group of antibiotics in Clostridium difficile is generally due to erm(B) genes. Tn6194, a conjugative transposon initially detected in PCR-ribotype 027 isolates, is an erm(B)-containing element also detected in other relevant C. difficile PCR-ribotypes. In this study, the genome of a C. difficile PCR-ribotype 001 strain was sequenced, and an element with two nucleotidic changes compared to Tn6194 was detected. This element was transferred by filter mating assays to recipient strains of C. difficile belonging to PCR-ribotype 009 and 027 and to a recipient strain of Enterococcus faecalis. Transconjugants were characterized by Southern blotting and genome sequencing, and integration sites in all transconjugants were identified. The element integrated the genome of C. difficile at different sites and the genome of E. faecalis at a unique site. This study is the first molecular characterization of an erm(B)-containing conjugative transposon in C. difficile and provides additional evidence of the antibiotic resistance transmission risk among pathogenic bacteria occupying the same human intestinal niche. PMID:25055190

  1. 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

  2. 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.

  3. Three dimensional fabrication of optical waveguiding elements for on-chip integration

    NASA Astrophysics Data System (ADS)

    Parsi Sreenivas, V. V.; Bülters, M.; Schröder, M.; Bergmann, R. B.

    2014-05-01

    We present micro polymer optical waveguide elements fabricated using femtosecond laser and two-photon absorption (TPA) process. The POWs are constructed by tightly focusing a laser beam in SU-8 based resists transparent to the laser wavelength for single-photon absorption. The TPA process enables the patterning of the resist in three dimensions at a resolution of 100-200 nm, which provides a high degree of freedom for POW designs. Using this technology, we provide a novel approach to fabricate Three dimensional Polymer Optical Waveguides (3D-POW) and coupling with single mode fibers in the visible wavelength regions. Our research is also focused on fabricating passive micro optical elements such as splitters, combiners and simple logical gates. For this reason we are aiming to achieve optimum coupling efficiency between the 3D-POW and fibers. The technology also facilitates 3D-POW fabrication independent of the substrate material. We present these fabrication techniques and designs, along with supporting numerical simulations and its transmission properties. With a length of 270 μm and polymer core diameter of 9 μm with air cladding, the waveguides possess a total loss of 12 dB. This value also includes the external in and out mode coupling and in continuously being improved upon by design optimization and simulations. We verify the overall feasibility of the design and coupling mechanisms that can be exploited to execute waveguide based optical functions such as filtering and logical operations.

  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. Semi-implicit time-integrators for a scalable spectral element atmospheric model

    NASA Astrophysics Data System (ADS)

    Giraldo, Francis X.

    2005-07-01

    The Naval Research Laboratory's spectral element atmospheric model (NSEAM) for scalable computer architectures is presented. This new dynamical core is based on a high-order spectral element (SE) method in space and uses semi-implicit methods in time based on either the traditional second-order leapfrog (LF2) or second-order backward difference formulas (BDF2). The novelties of NSEAM are: it is geometrically flexible and thereby can accommodate any type of grid; LF2 or BDF2 are used to construct the semi-implicit method; and the horizontal operators are written, discretized, and solved in three-dimensional Cartesian space. The semi-implicit NSEAM is validated using: five baroclinic test cases; direct comparisons to the explicit version of NSEAM which has been extensively tested and the results previously reported in the literature; and comparisons with operational weather prediction and well-established climate models. A comparison with the US Navy's spectral transform global forecast model illustrates that NSEAM is 60% faster on an IBM SP4 using 96 processors for the current operational resolution of T239 L30. However, NSEAM can accommodate many more processors while continuing to scale efficiently even at higher grid resolutions. In fact, we show that at T498 L60, NSEAM scales linearly up to 384 processors.

  6. 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.

  7. 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.

  8. A Fully Integrated RF-Powered Contact Lens With a Single Element Display.

    PubMed

    Pandey, J; Yu-Te Liao; Lingley, Andrew; Mirjalili, R; Parviz, B; Otis, B

    2010-12-01

    We present progress toward a wirelessly-powered active contact lens comprised of a transparent polymer substrate, loop antenna, power harvesting IC, and micro-LED. The fully integrated radio power harvesting and power management system was fabricated in a 0.13 μm CMOS process with a total die area of 0.2 mm(2). It utilizes a small on-chip capacitor for energy storage to light up a micro-LED pixel. We have demonstrated wireless power transfer at 10 cm distance using the custom IC and on-lens antenna. PMID:23853383

  9. 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.

  10. 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.

  11. 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. PMID:26208335

  12. 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

  13. Manufacturing and characterization of a ceramic microcombustor with integrated oxygen storage and release element

    NASA Astrophysics Data System (ADS)

    Khaji, Z.; Sturesson, P.; Klintberg, L.; Hjort, K.; Thornell, G.

    2015-10-01

    A microscale ceramic high-temperature combustor with a built-in temperature sensor and source of oxygen has been designed, manufactured and characterized. The successful in situ electroplating and oxidation of copper, and the use of copper oxide as the source of oxygen were demonstrated. It was shown that residual stresses from electroplating, copper oxidation and oxide decomposition did not cause much deformation of the substrate but influenced mainly the integrity and adhesion of the metal films. The process had influence on the electrical resistances, however. Calibration of the temperature sensor and correlation with IR thermography up to 1000 °C revealed a nearly linear sensor behavior. Demonstration of combustion in a vacuum chamber proved that no combustion had occurred before release of oxygen from the metal oxide resource.

  14. 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

  15. 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.

  16. Integrating 128-element linear imager for the 1 to 5 microns region

    NASA Technical Reports Server (NTRS)

    Bailey, G. C.

    1982-01-01

    Useful charge integration has been achieved in high quality photovoltaic InSb diodes when combined with a FET multiplexing (MUX) scheme. An experimental detector assembly with a linear array of 128 InSb diodes coupled to a FEX MUX has been developed. The first stage J-FET preamp, pixel reset switch, MUX, and the InSb array are contained in a hybrid microcircuit of compact dimensions. A low noise preamplifier topology which capitalizes on the low video line capacitance inherent with hybrid fabrication techniques is also utilized. Measurements indicate a signal-to-noise ratio of over 1000:1 and response uniformity of + or - 2 percent. Sample images show subtle detail which supports the estimated radiometric sensitivity of 0.01 K.

  17. Conjugate field approaches for active array compensation

    NASA Technical Reports Server (NTRS)

    Acosta, R. J.

    1989-01-01

    Two approaches for calculating the compensating feed array complex excitations are namely, the indirect conjugate field matching (ICFM) and the direct conjugate field matching (DCFM) approach. In the ICFM approach the compensating feed array excitations are determined by considering the transmitting mode and the reciprocity principle. The DCF, in contrast calculates the array excitations by integrating directly the induced surface currents on the reflector under a receiving mode. DCFM allows the reflector to be illuminated by an incident plane wave with a tapered amplitude. The level of taper can effectively control the sidelobe level of the compensated antenna pattern. Both approaches are examined briefly.

  18. 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.

  19. An integrated finite element simulation of cardiomyocyte function based on triphasic theory

    PubMed Central

    Hatano, Asuka; Okada, Jun-Ichi; Washio, Takumi; Hisada, Toshiaki; Sugiura, Seiryo

    2015-01-01

    In numerical simulations of cardiac excitation-contraction coupling, the intracellular potential distribution and mobility of cytosol and ions have been mostly ignored. Although the intracellular potential gradient is small, during depolarization it can be a significant driving force for ion movement, and is comparable to diffusion in terms of net flux. Furthermore, fluid in the t-tubules is thought to advect ions to facilitate their exchange with the extracellular space. We extend our previous finite element model that was based on triphasic theory to examine the significance of these factors in cardiac physiology. Triphasic theory allows us to study the behavior of solids (proteins), fluids (cytosol) and ions governed by mechanics and electrochemistry in detailed subcellular structures, including myofibrils, mitochondria, the sarcoplasmic reticulum, membranes, and t-tubules. Our simulation results predicted an electrical potential gradient inside the t-tubules at the onset of depolarization, which corresponded to the Na+ channel distribution therein. Ejection and suction of fluid between the t-tubules and the extracellular compartment during isometric contraction were observed. We also examined the influence of t-tubule morphology and mitochondrial location on the electrophysiology and mechanics of the cardiomyocyte. Our results confirm that the t-tubule structure is important for synchrony of Ca2+ release, and suggest that mitochondria in the sub-sarcolemmal region might serve to cancel Ca2+ inflow through surface sarcolemma, thereby maintaining the intracellular Ca2+ environment in equilibrium. PMID:26539124

  20. An integrated finite element simulation of cardiomyocyte function based on triphasic theory.

    PubMed

    Hatano, Asuka; Okada, Jun-Ichi; Washio, Takumi; Hisada, Toshiaki; Sugiura, Seiryo

    2015-01-01

    In numerical simulations of cardiac excitation-contraction coupling, the intracellular potential distribution and mobility of cytosol and ions have been mostly ignored. Although the intracellular potential gradient is small, during depolarization it can be a significant driving force for ion movement, and is comparable to diffusion in terms of net flux. Furthermore, fluid in the t-tubules is thought to advect ions to facilitate their exchange with the extracellular space. We extend our previous finite element model that was based on triphasic theory to examine the significance of these factors in cardiac physiology. Triphasic theory allows us to study the behavior of solids (proteins), fluids (cytosol) and ions governed by mechanics and electrochemistry in detailed subcellular structures, including myofibrils, mitochondria, the sarcoplasmic reticulum, membranes, and t-tubules. Our simulation results predicted an electrical potential gradient inside the t-tubules at the onset of depolarization, which corresponded to the Na(+) channel distribution therein. Ejection and suction of fluid between the t-tubules and the extracellular compartment during isometric contraction were observed. We also examined the influence of t-tubule morphology and mitochondrial location on the electrophysiology and mechanics of the cardiomyocyte. Our results confirm that the t-tubule structure is important for synchrony of Ca(2+) release, and suggest that mitochondria in the sub-sarcolemmal region might serve to cancel Ca(2+) inflow through surface sarcolemma, thereby maintaining the intracellular Ca(2+) environment in equilibrium. PMID:26539124

  1. Efficient conjugate gradient algorithms for computation of the manipulator forward dynamics

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Scheid, Robert E.

    1989-01-01

    The applicability of conjugate gradient algorithms for computation of the manipulator forward dynamics is investigated. The redundancies in the previously proposed conjugate gradient algorithm are analyzed. A new version is developed which, by avoiding these redundancies, achieves a significantly greater efficiency. A preconditioned conjugate gradient algorithm is also presented. A diagonal matrix whose elements are the diagonal elements of the inertia matrix is proposed as the preconditioner. In order to increase the computational efficiency, an algorithm is developed which exploits the synergism between the computation of the diagonal elements of the inertia matrix and that required by the conjugate gradient algorithm.

  2. 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

  3. 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

  4. Connecting Mechanics and Bone Cell Activities in the Bone Remodeling Process: An Integrated Finite Element Modeling

    PubMed Central

    Hambli, Ridha

    2014-01-01

    Bone adaptation occurs as a response to external loadings and involves bone resorption by osteoclasts followed by the formation of new bone by osteoblasts. It is directly triggered by the transduction phase by osteocytes embedded within the bone matrix. The bone remodeling process is governed by the interactions between osteoblasts and osteoclasts through the expression of several autocrine and paracrine factors that control bone cell populations and their relative rate of differentiation and proliferation. A review of the literature shows that despite the progress in bone remodeling simulation using the finite element (FE) method, there is still a lack of predictive models that explicitly consider the interaction between osteoblasts and osteoclasts combined with the mechanical response of bone. The current study attempts to develop an FE model to describe the bone remodeling process, taking into consideration the activities of osteoclasts and osteoblasts. The mechanical behavior of bone is described by taking into account the bone material fatigue damage accumulation and mineralization. A coupled strain–damage stimulus function is proposed, which controls the level of autocrine and paracrine factors. The cellular behavior is based on Komarova et al.’s (2003) dynamic law, which describes the autocrine and paracrine interactions between osteoblasts and osteoclasts and computes cell population dynamics and changes in bone mass at a discrete site of bone remodeling. Therefore, when an external mechanical stress is applied, bone formation and resorption is governed by cells dynamic rather than adaptive elasticity approaches. The proposed FE model has been implemented in the FE code Abaqus (UMAT routine). An example of human proximal femur is investigated using the model developed. The model was able to predict final human proximal femur adaptation similar to the patterns observed in a human proximal femur. The results obtained reveal complex spatio-temporal bone

  5. Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia.

    PubMed

    Almamun, Md; Levinson, Benjamin T; van Swaay, Annette C; Johnson, Nathan T; McKay, Stephanie D; Arthur, Gerald L; Davis, J Wade; Taylor, Kristen H

    2015-01-01

    Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children under the age of 15. In addition to genetic aberrations, epigenetic modifications such as DNA methylation are altered in cancer and impact gene expression. To identify epigenetic alterations in ALL, genome-wide methylation profiles were generated using the methylated CpG island recovery assay followed by next-generation sequencing. More than 25,000 differentially methylated regions (DMR) were observed in ALL patients with ∼ 90% present within intronic or intergenic regions. To determine the regulatory potential of the DMR, whole-transcriptome analysis was performed and integrated with methylation data. Aberrant promoter methylation was associated with the altered expression of genes involved in transcriptional regulation, apoptosis, and proliferation. Novel enhancer-like sequences were identified within intronic and intergenic DMR. Aberrant methylation in these regions was associated with the altered expression of neighboring genes involved in cell cycle processes, lymphocyte activation and apoptosis. These genes include potential epi-driver genes, such as SYNE1, PTPRS, PAWR, HDAC9, RGCC, MCOLN2, LYN, TRAF3, FLT1, and MELK, which may provide a selective advantage to leukemic cells. In addition, the differential expression of epigenetic modifier genes, pseudogenes, and non-coding RNAs was also observed accentuating the role of erroneous epigenetic gene regulation in ALL. PMID:26308964

  6. Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia

    PubMed Central

    Almamun, Md; Levinson, Benjamin T; van Swaay, Annette C; Johnson, Nathan T; McKay, Stephanie D; Arthur, Gerald L; Davis, J Wade; Taylor, Kristen H

    2015-01-01

    Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children under the age of 15. In addition to genetic aberrations, epigenetic modifications such as DNA methylation are altered in cancer and impact gene expression. To identify epigenetic alterations in ALL, genome-wide methylation profiles were generated using the methylated CpG island recovery assay followed by next-generation sequencing. More than 25,000 differentially methylated regions (DMR) were observed in ALL patients with ∼90% present within intronic or intergenic regions. To determine the regulatory potential of the DMR, whole-transcriptome analysis was performed and integrated with methylation data. Aberrant promoter methylation was associated with the altered expression of genes involved in transcriptional regulation, apoptosis, and proliferation. Novel enhancer-like sequences were identified within intronic and intergenic DMR. Aberrant methylation in these regions was associated with the altered expression of neighboring genes involved in cell cycle processes, lymphocyte activation and apoptosis. These genes include potential epi-driver genes, such as SYNE1, PTPRS, PAWR, HDAC9, RGCC, MCOLN2, LYN, TRAF3, FLT1, and MELK, which may provide a selective advantage to leukemic cells. In addition, the differential expression of epigenetic modifier genes, pseudogenes, and non-coding RNAs was also observed accentuating the role of erroneous epigenetic gene regulation in ALL. PMID:26308964

  7. 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

  8. 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

  9. 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

  10. Diverse CRISPR-Cas responses and dramatic cellular DNA changes and cell death in pKEF9-conjugated Sulfolobus species.

