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Sample records for 24-bp consensus sequence

  1. SSCP analysis and sequencing of the human prion protein gene (PRNP) detects two different 24 bp deletions in an atypical Alzheimer`s disease family

    SciTech Connect

    Perry, R.T.; Go, R.C.P.; Harrell, L.E.; Acton, R.T.

    1995-02-27

    Alzheimer`s disease (AD) is a progressive, degenerative neurological disorder of the central nervous system. AD is the fourth leading cause of death in elderly persons 65 years or older in Western industrialized societies. The etiology of AD is unknown, but clinical, pathological, epidemiological, and molecular investigations suggest it is etiologically heterogeneous. Mutations in the amyloid protein are rare and segregate with the disease in a few early-onset familial AD (FAD) families. Similarities between AD and the unconventional viral (UCV) diseases, and between the amyloid and prion proteins, implicate the human prion protein gene (PRNP) as another candidate gene. Single strand conformation polymorphism (SSCP) analysis was used to screen for mutations at this locus in 82 AD patients from 54 families (30 FAD), vs. 39 age-matched controls. A 24-bp deletion around codon 68 that codes for one of five Gly-Pro rich octarepeats was identified in two affected sibs and one offspring of one late-onset FAD family. Two other affected sibs, three unaffected sibs, and three offspring from this family, in addition to one sporadic AD patient and three age-matched controls, were heterozygous for another octarepeat deletion located around codon 82. Two of the four affected sibs had features of PD, including one who was autopsy-verified AD and PD. Although these deletions were found infrequently in other AD patients and controls, they appear to be a rare polymorphism that is segregating in this FAD family. It does not appear that mutations at the PRNP locus are frequently associated with AD in this population. 54 refs., 4 figs.

  2. Sequence logos: a new way to display consensus sequences.

    PubMed Central

    Schneider, T D; Stephens, R M

    1990-01-01

    A graphical method is presented for displaying the patterns in a set of aligned sequences. The characters representing the sequence are stacked on top of each other for each position in the aligned sequences. The height of each letter is made proportional to its frequency, and the letters are sorted so the most common one is on top. The height of the entire stack is then adjusted to signify the information content of the sequences at that position. From these 'sequence logos', one can determine not only the consensus sequence but also the relative frequency of bases and the information content (measured in bits) at every position in a site or sequence. The logo displays both significant residues and subtle sequence patterns. PMID:2172928

  3. Definition of the bacterial N-glycosylation site consensus sequence.

    PubMed

    Kowarik, Michael; Young, N Martin; Numao, Shin; Schulz, Benjamin L; Hug, Isabelle; Callewaert, Nico; Mills, Dominic C; Watson, David C; Hernandez, Marcela; Kelly, John F; Wacker, Michael; Aebi, Markus

    2006-05-01

    The Campylobacter jejuni pgl locus encodes an N-linked protein glycosylation machinery that can be functionally transferred into Escherichia coli. In this system, we analyzed the elements in the C. jejuni N-glycoprotein AcrA required for accepting an N-glycan. We found that the eukaryotic primary consensus sequence for N-glycosylation is N terminally extended to D/E-Y-N-X-S/T (Y, X not equalP) for recognition by the bacterial oligosaccharyltransferase (OST) PglB. However, not all consensus sequences were N-glycosylated when they were either artificially introduced or when they were present in non-C. jejuni proteins. We were able to produce recombinant glycoproteins with engineered N-glycosylation sites and confirmed the requirement for a negatively charged side chain at position -2 in C. jejuni N-glycoproteins. N-glycosylation of AcrA by the eukaryotic OST in Saccharomyces cerevisiae occurred independent of the acidic residue at the -2 position. Thus, bacterial N-glycosylation site selection is more specific than the eukaryotic equivalent with respect to the polypeptide acceptor sequence. PMID:16619027

  4. Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III.

    PubMed Central

    Van Houten, J V; Newlon, C S

    1990-01-01

    Yeast autonomously replicating sequence (ARS) elements contain an 11-base-pair core consensus sequence (5'-[A/T]TTTAT[A/G]TTT[A/T]-3') that is required for function. The contribution of each position within this sequence to ARS activity was tested by creating all possible single-base mutations within the core consensus sequence of ARS307 (formerly called the C2G1 ARS) and testing their effects on high-frequency transformation and on plasmid stability. Of the 33 mutations, 22 abolished ARS function as measured by high-frequency transformation, 7 caused more than twofold reductions in plasmid stability, and 4 had no effect on plasmid stability. Mutations that reduced or abolished ARS activity occurred at each position in the consensus sequence, demonstrating that each position of this sequence contributes to ARS function. Of the four mutations that had no effect on ARS activity, three created alternative perfect matches to the core consensus sequence, demonstrating that the alternate bases allowed by the consensus sequence are, indeed, interchangeable. In addition, a change from T to C at position 6 did not perturb wild-type efficiency. To test whether the essential region extends beyond the 11-base-pair consensus sequence, the effects on plasmid stability of point mutations one base 3' to the T-rich strand of the core consensus sequence (position 12) and deletion mutations that altered bases 5' to the T-rich strand of the core consensus sequence were examined. An A at position 12 or the removal of three T residues 5' to the core consensus sequence severely diminished ARS efficiency, showing that the region required for full ARS efficiency extends beyond the core consensus sequence in both directions. PMID:2196439

  5. Interferon Consensus Sequence Binding Protein Confers Resistance against Yersinia enterocolitica

    PubMed Central

    Hein, Joachim; Kempf, Volkhard A. J.; Diebold, Joachim; Bücheler, Nicole; Preger, Sonja; Horak, Ivan; Sing, Andreas; Kramer, Uwe; Autenrieth, Ingo B.

    2000-01-01

    Interferon consensus sequence binding protein (ICSBP)-deficient mice display enhanced susceptibility to intracellular pathogens. At least two distinct immunoregulatory defects are responsible for this phenotype. First, diminished production of reactive oxygen intermediates in macrophages results in impaired intracellular killing of microorganisms. Second, defective early interleukin-12 (IL-12) production upon microbial challenge leads to a failure in gamma interferon (IFN-γ) induction and subsequently in T helper 1 immune responses. Here, we investigated the role of ICSBP in resistance against the extracellular bacterium Yersinia enterocolitica. ICSBP−/− mice failed to produce IL-12 and IFN-γ, but also IL-4, after Yersinia challenge. In addition, granuloma formation was highly disturbed in infected ICSBP−/− mice, leading to multiple necrotic abscesses in affected organs. Consequently, ICSBP−/− mice rapidly succumbed to acute Yersinia infection. In vitro treatment of spleen cells from ICSBP−/− mice with recombinant IL-12 (rIL-12) or rIL-18 in combination with a second stimulus resulted in IFN-γ induction. In experimental therapy of infected ICSBP−/− mice, we observed that administration of rIL-12 induced IFN-γ production which was associated with improved resistance to Yersinia. In contrast, treatment with rIL-18 failed to enhance endogenous IFN-γ production but nevertheless reduced bacterial burden in ICSBP−/− mice. Although cytokine therapy with rIL-12 or rIL-18 ameliorated the course of Yersinia infection in ICSBP−/− mice, both cytokines failed to completely restore impaired immunity. Taken together, the results indicate that the transcription factor ICSBP is essential for efficient host immune defense against Yersinia. These results are important for understanding the complex host immune responses in bacterial infections. PMID:10678954

  6. Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads.