    PubMed

    Liu, Guannan; She, Qunxin; Garrett, Roger A

    2016-05-19

    The Sulfolobales host a unique family of crenarchaeal conjugative plasmids some of which undergo complex rearrangements intracellularly. Here we examined the conjugation cycle of pKEF9 in the recipient strain Sulfolobus islandicus REY15A. The plasmid conjugated and replicated rapidly generating high average copy numbers which led to strong growth retardation that was coincident with activation of CRISPR-Cas adaptation. Simultaneously, intracellular DNA was extensively degraded and this also occurred in a conjugated Δcas6 mutant lacking a CRISPR-Cas immune response. Furthermore, the integrated forms of pKEF9 in the donor Sulfolobus solfataricus P1 and recipient host were specifically corrupted by transposable orfB elements, indicative of a dual mechanism for inactivating free and integrated forms of the plasmid. In addition, the CRISPR locus of pKEF9 was progressively deleted when conjugated into the recipient strain. Factors influencing activation of CRISPR-Cas adaptation in the recipient strain are considered, including the first evidence for a possible priming effect in Sulfolobus The 3-Mbp genome sequence of the donor P1 strain is presented. PMID:27098036

  11. Diagnosis System for Hepatocellular Carcinoma Based on Fractal Dimension of Morphometric Elements Integrated in an Artificial Neural Network

    PubMed Central

    Gheonea, Dan Ionuț; Streba, Costin Teodor; Vere, Cristin Constantin; Șerbănescu, Mircea; Pirici, Daniel; Comănescu, Maria; Streba, Letiția Adela Maria; Ciurea, Marius Eugen; Mogoantă, Stelian; Rogoveanu, Ion

    2014-01-01

    Background and Aims. Hepatocellular carcinoma (HCC) remains a leading cause of death by cancer worldwide. Computerized diagnosis systems relying on novel imaging markers gained significant importance in recent years. Our aim was to integrate a novel morphometric measurement—the fractal dimension (FD)—into an artificial neural network (ANN) designed to diagnose HCC. Material and Methods. The study included 21 HCC and 28 liver metastases (LM) patients scheduled for surgery. We performed hematoxylin staining for cell nuclei and CD31/34 immunostaining for vascular elements. We captured digital images and used an in-house application to segment elements of interest; FDs were calculated and fed to an ANN which classified them as malignant or benign, further identifying HCC and LM cases. Results. User intervention corrected segmentation errors and fractal dimensions were calculated. ANNs correctly classified 947/1050 HCC images (90.2%), 1021/1050 normal tissue images (97.23%), 1215/1400 LM (86.78%), and 1372/1400 normal tissues (98%). We obtained excellent interobserver agreement between human operators and the system. Conclusion. We successfully implemented FD as a morphometric marker in a decision system, an ensemble of ANNs designed to differentiate histological images of normal parenchyma from malignancy and classify HCCs and LMs. PMID:25025042

  12. 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.

  13. 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.

  14. Multi-Analyte Biosensing -- The Integration of Sensing Elements into a Photolithographically Constructed Hydrogel Based Biosensor Platform

    NASA Astrophysics Data System (ADS)

    Schmid, Matthew John

    together and then assembled into randomly ordered arrays using highly-parallelized self-assembly techniques. The three-dimensional hydrogel features accommodate a wide variety of sensing elements, such as enzymes, antibodies and cells, which cannot be deployed using the traditional designs. This dissertation presents methods developed to integrate cellular and oligonucleotide sensing elements into the hydrogel features which preserve their biological activity and optimize the sensor's performance.

  15. ICE Afe 1, an actively excising genetic element from the biomining bacterium Acidithiobacillus ferrooxidans.

    PubMed

    Bustamante, Paula; Covarrubias, Paulo C; Levicán, Gloria; Katz, Assaf; Tapia, Pablo; Holmes, David; Quatrini, Raquel; Orellana, Omar

    2012-01-01

    Integrative conjugative elements (ICEs) are self-transferred mobile genetic elements that contribute to horizontal gene transfer. An ICE (ICEAfe1) was identified in the genome of Acidithiobacillus ferrooxidans ATCC 23270. Excision of the element and expression of relevant genes under normal and DNA-damaging growth conditions was analyzed. Bioinformatic tools and DNA amplification methods were used to identify and to assess the excision and expression of genes related to the mobility of the element. Both basal and mitomycin C-inducible excision as well as expression and induction of the genes for integration/excision are demonstrated, suggesting that ICEAfe1 is an actively excising SOS-regulated mobile genetic element. The presence of a complete set of genes encoding self-transfer functions that are induced in response to DNA damage caused by mitomycin C additionally suggests that this element is capable of conjugative transfer to suitable recipient strains. Transfer of ICEAfe1 may provide selective advantages to other acidophiles in this ecological niche through dissemination of gene clusters expressing transfer RNAs, CRISPRs, and exopolysaccharide biosynthesis enzymes, probably by modification of translation efficiency, resistance to bacteriophage infection and biofilm formation, respectively. These data open novel avenues of research on conjugative transformation of biotechnologically relevant microorganisms recalcitrant to genetic manipulation. PMID:23486178

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. Quench characteristics of HTSC elements in integrated three-phase flux-lock type SFCL according to ground-fault types

    NASA Astrophysics Data System (ADS)

    Lim, S. H.; Han, T. H.; Cho, Y. S.; Choi, H. S.; Han, B. S.; Lee, Su-Won

    2007-10-01

    The quench characteristics of high-TC superconducting (HTSC) elements in the integrated three-phase flux-lock type superconducting fault current limiter (SFCL), which consisted of HTSC elements and a three-phase flux-lock reactor wound on one iron core with the same turn's ratio between coil 1 and coil 2 in each single phase, were investigated. In a normal condition, the magnetic flux generated in the iron core is zero because the magnetic flux generated between two coils of each single phase is canceled out. However, unlike other three-phase SFCL with three isolated iron cores, the integrated three-phase flux-lock type SFCL showed the different fault current limiting characteristics for the three-phase faults such as the single line-to-ground fault, the double line-to-ground fault, the line-to-line fault and the triple line-to-ground fault. In addition, the power burden of HTSC elements comprising the integrated three-phase flux-lock type SFCL can be decreased. In this paper, we investigated the quench characteristics of HTSC elements in the integrated three-phase flux-lock type SFCL according to three-phase ground fault types. Through the experiments for the fault current limiting characteristics of this type SFCL according to three-phase ground fault types, the quench characteristics of HTSC elements were analyzed and compared with those of three-phase resistive type SFCL.

  3. Soviet phase conjugation research

    SciTech Connect

    Fisher, R.A.; Boyd, R.W.; Klein, M.B.; Kurnit, N.A.; Milonni, P.W.; Rockwell, D.A.; Yeh, P.

    1990-09-01

    Optical phase conjugation is a Soviet-discovered technique that applies nonlinear optical effects to automatically manipulate laser beams while automatically correcting for arbitrary distortions. Optical phase conjugation can aid in providing improved configurations for average-power and high-peak-power laser systems; it can provide nearly automatic pointing and tracking laser systems; and it can provide many other practical applications (both military and nonmilitary). Here it is important to note that 100- to 1000-watt systems are also of significant importance, not just ultra-high-energy or high-power lasers designed to do significant structural damage at significant distances. One class of phase conjugation techniques, namely, stimulated Brillouin scattering, along with its four-wave mixing counterpart, Brillioun-enhanced four-wave mixing, has been the hallmark of the Soviet effort -- with nearly all contributions (both theoretical and experimental) arising from the Soviet Union. Both stimulated Brillouin scattering and Brillouin-enhanced four-wave mixing arise from the same electrostrictive nonlinearity, where the presence of a gradient in the optical intensity produces a force on the fluid. Scientists in the United States started studying optical phase conjugation approximately five years after Soviet scientists, and initially concentrated on areas quite different from those of Soviet emphasis.

  4. 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…

  5. 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.

  6. 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)

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Conjugate flow action functionals

    NASA Astrophysics Data System (ADS)

    Venturi, Daniele

    2013-11-01

    We present a new general framework to construct an action functional for a non-potential field theory. The key idea relies on representing the governing equations relative to a diffeomorphic flow of curvilinear coordinates which is assumed to be functionally dependent on the solution field. Such flow, which will be called the conjugate flow, evolves in space and time similarly to a physical fluid flow of classical mechanics and it can be selected in order to symmetrize the Gâteaux derivative of the field equations with respect to suitable local bilinear forms. This is equivalent to requiring that the governing equations of the field theory can be derived from a principle of stationary action on a Lie group manifold. By using a general operator framework, we obtain the determining equations of such manifold and the corresponding conjugate flow action functional. In particular, we study scalar and vector field theories governed by second-order nonlinear partial differential equations. The identification of transformation groups leaving the conjugate flow action functional invariant could lead to the discovery of new conservation laws in fluid dynamics and other disciplines.

  13. 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.

  14. Prediction of plasma-facing ICRH antenna behavior via a Finite-Element solution of coupled Integral Equations

    NASA Astrophysics Data System (ADS)

    Lancellotti, V.; Milanesio, D.; Maggiora, R.; Vecchi, G.; Kyrytsya, V.

    2005-09-01

    The demand for a predictive tool to help designing ICRH antennas for fusion experiments has driven the development of codes like ICANT, RANT3D, and the early developments and further upgrades of TOPICA code. Currently, TOPICA handles the actual geometry of ICRH antennas (with their housing, etc.) as well as a realistic plasma model, including density and temperature profiles and FLR effects. Both goals have been attained by formally splitting the problem into two parts: the vacuum region around the antenna, and the plasma region inside the toroidal chamber. Field continuity and boundary conditions allow writing a set of coupled integral equations for the unknown equivalent (current) sources; finite elements are used on a triangular-cell mesh and a linear system is obtained on application of the weighted-residual solution scheme. In the vacuum region calculations are done in the spatial domain, whereas in the plasma region a spectral (wavenumber) representation of fields and currents is adopted, thus allowing a description of the plasma by a surface impedance matrix. Thanks to this approach, any plasma model can be used in principle, and at present Brambilla's FELICE code has been employed. The natural outputs of TOPICA are the induced currents on the conductors and the electric field in front of the plasma, whence the antenna circuit parameters (impedance/scattering matrices), the radiated power and the fields (at locations other than the chamber aperture) are then obtained. An accurate model of the feeding coaxial lines is also included. This paper is precisely devoted to the description of TOPICA, whereas examples of results for real-life antennas are reported in a companion paper [1] in this proceedings.

  15. Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition.

    PubMed

    Shakoor, Nadia; Ziegler, Greg; Dilkes, Brian P; Brenton, Zachary; Boyles, Richard; Connolly, Erin L; Kresovich, Stephen; Baxter, Ivan

    2016-04-01

    Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. The identification of genes and alleles that modify element content in the grains of cereals, including sorghum (Sorghum bicolor), is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high-throughput work flow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel, representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome-wide association was demonstrated by implementing rank transformation and a multilocus mixed model to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc, manganese, nickel, calcium, and cadmium in sorghum seeds. In addition to strong candidates for these five elements, we provide a list of candidate loci for several other elements. Our approach enabled the identification of single-nucleotide polymorphisms in strong linkage disequilibrium with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement. PMID:26896393

  16. 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

  17. pDGO100, a type 1 IncC plasmid from 1981 carrying ARI-A and a Tn1696-like transposon in a novel integrating element.

    PubMed

    Harmer, Christopher J; Partridge, Sally R; Hall, Ruth M

    2016-07-01

    Most A/C plasmids sequenced to date were recovered in the last two decades. To gain insight into the evolution of this group, the IncC plasmid pDGO100, found in a multiply antibiotic-resistant Escherichia coli strain isolated in 1981, was sequenced. pDGO100 belongs to the type 1 lineage and carries an ARI-A antibiotic resistance island but not an ARI-B island. The A/C2 backbone of pDGO100 has a deletion in the rhs1 gene previously found in pRMH760 and differs by only six single base pair substitutions from pRMH760, recovered at the same hospital 16years later. This confirms that the separation of type 1 and type 2 IncC plasmids is long standing. The ARI-A islands are also closely related, but pRMH760 contains Tn4352B in tniA of Tn402, while in pDGO100, Tn4352 has inserted into merA of pDUmer. pDGO100 also carries an additional 46kb insertion that includes a Tn1696-like transposon with the dfrB3 gene cassette. This insertion was identified as a novel integrating element, with an int gene at one end, and also includes the fec iron uptake operon that has been acquired from the E. coli chromosome. Related integrating elements carrying the same int gene were found in A/C2, IncHI1, and IncHI2 plasmids, and in the chromosomes of Enterobacter cloacae, Klebsiella oxytoca, and Cronobacter sakazakii isolates. In the Enterobacteriaceae chromosomes, these integrating elements appear to target a gene encoding a radical SAM superfamily protein. In the A/C2, IncHI1, and IncHI2 plasmids, genes encoding a phosphoadenosine phosphosulfate reductase were interrupted. The extremities of the integrating element are highly conserved, whilst the internal gene content varies. The detection of integrative elements in plasmids demonstrates an increased range of locations into which this type of mobile element can integrate and insertion in plasmids is likely to assist their spread. PMID:27318267

  18. An integrated approach for risk object re-entry predictions in terms of KS elements and genetic algorithm

    NASA Astrophysics Data System (ADS)

    Sharma, R. K.; Anil Kumar, A. K.; Xavier James Raj, M.

    strategy (Sharma & Anilkumar 2003) adopted for the re-entry prediction of the risk objects by estimating the ballistic coefficient based on the TLEs. The estimation of the ballistic coefficient Bn = m/(CDA), where CD is the drag coefficient, A is the reference area, and m is the mass of the object, is done by minimizing a cost function (variation in the re-entry prediction time) using Genetic algorithm. The KS element equations of motion are numerically integrated with a suitable integration step size with the 4th - order Runge-Kutta-Gill method till the end of the orbital life, by including the Earth's oblateness with J2 to J6 terms, and modelling the air drag forces through an analytical oblate diurnal atmosphere with the density scale height varying with altitude. Jacchia (1977) atmospheric model, which takes into consideration the epoch, daily solar flux (F10.7) and geomagnetic index (Ap) for computation of density and density scale height, is utilized. The basic feature of the present approach is that the model and measurement errors are accountable in terms of adjusting the ballistic coefficient and hence the estimated Bn is not the actual ballistic coefficient but an effective ballistic coefficient. It is demonstrated that the inaccuracies or deficiencies in the inputs, like F10.7 and Ap values, are absorbed in the estimated Bn. The details of the re-entry results based on this approach, utilizing the TLE of debris objects, US Sat No. 25947 and SROSS-C2 Satellite, which re-entered the Earth's atmosphere on 4th March 2000 and 12th July 2001, are provided. Details of the re-entry predictions with respect to the 4th and 5th IADC re-entry campaigns, related to COSMOS 1043 rocket body and COSMOS 389 satellite, which re-entered the Earth's atmosphere on 19 January 2002 and 24 November 2003, respectively, are described. The predicted re-entries were found to be all along quite close to the actual re-entry time, with quite less uncertainties bands on the predictions. A

  19. Prospectivity modeling of porphyry-Cu deposits by identification and integration of efficient mono-elemental geochemical signatures

    NASA Astrophysics Data System (ADS)

    Parsa, Mohammad; Maghsoudi, Abbas; Yousefi, Mahyar; Sadeghi, Martiya

    2016-02-01

    Dispersion pattern of geochemical elements in stream sediment data of a study area is affected by several factors, e.g., geological and geomorphological characteristics of the area. In this paper, we demonstrated recognition of efficient and inefficient mono-elemental geochemical signatures in a study area and exclusion of inefficient elements is worthwhile for increasing the probability of exploration success. For this, we adapted prediction-area (P-A) plot, normalized density and success-rate curve as tools that evaluate the ability of geochemical signatures in prediction of undiscovered mineral deposits and in delimiting exploration targets. After identification of efficient and inefficient elements, we combined efficient indicator elements to generate an effective prospectivity model. To illustrate the procedure we used a stream sediment data set for prospecting porphyry-Cu deposits in the Noghdouz area, Iran.

  20. Frequency translating phase conjugation circuit for active retrodirective antenna array

    NASA Astrophysics Data System (ADS)

    Chernoff, R.

    1980-11-01

    An active retrodirective antenna array which has central phasing from a reference antenna element through a "tree" structured network of transmission lines utilizes a number of phase conjugate circuits (PCCs) at each node and a phase reference regeneration circuit (PRR) at each node except the initial node. Each node virtually coincides with an element of the array. A PCC generates the exact conjugate phase of an incident signal using a phase locked loop which combines the phases in an up converter, divides the sum by 2 and mixes the result with the phase in a down converter for phase detection. The PRR extracts the phase from the conjugate phase. Both the PCC and the PRR are not only exact but also free from mixer degeneracy.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. Novel Tn4371-ICE like element in Ralstonia pickettii and Genome mining for comparative elements

    PubMed Central

    2009-01-01

    Background Integrative Conjugative Elements (ICEs) are important factors in the plasticity of microbial genomes. An element related to the ICE Tn4371 was discovered during a bioinformatic search of the Ralstonia pickettii 12J genome. This element was analysed and further searches carried out for additional elements. A PCR method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight Ralstonia pickettii and Ralstonia insidiosa strains were analysed for the presence of the element. Results Comparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several β and γ- Proteobacteria. These elements vary in size, GC content, putative function and have a mosaic-like structure of plasmid- and phage-like sequences which is typical of Tn4371-like ICEs. These elements were found after a through search of the GenBank database. The elements, which are found in Ralstonia, Delftia, Acidovorax, Bordetella, Comamonas, Acidovorax, Congregibacter, Shewanella, Pseudomonas Stenotrophomonas, Thioalkalivibrio sp. HL-EbGR7, Polaromonas, Burkholderia and Diaphorobacter sp. share a common scaffold. A PCR method was designed (based on the Tn4371- like element detected in the Ralstonia pickettii 12J genome) to detect and characterise new elements of this type. Conclusion All elements found in this study possess a common scaffold of core genes but contain different accessory genes. A new uniform nomenclature is suggested for ICEs of the Tn4371 family. Two novel Tn4371-like ICE were discovered and characterised, using the novel PCR method described in two different isolates of Ralstonia pickettii from laboratory purified water. PMID:19941653

  7. Non Linear Conjugate Gradient

    Energy Science and Technology Software Center (ESTSC)

    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

  8. 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.

  9. 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°. PMID:24385032

  10. 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

  11. Use of geochemical signatures, including rare earth elements, in mosses and lichens to assess spatial integration and the influence of forest environment

    NASA Astrophysics Data System (ADS)

    Gandois, L.; Agnan, Y.; Leblond, S.; Séjalon-Delmas, N.; Le Roux, G.; Probst, A.

    2014-10-01

    In order to assess the influence of local environment and spatial integration of Trace Metals (TM) by biomonitors, Al, As, Cd, Cr, Cs, Cu, Fe, Mn, Ni, Pb, Sb, Sn, V and Zn and some rare earth element (REE) concentrations have been measured in lichens and mosses collected in three French forest sites located in three distinct mountainous areas, as well as in the local soil and bedrock, and in both bulk deposition (BD) and throughfall (TF). Similar enrichment factors (EF) were calculated using lichens and mosses and local bedrock for most elements, except for Cs, Mn, Ni, Pb, and Cu which were significantly (KW, p < 0.05) more enriched in mosses. Similar REE ratios were measured in soils, bedrock, lichens and mosses at each study sites, indicating a regional integration of atmospheric deposition by both biomonitors. Both TM signature and REE composition of mosses revealed that this biomonitor is highly influenced by throughfall composition, and reflect atmospheric deposition interaction with the forest canopy. This explained the higher enrichment measured in mosses for elements which concentration in deposition were influenced by the canopy, either due to leaching (Mn), direct uptake (Ni), or dry deposition dissolution (Pb, Cu, Cs).

  12. 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.

  13. A Strategy for Preservice Teachers to Integrate Cultural Elements within Planning and Instruction: Cultural L.I.V.E.S.

    ERIC Educational Resources Information Center

    Salsbury, Denise E.

    2008-01-01

    The large percentages of teachers in the United States are white, middle class people who may not understand or identify their own cultural connections within the American culture, let alone elaborate their own ancestral cultural elements. Educators are expected to teach a diverse student population, and preservice teachers should be prepared to…

  14. 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

  15. 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

  16. Conjugate-Gradient Algorithms For Dynamics Of Manipulators

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Scheid, Robert E.

    1993-01-01

    Algorithms for serial and parallel computation of forward dynamics of multiple-link robotic manipulators by conjugate-gradient method developed. Parallel algorithms have potential for speedup of computations on multiple linked, specialized processors implemented in very-large-scale integrated circuits. Such processors used to stimulate dynamics, possibly faster than in real time, for purposes of planning and control.

  17. Characterization of the genetic elements required for site-specific integration of plasmid pSE211 in Saccharopolyspora erythraea.

    PubMed

    Brown, D P; Idler, K B; Katz, L

    1990-04-01

    The 18.1-kilobase plasmid pSE211 integrates into the chromosome of Saccharopolyspora erythraea at a specific attB site. Restriction analysis of the integrated plasmid, pSE211int, and adjacent chromosomal sequences allowed identification of attP, the plasmid attachment site. Nucleotide sequencing of attP, attB, attL, and attR revealed a 57-base-pair sequence common to all sites with no duplications of adjacent plasmid or chromosomal sequences in the integrated state, indicating that integration takes place through conservative, reciprocal strand exchange. An analysis of the sequences indicated the presence of a putative gene for Phe-tRNA at attB which is preserved at attL after integration has occurred. A comparison of the attB site for a number of actinomycete plasmids is presented. Integration at attB was also observed when a 2.4-kilobase segment of pSE211 containing attP and the adjacent plasmid sequence was used to transform a pSE211- host. Nucleotide sequencing of this segment revealed the presence of two complete open reading frames (ORFs) and a segment of a third ORF. The ORF adjacent to attP encodes a putative polypeptide 437 amino acids in length that shows similarity, at its C-terminal domain, to sequences of site-specific recombinases of the integrase family. The adjacent ORF encodes a putative 98-amino-acid basic polypeptide that contains a helix-turn-helix motif at its N terminus which corresponds to domains in the Xis proteins of a number of bacteriophages. A proposal for the function of this polypeptide is presented. The deduced amino acid sequence of the third ORF did not reveal similarities to polypeptide sequences in the current data banks. PMID:2180909

  18. 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.

  19. Poro-viscoelastic constitutive modeling of unconfined creep of hydrogels using finite element analysis with integrated optimization method.

    PubMed

    Liu, Kaifeng; Ovaert, Timothy C

    2011-04-01

    Hydrogels are cross-linked polymer networks swollen with water and are being considered as potential replacements for deceased load bearing tissues such as cartilage. Hydrogels show nonlinear time dependent behavior, and are a challenge to model. A three-element poro-viscoelastic constitutive model was developed based on the structure and nature of the hydrogel. To identify the material parameters, an inverse finite element (FE) technique was used that combines experimental results with FE modeling and an optimization method. Unconfined compression creep tests were conducted on poly(vinyl alcohol) (PVA) and poly(ethylene-co-vinyl alcohol)-poly(vinyl pyrrolidone) (EVAL-PVP) hydrogels manufactured by injection molding. Results from the creep experiments showed that for PVA hydrogels, an increase in polymer concentration correlates with a decrease in the equilibrium water content (EWC) and the creep strain. In EVAL-PVP hydrogels, an increase in the hydrophobic segments (EVAL) correlates with a decrease in the EWC as well as the creep strain. An inverse FE method was used to identify the viscoelastic material parameters of the hydrogels in combination with creep testing using the poro-viscoelastic three-element constitutive model. The elastic modulus estimated from the inverse FE technique showed good agreement with the modulus estimated directly from the test data. PMID:21316632

  20. Is emergency management an integrated element of business continuity management? A case study with security professionals in Western Australia.

    PubMed

    Frohde, Kenny; Brooks, David J

    2014-01-01

    Emergency management (EM) and business continuity management (BCM) frameworks incorporate various strategic and operational measures. Defined within a number of national and international standards and guidelines, such concepts may be integrated within one another to provide increased resilience to disruptive events. Nevertheless, there is a degree of dispute regarding concept integration among security and EM professionals and bodies of knowledge. In line with cognitive psychology exemplar-based concepts, such disputes may be associated with a lack of precision in communality in the approach to EM and BCM. This paper presents a two-stage study, where stage 1 critiqued national and international literature and stage 2 applied semi-structured interviews with security managers in Western Australia. Findings indicate the existence of contradictory views on EM and its integration within BCM. As such, this study concludes that EM is considered a vital component of BCM by the majority of security managers. However, there is broader dispute regarding its degree of integration. Understanding the underpinnings of such disputes will aid in raising the standards and application of professionalism within security, EM and BCM domains, supporting clarification and definition of professional boundaries. PMID:25193457

  1. 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…

  2. Defined DNA/nanoparticle conjugates.

    PubMed

    Ackerson, Christopher J; Sykes, Michael T; Kornberg, Roger D

    2005-09-20

    Glutathione monolayer-protected gold clusters were reacted by place exchange with 19- or 20-residue thiolated oligonucleotides. The resulting DNA/nanoparticle conjugates could be separated on the basis of the number of bound oligonucleotides by gel electrophoresis and assembled with one another by DNA-DNA hybridization. This approach overcomes previous limitations of DNA/nanoparticle synthesis and yields conjugates that are precisely defined with respect to both gold and nucleic acid content. PMID:16155122

  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. 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

  5. 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.

  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. PMID:25529239

  7. Three-dimensional/two-dimensional convertible projection screen using see-through integral imaging based on holographic optical element.

    PubMed

    Yeom, Jiwoon; Jeong, Jinsoo; Jang, Changwon; Li, Gang; Hong, Keehoon; Lee, Byoungho

    2015-10-20

    We propose a 3D/2D convertible screen using a holographic optical element and angular multiplexing method of volume hologram. The proposed screen, named a multiplexed holographic optical element screen (MHOES), is composed of passive optical components, and displaying modes between 3D and 2D modes are converted according to projection directions. In a recording process, the angular multiplexing method by using two reference waves with different incidence angles enables the functions of 3D and 2D screens to be recorded in a single holographic material. Also, in order to avoid the bulky experimental setup due to adopting different projectors for the 3D and 2D modes, the projection part is realized based on a prism. The designed projection part enables the single projector to present 3D on 2D mode, where the 3D and 2D contents are simultaneously displayed in one scene, without active components. The optical characteristics of MHOES are experimentally analyzed, and displaying experiments with a full-color MHOES are presented in order to verify the 3D/2D convertibility and see-through properties. PMID:26560370

  8. 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

  9. 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

  10. Mapping synapses by conjugate light-electron array tomography.

    PubMed

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

    2015-04-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    1993-08-01

    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

  12. 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

  13. 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

  14. Prospects of Bacteriotherapy with Nanotechnology in Nanoparticledrug Conjugation Approach for Cancer Therapy.

    PubMed

    Raj, Ritu; Das, Surajit

    2016-01-01

    Bacteriotherapy and nanotechnology have shown remarkable potential in diagnostic and therapeutic applications for various diseases. Individual impacts of these micro-nano systems over different aspects of human health are well studied; however, an integrated system of bacteria-nanoparticle (NP) conjugation is less explored. The untamed potential of bacteria-NP conjugation could be a new tool for diagnosis and treatment of invasive diseases like malaria, tuberculosis and cancer. Mammalian cells exhibit cytosis as their defense mechanism when they encounter foreign elements such as bacteria. In these mammalian cells, during phagocytosis, bacteria are ruptured and lysed by lysozymes. A bacterium carrying the drug-tagged NP would be engulfed in the same manner and ultimately reaches the target cells. Rapid and continuous cell divisions in the cancer tissues lead to defective vessels, underdeveloped cellcell interconnects, development of hypoxic areas and heterogeneous population of tumor cells. This unorganized and poorly developed angiogenesis in tumor cells makes it difficult for conventional chemotherapeutic drugs to localize the tumors selectively. In the present scenario of diagnosis and treatment of cancer/tumor cells, it could be expected that the existing bacteriotherapy with the advanced nanotechnology would be a way further in the targeted drug delivery for cancer therapy. This review emphasizes the potential applications of bacteriotherapy with nanotechnology for the diagnosis and treatment of cancer. PMID:27048378

  15. 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

  16. 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. PMID:18321254

  17. IS5 Element Integration, a Novel Mechanism for Rapid In Vivo Emergence of Tigecycline Nonsusceptibility in Klebsiella pneumoniae

    PubMed Central

    Snesrud, Erik C.; Onmus-Leone, Fatma; Kwak, Yoon I.; Avilés, Ricardo; Steele, Eric D.; Sutter, Deena E.; Waterman, Paige E.; Lesho, Emil P.