    PubMed

    Ye, Chengxi; Ma, Zhanshan Sam

    2016-01-01

    Motivation. The third generation sequencing (3GS) technology generates long sequences of thousands of bases. However, its current error rates are estimated in the range of 15-40%, significantly higher than those of the prevalent next generation sequencing (NGS) technologies (less than 1%). Fundamental bioinformatics tasks such as de novo genome assembly and variant calling require high-quality sequences that need to be extracted from these long but erroneous 3GS sequences. Results. We describe a versatile and efficient linear complexity consensus algorithm Sparc to facilitate de novo genome assembly. Sparc builds a sparse k-mer graph using a collection of sequences from a targeted genomic region. The heaviest path which approximates the most likely genome sequence is searched through a sparsity-induced reweighted graph as the consensus sequence. Sparc supports using NGS and 3GS data together, which leads to significant improvements in both cost efficiency and computational efficiency. Experiments with Sparc show that our algorithm can efficiently provide high-quality consensus sequences using both PacBio and Oxford Nanopore sequencing technologies. With only 30× PacBio data, Sparc can reach a consensus with error rate <0.5%. With the more challenging Oxford Nanopore data, Sparc can also achieve similar error rate when combined with NGS data. Compared with the existing approaches, Sparc calculates the consensus with higher accuracy, and uses approximately 80% less memory and time. Availability. The source code is available for download at https://github.com/yechengxi/Sparc. PMID:27330851

  7. Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads

    PubMed Central

    2016-01-01

    Motivation. The third generation sequencing (3GS) technology generates long sequences of thousands of bases. However, its current error rates are estimated in the range of 15–40%, significantly higher than those of the prevalent next generation sequencing (NGS) technologies (less than 1%). Fundamental bioinformatics tasks such as de novo genome assembly and variant calling require high-quality sequences that need to be extracted from these long but erroneous 3GS sequences. Results. We describe a versatile and efficient linear complexity consensus algorithm Sparc to facilitate de novo genome assembly. Sparc builds a sparse k-mer graph using a collection of sequences from a targeted genomic region. The heaviest path which approximates the most likely genome sequence is searched through a sparsity-induced reweighted graph as the consensus sequence. Sparc supports using NGS and 3GS data together, which leads to significant improvements in both cost efficiency and computational efficiency. Experiments with Sparc show that our algorithm can efficiently provide high-quality consensus sequences using both PacBio and Oxford Nanopore sequencing technologies. With only 30× PacBio data, Sparc can reach a consensus with error rate <0.5%. With the more challenging Oxford Nanopore data, Sparc can also achieve similar error rate when combined with NGS data. Compared with the existing approaches, Sparc calculates the consensus with higher accuracy, and uses approximately 80% less memory and time. Availability. The source code is available for download at https://github.com/yechengxi/Sparc. PMID:27330851

  8. Newly Exerted T Cell Pressures on Mutated Epitopes following Transmission Help Maintain Consensus HIV-1 Sequences

    PubMed Central

    Eriksson, Emily M.; Liegler, Teri; Keh, Chris E.; Karlsson, Annika C.; Holditch, Sara J.; Pilcher, Christopher D.; Loeb, Lisa; Nixon, Douglas F.; Hecht, Frederick M.

    2015-01-01

    CD8+ T cells are important for HIV-1 virus control, but are also a major contributing factor that drives HIV-1 virus sequence evolution. Although HIV-1 cytotoxic T cell (CTL) escape mutations are a common aspect during HIV-1 infection, less is known about the importance of T cell pressure in reversing HIV-1 virus back to a consensus sequences. In this study we aimed to assess the frequency with which reversion of transmitted mutations in T cell epitopes were associated with T cell responses to the mutation. This study included 14 HIV-1 transmission pairs consisting of a ‘source’ (virus-donor) and a ‘recipient’ (newly infected individual). Non-consensus B sequence amino acids (mutations) in T cell epitopes in HIV-1 gag regions p17, p24, p2 and p7 were identified in each pair and transmission of mutations to the recipient was verified with population viral sequencing. Longitudinal analyses of the recipient’s viral sequence were used to identify whether reversion of mutations back to the consensus B sequence occurred. Autologous 12-mer peptides overlapping by 11 were synthesized, representing the sequence region surrounding each reversion and longitudinal analysis of T cell responses to source-derived mutated and reverted epitopes were assessed. We demonstrated that mutations in the source were frequently transmitted to the new host and on an average 17 percent of mutated epitopes reverted to consensus sequence in the recipient. T cell responses to these mutated epitopes were detected in 7 of the 14 recipients in whom reversion occurred. Overall, these findings indicate that transmitted non-consensus B epitopes are frequently immunogenic in HLA-mismatched recipients and new T cell pressures to T cell escape mutations following transmission play a significant role in maintaining consensus HIV-1 sequences. PMID:25919393

  9. Haplotype and minimum-chimerism consensus determination using short sequence data

    PubMed Central

    2012-01-01

    Background Assembling haplotypes given sequence data derived from a single individual is a well studied problem, but only recently has haplotype assembly been considered for population-sampled data. We discuss a software tool called Hapler, which is designed specifically for low-diversity, low-coverage data such as ecological samples derived from natural populations. Because such data may contain error as well as ambiguous haplotype information, we developed methods that increase confidence in these assemblies. Hapler also reconstructs full consensus sequences while minimizing and identifying possible chimeric points. Results Experiments on simulated data indicate that Hapler is effective at assembling haplotypes from gene-sized alignments of short reads. Further, in our tests Hapler-generated consensus sequences are less chimeric than the alternative consensus approaches of majority vote and viral quasispecies estimation regardless of error rate, read length, or population haplotype bias. Conclusions The analysis of genetically diverse sequence data is increasingly common, particularly in the field of ecoinformatics where transcriptome sequencing of natural populations is a cost effective alternative to genome sequencing. For such studies, it is important to consider and identify haplotype diversity. Hapler provides robust haplotype information and identifies possible phasing errors in consensus sequences, providing valuable information for population studies and downstream usage of resulting assemblies. PMID:22537299

  10. Scoring consensus of multiple ECG annotators by optimal sequence alignment.

    PubMed

    Haghpanahi, Masoumeh; Sameni, Reza; Borkholder, David A

    2014-01-01

    Development of ECG delineation algorithms has been an area of intense research in the field of computational cardiology for the past few decades. However, devising evaluation techniques for scoring and/or merging the results of such algorithms, both in the presence or absence of gold standards, still remains as a challenge. This is mainly due to existence of missed or erroneous determination of fiducial points in the results of different annotation algorithms. The discrepancy between different annotators increases when the reference signal includes arrhythmias or significant noise and its morphology deviates from a clean ECG signal. In this work, we propose a new approach to evaluate and compare the results of different annotators under such conditions. Specifically, we use sequence alignment techniques similar to those used in bioinformatics for the alignment of gene sequences. Our approach is based on dynamic programming where adequate mismatch penalties, depending on the type of the fiducial point and the underlying signal, are defined to optimally align the annotation sequences. We also discuss how to extend the algorithm for more than two sequences by using suitable data structures to align multiple annotation sequences with each other. Once the sequences are aligned, different heuristics are devised to evaluate the performance against a gold standard annotation, or to merge the results of multiple annotations when no gold standard exists. PMID:25570339

  11. Splice site consensus sequences are preferentially accessible to nucleases in isolated adenovirus RNA.

    PubMed Central

    Munroe, S H; Duthie, R S

    1986-01-01

    The conformation of RNA sequences spanning five 3' splice sites and two 5' splice sites in adenovirus mRNA was probed by partial digestion with single-strand specific nucleases. Although cleavage of nucleotides near both 3' and 5' splice sites was observed, most striking was the preferential digestion of sequences near the 3' splice site. At each 3' splice site a region of very strong cleavage is observed at low concentrations of enzyme near the splice site consensus sequence or the upstream branch point consensus sequence. Additional sites of moderately strong cutting near the branch point consensus sequence were observed in those sequences where the splice site was the preferred target. Since recognition of the 3' splice site and branch site appear to be early events in mRNA splicing these observations may indicate that the local conformation of the splice site sequences may play a direct or indirect role in enhancing the accessibility of sequences important for splicing. Images PMID:3024107

  12. Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing.

    PubMed

    Zhao, Yuqi; Wang, Yanjie; Zou, Lei; Huang, Jingfei

    2016-04-01

    One practical application of genome-scale metabolic reconstructions is to interrogate multispecies relationships. Here, we report a consensus metabolic model in four yeast species (Saccharomyces cerevisiae, S. paradoxus, S. mikatae, and S. bayanus) by integrating metabolic network simulations with RNA sequencing (RNA-seq) datasets. We generated high-resolution transcriptome maps of four yeast species through de novo assembly and genome-guided approaches. The transcriptomes were annotated and applied to build the consensus metabolic network, which was verified using independent RNA-seq experiments. The expression profiles reveal that the genes involved in amino acid and lipid metabolism are highly coexpressed. The diverse phenotypic characteristics, such as cellular growth and gene deletions, can be simulated using the metabolic model. We also explored the applications of the consensus model in metabolic engineering using yeast-specific reactions and biofuel production as examples. Similar strategies will benefit communities studying genome-scale metabolic networks of other organisms. PMID:27239440

  13. The iceLogo web server and SOAP service for determining protein consensus sequences.

    PubMed

    Maddelein, Davy; Colaert, Niklaas; Buchanan, Iain; Hulstaert, Niels; Gevaert, Kris; Martens, Lennart

    2015-07-01

    The iceLogo web server and SOAP service implement the previously published iceLogo algorithm. iceLogo builds on probability theory to visualize protein consensus sequences in a format resembling sequence logos. Peptide sequences are compared against a reference sequence set that can be tailored to the studied system and the used protocol. As such, not only over- but also underrepresented residues can be visualized in a statistically sound manner, which further allows the user to easily analyse and interpret conserved sequence patterns in proteins. The web application and SOAP service can be found free and open to all users without the need for a login on http://iomics.ugent.be/icelogoserver/main.html. PMID:25897125

  14. Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence.

    PubMed

    Scott, A F; Schmeckpeper, B J; Abdelrazik, M; Comey, C T; O'Hara, B; Rossiter, J P; Cooley, T; Heath, P; Smith, K D; Margolet, L

    1987-10-01

    A consensus sequence for the human long interspersed repeated DNA element, L1Hs (LINE or KpnI sequence), is presented. The sequence contains two open reading frames (ORFs) which are homologous to ORFs in corresponding regions of L1 elements in other species. The L1Hs ORFs are separated by a small evolutionarily nonconserved region. The 5' end of the consensus contains frequent terminators in all three reading frames and has a relatively high GC content with numerous stretches of weak homology with AluI repeats. The 5' ORF extends for a minimum of 723 bp (241 codons). The 3' ORF is 3843 bp (1281 codons) and predicts a protein of 149 kD which has regions of weak homology to the polymerase domain of various reverse transcriptases. The 3' end of the consensus has a 208-bp nonconserved region followed by an adenine-rich end. The organization of the L1Hs consensus sequence resembles the structure of eukaryotic mRNAs except for the noncoding region between ORFs. However, due to base substitutions or truncation most elements appear incapable of producing mRNA that can be translated. Our observation that individual elements cluster into subfamilies on the basis of the presence or absence of blocks of sequence, or by the linkage of alternative bases at multiple positions, suggests that most L1 sequences were derived from a small number of structural genes. An estimate of the mammalian L1 substitution rate was derived and used to predict the age of individual human elements. From this it follows that the majority of human L1 sequences have been generated within the last 30 million years. The human elements studied here differ from each other, yet overall the L1Hs sequences demonstrate a pattern of species-specificity when compared to the L1 families of other mammals. Possible mechanisms that may account for the origin and evolution of the L1 family are discussed. These include pseudogene formation (retroposition), transposition, gene conversion, and RNA recombination. PMID

  15. Stimulatory and inhibitory protein kinase C consensus sequences regulate the cystic fibrosis transmembrane conductance regulator.

    PubMed

    Chappe, Valerie; Hinkson, Deborah A; Howell, L Daniel; Evagelidis, Alexandra; Liao, Jie; Chang, Xiu-Bao; Riordan, John R; Hanrahan, John W

    2004-01-01

    Protein kinase C (PKC) phosphorylation stimulates the cystic fibrosis transmembrane conductance regulator (CFTR) channel and enhances its activation by protein kinase A (PKA) through mechanisms that remain poorly understood. We have examined the effects of mutating consensus sequences for PKC phosphorylation and report here evidence for both stimulatory and inhibitory sites. Sequences were mutated in subsets and the mutants characterized by patch clamping. Activation of a 4CA mutant (S707A/S790A/T791A/S809A) by PKA was similar to that of wild-type CFTR and was enhanced by PKC, whereas responses of 3CA (T582A/T604A/S641A) and 2CA (T682A/S686A) channels to PKA were both drastically reduced (>90%). When each mutation in the 3CA and 2CA constructs was studied individually in a wild-type background, T582, T604, and S686 were found to be essential for PKA activation. Responses were restored when these three residues were reintroduced simultaneously into a 9CA mutant lacking all nine PKC consensus sequences (R6CA revertant); however, PKC phosphorylation was not required for this rescue. Nevertheless, two of the sites (T604 and S686) were phosphorylated in vitro, and PKC alone partially activated wild-type CFTR, the 4CA mutant, and the point mutants T582A and T604A, but not S686A channels, indicating that PKC does act at S686. The region encompassing S641 and T682 is inhibitory, because S641A enhanced activation by PKA, and T682A channels had 4-fold larger responses to PKC compared to wild-type channels. These results identify functionally important PKC consensus sequences on CFTR and will facilitate studies of its convergent regulation by PKC and PKA. PMID:14695900

  16. Stimulatory and inhibitory protein kinase C consensus sequences regulate the cystic fibrosis transmembrane conductance regulator

    PubMed Central

    Chappe, Valerie; Hinkson, Deborah A.; Howell, L. Daniel; Evagelidis, Alexandra; Liao, Jie; Chang, Xiu-Bao; Riordan, John R.; Hanrahan, John W.

    2004-01-01

    Protein kinase C (PKC) phosphorylation stimulates the cystic fibrosis transmembrane conductance regulator (CFTR) channel and enhances its activation by protein kinase A (PKA) through mechanisms that remain poorly understood. We have examined the effects of mutating consensus sequences for PKC phosphorylation and report here evidence for both stimulatory and inhibitory sites. Sequences were mutated in subsets and the mutants characterized by patch clamping. Activation of a 4CA mutant (S707A/S790A/T791A/S809A) by PKA was similar to that of wild-type CFTR and was enhanced by PKC, whereas responses of 3CA (T582A/T604A/S641A) and 2CA (T682A/S686A) channels to PKA were both drastically reduced (>90%). When each mutation in the 3CA and 2CA constructs was studied individually in a wild-type background, T582, T604, and S686 were found to be essential for PKA activation. Responses were restored when these three residues were reintroduced simultaneously into a 9CA mutant lacking all nine PKC consensus sequences (R6CA revertant); however, PKC phosphorylation was not required for this rescue. Nevertheless, two of the sites (T604 and S686) were phosphorylated in vitro, and PKC alone partially activated wild-type CFTR, the 4CA mutant, and the point mutants T582A and T604A, but not S686A channels, indicating that PKC does act at S686. The region encompassing S641 and T682 is inhibitory, because S641A enhanced activation by PKA, and T682A channels had 4-fold larger responses to PKC compared to wild-type channels. These results identify functionally important PKC consensus sequences on CFTR and will facilitate studies of its convergent regulation by PKC and PKA. PMID:14695900

  17. Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography.