    2014-01-01

    Tigecycline nonsusceptibility is concerning because tigecycline is increasingly relied upon to treat carbapenem- or colistin-resistant organisms. In Enterobacteriaceae, tigecycline nonsusceptibility is mediated by the AcrAB-TolC efflux pump, among others, and pump activity is often a downstream effect of mutations in their transcriptional regulators, cognate repressor genes, or noncoding regions, as demonstrated in Enterobacteriaceae and Acinetobacter isolates. Here, we report the emergence of tigecycline nonsusceptibility in a longitudinal series of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Klebsiella pneumoniae isolates collected during tigecycline therapy and the elucidation of its resistance mechanisms. Clinical isolates were recovered prior to and during tigecycline therapy of a 2.5-month-old Honduran neonate. Antimicrobial susceptibility tests to tigecycline determined that the MIC increased from 1 to 4 μg/ml prior to the completion of tigecycline therapy. Unlike other studies, we did not find increased expression of ramA, ramR, oqxA, acrB, marA, or rarA genes by reverse transcription-quantitative PCR (qRT-PCR). Whole-genome sequencing revealed an IS5 insertion element in nonsusceptible isolates 85 bp upstream of a putative efflux pump operon, here named kpgABC, previously unknown to be involved in resistance. Introduction of the kpgABC genes in a non-kpgABC background increased the MIC of tigecycline 4-fold and is independent of a functional AcrAB-TolC pump. This is the first report to propose a function for kpgABC and identify an insertion element whose presence correlated with the in vivo development of tigecycline nonsusceptibility in K. pneumoniae. PMID:25092708

  18. 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.

  19. Haematological malignancies: the rationale for integrated haematopathology services, key elements of organization and wider contribution to patient care.

    PubMed

    Ireland, Robin

    2011-01-01

    The National Institute for Clinical Excellence (NICE) defined the process of care for haematological malignancies in Improving outcomes in haematological cancers. The manual in 2003. The most challenging recommendation has been the requirement to develop integrated laboratory services for accurate diagnosis. This is an aim that has not been fully achieved. The unified concept of haematological malignancy is recent and based on an understanding of the cellular pathology of the bone marrow and immune systems. Historical UK pathology practice has previously resulted in the separation of laboratory haematology from histopathology and of liquid and tissue specimens. Proposals for reintegration and centralization with specialist-led, centralized diagnostic and reporting services challenge the fragmented historical model. Accuracy and certainty of diagnosis remains problematic, particularly for lymphomas, with evidence that the accuracy of diagnosis is slowly improving but still only approaches 85%. There is a potentially significant human and financial cost of diagnostic errors. No nationwide, validated and comparable epidemiology/population-based data exist for accurate and complete ascertainment of new cases of haematological cancer, service planning or clinical outcomes monitoring. This article examines the original rationale behind the NICE guidance and outlines the key components and processes of an integrated diagnostic service. PMID:21261689

  20. Analysis of dynamic characteristics and ways of development of bipolar main memory with miniaturization of integrated circuit elements

    NASA Astrophysics Data System (ADS)

    Sergeyev, A. G.; Savenkov, V. N.; Parmenov, Y. A.; Neklyudov, V. A.; Mindeyeva, A. A.

    1984-08-01

    A forecast estimate of the characteristics of a super large scale integrated circuit (super-BIS) memory as applied to bipolar main memory (OZU) circuits is presented. The limiting speed of bipolar OSU with d 2 micrometer will be determined by the characteristics of the interconnections and not by the parameters of bipolar devices. With d 2 micrometer, slowing down of the rate of growth of the response speed of OZU must be expected as the result of miniaturization as a consequence of the increase of the specific capacities of the p-n junctions and the metallization and constraint on the current density in the interconnections. The limitation and the specific properties of the energetics of bipolar OZU--localization of the current in separate lines, leads to a variance between speed of response and the decree of integration. For realization of the potentially high speed of response of bipolar OSU an improvement is necessary of the technology of the interconnections with the object of an increase of the current density to master a three layered system of interconnections.

  1. 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

  2. The overview of reviews: unique challenges and opportunities when research syntheses are the principal elements of new integrative scholarship.

    PubMed

    Cooper, Harris; Koenka, Alison C

    2012-09-01

    In the past two decades, a new form of scholarship has appeared in which researchers present an overview of previously conducted research syntheses on the same topic. In these efforts, research syntheses are the principal units of evidence. Overviews of reviews introduce unique problems that require unique solutions. This article describes what methods overviewers have developed or have adopted from other forms of scholarship. These methods concern how to (a) define the broader problem space of an overview, (b) conduct literature searches that specifically look for research syntheses, (c) address the overlap in evidence in related reviews, (d) evaluate the quality of both primary research and research syntheses, (e) integrate the outcomes of research syntheses, especially when they produce discordant results, (f) conduct a second-order meta-analysis, and (g) present findings. The limitations of overviews are also discussed, especially with regard to the age of the included evidence. PMID:22352742

  3. 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.

  4. 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.

  5. [Hypno-analysis: On the integration of hypnotic elements in individual uncovering psychotherapy in patients with anxiety disorder].

    PubMed

    Hinrichs, R

    2001-01-01

    Following a short history of the development of the therapeutic techniques of psychoanalysis as derived from the basic rules of hypnosis, the apparent contradictions between the two approaches are called into question, with particular reference to the importance and efficacy of suggestion and suggestibility in both methods. How the integration of hypnotic interventions can both intensify and at the same time shorten the process of analytic therapy is demonstrated by two vignettes. The range of indications for the use of hypnosis as a complementary measure is currently restricted to the analysis of resistance and of the making conscious of past traumatic experiences that are involved in the psychogenesis of anxiety disorders. Particular importance is attached to the careful establishment of the indication and then psychoanalytic working-through of the accompanying transference-countertransference-dynamics following the completion of the hypno-analytic phase and in the course of the ongoing uncovering therapeutic process. PMID:11568865

  6. 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

  7. Oligonucleotide conjugates for therapeutic applications

    PubMed Central

    Winkler, Johannes

    2013-01-01

    Insufficient pharmacokinetic properties and poor cellular uptake are the main hurdles for successful therapeutic development of oligonucleotide agents. The covalent attachment of various ligands designed to influence the biodistribution and cellular uptake or for targeting specific tissues is an attractive possibility to advance therapeutic applications and to expand development options. In contrast to advanced formulations, which often consist of multiple reagents and are sensitive to a variety of preparation conditions, oligonucleotide conjugates are defined molecules, enabling structure-based analytics and quality control techniques. This review gives an overview of current developments of oligonucleotide conjugates for therapeutic applications. Attached ligands comprise peptides, proteins, carbohydrates, aptamers and small molecules, including cholesterol, tocopherol and folic acid. Important linkage types and conjugation methods are summarized. The distinct ligands directly influence biochemical parameters, uptake machanisms and pharmacokinetic properties. PMID:23883124

  8. 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.

  9. Integrated geophysical interpretation for delineating the structural elements and groundwater aquifers at central part of Sinai Peninsula, Egypt

    NASA Astrophysics Data System (ADS)

    Araffa, Sultan Awad Sultan; Sabet, Hassan S.; Gaweish, Wael R.

    2015-05-01

    The study area is inhabited by Bedouins, suffering from scarcity of water necessary for domestic use and agricultural activities. The study area is located at central part of Sinai between Nakhl area and El Thamed area. Magnetic, gravity and geoelectric methods were used in this investigation to determine the groundwater aquifers and delineate the structural elements in the study area. Two hundreds and eighty eight magnetic and gravity stations were acquired by the EnviMag and Autograv CG3 instruments respectively. The magnetic data were processed by using Oasis Montaj. Reductions to the pole and 2D magnetic modeling were established to construct basement relief map. The depth to the basement rocks in the study area is ranging from 1200 m to 7000 m. The regional-residual separation and Euler deconvolution techniques were applied to the gravity data. Nine deep Vertical Electrical Sounding stations were measured to estimate the deep groundwater aquifer in the study area (Nubian Sandstone aquifer). The depth of upper surface of Nubian Sandstone aquifer is ranging between 975 m and 1100 m and affected by two major fault trends in the NE-SW and NW-SE directions.

  10. Defined DNA/nanoparticle conjugates

    NASA Astrophysics Data System (ADS)

    Ackerson, Christopher J.; Sykes, Michael T.; Kornberg, Roger D.

    2005-09-01

    Glutathione monolayer-protected gold clusters were reacted by place exchange with 19- or 20-residue thiolated oligonucleotides. The resulting DNA/nanoparticle conjugates could be separated on the basis of the number of bound oligonucleotides by gel electrophoresis and assembled with one another by DNA-DNA hybridization. This approach overcomes previous limitations of DNA/nanoparticle synthesis and yields conjugates that are precisely defined with respect to both gold and nucleic acid content. Freely available online through the PNAS open access option.

  11. 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

  12. Enzyme-Regulated Supramolecular Assemblies of Cholesterol Conjugates against Drug-Resistant Ovarian Cancer Cells.

    PubMed

    Wang, Huaimin; Feng, Zhaoqianqi; Wu, Dongdong; Fritzsching, Keith J; Rigney, Mike; Zhou, Jie; Jiang, Yujie; Schmidt-Rohr, Klaus; Xu, Bing

    2016-08-31

    We report that phosphotyrosine-cholesterol conjugates effectively and selectively kill cancer cells, including platinum-resistant ovarian cancer cells. The conjugate increases the degree of noncovalent oligomerization upon enzymatic dephosphorylation in aqueous buffer. This enzymatic conversion also results in the assembly of the cholesterol conjugates inside and outside cells and leads to cell death. Preliminary mechanistic studies suggest that the formed assemblies of the conjugates not only interact with actin filaments and microtubules but also affect lipid rafts. As the first report of multifaceted supramolecular assemblies of cholesterol conjugates against cancer cells, this work illustrates the integration of enzyme catalysis and self-assembly of essential biological small molecules on and inside cancer cells as a promising strategy for developing multifunctional therapeutics to treat drug-resistant cancers. PMID:27529637

  13. Synthesis, characterization, and application of microbe-triggered controlled-release kasugamycin-pectin conjugate.

    PubMed

    Liu, Yao; Sun, Yan; Ding, Guanglong; Geng, Qianqian; Zhu, Juanli; Guo, Mingcheng; Duan, Yongheng; Wang, Baitao; Cao, Yongsong

    2015-05-01

    The controlled and targeted release of pesticides with high water solubility has been a challenge for integrated pest management. In this paper, kasugamycin, an antibiotic broadly used in plant disease control, was covalently conjugated to pectin to form a kasugamycin-pectin conjugate by an amide bond. The conjugate was structurally characterized by Fourier transform infrared spectroscopy, ultraviolet spectrophotometry, and thermal gravimetric analysis. The results showed that the conjugate was stable over a wide range of pH and temperatures, as well as under UV irradiation. When incubated with Pseudomonas syringae pv. lachrymans, the conjugate could be activated, releasing the kasugamycin, which made it a promising controlled-release formulation of pesticide. PMID:25876441

  14. 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

  15. Antibody conjugates with unnatural amino acids.

    PubMed

    Hallam, Trevor J; Wold, Erik; Wahl, Alan; Smider, Vaughn V

    2015-06-01

    Antibody conjugates are important in many areas of medicine and biological research, and antibody-drug conjugates (ADCs) are becoming an important next generation class of therapeutics for cancer treatment. Early conjugation technologies relied upon random conjugation to multiple amino acid side chains, resulting in heterogeneous mixtures of labeled antibody. Recent studies, however, strongly support the notion that site-specific conjugation produces a homogeneous population of antibody conjugates with improved pharmacologic properties over randomly coupled molecules. Genetically incorporated unnatural amino acids (uAAs) allow unique orthogonal coupling strategies compared to those used for the 20 naturally occurring amino acids. Thus, uAAs provide a novel paradigm for creation of next generation ADCs. Additionally, uAA-based site-specific conjugation could also empower creation of additional multifunctional conjugates important as biopharmaceuticals, diagnostics, or reagents. PMID:25898256

  16. 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.

  17. A spreadable, non-integrative and high copy number shuttle vector for Sulfolobus solfataricus based on the genetic element pSSVx from Sulfolobus islandicus.

    PubMed

    Aucelli, Tiziana; Contursi, Patrizia; Girfoglio, Michele; Rossi, Mosè; Cannio, Raffaele

    2006-01-01

    The pSSVx genetic element from Sulfolobus islandicus REY15/4 is a hybrid between a plasmid and a fusellovirus, able to be maintained in non-integrative form and to spread when the helper SSV2 virus is present in the cells. In this work, the satellite virus was engineered to obtain an Escherichia coli-Sulfolobus solfataricus shuttle vector for gene transfer and expression in S.solfataricus by fusing site-specifically the pSSVx chromosome with an E.coli plasmid replicon and the ampicillin resistance gene. The pSSVx-based vector was proven functional like the parental virus, namely it was able to spread efficiently through infected S.solfataricus cells. Moreover, the hybrid plasmid stably transformed S.solfataricus and propagated with no rearrangement, recombination or integration into the host chromosome. The high copy number of the artificial genetic element was found comparable with that calculated for the wild-type pSSVx in the new host cells, with no need of genetic markers for vector maintenance in the cells and for transfomant enrichment. The newly constructed vector was also shown to be an efficient cloning vehicle for the expression of passenger genes in S.solfataricus. In fact, a derivative plasmid carrying an expression cassette of the lacS gene encoding the beta-glycosidase from S.solfataricus under the control of the Sulfolobus chaperonine (thermosome tf55) heat shock promoter was also able to drive the expression of a functional enzyme. Complementation of the beta-galactosidase deficiency in a deletion mutant strain of S.solfataricus demonstrated that lacS gene was an efficient marker for selection of single transformants on solid minimal lactose medium. PMID:16971457

  18. 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

  19. Hybridization of the Vector Finite Element Method with the Boundary Integral Method for the Solution of Finite Arrays of Cavity-Backed Slot Antennas

    NASA Astrophysics Data System (ADS)

    Polycarpou, A. C.

    2009-10-01

    The vector finite element method (FEM) is hybridized with the boundary integral (BI) method to solve for the radiation characteristics of a cavity-backed slot (CBS) antenna. The hybridization of the two methods is made possible at the aperture of the antenna separating the cavity interior and the half-space exterior region above an infinite conducting ground plane. Having to solve for a finite array of CBS antennas requires an excessive amount of memory, in order to store the system matrix, and considerable CPU time for the solution of the resulting linear system of equations. Increasing the number of array elements results in a non-linear increase in the number of unknowns, thus making the solution of the linear system impossible. In this paper, we adopt array domain decomposition (ADD) and by taking advantage of the repetitive features of the array, we can reduce the memory requirements to a minimum. In addition, we introduce stationary and non-stationary iteration techniques, with or without preconditioning, to solve the system of linear equations in an efficient manner. Singular value decomposition (SVD) is also used in order to further reduce memory requirements and speed-up matrix-vector multiplications that are inherent in either type of iterative techniques. Computational statistics and comparisons between stationary and non-stationary techniques are presented and discussed.

  20. Antibody-drug conjugate payloads.

    PubMed

    Anderl, Jan; Faulstich, Heinz; Hechler, Torsten; Kulke, Michael

    2013-01-01

    Toxin payloads, or drugs, are the crucial components of therapeutic antibody-drug conjugates (ADCs). This review will give an introduction on the requirements that make a toxic compound suitable to be used in an antitumoral ADC and will summarize the structural and mechanistic features of four drug families that yielded promising results in preclinical and clinical studies. PMID:23913141

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. Airborne LiDAR data as a key element of the integrated monitoring of the reservoir shore zone development

    NASA Astrophysics Data System (ADS)

    Kaczmarek, Halina

    2015-04-01

    formats, the raster with a resolution of 0.5 m and the point cloud of the resolution of min. 4 points per m2. Their compilation with the materials previously used in the study, such as surveying, the DGP measurements of the upper edge of the cliff (2009), aerial photographs (1991 and 2004), and orthophotomap (1992) made it possible to determine the rate and direction of the transformation of the shore of the Jeziorsko Reservoir since its construction until 2011. This study was supported by the Virtual Institute of Integrated Climate and Landscape Evolution (ICLEA) of the Helmholtz Association.

  7. Parallel conjugate gradient algorithms for manipulator dynamic simulation

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Scheld, Robert E.

    1989-01-01

    Parallel conjugate gradient algorithms for the computation of multibody dynamics are developed for the specialized case of a robot manipulator. For an n-dimensional positive-definite linear system, the Classical Conjugate Gradient (CCG) algorithms are guaranteed to converge in n iterations, each with a computation cost of O(n); this leads to a total computational cost of O(n sq) on a serial processor. A conjugate gradient algorithms is presented that provide greater efficiency using a preconditioner, which reduces the number of iterations required, and by exploiting parallelism, which reduces the cost of each iteration. Two Preconditioned Conjugate Gradient (PCG) algorithms are proposed which respectively use a diagonal and a tridiagonal matrix, composed of the diagonal and tridiagonal elements of the mass matrix, as preconditioners. Parallel algorithms are developed to compute the preconditioners and their inversions in O(log sub 2 n) steps using n processors. A parallel algorithm is also presented which, on the same architecture, achieves the computational time of O(log sub 2 n) for each iteration. Simulation results for a seven degree-of-freedom manipulator are presented. Variants of the proposed algorithms are also developed which can be efficiently implemented on the Robot Mathematics Processor (RMP).

  8. 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.

  9. D-π-A conjugated molecules for optoelectronic applications.

    PubMed

    Kim, Tae-Dong; Lee, Kwang-Sup

    2015-06-01

    Dipolar chromophores consisting of electron donor (D) and electron acceptor (A) groups connected through a conjugated π-bridge have been actively studied and integrated in optoelectronic and electronic devices. Generally, such π-conjugated molecules provide substantial delocalization of π-electrons over the molecules. Here, a brief overview of recent research on D-π-A dipolar chromophores including their syntheses and several promising applications is reported, especially in nonlinear optical devices and organic photovoltaics. Structure/property relationships are discussed in order to exploit the potentials by tuning the π-electron density, polarizability, and HOMO-LUMO band gap of the chromophores. Some of the examples may well set the stage for chip-scale integration of optoelectronics as well as the realization of an important array of new device technologies. PMID:25820642

  10. 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)

  11. Conjugative Plasmids of Neisseria gonorrhoeae

    PubMed Central

    Pachulec, Emilia; van der Does, Chris

    2010-01-01

    Many clinical isolates of the human pathogen Neisseria gonorrhoeae contain conjugative plasmids. The host range of these plasmids is limited to Neisseria species, but presence of a tetracycline (tetM) determinant inserted in several of these plasmids is an important cause of the rapid spread of tetracycline resistance. Previously plasmids with different backbones (Dutch and American type backbones) and with and without different tetM determinants (Dutch and American type tetM determinants) have been identified. Within the isolates tested, all plasmids with American or Dutch type tetM determinants contained a Dutch type plasmid backbone. This demonstrated that tetM determinants should not be used to differentiate between conjugal plasmid backbones. The nucleotide sequences of conjugative plasmids with Dutch type plasmid backbones either not containing the tetM determinant (pEP5233) or containing Dutch (pEP5289) or American (pEP5050) type tetM determinants were determined. Analysis of the backbone sequences showed that they belong to a novel IncP1 subfamily divergent from the IncP1α, β, γ, δ and ε subfamilies. The tetM determinants were inserted in a genetic load region found in all these plasmids. Insertion was accompanied by the insertion of a gene with an unknown function, and rearrangement of a toxin/antitoxin gene cluster. The genetic load region contains two toxin/antitoxins of the Zeta/Epsilon toxin/antitoxin family previously only found in Gram positive organisms and the virulence associated protein D of the VapD/VapX toxin/antitoxin family. Remarkably, presence of VapX of pJD1, a small cryptic neisserial plasmid, in the acceptor strain strongly increased the conjugation efficiency, suggesting that it functions as an antitoxin for the conjugative plasmid. The presence of the toxin and antitoxin on different plasmids might explain why the host range of this IncP1 plasmid is limited to Neisseria species. The isolated plasmids conjugated efficiently between

  12. Self-organizing conjugated polymers

    NASA Astrophysics Data System (ADS)

    Hong, Xiaoyong Michael

    2000-10-01

    A general and efficient synthetic route to semifluoroalkyl substituted thiophenes has been developed and a series of 3-semifluoroalkylthiophenes were synthesized. The lengths of the fluorocarbon chain and hydrocarbon spacer between thiophene and fluorocarbon were systematically altered to study their effect on the properties of the resulting polymers. Oxidative polymerization (FeCl3) and electrochemical polymerization of 3-semifluoroalkylthiophenes afforded regiorandom (head-to-tail coupling ˜70%) homopolymers. The solubility and thermal transition temperatures of the polymers are also dependent on the nature of side chains. The surface properties of the polymers are also a function of the length of fluoroalkyl side chains. From x-ray diffraction, the regiorandom polymers have low crystallinity. Two synthetic methods have been successfully utilized to prepare regioregular poly(3-semifluoroalkylthiophene)s (head-to-tail coupling >90%) and gave identical polymers. The regioregular polymers are highly conjugated and highly ordered. The long side chain substituted polythiophenes form a liquid crystal mesophase between the crystal solid and isotropic liquid phases. To prepare polymers bearing alternating 3-semifluoroalkylthiophene and alkylthiophene units, we developed synthetic methods to 3-semifluoroalkyl-4 '-alkyl-2,2'-bithiophenes. The 3-semifluoroalkyl-4 '-alkyl-2,2'-bithiophenes were polymerized to afford regiorandom and regioregular polymers. Regiorandom polymers have low crystallinity and conjugation. Regioregular, strictly alternating copolymer with 3-semifluoroalkylthiophene and alkylthiophene units are highly conjugated and ordered. The regioregular polymers self-assemble into bilayer structure in solid state due to phase separation between fluorocarbon and hydrocarbon. At high temperatures close to melting transition, the thiophene rings rotate and twist along the molecular axis to give a single layer structure. Methylene bridges were placed between the

  13. Multifunctional Aptamer-miRNA Conjugates for Targeted Cancer Therapy

    PubMed Central

    Esposito, Carla L; Cerchia, Laura; Catuogno, Silvia; De Vita, Gennaro; Dassie, Justin P; Santamaria, Gianluca; Swiderski, Piotr; Condorelli, Gerolama; Giangrande, Paloma H; de Franciscis, Vittorio

    2014-01-01

    While microRNAs (miRNAs) clearly regulate multiple pathways integral to disease development and progression, the lack of safe and reliable means for specific delivery of miRNAs to target tissues represents a major obstacle to their broad therapeutic application. Our objective was to explore the use of nucleic acid aptamers as carriers for cell-targeted delivery of a miRNA with tumor suppressor function, let-7g. Using an aptamer that binds to and antagonizes the oncogenic receptor tyrosine kinase Axl (GL21.T), here we describe the development of aptamer-miRNA conjugates as multifunctional molecules that inhibit the growth of Axl-expressing tumors. We conjugated the let-7g miRNA to GL21.T and demonstrate selective delivery to target cells, processing by the RNA interference machinery, and silencing of let-7g target genes. Importantly, the multifunctional conjugate reduced tumor growth in a xenograft model of lung adenocarcinoma. Therefore, our data establish aptamer-miRNA conjugates as a novel tool for targeted delivery of miRNAs with therapeutic potential. PMID:24441398

  14. Recent Advances in Conjugated Polymer Materials for Disease Diagnosis.

    PubMed

    Lv, Fengting; Qiu, Tian; Liu, Libing; Ying, Jianming; Wang, Shu

    2016-02-10

    The extraordinary optical amplification and light-harvesting properties of conjugated polymers impart sensing systems with higher sensitivity, which meets the primary demands of early cancer diagnosis. Recent advances in the detection of DNA methylation and mutation with polyfluorene derivatives based fluorescence resonance energy transfer (FRET) as a means to modulate fluorescent responses attest to the great promise of conjugated polymers as powerful tools for the clinical diagnosis of diseases. To facilitate the ever-changing needs of diagnosis, the development of detection approaches and FRET signal analysis are highlighted in this review. Due to their exceptional brightness, excellent photostability, and low or absent toxicity, conjugated polymers are verified as superior materials for in-vivo imaging, and provide feasibility for future clinical molecular-imaging applications. The integration of conjugated polymers with clinical research has shown profound effects on diagnosis for the early detection of disease-related biomarkers, as well as in-vivo imaging, which leads to a multidisciplinary scientific field with perspectives in both basic research and application issues. PMID:26679834

  15. 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

  16. Single conjugated polymer nanoparticle capacitors

    NASA Astrophysics Data System (ADS)

    Palacios, Rodrigo E.; Lee, Kwang-Jik; Rival, Arnaud; Adachi, Takuji; Bolinger, Joshua C.; Fradkin, Leonid; Barbara, Paul F.

    2009-02-01

    The hole injection from a carbazole derivative hole transport layer into nanoparticles ( r = 25 ± 15 nm) of the conjugated polymer MEH-PPV was investigated by an indirect single-particle fluorescence-quenching technique. The results suggest that there is a kinetic barrier for hole injection that prevents polymer particles from being charged in the dark. This barrier can be overcome with the assistance of optical excitation of the MEH-PPV nanoparticles, achieving a thermodynamic population of injected holes at positive bias. The amount of injected holes at equilibrium is observed to depend upon the bias in a manner highly consistent with device simulations based on a continuum model. Overall, the results demonstrate that the hole injection into nano domains of conjugated polymers is a complex process depending upon molecular interfacial effects determined by device geometry and electrostatic interactions.

  17. 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.

  18. 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

  19. 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.

  20. Globular Cluster Abundances from High-resolution, Integrated-light Spectroscopy. IV. The Large Magellanic Cloud: α, Fe-peak, Light, and Heavy Elements

    NASA Astrophysics Data System (ADS)

    Colucci, Janet E.; Bernstein, Rebecca A.; Cameron, Scott A.; McWilliam, Andrew

    2012-02-01

    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 ~ 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 χ2-minimization spectral synthesis technique to facilitate measurement of weak (~15 mÅ) spectral lines and abundances in low signal-to-noise ratio data (S/N ~ 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 [α/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 results can be used to constrain both

  1. 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

  2. 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.

  3. 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. PMID:25523211

  4. 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. PMID:26784936

  5. 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.

  6. 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.

  7. GHF-1/Pit-1 functions as a cell-specific integrator of Ras signaling by targeting the Ras pathway to a composite Ets-1/GHF-1 response element.

    PubMed

    Bradford, A P; Conrad, K E; Tran, P H; Ostrowski, M C; Gutierrez-Hartmann, A

    1996-10-01

    Activation of the rat prolactin (rPRL) promoter by Ras is a prototypical example of tissue-specific transcriptional regulation in a highly differentiated cell type. Using a series of site-specific mutations and deletions of the proximal rPRL promoter we have mapped the major Ras/Raf response element (RRE) to a composite Ets-1/GHF-1 binding site located between positions -217 and -190. Mutation of either the Ets-1 or GHF-1 binding sites inhibits Ras and Raf activation of the rPRL promoter, and insertion of this RRE into the rat growth hormone promoter confers Ras responsiveness. We show that Ets-1 is expressed in GH4 cells and, consistent with their functional synergistic interaction, both Ets-1 and GHF-1 are able to bind specifically to this bipartite RRE. We confirm that Ets-1 or a related Ets factor is the nuclear target of the Ras pathway leading to activation of the rPRL promoter and demonstrate that Elk-1 and Net do not mediate the Ras response. Thus, the pituitary-specific POU homeodomain transcription factor, GHF-1, serves as a cell-specific signal integrator by functionally interacting with an Ets-1-like factor, at uniquely juxtaposed binding sites, thereby targeting an otherwise ubiquitous Ras signaling pathway to a select subset of cell-specific GHF-1-dependent genes. PMID:8798730

  8. 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

  9. 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.

  10. 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.

  11. 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…

  12. Some Theoretical Aspects for Elastic Wave Modeling in a Recently Developed Spectral Element Method

    NASA Astrophysics Data System (ADS)

    Wang, X. M.; Seriani, G.; Lin, W. J.

    2006-10-01

    A spectral element method has been recently developed for solving elastodynamic problems. The numerical solutions are obtained by using the weak formulation of the elastodynamic equation for heterogeneous media and by the Galerkin approach applied to a partition, in small subdomains, of the original physical domain under investigation. In the present work some mathematical aspects of the method and of the associated algorithm implementation are systematically investigated. Two kinds of orthogonal basis functions, constructed with Legendre and Chebyshev polynomials, and their related Gauss-Lobbatto collocation points, used in reference element quadrature, are introduced. The related analytical integration formulas are obtained. The standard error estimations and expansion convergence are discussed. In order to improve the computation accuracy and efficiency, an element-by-element pre-conditioned conjugate gradient linear solver in the space domain and a staggered predictor/multi-corrector algorithm in the time integration are used for strong heterogeneous elastic media. As a consequence neither the global matrices, nor the effective force vector is assembled. When analytical formula are used for the element quadrature, there is even no need for forming element matrix in order to further save memory without loosing much in computational efficiency. The element-by-element algorithm uses an optimal tensor product scheme which makes spectral element methods much more efficient than finite-element methods from the point of view of both memory storage and computational time requirements. This work is divided into two parts. The second part will give the algorithm implementation, numerical accuracy and efficiency analyses, and then the modelling example comparison of the proposed spectral element method with a conventional finite-element method and a staggered pseudo-spectral method that is to be reported in the other work.

  13. Enhanced optical phase conjugation in nonlinear metamaterials.

    PubMed

    Kim, Kihong

    2014-12-15

    Optical phase conjugation by degenerate four-wave mixing in nonlinear metamaterials is studied theoretically by solving the coupled wave equations using a generalized version of the invariant imbedding method. The phase-conjugate reflectance and the lateral shift of the phase-conjugate reflected beams are calculated and their dependencies on the frequency, the polarization, the incident angle, the material properties and the structure are investigated in detail. It is found that the efficiency of phase conjugation can be significantly enhanced due to the enhancement of electromagnetic fields in various metamaterial structures. PMID:25607488

  14. 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.

  15. Conjugative Transfer in Staphylococcus aureus.

    PubMed

    Halsey, Cortney R; Fey, Paul D

    2016-01-01

    The acquisition of plasmids has led to a significant increase in antimicrobial resistance within the staphylococci. In order to study these plasmids effectively, one must be able move the plasmid DNA into genetically clean backgrounds. While the smaller staphylococcal class I (1-5 kb) and class II (10-30 kb) plasmids are readily transferred using bacteriophage transduction or electroporation, these methods are inefficient at moving the larger class III (30-60 kb) plasmids. This review describes methods to transfer class III plasmids via conjugative mobilization. PMID:26194708

  16. Phase conjugated slab laser designator

    SciTech Connect

    Chandra, S.; Paul, J.L.