    PubMed

    Mandal, Pradeep K; Collie, Gavin W; Srivastava, Suresh C; Kauffmann, Brice; Huc, Ivan

    2016-07-01

    It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods-that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence 'TATAAT'. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65-2.3 Å), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence. PMID:27137886

  18. PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach.

    PubMed

    Chatterjee, Piyali; Basu, Subhadip; Zubek, Julian; Kundu, Mahantapas; Nasipuri, Mita; Plewczynski, Dariusz

    2016-04-01

    The prediction of domain/linker residues in protein sequences is a crucial task in the functional classification of proteins, homology-based protein structure prediction, and high-throughput structural genomics. In this work, a novel consensus-based machine-learning technique was applied for residue-level prediction of the domain/linker annotations in protein sequences using ordered/disordered regions along protein chains and a set of physicochemical properties. Six different classifiers-decision tree, Gaussian naïve Bayes, linear discriminant analysis, support vector machine, random forest, and multilayer perceptron-were exhaustively explored for the residue-level prediction of domain/linker regions. The protein sequences from the curated CATH database were used for training and cross-validation experiments. Test results obtained by applying the developed PDP-CON tool to the mutually exclusive, independent proteins of the CASP-8, CASP-9, and CASP-10 databases are reported. An n-star quality consensus approach was used to combine the results yielded by different classifiers. The average PDP-CON accuracy and F-measure values for the CASP targets were found to be 0.86 and 0.91, respectively. The dataset, source code, and all supplementary materials for this work are available at https://cmaterju.org/cmaterbioinfo/ for noncommercial use. PMID:26969678

  19. Identification of Phosphorylation Consensus Sequences and Endogenous Neuronal Substrates of the Psychiatric Risk Kinase TNIK.

    PubMed

    Wang, Qi; Amato, Stephen P; Rubitski, David M; Hayward, Matthew M; Kormos, Bethany L; Verhoest, Patrick R; Xu, Lan; Brandon, Nicholas J; Ehlers, Michael D

    2016-02-01

    Traf2- and Nck-interacting kinase (TNIK) is a serine/threonine kinase highly expressed in the brain and enriched in the postsynaptic density of glutamatergic synapses in the mammalian brain. Accumulating genetic evidence and functional data have implicated TNIK as a risk factor for psychiatric disorders. However, the endogenous substrates of TNIK in neurons are unknown. Here, we describe a novel selective small molecule inhibitor of the TNIK kinase family. Using this inhibitor, we report the identification of endogenous neuronal TNIK substrates by immunoprecipitation with a phosphomotif antibody followed by mass spectrometry. Phosphorylation consensus sequences were defined by phosphopeptide sequence analysis. Among the identified substrates were members of the delta-catenin family including p120-catenin, δ-catenin, and armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF), each of which is linked to psychiatric or neurologic disorders. Using p120-catenin as a representative substrate, we show TNIK-induced p120-catenin phosphorylation in cells requires intact kinase activity and phosphorylation of TNIK at T181 and T187 in the activation loop. Addition of the small molecule TNIK inhibitor or knocking down TNIK by two shRNAs reduced endogenous p120-catenin phosphorylation in cells. Together, using a TNIK inhibitor and phosphomotif antibody, we identify endogenous substrates of TNIK in neurons, define consensus sequences for TNIK, and suggest signaling pathways by which TNIK influences synaptic development and function linked to psychiatric and neurologic disorders. PMID:26645429

  20. Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire

    PubMed Central

    2012-01-01

    Background Vertebrate immune systems generate diverse repertoires of antibodies capable of mediating response to a variety of antigens. Next generation sequencing methods provide unique approaches to a number of immuno-based research areas including antibody discovery and engineering, disease surveillance, and host immune response to vaccines. In particular, single-molecule circular consensus sequencing permits the sequencing of antibody repertoires at previously unattainable depths of coverage and accuracy. We approached the bovine immunoglobulin G (IgG) repertoire with the objective of characterizing diversity of expressed IgG transcripts. Here we present single-molecule real-time sequencing data of expressed IgG heavy-chain repertoires of four individual cattle. We describe the diversity observed within antigen binding regions and visualize this diversity using a network-based approach. Results We generated 49,945 high quality cDNA sequences, each spanning the entire IgG variable region from four Bos taurus calves. From these sequences we identified 49,521 antigen binding regions using the automated Paratome web server. Approximately 9% of all unique complementarity determining 2 (CDR2) sequences were of variable lengths. A bimodal distribution of unique CDR3 sequence lengths was observed, with common lengths of 5–6 and 21–25 amino acids. The average number of cysteine residues in CDR3s increased with CDR3 length and we observed that cysteine residues were centrally located in CDR3s. We identified 19 extremely long CDR3 sequences (up to 62 amino acids in length) within IgG transcripts. Network analyses revealed distinct patterns among the expressed IgG antigen binding repertoires of the examined individuals. Conclusions We utilized circular consensus sequencing technology to provide baseline data of the expressed bovine IgG repertoire that can be used for future studies important to livestock research. Somatic mutation resulting in base insertions and

  1. MRX87 family with Aristaless X dup24bp mutation and implication for polyAlanine expansions

    PubMed Central

    Laperuta, Carmela; Spizzichino, Letizia; D'Adamo, Pio; Monfregola, Jlenia; Maiorino, Antonio; D'Eustacchio, Angela; Ventruto, Valerio; Neri, Giovanni; D'Urso, Michele; Chiurazzi, Pietro; Ursini, Matilde Valeria; Miano, Maria Giuseppina

    2007-01-01

    Background Cognitive impairments are heterogeneous conditions, and it is estimated that 10% may be caused by a defect of mental function genes on the X chromosome. One of those genes is Aristaless related homeobox (ARX) encoding a polyA-rich homeobox transcription factor essential for cerebral patterning and its mutations cause different neurologic disorders. We reported on the clinical and genetic analysis of an Italian family with X-linked mental retardation (XLMR) and intra-familial heterogeneity, and provided insight into its molecular defect. Methods We carried out on linkage-candidate gene studies in a new MRX family (MRX87). All coding regions and exon-intron boundaries of ARX gene were analysed by direct sequencing. Results MRX87 patients had moderate to profound cognition impairment and a combination of minor congenital anomalies. The disease locus, MRX87, was mapped between DXS7104 and DXS1214, placing it in Xp22-p21 interval, a hot spot region for mental handicap. An in frame duplication of 24 bp (ARXdup24) in the second polyAlanine tract (polyA_II) in ARX was identified. Conclusion Our study underlines the role of ARXdup24 as a critical mutational site causing mental retardation linked to Xp22. Phenotypic heterogeneity of MRX87 patients represents a new observation relevant to the functional consequences of polyAlanine expansions enriching the puzzling complexity of ARXdup24-linked diseases. PMID:17480217

  2. Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM

    PubMed Central

    Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

    2015-01-01

    Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM). Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS), segmented PsePSSM, and segmented autocovariance transformation (ACT) based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640) are adopted in this paper. Then a 700-dimensional (700D) feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA). To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to other PSSM-based methods for prediction of protein structural classes for low-similarity sequences. PMID:26788119

  3. Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM.

    PubMed

    Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

    2015-01-01

    Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM). Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS), segmented PsePSSM, and segmented autocovariance transformation (ACT) based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640) are adopted in this paper. Then a 700-dimensional (700D) feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA). To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to other PSSM-based methods for prediction of protein structural classes for low-similarity sequences. PMID:26788119

  4. Consensus Sequence of 27 African Horse Sickness Virus Genomes from Viruses Collected over a 76-Year Period (1933 to 2009)

    PubMed Central

    Wright, Isabella M.; van Dijk, Alberdina A.

    2015-01-01

    We announce the complete consensus genome sequence of 27 African horse sickness viruses, representing all nine African horse sickness virus (AHSV) serotypes from historical and recent isolates collected over a 76-year period (1933 to 2009). The data set includes the sequence of the virulent Office International des Epizooties AHSV reference strains which are not adapted to cell culture. PMID:26358586

  5. A Comprehensive Approach to Clustering of Expressed Human Gene Sequence: The Sequence Tag Alignment and Consensus Knowledge Base

    PubMed Central

    Miller, Robert T.; Christoffels, Alan G.; Gopalakrishnan, Chella; Burke, John; Ptitsyn, Andrey A.; Broveak, Tania R.; Hide, Winston A.