    1989-06-06

    A laser designator is described comprising a laser pump means; a high power phase conjugated slab laser amplifier formed of GSGG:Cr:Nd as a lasing material on one side of the pump means; a low power rod shaped laser oscillator on the opposite side of the pump means; and a first plurality of optical reflecting and refracting means for directing and shaping a laser beam which surrounds the pump means and passes through the rod and slab; and a telescope means coupled to the beam to direct it to a distant target.

  17. A physico-chemical assessment of the thermal stability of pneumococcal conjugate vaccine components

    PubMed Central

    Gao, Fang; Lockyer, Kay; Burkin, Karena; Crane, Dennis T; Bolgiano, Barbara

    2014-01-01

    Physico-chemical analysis of pneumococcal polysaccharide (PS)-protein conjugate vaccine components used for two commercially licensed vaccines was performed to compare the serotype- and carrier protein-specific stabilities of these vaccines. Nineteen different monovalent pneumococcal conjugates from commercial vaccines utilizing CRM197, diphtheria toxoid (DT), Protein D (PD) or tetanus toxoid (TT) as carrier proteins were incubated at temperatures up to 56°C for up to eight weeks or were subjected to freeze-thawing (F/T). Structural stability was evaluated by monitoring their size, integrity and carrier protein conformation. The molecular size of the vaccine components was well maintained for Protein D, TT and DT conjugates at -20°C, 4°C and F/T, and for CRM197 conjugates at 4°C and F/T. It was observed that four of the eight serotypes of Protein D conjugates tended to form high molecular weight complexes at 37°C or above. The other conjugated carrier proteins also appeared to form oligomers or ‘aggregates’ at elevated temperatures, but rarely when frozen and thawed. There was evidence of degradation in some of the conjugates as evidenced by the formation of lower molecular weight materials which correlated with measured free saccharide. In conclusion, pneumococcal-Protein D/TT/DT and most CRM197 bulk conjugate vaccines were stable when stored at 2–8°C, the recommended temperature. In common between the conjugates produced by the two manufacturers, serotypes 1, 5, and 19F were relatively less stable and 6B was the most stable, with types 7F and 23F also showing good stability. PMID:25483488

  18. 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.

  19. Quasi-Optimal Schwarz Methods for the Conforming Spectral Element Discretization

    NASA Technical Reports Server (NTRS)

    Casarin, Mario

    1996-01-01

    Fast methods are proposed for solving the system K(sub N)x = b resulting from the discretization of self-adjoint elliptic equations in three dimensional domains by the spectral element method. The domain is decomposed into hexahedral elements, and in each of these elements the discretization space is formed by polynomials of degree N in each variable. Gauss-Lobatto-Legendre (GLL) quadrature rules replace the integrals in the Galerkin formulation. This system is solved by the preconditioned conjugate gradients method. The conforming finite element space on the GLL mesh consisting of piecewise Q(sub 1) elements produces a stiffness matrix K(sub h) that is spectrally equivalent to the spectral element stiffness matrix K(sub N). The action of the inverse of K(sub h) is expensive for large problems, and is therefore replaced by a Schwarz preconditioner B(sub h) of this finite element stiffness matrix. The preconditioned operator then becomes B(sub h)(exp -l)K(sub N). The technical difficulties stem from the nonregularity of the mesh. Tools to estimate the convergence of a large class of new iterative substructuring and overlapping Schwarz preconditioners are developed. This technique also provides a new analysis for an iterative substructuring method proposed by Pavarino and Widlund for the spectral element discretization.

  20. Operational mechanism of conjugated polyelectrolytes.

    PubMed

    Tordera, Daniel; Kuik, Martijn; Rengert, Zachary D; Bandiello, Enrico; Bolink, Henk J; Bazan, Guillermo C; Nguyen, Thuc-Quyen

    2014-06-18

    Conjugated polyelectrolytes (CPEs) are versatile materials used in a range of organic optoelectronic applications. Because of their ionic/electronic nature, characterizing these materials is nontrivial, and their operational mechanism is not fully understood. In this work we use a methodology that combines constant-voltage-driven current-density transient measurements with fast current vs voltage scans to allow decoupling of ionic and electronic phenomena. This technique is applied to diodes prepared with cationic CPEs having different charge-compensating anions. Our results indicate that the operational mechanism of these devices is governed by electrochemical doping of the CPE. On the basis of the notion that the saturated depletion layer for the anions consists of the same π-conjugated backbone material, we discern how the extent and speed of formation of the doped region depend on the anion structure. Apart from addressing fundamental transport questions, this work provides a tool for future characterization of different CPEs and other similar systems. PMID:24855971

  1. Solution assembly of conjugated polymers

    NASA Astrophysics Data System (ADS)

    Bokel, Felicia A.

    This dissertation focuses on the solution-state polymer assembly of conjugated polymers with specific attention to nano- and molecular-scale morphology. Understanding how to control these structures holds potential for applications in polymer-based electronics. Optimization of conjugated polymer morphology was performed with three objectives: 1) segregation of donor and acceptor materials on the nanometer length-scale, 2) achieving molecular-scale ordering in terms of crystallinity within distinct domains, and 3) maximizing the number and quality of well-defined donor/acceptor interfaces. Chapter 1 introduces the development of a mixed solvent method to create crystalline poly(3-hexyl thiophene) (P3HT) fibrils in solution. Chapter 2 describes fibril purification and approaches to robust and functional fibrils, while chapters 3 and 4 demonstrate the formation of hybrid nanocomposite wires of P3HT and cadmium selenide (CdSe) nanoparticles by two methods: 1) co-crystallization of free and P3HT-grafted CdSe for composite nanowires and 2) direct attachment of CdSe nanoparticles at fibril edges to give superhighway structures. These composite structures show great potential in the application of optoelectronic devices, such as the active layer of solar cells. Finally, ultrafast photophysical characterization of these polymers, using time-resolved photoluminescence and transient absorption, was performed to determine the aggregation types present in suspended fibrils and monitor the formation and decay of charged species in fibrils and donor-acceptor systems.

  2. Photoluminescence of Conjugated Star Polymers

    NASA Astrophysics Data System (ADS)

    Ferguson, J. B.; Prigodin, N. V.; Epstein, A. J.; Wang, F.

    2000-10-01

    Higher dimensionality "star" polymers provide new properties beyond those found in their linear analogs. They have been used to improving electronic properties for nonlinear optics through exciton transfer and molecular antenna structures for example (M. Kawa, J. M. J. Frechet, Chem. Mater. 10, 286 (1998).). We report on photoluminescence properties of star polymers with a hyperbranched core (both hyperbranched phenlyene and hyperbranched triphenylamine) and polyhexylthiophene arms. The arm is a conjugated oligomer of polythiophene that has been investigated extensively for metallic like conductivity when doped as well as utilized in field effect transistors in its undoped form (A. Tsumara, H. Koezuka, T. Ando, Appl. Phys. Lett. 49, 1210 (1986).). The cores are respectively, a nonconjugated polymer in the case of hyperbranched phenlyene and a conjugated polymer in the case of hyperbranched triphenylamine. The photoluminesce spectrum (λ_max at 575 nm) is identical for both star polymers with the two electronically different hyperbranched cores and for linear polythiophene alone. We conclude the wave functions of the core and arms do not strongly interact to form states different from their individual states and excitons formed on the hyperbranched cores migrate to the lower bandgap polythiophene before recombining.

  3. Analysis of diffraction imaging in non-conjugate configurations.

    PubMed

    Pan, Ran; Feng, Yuanming; Sa, Yu; Lu, Jun Q; Jacobs, Kenneth M; Hu, Xin-Hua

    2014-12-15

    Diffraction imaging of scattered light allows extraction of information on scatterer's morphology. We present a method for accurate simulation of diffraction imaging of single particles by combining rigorous light scattering model with ray-tracing software. The new method has been validated by comparison to measured images of single microspheres. Dependence of fringe patterns on translation of an objective based imager to off-focus positions has been analyzed to clearly understand diffraction imaging with multiple optical elements. The calculated and measured results establish unambiguously that diffraction imaging should be pursued in non-conjugate configurations to ensure accurate sampling of coherent light distribution from the scatterer. PMID:25607106

  4. Shape-Encoded Chitosan-Polyacrylamide Hybrid Hydrogel Microparticles with Controlled Macroporous Structures via Replica Molding for Programmable Biomacromolecular Conjugation.

    PubMed

    Kang, Eunae; Jung, Sukwon; Abel, John H; Pine, Allison; Yi, Hyunmin

    2016-05-31

    Polymeric hydrogel microparticle-based suspension arrays with shape-based encoding offer powerful alternatives to planar and bead-based arrays toward high throughput biosensing and medical diagnostics. We report a simple and robust micromolding technique for polyacrylamide- (PAAm-) based biopolymeric-synthetic hybrid microparticles with controlled 2D shapes containing a potent aminopolysaccharide chitosan as an efficient conjugation handle uniformly incorporated in PAAm matrix. A postfabrication conjugation approach utilizing amine-reactive chemistries on the chitosan shows stable incorporation and retained chemical reactivity of chitosan, readily tunable macroporous structures via simple addition of low content long-chain PEG porogens for improved conjugation capacity and kinetics, and one-pot biomacromolecular assembly via bioorthogonal click reactions with minimal nonspecific binding. We believe that the integrated fabrication-conjugation approach reported here could offer promising routes to programmable manufacture of hydrogel microparticle-based biomacromolecular conjugation and biofunctionalization platforms for a large range of applications. PMID:27191399

  5. Block copolymer modified surfaces for conjugation of biomacromolecules with control of quantity and activity.

    PubMed

    Li, Xin; Wang, Mengmeng; Wang, Lei; Shi, Xiujuan; Xu, Yajun; Song, Bo; Chen, Hong

    2013-01-29

    Polymer brush layers based on block copolymers of poly(oligo(ethylene glycol) methacrylate) (POEGMA) and poly(glycidyl methacrylate) (PGMA) were formed on silicon wafers by activators generated by electron transfer atom transfer radical polymerization (AGET ATRP). Different types of biomolecule can be conjugated to these brush layers by reaction of PGMA epoxide groups with amino groups in the biomolecule, while POEGMA, which resists nonspecific protein adsorption, provides an antifouling environment. Surfaces were characterized by water contact angle, ellipsometry, and Fourier transform infrared spectroscopy (FTIR) to confirm the modification reactions. Phase segregation of the copolymer blocks in the layers was observed by AFM. The effect of surface properties on protein conjugation was investigated using radiolabeling methods. It was shown that surfaces with POEGMA layers were protein resistant, while the quantity of protein conjugated to the diblock copolymer modified surfaces increased with increasing PGMA layer thickness. The activity of lysozyme conjugated on the surface could also be controlled by varying the thickness of the copolymer layer. When biotin was conjugated to the block copolymer grafts, the surface remained resistant to nonspecific protein adsorption but showed specific binding of avidin. These properties, that is, well-controlled quantity and activity of conjugated biomolecules and specificity of interaction with target biomolecules may be exploited for the improvement of signal-to-noise ratio in sensor applications. More generally, such surfaces may be useful as biological recognition elements of high specificity for functional biomaterials. PMID:23265296

  6. 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.

  7. 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.

  8. 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)

  9. 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.

  10. 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.

  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. New TFO conjugates containing a carminomycinone-derived chromophore.

    PubMed

    Capobianco, M L; De Champdoré, M; Francini, L; Lena, S; Garbesi, A; Arcamone, F

    2001-01-01

    Conjugates obtained by linking the anthracycline intercalating chromophore to triple helix forming oligonucleotides (TFOs) have been used in a physicochemical study of the stability of triple helices with DNA sequences of pharmacological relevance. The intercalating moiety is represented by carminomycinone derivatives obtained upon O-demethylation and hydrolysis of the glycosidic linkage of daunomycin followed by the introduction of an alkylating residue at two different positions. Results of experiments with a polypurinic region present in the multidrug resistance (MDR) gene indicate that the stability of the triple helix is significantly enhanced by replacement of C's with (5-Me)C's in the TFO sequences tested. The stability is not changed when a 3'-TpT is present in place of a 3'-CpG at the presumed intercalation site of the anthraquinone chromophore. The same carminomycinone derivatives were used for the preparation of conjugates able to form triple helices with the polypurine tract (PPT) present in the human integrated genome of HIV-1 infected cells. Three different TFOs (T(4)(Me)CT(4)(Me)CC, C2; T(4)(Me)CT(4)(Me)CC(Me)CC(Me)CCT, C6; and T(4)(Me)CT(4)G(6), G6) were designed and linked to the anthraquinone moiety. These conjugates showed a significantly enhanced ability to bind the PPT region of HIV with respect to the nonconjugated TFOs. PMID:11459456

  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. New porphyrin glyco-conjugates

    NASA Astrophysics Data System (ADS)

    Drain, Charles M.; Singh, Sunaina; Samaroo, Diana; Thompson, Sebastian; Vinodu, Mikki; Tome, Joao P. C.

    2009-06-01

    Porphyrins bearing sugars and other motifs are proposed for a variety of therapeutic applications. Non-hydrolysable glyco conjugates of porphyrins can be formed in rapid, room temperature reacting in greater than 90% yields from tetraperfluorophenyporphyrin. Additional functional groups can be appended using the same chemistry but different stoichiometries of the reagents. Thus sugars, amines, peptides, and cationic moieties designed to target cancer cells or other diseased or disease-causing cells are made rapidly and cleanly. These compounds can then be rapidly screened for cell uptake, or selected from combinatorial libraries by cell uptake assays using a combination of fluorescence microscopy and mass spectrometry. Modifications of the macrocycle allow fine-tuning of the photonic properties for specific medical, imaging, or biochemical applications.

  15. Characterization of the Ends and Target Sites of the Novel Conjugative Transposon Tn5397 from Clostridium difficile: Excision and Circularization Is Mediated by the Large Resolvase, TndX

    PubMed Central

    Wang, Hongmei; Roberts, Adam P.; Lyras, Dena; Rood, Julian I.; Wilks, Mark; Mullany, Peter

    2000-01-01

    Tn5397 is a conjugative transposon that was originally isolated from Clostridium difficile. Previous analysis had shown that the central region of Tn5397 was closely related to the conjugative transposon Tn916. However, in this work we obtained the DNA sequence of the ends of Tn5397 and showed that they are completely different to those of Tn916. Tn5397 did not contain the int and xis genes, which are required for the excision and integration of Tn916. Instead, the right end of Tn5397 contained a gene, tndX, that appears to encode a member of the large resolvase family of site-specific recombinases. TndX is closely related to the TnpX resolvase from the mobilizable but nonconjugative chloramphenicol resistance transposons, Tn4451 from Clostridium perfringens and Tn4453 from C. difficile. Like the latter elements, inserted copies of Tn5397 were flanked by a direct repeat of a GA dinucleotide. The Tn5397 target sites were also shown to contain a central GA dinucleotide. Excision of the element in C. difficile completely regenerated the original target sequence. A circular form of the transposon, in which the left and right ends of the element were separated by a GA dinucleotide, was detected by PCR in both Bacillus subtilis and C. difficile. A Tn5397 mutant in which part of tndX was deleted was constructed in B. subtilis. This mutant was nonconjugative and did not produce the circular form of Tn5397, indicating that the TndX resolvase has an essential role in the excision and transposition of Tn5397 and is thus the first example of a member of the large resolvase family of recombinases being involved in conjugative transposon mobility. Finally, we showed that introduction of Tn916 into a strain containing Tn5397 induced the loss of the latter element in 95.6% of recipients. PMID:10850994

  16. Staining Fission Yeast Filamentous Actin with Fluorescent Phalloidin Conjugates.

    PubMed

    Hagan, Iain M

    2016-01-01

    The Schizosaccharomyces pombe filamentous (F)-actin cytoskeleton drives cell growth, morphogenesis, endocytosis, and cytokinesis. The protocol described here reveals the distribution of F-actin in fixed cells through the use of fluorescently conjugated phalloidin. Simultaneous staining of cell wall landmarks (with calcofluor) and chromatin (with 4',6-diamidino-2-phenylindole, or DAPI) makes this rapid staining procedure highly effective for staging cell cycle progression, monitoring morphogenetic abnormalities, and assessing the impact of environmental and genetic changes on the integrity of the F-actin cytoskeleton. PMID:27250943

  17. 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

  18. 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.