    1999-01-01

    The expressed human genome is being sequenced and analyzed by disparate groups producing disparate data. The majority of the identified coding portion is in the form of expressed sequence tags (ESTs). The need to discover exonic representation and expression forms of full-length cDNAs for each human gene is frustrated by the partial and variable quality nature of this data delivery. A highly redundant human EST data set has been processed into integrated and unified expressed transcript indices that consist of hierarchically organized human transcript consensi reflecting gene expression forms and genetic polymorphism within an index class. The expression index and its intermediate outputs include cleaned transcript sequence, expression, and alignment information and a higher fidelity subset, SANIGENE. The STACK_PACK clustering system has been applied to dbEST release 121598 (GenBank version 110). Sixty-four percent of 1,313,103 Homo sapiens ESTs are condensed into 143,885 tissue level multiple sequence clusters; linking through clone-ID annotations produces 68,701 total assemblies, such that 81% of the original input set is captured in a STACK multiple sequence or linked cluster. Indexing of alignments by substituent EST accession allows browsing of the data structure and its cross-links to UniGene. STACK metaclusters consolidate a greater number of ESTs by a factor of 1.86 with respect to the corresponding UniGene build. Fidelity comparison with genome reference sequence AC004106 demonstrates consensus expression clusters that reflect significantly lower spurious repeat sequence content and capture alternate splicing within a whole body index cluster and three STACK v.2.3 tissue-level clusters. Statistics of a staggered release whole body index build of STACK v.2.0 are presented. PMID:10568754

  6. Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome.

    PubMed

    Singh, Vinod Kumar; Krishnamachari, Annangarachari

    2016-09-01

    Genome-wide experimental studies in Saccharomyces cerevisiae reveal that autonomous replicating sequence (ARS) requires an essential consensus sequence (ACS) for replication activity. Computational studies identified thousands of ACS like patterns in the genome. However, only a few hundreds of these sites act as replicating sites and the rest are considered as dormant or evolving sites. In a bid to understand the sequence makeup of replication sites, a content and context-based analysis was performed on a set of replicating ACS sequences that binds to origin-recognition complex (ORC) denoted as ORC-ACS and non-replicating ACS sequences (nrACS), that are not bound by ORC. In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS motifs in the non-coding segments points to the locations of ORC-ACS which are found far away from the adjacent gene start position compared to nrACS thereby enabling an accessible environment for ORC-proteins. Our attempt is novel in considering the contextual view of ACS and its flanking region along with nucleosome positioning in the S. cerevisiae genome and may be useful for any computational prediction scheme. PMID:27508123

  7. The effect of two closely inserted transcription consensus sequences on coronavirus transcription.

    PubMed Central

    Joo, M; Makino, S

    1995-01-01

    Insertion of an intergenic region from the murine coronavirus mouse hepatitis virus into a mouse hepatitis virus defective interfering (DI) RNA led to transcription of subgenomic DI RNA in helper virus-infected cells. Using this system, we studied how two intergenic regions in close proximity affected subgenomic RNA synthesis. When two intergenic regions were separated by more than 100 nucleotides, slightly less of the larger subgenomic DI RNA (synthesized from the upstream intergenic region) was made; this difference was significant when the intergenic region separation was less than about 35 nucleotides. Deletion of sequences flanking the two intergenic regions inserted in close proximity did not affect transcription. No significant change in the ratio of the two subgenomic DI RNAs was observed when the sequence between the two intergenic regions was altered. Removal of the downstream intergenic region restored transcription of the larger subgenomic DI RNA. The UCUAAAC consensus sequence was needed for efficient suppression of the larger subgenomic DI RNA synthesis. These results demonstrated that the downstream intergenic sequence was suppressing subgenomic DI RNA synthesis from the upstream intergenic region. We discuss possible mechanisms to account for the regulation of this suppression of subgenomic DI RNA synthesis and the ways in which they relate to the general regulation of coronavirus transcription. PMID:7983719

  8. A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety

    PubMed Central

    Cartwright, Dustin A.; Cestaro, Alessandro; Pruss, Dmitry; Pindo, Massimo; FitzGerald, Lisa M.; Vezzulli, Silvia; Reid, Julia; Malacarne, Giulia; Iliev, Diana; Coppola, Giuseppina; Wardell, Bryan; Micheletti, Diego; Macalma, Teresita; Facci, Marco; Mitchell, Jeff T.; Perazzolli, Michele; Eldredge, Glenn; Gatto, Pamela; Oyzerski, Rozan; Moretto, Marco; Gutin, Natalia; Stefanini, Marco; Chen, Yang; Segala, Cinzia; Davenport, Christine; Demattè, Lorenzo; Mraz, Amy; Battilana, Juri; Stormo, Keith; Costa, Fabrizio; Tao, Quanzhou; Si-Ammour, Azeddine; Harkins, Tim; Lackey, Angie; Perbost, Clotilde; Taillon, Bruce; Stella, Alessandra; Solovyev, Victor; Fawcett, Jeffrey A.; Sterck, Lieven; Vandepoele, Klaas; Grando, Stella M.; Toppo, Stefano; Moser, Claudio; Lanchbury, Jerry; Bogden, Robert; Skolnick, Mark; Sgaramella, Vittorio; Bhatnagar, Satish K.; Fontana, Paolo; Gutin, Alexander; Van de Peer, Yves; Salamini, Francesco; Viola, Roberto

    2007-01-01

    Background Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. Principal Findings We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before). Conclusions Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape. PMID:18094749

  9. Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography

    PubMed Central

    Mandal, Pradeep K.; Collie, Gavin W.; Srivastava, Suresh C.; Kauffmann, Brice; Huc, Ivan

    2016-01-01

    It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods—that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence ‘TATAAT’. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65–2.3 Å), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence. PMID:27137886

  10. Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

    PubMed Central

    Frank, J. A.; Pan, Y.; Tooming-Klunderud, A.; Eijsink, V. G. H.; McHardy, A. C.; Nederbragt, A. J.; Pope, P. B.

    2016-01-01

    DNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomic projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample that averaged 1319 nt in length and 99.7% accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62% of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications. PMID:27156482

  11. Eliciting neutralizing antibodies with gp120 outer domain constructs based on M-group consensus sequence.

    PubMed

    Qin, Yali; Banasik, Marisa; Kim, SoonJeung; Penn-Nicholson, Adam; Habte, Habtom H; LaBranche, Celia; Montefiori, David C; Wang, Chong; Cho, Michael W

    2014-08-01

    One strategy being evaluated for HIV-1 vaccine development is focusing immune responses towards neutralizing epitopes on the gp120 outer domain (OD) by removing the immunodominant, but non-neutralizing, inner domain. Previous OD constructs have not elicited strong neutralizing antibodies (nAbs). We constructed two immunogens, a monomeric gp120-OD and a trimeric gp120-OD×3, based on an M group consensus sequence (MCON6). Their biochemical and immunological properties were compared with intact gp120. Results indicated better preservation of critical neutralizing epitopes on gp120-OD×3. In contrast to previous studies, our immunogens induced potent, cross-reactive nAbs in rabbits. Although nAbs primarily targeted Tier 1 viruses, they exhibited significant breadth. Epitope mapping analyses indicated that nAbs primarily targeted conserved V3 loop elements. Although the potency and breadth of nAbs were similar for all three immunogens, nAb induction kinetics indicated that gp120-OD×3 was superior to gp120-OD, suggesting that gp120-OD×3 is a promising prototype for further gp120 OD-based immunogen development. PMID:25046154