  19. 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. PMID:26118338

  20. Fullerene isoniazid conjugate--a tuberculostat with increased lipophilicity: synthesis and evaluation of antimycobacterial activity.

    PubMed

    Kumar, Anish; Patel, Gaurang; Menon, Shobhana Karuveettil

    2009-05-01

    A fullerene-isoniazid conjugate has been synthesized by 1, 3 dipolar cycloaddition reaction of fullerene (C(60)) with isonicotinic acid (4-formyl-benzylidene) hydrazide and N-methylglycine. The identity and purity of the compound was confirmed by elemental analysis, (1)H NMR, (13)C NMR and MALDI-TOF mass spectral analysis. Stable water suspension, in which the particles of the synthesized conjugate were made to aggregate in nanosize, was successfully tested for antimycobacterial activity against Mycobacterium avium and strains of Mycobacterium tuberculosis- H(37)Rv & H6/99 at concentration as low as 0.50 microg/mL. PMID:19366360

  1. 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.

  2. Ultraviolet phase conjugation and its practical implications

    SciTech Connect

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

    1980-01-01

    The first demonstration of uv phase conjugation is reported. 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 to 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. Xenobiotic conjugation with phosphate - a metabolic rarity.

    PubMed

    Mitchell, Stephen C

    2016-08-01

    1. Although not unknown, the conjugation of a xenobiotic with phosphate appears a rarity amongst the routes available for foreign compound metabolism. This is especially true in mammals and may be somewhat surprising as conjugation with sulphate, a seemingly similar moiety, is commonplace. 2. Information from the literature, where xenobiotic phosphate conjugates have been described or suggested, has been collated and presented in this article. By bringing together this diverse material, hopefully interest will be generated in this unusual xenobiotic reaction, and perhaps further research undertaken to better understand and delineate the reasons for its relative absence from the xenobiotic scene. PMID:26611118

  4. 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.

  5. 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.

  6. Design and Application of Antimicrobial Peptide Conjugates.

    PubMed

    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

  7. Mitochondria-specific Conjugated Polymer Nanoparticles

    PubMed Central

    Twomey, Megan; Mendez, Eladio; Manian, Rajesh Kumar

    2016-01-01

    Biodegradable conjugated polymer nanoparticles (CPNs) were prepared for high mitochondria targeting in live cancer cells. The degradable CPNs are nontoxic and specifically localized to mitochondria of live tumor cells through macropinocytosis followed by intracellular degradation and trafficking. PMID:26974193

  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. 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.

  10. Atomic phase conjugation from a Bose condensate

    SciTech Connect

    Goldstein, E.V.; Plaettner, K.; Meystre, P.

    1996-08-01

    The authors discuss the possibility of observing atomic phase conjugation from Bose condensates, and using it as a diagnostic tool to access the spatial coherence properties and to measure the lifetime of the condensate. They argue that since phase conjugation results from the scattering of a partial matter wave off the spatial grating produced by two other waves, it offers a natural way to directly measure such properties, and as such provides an attractive alternative to the optical methods proposed in the past.

  11. Periodic amplification and conjugation of optical solitons.

    PubMed

    Goedde, C G; Kath, W L; Kumar, P

    1995-06-15

    Nondegenerate optical parametric amplifiers can be used to simultaneously phase conjugate and amplify a pulse in a nonlinear optical fiber. The gain in the amplifiers compensates the linear loss in the fiber, while the phase conjugation effectively neutralizes second-order dispersion, self-phase modulation, the Raman self-frequency shift, and Gordon-Haus jitter. If the remaining third-order and nonlinear dispersions balance, solitonlike pulses are able to propagate with subpicosecond pulse widths. PMID:19862016

  12. 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

  13. Lens collimation and testing using a Twyman-Green interferometer with a self-pumped phase-conjugating mirror

    NASA Technical Reports Server (NTRS)

    Howes, W. L.

    1986-01-01

    Ordinarily Twyman-Green interferometers are employed testing optical elements. In a modification of the basic configuration, the ordinary mirror in the test arm is replaced with a self-pumped phase-conjugating mirror using a barium titanate crystal. It is shown that, with a redefinition of components, the new configuration permits retention and improvement of the optical element testing function while simultaneously serving as a sensitive test for collimation. The optical path difference resulting from the double pass in the original Twyman-Green interferometer approximately equals that of the single pass and phase conjugation in the modification.

  14. Neurotoxin quantum dot conjugates detect endogenous targets expressed in live cancer cells.

    PubMed

    Orndorff, Rebecca L; Rosenthal, Sandra J

    2009-07-01

    High affinity peptide neurotoxins are effective agents for integrating technological advances with biological inquiries. Both chlorotoxin (CTX) and dendrotoxin-1 (DTX-1) are peptide neurotoxins demonstrated to bind targets expressed by glioma cancer cells and are suitable ligands for quantum dot (QD) live cell investigations. Here, we present dual labeling of endogenously expressed cellular proteins within living cells utilizing high affinity peptide neurotoxins conjugated to QDs. Multiplexing experiments reveal quantifiable evidence that CTX and DTX-1 conjugated QDs may potentially be used as a live assessment of markers toward identification of cancer cell presence. PMID:19507837

  15. 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.

  16. Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation.

    PubMed

    Baharoglu, Zeynep; Bikard, David; Mazel, Didier

    2010-10-01

    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

  17. 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

  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. 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)

  20. 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

  1. 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

  2. Transfer of the methicillin resistance genomic island among staphylococci by conjugation.

    PubMed

    Ray, M D; Boundy, S; Archer, G L

    2016-05-01

    Methicillin resistance creates a major obstacle for treatment of Staphylococcus aureus infections. The resistance gene, mecA, is carried on a large (20 kb to > 60 kb) genomic island, staphylococcal cassette chromosome mec (SCCmec), that excises from and inserts site-specifically into the staphylococcal chromosome. However, although SCCmec has been designated a mobile genetic element, a mechanism for its transfer has not been defined. Here we demonstrate the capture and conjugative transfer of excised SCCmec. SCCmec was captured on pGO400, a mupirocin-resistant derivative of the pGO1/pSK41 staphylococcal conjugative plasmid lineage, and pGO400::SCCmec (pRM27) was transferred by filter-mating into both homologous and heterologous S. aureus recipients representing a range of clonal complexes as well as S. epidermidis. The DNA sequence of pRM27 showed that SCCmec had been transferred in its entirety and that its capture had occurred by recombination between IS257/431 elements present on all SCCmec types and pGO1/pSK41 conjugative plasmids. The captured SCCmec excised from the plasmid and inserted site-specifically into the chromosomal att site of both an isogenic S. aureus and a S. epidermidis recipient. These studies describe a means by which methicillin resistance can be environmentally disseminated and a novel mechanism, IS-mediated recombination, for the capture and conjugative transfer of genomic islands. PMID:26822382

  3. 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.

  4. Cellular Uptake and Cytotoxicity of Drug-Peptide Conjugates Regulated by Conjugation Site

    PubMed Central

    Zhang, Pengcheng; Cheetham, Andrew G.; Lock, Lye Lin; Cui, Honggang

    2013-01-01

    Conjugation of anticancer drugs to hydrophilic peptides such as Tat is a widely adopted strategy to improve the drug’s solubility, cellular uptake and potency against cancerous cells. Here we report that attachment of an anticancer drug doxorubicin to the N- or C-terminal of the Tat peptide can have a significant impact on their cellular uptake, cytotoxicity against both drug-sensitive and drug-resistant cancer cells. We observed higher cellular uptake by both cell lines for C-terminal conjugate relative to the N-terminal analogue. Our results reveal that the C-terminal conjugate partially overcame the multi-drug resistance of cervical cancer cells, while the N-terminal conjugate showed no significant improvement in cytotoxicity when compared with free doxorubicin. We also found that both N- and C- conjugates offers a mechanism to circumvent drug efflux associated with multidrug resistance. PMID:23514455

  5. 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.

  6. 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

  7. 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.

  8. Triplex glue by synthesizing conjugated flexible intercalators.

    PubMed

    Pedersen, Erik B; Osman, Amany M A; Globisch, Daniel; Paramasivam, Manikandan; Cogoi, Susanna; Bomholt, Niels; Jørgensen, Per T; Xodo, Luigi E; Filichev, Vyacheslav V

    2008-01-01

    Bulge insertions of conjugated intercalators into the DNA triplex structure are found to give a dramatic contribution to the triplex stability. On the other hand insertions of conjugated intercalators are found to diminish quadruplex structures and in this way breaking down the self association of G-rich oligonucleotides under physiologically potassium ion conditions. A large number of intercalators are described here and they all result in dramatic increases of thermal stability of the corresponding triplexes. Another interesting aspect of conjugated intercalators is their use for assembling alternate strand triplexes. Targeting of neighbouring purine sequences on each their strand in the duplex DNA is a challenge for the 5'- 5' connectivity of the TFOs because of a large distance between the 5'-ends. The intercalator approach offers a linkage with the proper combination of flexibility and rigidity to produce alternate strand triplexes with higher stability than a similar wild type triplex of the same total length. PMID:18776241

  9. Multicolor Upconversion Nanoparticles for Protein Conjugation

    PubMed Central

    Wilhelm, Stefan; Hirsch, Thomas; Patterson, Wendy M.; Scheucher, Elisabeth; Mayr, Torsten; Wolfbeis, Otto S.

    2013-01-01

    We describe the preparation of monodisperse, lanthanide-doped hexagonal-phase NaYF4 upconverting luminescent nanoparticles for protein conjugation. Their core was coated with a silica shell which then was modified with a poly(ethylene glycol) spacer and N-hydroxysuccinimide ester groups. The nanoparticles were characterized by transmission electron microscopy, Raman spectroscopy, X-ray diffraction, and dynamic light scattering. The N-hydroxysuccinimide ester functionalization renders them highly reactive towards amine nucleophiles (e.g., proteins). We show that such particles can be conjugated to proteins. The protein-reactive UCLNPs and their conjugates to streptavidin and bovine serum albumin display multicolor emissions upon 980-nm continuous wave laser excitation. Surface plasmon resonance studies were carried out to prove bioconjugation and to compare the affinity of the particles for proteins immobilized on a thin gold film. PMID:23606910

  10. 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.

  11. A rapid approach for characterization of thiol-conjugated antibody-drug conjugates and calculation of drug-antibody ratio by liquid chromatography mass spectrometry.

    PubMed

    Firth, David; Bell, Leonard; Squires, Martin; Estdale, Sian; McKee, Colin

    2015-09-15

    We present the demonstration of a rapid "middle-up" liquid chromatography mass spectrometry (LC-MS)-based workflow for use in the characterization of thiol-conjugated maleimidocaproyl-monomethyl auristatin F (mcMMAF) and valine-citrulline-monomethyl auristatin E (vcMMAE) antibody-drug conjugates. Deconvoluted spectra were generated following a combination of deglycosylation, IdeS (immunoglobulin-degrading enzyme from Streptococcus pyogenes) digestion, and reduction steps that provide a visual representation of the product for rapid lot-to-lot comparison-a means to quickly assess the integrity of the antibody structure and the applied conjugation chemistry by mass. The relative abundance of the detected ions also offer information regarding differences in drug conjugation levels between samples, and the average drug-antibody ratio can be calculated. The approach requires little material (<100 μg) and, thus, is amenable to small-scale process development testing or as an early component of a complete characterization project facilitating informed decision making regarding which aspects of a molecule might need to be examined in more detail by orthogonal methodologies. PMID:26070852

  12. Phase conjugation of high energy lasers.

    SciTech Connect

    Bliss, David Emery; Valley, Michael T.; Atherton, Briggs W.; Bigman, Verle; 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.

  13. 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.

  14. Conjugate mixed convection heat and mass transfer in brick drying

    NASA Astrophysics Data System (ADS)

    Suresh, H. N.; Aswatha Narayana, P. A.; Seetharamu, K. N.

    In this study, a numerical methodology for the solution of conjugate heat and mass transfer problem is presented. Fluid flow, heat and mass transfer over a rectangular brick due to transient laminar mixed convection has been numerically simulated. The coupled non-linear partial differential equations, for both gas phase and solid are solved using finite element procedure. Flow is assumed to be incompressible, two-dimensional, laminar. Analysis has been carried out at a Reynolds number of 200 with Pr=0.71. The effect of buoyancy on the brick drying has been investigated. Velocity vectors, streamlines in the flow field and temperature and moisture contours and temperature distribution along the solid surface are presented. It is observed that there is considerable effect of buoyancy during drying. The results indicate a non-uniform drying of the brick with the leading edge drying faster than the rest of the brick.

  15. 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.

  16. 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.

  17. Ubiquitin in Motion: Structural Studies of the Ubiquitin-Conjugating Enzyme~Ubiquitin Conjugate

    SciTech Connect

    Pruneda, Jonathan N.; Stoll, Kate E.; Bolton, Laura J.; Brzovic, Peter S.; Klevit, Rachel E.

    2011-03-15

    Ubiquitination of proteins provides a powerful and versatile post-translational signal in the eukaryotic cell. The formation of a thioester bond between ubiquitin (Ub) and the active site of a ubiquitin-conjugating enzyme (E2) is critical for the transfer of Ub to substrates. Assembly of a functional ubiquitin ligase (E3) complex poised for Ub transfer involves recognition and binding of an E2~Ub conjugate. Therefore, full characterization of the structure and dynamics of E2~Ub conjugates is required for further mechanistic understanding of Ub transfer reactions. Here we present characterization of the dynamic behavior of E2~Ub conjugates of two human enzymes, UbcH5c~Ub and Ubc13~Ub, in solution as determined by nuclear magnetic resonance and small-angle X-ray scattering. Within each conjugate, Ub retains great flexibility with respect to the E2, indicative of highly dynamic species that adopt manifold orientations. The population distribution of Ub conformations is dictated by the identity of the E2: the UbcH5c~Ub conjugate populates an array of extended conformations, and the population of Ubc13~Ub conjugates favors a closed conformation in which the hydrophobic surface of Ub faces helix 2 of Ubc13. Finally, we propose that the varied conformations adopted by Ub represent available binding modes of the E2~Ub species and thus provide insight into the diverse E2~Ub protein interactome, particularly with regard to interaction with Ub ligases.