  12. Eliciting Neutralizing Antibodies with gp120 Outer Domain Constructs Based on M-Group Consensus Sequence

    PubMed Central

    Qin, Yali; Banasik, Marisa; Kim, SoonJeung; Penn-Nicholson, Adam; Habte, Habtom H; Labranche, Celia; Montefiori, David C; Wang, Chong; Cho, Michael W

    2014-01-01

    One strategy being evaluated for HIV-1 vaccine development is focusing immune responses towards neutralizing epitopes on the gp120 outer domain (OD) by removing the immunodominant, but non-neutralizing, inner domain. Previous OD constructs have not elicited strong neutralizing antibodies (nAbs). We constructed two immunogens, a monomeric gp120-OD and a trimeric gp120-OD×3, based on an M group consensus sequence (MCON6). Their biochemical and immunological properties were compared with intact gp120. Results indicated better preservation of critical neutralizing epitopes on gp120-OD×3. In contrast to previous studies, our immunogens induced potent, cross-reactive nAbs in rabbits. Although nAbs primarily targeted Tier 1 viruses, they exhibited significant breadth. Epitope mapping analyses indicated that nAbs primarily targeted conserved V3 loop elements. Although the potency and breadth of nAbs were similar for all three immunogens, nAb induction kinetics indicated that gp120-OD×3 was superior to gp120-OD, suggesting that gp120-OD×3 is a promising prototype for further gp120 OD-based immunogen development. PMID:25046154

  13. Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.

    PubMed

    Frank, J A; Pan, Y; Tooming-Klunderud, A; Eijsink, V G H; McHardy, A C; Nederbragt, A J; Pope, P B

    2016-01-01

    DNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomic projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample that averaged 1319 nt in length and 99.7% accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62% of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications. PMID:27156482

  14. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

    PubMed

    Washietl, Stefan; Bernhart, Stephan H; Kellis, Manolis

    2014-01-01

    Many biologically important RNA structures are conserved in evolution leading to characteristic mutational patterns. RNAalifold is a widely used program to predict consensus secondary structures in multiple alignments by combining evolutionary information with traditional energy-based RNA folding algorithms. Here we describe the theory and applications of the RNAalifold algorithm. Consensus secondary structure prediction not only leads to significantly more accurate structure models, but it also allows to study structural conservation of functional RNAs. PMID:24639158

  15. A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags.

    PubMed Central

    Tani, Naoki; Takahashi, Tomokazu; Iwata, Hiroyoshi; Mukai, Yuzuru; Ujino-Ihara, Tokuko; Matsumoto, Asako; Yoshimura, Kensuke; Yoshimaru, Hiroshi; Murai, Masafumi; Nagasaka, Kazutoshi; Tsumura, Yoshihiko

    2003-01-01

    A consensus map for sugi (Cryptomeria japonica) was constructed by integrating linkage data from two unrelated third-generation pedigrees, one derived from a full-sib cross and the other by self-pollination of F1 individuals. The progeny segregation data of the first pedigree were derived from cleaved amplified polymorphic sequences, microsatellites, restriction fragment length polymorphisms, and single nucleotide polymorphisms. The data of the second pedigree were derived from cleaved amplified polymorphic sequences, isozyme markers, morphological traits, random amplified polymorphic DNA markers, and restriction fragment length polymorphisms. Linkage analyses were done for the first pedigree with JoinMap 3.0, using its parameter set for progeny derived by cross-pollination, and for the second pedigree with the parameter set for progeny derived from selfing of F1 individuals. The 11 chromosomes of C. japonica are represented in the consensus map. A total of 438 markers were assigned to 11 large linkage groups, 1 small linkage group, and 1 nonintegrated linkage group from the second pedigree; their total length was 1372.2 cM. On average, the consensus map showed 1 marker every 3.0 cM. PCR-based codominant DNA markers such as cleaved amplified polymorphic sequences and microsatellite markers were distributed in all linkage groups and occupied about half of mapped loci. These markers are very useful for integration of different linkage maps, QTL mapping, and comparative mapping for evolutional study, especially for species with a large genome size such as conifers. PMID:14668402

  16. Flagellar transcriptional activators FlbB and FlaI: gene sequences and 5' consensus sequences of operons under FlbB and FlaI control.

    PubMed Central

    Bartlett, D H; Frantz, B B; Matsumura, P

    1988-01-01

    The regulation of the expression of the operons in the flagella-chemotaxis regulon in Escherichia coli has been shown to be a highly ordered cascade which closely parallels the assembly of the flagellar structure and the chemotaxis machinery (T. Iino, Annu. Rev. Genet. 11:161-182, 1977; Y. Komeda, J. Bacteriol. 168: 1315-1318). The master operon, flbB, has been sequenced, and one of its gene products (FlaI) has been identified. On the basis of the deduced amino acid sequence, the FlbB protein has similarity to an alternate sigma factor which is responsible for expression of flagella in Bacillus subtilis. In addition, we have sequenced the 5' regions of a number of flagellar operons and compared these sequences with the 5' region of flagellar operons directly and indirectly under FlbB and FlaI control. We found both a consensus sequence which has been shown to be in all other flagellar operons (J. D. Helmann and M. J. Chamberlin, Proc. Natl. Acad. Sci. USA 84:6422-6424) and a derivative consensus sequence, which is found only in the 5' region of operons directly under FlbB and FlaI control. Images PMID:2832369

  17. Defining a Conformational Consensus Motif in Cotransin-Sensitive Signal Sequences: A Proteomic and Site-Directed Mutagenesis Study

    PubMed Central

    Klein, Wolfgang; Westendorf, Carolin; Schmidt, Antje; Conill-Cortés, Mercè; Rutz, Claudia; Blohs, Marcus; Beyermann, Michael; Protze, Jonas; Krause, Gerd; Krause, Eberhard; Schülein, Ralf

    2015-01-01

    The cyclodepsipeptide cotransin was described to inhibit the biosynthesis of a small subset of proteins by a signal sequence-discriminatory mechanism at the Sec61 protein-conducting channel. However, it was not clear how selective cotransin is, i.e. how many proteins are sensitive. Moreover, a consensus motif in signal sequences mediating cotransin sensitivity has yet not been described. To address these questions, we performed a proteomic study using cotransin-treated human hepatocellular carcinoma cells and the stable isotope labelling by amino acids in cell culture technique in combination with quantitative mass spectrometry. We used a saturating concentration of cotransin (30 micromolar) to identify also less-sensitive proteins and to discriminate the latter from completely resistant proteins. We found that the biosynthesis of almost all secreted proteins was cotransin-sensitive under these conditions. In contrast, biosynthesis of the majority of the integral membrane proteins was cotransin-resistant. Cotransin sensitivity of signal sequences was neither related to their length nor to their hydrophobicity. Instead, in the case of signal anchor sequences, we identified for the first time a conformational consensus motif mediating cotransin sensitivity. PMID:25806945

  18. Plasmodium falciparum Variability and Immune Evasion Proceed from Antigenicity of Consensus Sequences from DBL6ε; Generalization to All DBL from VAR2CSA

    PubMed Central

    Deloron, Philippe; Milet, Jacqueline; Badaut, Cyril

    2013-01-01

    We studied all consensus sequences within the four least ‘variable blocks’ (VB) present in the DBL6ε domain of VAR2CSA, the protein involved in the adhesion of infected red blood cells by Plasmodium falciparum that causes the Pregnancy-Associated Malaria (PAM). Characterising consensus sequences with respect to recognition of antibodies and percentage of responders among pregnant women living in areas where P. falciparum is endemic allows the identification of the most antigenic sequences within each VB. When combining these consensus sequences among four serotypes from VB1 or VB5, the most often recognized ones are expected to induce pan-reactive antibodies recognizing VAR2CSA from all plasmodial strains. These sequences are of main interest in the design of an immunogenic molecule. Using a similar approach than for DBL6ε, we studied the five other DBL and the CIDRpam from VAR2CSA, and again identified VB segments with highly conserved consensus sequences. In addition, we identified consensus sequences in other var genes expressed by non-PAM parasites. This finding paves the way for vaccine design against other pathologies caused by P. falciparum. PMID:23372786

  19. International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons.

    PubMed

    Olson, Nathan D; Lund, Steven P; Zook, Justin M; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B

    2015-03-01

    This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing(®), or Ion Torrent PGM(®). The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

  20. Consensus Rules in Variant Detection from Next-Generation Sequencing Data

    PubMed Central

    Jia, Peilin; Li, Fei; Xia, Jufeng; Chen, Haiquan; Ji, Hongbin; Pao, William; Zhao, Zhongming

    2012-01-01

    A critical step in detecting variants from next-generation sequencing data is post hoc filtering of putative variants called or predicted by computational tools. Here, we highlight four critical parameters that could enhance the accuracy of called single nucleotide variants and insertions/deletions: quality and deepness, refinement and improvement of initial mapping, allele/strand balance, and examination of spurious genes. Use of these sequence features appropriately in variant filtering could greatly improve validation rates, thereby saving time and costs in next-generation sequencing projects. PMID:22715385

  1. Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Vertebrate immune systems generate diverse repertoires of antibodies capable of mediating response to a variety of antigens. Next generation sequencing methods provide unique approaches to a number of immuno-based research areas including antibody discovery and engineering, disease surve...

  2. Chimaeric virus-like particles derived from consensus genome sequences of human rotavirus strains co-circulating in Africa.

    PubMed

    Jere, Khuzwayo C; O'Neill, Hester G; Potgieter, A Christiaan; van Dijk, Alberdina A

    2014-01-01

    Rotavirus virus-like particles (RV-VLPs) are potential alternative non-live vaccine candidates due to their high immunogenicity. They mimic the natural conformation of native viral proteins but cannot replicate because they do not contain genomic material which makes them safe. To date, most RV-VLPs have been derived from cell culture adapted strains or common G1 and G3 rotaviruses that have been circulating in communities for some time. In this study, chimaeric RV-VLPs were generated from the consensus sequences of African rotaviruses (G2, G8, G9 or G12 strains associated with either P[4], P[6] or P[8] genotypes) characterised directly from human stool samples without prior adaptation of the wild type strains to cell culture. Codon-optimised sequences for insect cell expression of genome segments 2 (VP2), 4 (VP4), 6 (VP6) and 9 (VP7) were cloned into a modified pFASTBAC vector, which allowed simultaneous expression of up to four genes using the Bac-to-Bac Baculovirus Expression System (BEVS; Invitrogen). Several combinations of the genome segments originating from different field strains were cloned to produce double-layered RV-VLPs (dRV-VLP; VP2/6), triple-layered RV-VLPs (tRV-VLP; VP2/6/7 or VP2/6/7/4) and chimaeric tRV-VLPs. The RV-VLPs were produced by infecting Spodoptera frugiperda 9 and Trichoplusia ni cells with recombinant baculoviruses using multi-cistronic, dual co-infection and stepwise-infection expression strategies. The size and morphology of the RV-VLPs, as determined by transmission electron microscopy, revealed successful production of RV-VLPs. The novel approach of producing tRV-VLPs, by using the consensus insect cell codon-optimised nucleotide sequence derived from dsRNA extracted directly from clinical specimens, should speed-up vaccine research and development by by-passing the need to adapt rotaviruses to cell culture. Other problems associated with cell culture adaptation, such as possible changes in epitopes, can also be circumvented

  3. Enterocytozoon bieneusi genotype nomenclature based on the internal transcribed spacer sequence: a consensus.

    PubMed

    Santín, Mónica; Fayer, Ronald

    2009-01-01

    The standard method for determining the genotypes of Enterocytozoon bieneusi is based on the DNA sequence of the internal transcribed spacer (ITS) region of the rRNA gene. There are 81 genotypes with 111 genotype names: 26 genotypes have been identified exclusively in humans, eight have been identified in humans and in other hosts, 27 have been identified exclusively in cattle and pigs, six have been identified exclusively in cats and dogs, and 14 have been identified in miscellaneous hosts. Because none of these genotypes has taxonomic status and therefore do not adhere to the International Code of Zoological Nomenclature regarding naming, some genotypes have received multiple names, each different and in separate publications by different authors. Because of the proliferation of genotypes with overlapping names and multiple hosts the scientific literature has become confusing and difficult to efficiently utilize. To reduce confusion and provide guidance for future publications we tabulated all names, GenBank accession numbers, and author citations and propose that the first published name has precedence and should become the primary name used in all subsequent publications in which genotyping is based on ITS sequencing. In those publications the names and GenBank numbers that were submitted at later dates should also be provided by the authors as synonyms to aid readers and reviewers. PMID:19335772

  4. Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences

    PubMed Central

    Cao, Bo; Chen, Chao; DeMott, Michael S.; Cheng, Qiuxiang; Clark, Tyson A.; Xiong, Xiaolin; Zheng, Xiaoqing; Butty, Vincent; Levine, Stuart S.; Yuan, George; Boitano, Matthew; Luong, Khai; Song, Yi; Zhou, Xiufen; Deng, Zixin; Turner, Stephen W.; Korlach, Jonas; You, Delin; Wang, Lianrong; Chen, Shi; Dedon, Peter C.

    2015-01-01

    Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other PT functions. To better understand PT biology, we report two novel, orthogonal technologies to map PTs across the genomes of B7A and FF75 with >90% agreement: real-time (SMRT) sequencing and deep sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of GpsAAC/GpsTTC motifs, but with only 18% of 40,701 possible sites modified. In contrast, PT in FF75 occurs as a single-strand modification at CpsCA, again with only 14% of 160,541 sites modified. Single-molecule analysis indicates that modification could be partial at any particular genomic site even with active restriction by DndF-H, with direct interaction of modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results point to highly unusual target selection by PT modification proteins and rule out known R-M mechanisms. PMID:24899568

  5. Allelic frequency determination of the 24-bp chitotriosidase duplication in the Portuguese population by real-time PCR.

    PubMed

    Rodrigues, M R; Sá Miranda, M C; Amaral, O

    2004-01-01

    Chitotriosidase is a human chitinase produced by macrophages. Its enzymatic activity is markedly elevated in serum of patients suffering from lysosomal storage disorders, as well as other diseases in which macrophages are activated. Therefore, it is a useful tool as a secondary marker in the diagnosis of several disorders including Gaucher disease type 1 and Niemann-Pick disease. The determination of chitotriosidase levels as a diagnosis complement in some lysosomal storage disorders and in enzyme replacement therapy follow-up of Gaucher disease patients is of great importance. However, the fact that a mutation caused by a 24-bp duplication in the CHIT1 gene resulting in deficiency of plasma chitotriosidase activity is very frequent makes the establishment of the frequency of this mutation in different population groups necessary. Furthermore, in order to validate the use of chitotriosidase activity as a marker, it is indispensable to screen individuals for this particular mutation. In this work, we present the results of a study where the allelic frequency of the above mentioned CHIT1 gene mutation was determined in the Portuguese population by real-time PCR. The frequency of carriers encountered in this sample of Portuguese individuals was of 37%. PMID:15528158

  6. A multiwavelength consensus on the main sequence of star-forming galaxies at z ˜ 2

    NASA Astrophysics Data System (ADS)

    Rodighiero, G.; Renzini, A.; Daddi, E.; Baronchelli, I.; Berta, S.; Cresci, G.; Franceschini, A.; Gruppioni, C.; Lutz, D.; Mancini, C.; Santini, P.; Zamorani, G.; Silverman, J.; Kashino, D.; Andreani, P.; Cimatti, A.; Sánchez, H. Domínguez; Le Floch, E.; Magnelli, B.; Popesso, P.; Pozzi, F.