  18. [Conjugate vaccines against bacterial infections: typhoid fever].

    PubMed

    Paniagua, J; García, J A; López, C R; González, C R; Isibasi, A; Kumate, J

    1992-01-01

    Capsular polysaccharides have been studied as possible vaccines against infectious diseases. However, they are capable to induce only short-run protection because of their T-independent properties and they would not be protective against infection in high-risk populations. The alternative to face this problem is to develop methods to join covalently the polysaccharide and proteins to both increase the immunogenicity of and to confer the property of T-dependence to this antigen. In order to obtain a conjugate vaccine against typhoid fever, in our laboratory we have tried to synthesize a conjugate immunogen between the Vi antigen and porins from Salmonella typhi. PMID:1377407

  19. 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

  20. A new nonlinear conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Abdelrahman, Awad; Mamat, Mustafa; Mohd, Ismail bin; Rivaie, Mohd; Omer, Osman

    2015-02-01

    Conjugate gradient (CG) methods are essential for solving large-scale unconstrained optimization problems. Many of studies and modifications have been practiced to improve this method. In this paper, a new class of conjugate gradient coefficients (βk) with a new parameter m = ‖g/k‖ ‖dk-1‖ that possess global convergence properties is presented. The global convergence and sufficient decent property result is established using inexact line searches to determine the step size of CG, denoted as ∝k. Numerical result shows that the new formula is superior and more efficient when compared to other CG coefficients.

  1. Synthesis of cyanopyridine based conjugated polymer

    PubMed Central

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

    2016-01-01

    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

  2. Conjugate Compressible Fluid Flow and Heat Transfer in Ducts

    NASA Technical Reports Server (NTRS)

    Cross, M. F.

    2011-01-01

    A computational approach to modeling transient, compressible fluid flow with heat transfer in long, narrow ducts is presented. The primary application of the model is for analyzing fluid flow and heat transfer in solid propellant rocket motor nozzle joints during motor start-up, but the approach is relevant to a wide range of analyses involving rapid pressurization and filling of ducts. Fluid flow is modeled through solution of the spatially one-dimensional, transient Euler equations. Source terms are included in the governing equations to account for the effects of wall friction and heat transfer. The equation solver is fully-implicit, thus providing greater flexibility than an explicit solver. This approach allows for resolution of pressure wave effects on the flow as well as for fast calculation of the steady-state solution when a quasi-steady approach is sufficient. Solution of the one-dimensional Euler equations with source terms significantly reduces computational run times compared to general purpose computational fluid dynamics packages solving the Navier-Stokes equations with resolved boundary layers. In addition, conjugate heat transfer is more readily implemented using the approach described in this paper than with most general purpose computational fluid dynamics packages. The compressible flow code has been integrated with a transient heat transfer solver to analyze heat transfer between the fluid and surrounding structure. Conjugate fluid flow and heat transfer solutions are presented. The author is unaware of any previous work available in the open literature which uses the same approach described in this paper.

  3. Synthesis, cellular uptake and HIV-1 Tat-dependent trans-activation inhibition activity of oligonucleotide analogues disulphide-conjugated to cell-penetrating peptides

    PubMed Central

    Turner, John J.; Arzumanov, Andrey A.; Gait, Michael J.

    2005-01-01

    Oligonucleotides composed of 2′-O-methyl and locked nucleic acid residues complementary to HIV-1 trans-activation responsive element TAR block Tat-dependent trans-activation in a HeLa cell assay when delivered by cationic lipids. We describe an improved procedure for synthesis and purification under highly denaturing conditions of 5′-disulphide-linked conjugates of 3′-fluorescein labelled oligonucleotides with a range of cell-penetrating peptides and investigate their abilities to enter HeLa cells and block trans-activation. Free uptake of 12mer OMe/LNA oligonucleotide conjugates to Tat (48–58), Penetratin and R9F2 was observed in cytosolic compartments of HeLa cells. Uptake of the Tat conjugate was enhanced by N-terminal addition of four Lys or Arg residues or a second Tat peptide. None of the conjugates entered the nucleus or inhibited trans-activation when freely delivered, but inhibition was obtained in the presence of cationic lipids. Nuclear exclusion was seen for free delivery of Tat (48–58), Penetratin and R9 conjugates of 16mer phosphorothioate OMe oligonucleotide. Uptake into human fibroblast cytosolic compartments was seen for Tat, Penetratin, R9F2 and Transportan conjugates. Large enhancements of HeLa cell uptake into cytosolic compartments were seen when free Tat peptide was added to Tat conjugate of 12mer OMe/LNA oligonucleotide or Penetratin peptide to Penetratin conjugate of the same oligonucleotide. PMID:15640444

  4. Conjugate-shear folding: A model for the relationships between foliations, folds and shear zones

    NASA Astrophysics Data System (ADS)

    Aerden, Domingo G. A. M.; Sayab, Mohammad; Bouybaouene, Mohamed L.

    2010-08-01

    Microstructural mapping of whole thin sections cut from two samples of micaschist containing cm-scale folds plus garnet porphyroblasts has provided new insight in the relationships between folding, shearing and foliation development. The garnets exhibit coherent inclusion-trail patterns that place important constraints on the kinematic development of both samples, which are shown to be representative of coaxial versus non-coaxial deformation in rocks containing a pre-existing schistosity. A comparison of crenulations-cleavages geometries in both samples and a review of the geometry of natural and experimental multilayer folds leads to the conclusion that folding involves conjugate shearing at different scales. At microscopic scales, crenulation cleavages nucleate as conjugate-kink or shear instabilities and develop further as a function of the macroscopic partitioning of deformation. In fold-hinge domains, bulk-coaxial deformation results in equal development of conjugate crenulations that progressively coalescence into symmetrical crenulation patterns so that, macroscopically, parallelism is achieved between foliation, fold-axial planes and long axes of strain ellipses. Fold-limb domains represent a system of conjugate-shear zones where single sets of crenulation instabilities with synthetic shearing component preferentially develop producing oblique relationships between the aforementioned elements. Cleavage fanning is inferred as a direct consequence of this conjugate-shear origin of folds. The model implies that crenulation cleavages and S-C fabrics in shear zones form by analogous processes, in both cases involving a component of shearing along foliation planes. The development of conjugate sets of foliation planes surrounding porphyroblasts during early, relatively coaxial stages of deformation explains continued "gyrostatic" behaviour during more advanced non-coaxial stages, as indicated by consistently oriented inclusion trails in the studied samples.

  5. Fast and high resolution thermal detector based on an aluminum nitride piezoelectric microelectromechanical resonator with an integrated suspended heat absorbing element

    NASA Astrophysics Data System (ADS)

    Hui, Yu; Rinaldi, Matteo

    2013-03-01

    This letter presents a miniaturized, fast, and high resolution thermal detector, in which a heat absorbing element and a temperature sensitive microelectromechanical system (MEMS) resonator are perfectly overlapped but separated by a microscale air gap. This unique design guarantees efficient and fast (˜10s μs) heat transfer from the absorbing element to the temperature sensitive device and enables high resolution thermal power detection (˜nW), thanks to the low noise performance of the high quality factor (Q = 2305) MEMS resonant thermal detector. A device prototype was fabricated, and its detection capabilities were experimentally characterized. A thermal power as low as 150 nW was experimentally measured, and a noise equivalent power of 6.5 nW/Hz1/2 was extracted. A device thermal time constant of only 350 μs was measured (smallest ever reported for MEMS resonant thermal detectors), indicating the great potential of the proposed technology for the implementation of ultra-fast and high resolution un-cooled resonant thermal detectors.

  6. Modeling energy and charge transports in pi-conjugated systems

    NASA Astrophysics Data System (ADS)

    Shin, Yongwoo

    Carbon based pi-conjugated materials, such as conducting polymers, fullerene, carbon nanotubes, graphene, and conjugated dendrimers have attracted wide scientific attentions in the past three decades. This work presents the first unified model Hamiltonian that can accurately capture the low-energy excitations among all these pi-conjugated systems, even with the presence of defects and heterogeneous sites. Two transferable physical parameters are incorporated into the Su-Schrieffer-Heeger Hamiltonian to model conducting polymers beyond polyacetylene: the parameter gamma scales the electronphonon coupling strength in aromatic rings and the other parameter epsilon specifies the heterogeneous core charges. This generic Hamiltonian predicts the fundamental band gaps of polythiophene, polypyrrole, polyfuran, poly-(p-phenylene), poly-(p-phenylene vinylene), polyacenes, fullerene, carbon nanotubes, graphene, and graphene nanoribbons with an accuracy exceeding time-dependent density functional theory. Its computational costs for moderate-length polymer chains are more than eight orders of magnitude lower than first-principles approaches. The charge and energy transports along -conjugated backbones can be modeled on the adiabatic potential energy surface. The adiabatic minimum-energy path of a self-trapped topological soliton is computed for trans-polyacetylene. The frequently cited activation barrier via a ridge shift of the hyper-tangent order parameter overestimates its true value by 14 orders of magnitude. Self-trapped solitons migrate along the Goldstone mode direction with continuously adjusted amplitudes so that a small-width soliton expands and a large-width soliton shrinks when they move uphill. A soliton with the critical width may migrate without any amplitude modifications. In an open chain as solitons move from the chain center toward a chain edge, the minimum-energy path first follows a tilted washboard. Such a generic constrained Goldstone mode relaxation

  7. 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.

  8. Resonant modes of optical cavities with phase-conjugate mirrors.

    PubMed

    Bélanger, P A; Hardy, A; Siegman, A E

    1980-02-15

    The lowest-order self-consistent Gaussian transverse modes are derived, also the resonant frequencies of an optical resonator formed by conventional paraxial optical components plus a phase-conjugate mirror (PCM) on one end. The conventional optical elements are described by an over-all ABCD matrix. Cavities with purely real elements (no aperturing) have a continuous set of self-reproducing Gaussian modes described by a semicircular locus in the 1/q plane for one round trip; all Gaussian beams are self-reproducing after two round trips. Complex ABCD matrices, such as are produced by Gaussian aperturing in the cavity, lead to unique self-consistent perturbation-stable Gaussian modes. The resonant frequency spectrum of a PCM cavity consists of a central resonance at the driving frequency omega(0) of the PCM element, independent of the cavity length L, plus half-axial sidebands spaced by Deltaomega(ax) = 2pi(c/4L), with phase and amplitude constraints on each pair of upper and lower sidebands. PMID:20216900

  9. A comparison of element-by-element preconditioned iterative methods for solid and structural mechanics

    SciTech Connect

    Ferencz, R.M.

    1988-10-01

    Past work with element-by-element (EBE) preconditioned conjugate gradient iterative solution strategies has shown these techniques can be effective for large-scale, three-dimensional calculations in solid and structural mechanics. Significant gains over the profile storage direct solution method traditionally used in implicit finite element codes have been observed for a variety of real engineering analyses, especially in solid mechanics. Structural mechanics applications have proved less successful due to the ill-conditioned linear systems engendered by standard structural discretizations. This lack of robustness has recently motivated reconsideration of Lanczos-based algorithms as alternative iterative drivers. In this paper we compare the relative strengths of the conjugate gradient and Lanczos drivers when coupled with EBE preconditioning. The performance of the two methods is characterized, and compared with direct solution, using a model problem and a number of real engineering meshes. 26 refs., 14 figs., 2 tabs.

  10. Pneumococcal conjugate vaccine (PCV13) - What you need to know

    MedlinePlus

    ... www.cdc.gov/vaccines/hcp/vis/vis-statements/pcv13.html CDC review information for Pneumococcal Conjugate VIS: ... the disease, through vaccination, even more important. 2. PCV13 vaccine Pneumococcal conjugate vaccine (called PCV13) protects against ...

  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. PMID:11236890

  12. 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.

  13. 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.

  14. Stress on Second Conjugation Infinitives in Italian.

    ERIC Educational Resources Information Center

    Davis, Stuart; And Others

    1987-01-01

    Reviews the limited amount of research regarding ways in which primary stress is assigned to second conjugation infinitives in Italian and then proposes a new perspective taking into consideration root vowels, root-final consonants, syllable onset, monosyllabic vs. polysyllabic roots, and canonical form. (CB)

  15. An Auxin-Conjugated Strawberry Fruit Protein

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Strawberry fruit contain indole-3-acetic acid (IAA) covalently attached to specific strawberry proteins. Immunoblotting using a specific antibody to IAA-glycine linked to BSA detected IAA proteins in both achenes and receptacles. Protein-conjugated IAA accounts for the majority of the total IAA pool...

  16. 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.

  17. 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

  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. New antibody conjugates in cancer therapy.

    PubMed

    Govindan, Serengulam V; Goldenberg, David M

    2010-01-01

    Targeting of radiation, drugs, and protein toxins to cancers selectively with monoclonal antibodies (MAbs) has been a topic of considerable interest and an area of continued development. Radioimmunotherapy (RAIT) of lymphoma using directly labeled MAbs is of current interest after approval of two radiolabeled anti-CD20 MAbs, as illustrated with the near 100% overall response rate obtained in a recent clinical trial using an investigational radiolabeled anti-CD22 MAb, 90Y-epratuzumab. The advantage of pretargeted RAIT over directly labeled MAbs is continuing to be validated in preclinical models of lymphoma and solid tumors. Importantly, the advantages of combining RAIT with radiation sensitizers, with immunotherapy, or a drug conjugate targeting a different antigen are being studied clinically and preclinically. The area of drug-conjugated antibodies is progressing with encouraging data published for the trastuzumab-DM1 conjugate in a phase I clinical trial in HER2-positive breast cancer. The Dock-and-Lock platform technology has contributed to the design and the evaluation of complex antibody-cytokine and antibody-toxin conjugates. This review describes the advances made in these areas, with illustrations taken from advances made in the authors' institutions. PMID:20953556

  20. Photorefractive phase-conjugation digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Chang, Chi-Ching; Chan, Huang-Tian; Shiu, Min-Tzung; Chew, Yang-Kun

    2015-05-01

    In this work, we propose an innovative method for digital holographic microscopy named as photorefractive phaseconjugation digital holographic microscopy (PPCDHM) technique based on the phase conjugation dynamic holographic process in photorefractive BaTiO3 crystal and the retrieval of phase and amplitude of the object wave were performed by a reflection-type digital holographic method. Both amplitude and phase reconstruction benefit from the prior amplification by self-pumped conjugation (SPPC) as they have an increased SNR. The interest of the PPCDHM is great, because its hologram is created by interfered the amplified phase-conjugate wave field generated from a photorefractive phase conjugator (PPC) correcting the phase aberration of the imaging system and the reference wave onto the digital CCD camera. Therefore, a precise three-dimensional description of the object with high SNR can be obtained digitally with only one hologram acquisition. The method requires the acquisition of a single hologram from which the phase distribution can be obtained simultaneously with distribution of intensity at the surface of the object.