    2014-09-01

    We compare various star formation rate (SFR) indicators for star-forming galaxies at 1.4 < z < 2.5 in the COSMOS field. The main focus is on the SFRs from the far-IR (PACS-Herschel data) with those from the ultraviolet, for galaxies selected according to the BzK criterion. FIR-selected samples lead to a vastly different slope of the SFR-stellar mass (M*) relation, compared to that of the dominant main-sequence population as measured from the UV, since the FIR selection picks predominantly only a minority of outliers. However, there is overall agreement between the main sequences derived with the two SFR indicators, when stacking on the PACS maps the BzK-selected galaxies. The resulting logarithmic slope of the SFR-M* relation is ˜0.8-0.9, in agreement with that derived from the dust-corrected UV luminosity. Exploiting deeper 24 μm Spitzer data, we have characterized a subsample of galaxies with reddening and SFRs poorly constrained, as they are very faint in the B band. The combination of Herschel with Spitzer data has allowed us to largely break the age/reddening degeneracy for these intriguing sources, by distinguishing whether a galaxy is very red in B-z because of being heavily dust reddened, or whether because star formation has been (or is being) quenched. Finally, we have compared our SFR(UV) to the SFRs derived by stacking the radio data and to those derived from the Hα luminosity of a sample of star-forming galaxies at 1.4 < z < 1.7. The two sets of SFRs are broadly consistent as they are with the SFRs derived from the UV and by stacking the corresponding PACS data in various mass bins.

  7. Characterization of Synthetic Chikungunya Viruses Based on the Consensus Sequence of Recent E1-226V Isolates

    PubMed Central

    Scholte, Florine E. M.; Tas, Ali; Martina, Byron E. E.; Cordioli, Paolo; Narayanan, Krishna; Makino, Shinji; Snijder, Eric J.; van Hemert, Martijn J.

    2013-01-01

    Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that re-emerged in 2004 and has caused massive outbreaks in recent years. The lack of a licensed vaccine or treatment options emphasize the need to obtain more insight into the viral life cycle and CHIKV-host interactions. Infectious cDNA clones are important tools for such studies, and for mechanism of action studies on antiviral compounds. Existing CHIKV cDNA clones are based on a single genome from an individual clinical isolate, which is expected to have evolved specific characteristics in response to the host environment, and possibly also during subsequent cell culture passaging. To obtain a virus expected to have the general characteristics of the recent E1-226V CHIKV isolates, we have constructed a new CHIKV full-length cDNA clone, CHIKV LS3, based on the consensus sequence of their aligned genomes. Here we report the characterization of this synthetic virus and a green fluorescent protein-expressing variant (CHIKV LS3-GFP). Their characteristics were compared to those of natural strain ITA07-RA1, which was isolated during the 2007 outbreak in Italy. In cell culture the synthetic viruses displayed phenotypes comparable to the natural isolate, and in a mouse model they caused lethal infections that were indistinguishable from infections with a natural strain. Compared to ITA07-RA1 and clinical isolate NL10/152, the synthetic viruses displayed similar sensitivities to several antiviral compounds. 3-deaza-adenosine was identified as a new inhibitor of CHIKV replication. Cyclosporin A had no effect on CHIKV replication, suggesting that cyclophilins -opposite to what was found for other +RNA viruses- do not play an essential role in CHIKV replication. The characterization of the consensus sequence-based synthetic viruses and their comparison to natural isolates demonstrated that CHIKV LS3 and LS3-GFP are suitable and representative tools to study CHIKV-host interactions, screen for antiviral compounds and

  8. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE) Consensus Sequence Repeats in the Viral Genome.

    PubMed

    Kumar, Ashutosh; Singh, Himanshu N; Pareek, Vikas; Raza, Khursheed; Dantham, Subrahamanyam; Kumar, Pavan; Mochan, Sankat; Faiq, Muneeb A

    2016-01-01

    Owing to the reports of microcephaly as a consistent outcome in the fetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV)-microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favor of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1) sequence homology between ZIKV genome and the response element of an early neural tube developmental marker "retinoic acid" in human DNA and (2) comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE) consensus sequence (5'-AGGTCA-3') in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly) and other viruses available in National Institute of Health genetic sequence database (GenBank) for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause fetal brain defects (for which maternal-fetal transmission during developing stage may be required). The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although, bioinformatic evidence and embryological

  9. Deduced consensus sequence of Sindbis virus strain AR339: mutations contained in laboratory strains which affect cell culture and in vivo phenotypes.

    PubMed Central

    McKnight, K L; Simpson, D A; Lin, S C; Knott, T A; Polo, J M; Pence, D F; Johannsen, D B; Heidner, H W; Davis, N L; Johnston, R E

    1996-01-01

    The consensus sequence of the Sindbis virus AR339 isolate, the prototype alphavirus, has been deduced. THe results presented here suggest (i) that a substantial proportion of the sequence divergence evident between the consensus sequence and sequences of laboratory strains of AR339 has resulted from selection for efficient growth in cell culture, (ii) that many of these changes affect the virulence of the virus in animal models, and (iii) that such modified genetic backgrounds present in laboratory strains can exert a significant influence on genetic studies of virus pathogenesis and host range. A laboratory strain of Sindbis virus AR339 was sequenced and cloned as a cDNA (pTRSB) from which infectious virus (TRSB) could be derived. The consensus sequence was deduced from the complete sequences of pTRSB and HRsp (E. G. Strauss, C. M. Rice, and J. H. Strauss, Virology 133:92-110, 1984), from partial sequences of the glycoprotein genes of three other AR339 laboratory strains, and by comparison with the sequences of the glycoprotein genes of three other AR339 sequence. HRsp differed form the consensus sequence by eight coding changes, and TRSB differed by three coding changes. In the 5' untranslated region, HRsp differed from the consensus sequence at nucleotide (nt) 5. These differences were likely the result of cell culture passage of the original AR339 isolate. At three of the difference loci (one in TRSB and two in HRsp), selection of cell-culture-adaptive mutations was documented with Sindbis virus or other alphaviruses. Selection in cell culture often results in attenuation of virulence in animals. Considering the TRSB and HRsp sequences together, one noncoding difference from the consensus (an A-for-G substitution in the 5' untranslated region at nt 5) and six coding differences in the glycoprotein genes (at E2 amino acids 1, 3, 70, and 172 and at E1 amino acids 72 and 237) were at loci which, either individually or in combination, significantly affected

  10. Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3'-UTR.

    PubMed

    Miyazaki, Saori; Sato, Yutaka; Asano, Tomoya; Nagamura, Yoshiaki; Nonomura, Ken-Ichi

    2015-10-01

    Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to cis-elements in the 3'-untranslated region (3'-UTR) is widely used in eukaryotes to complete various biological processes. Rice MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2) is the RRM protein that functions in the transition to meiosis in proper timing. The MEL2 RRM preferentially associated with the U-rich RNA consensus, UUAGUU[U/A][U/G][A/U/G]U, dependently on sequences and proportionally to MEL2 protein amounts in vitro. The consensus sequences were located in the putative looped structures of the RNA ligand. A genome-wide survey revealed a tendency of MEL2-binding consensus appearing in 3'-UTR of rice genes. Of 249 genes that conserved the consensus in their 3'-UTR, 13 genes spatiotemporally co-expressed with MEL2 in meiotic flowers, and included several genes whose function was supposed in meiosis; such as Replication protein A and OsMADS3. The proteome analysis revealed that the amounts of small ubiquitin-related modifier-like protein and eukaryotic translation initiation factor3-like protein were dramatically altered in mel2 mutant anthers. Taken together with transcriptome and gene ontology results, we propose that the rice MEL2 is involved in the translational regulation of key meiotic genes on 3'-UTRs to achieve the faithful transition of germ cells to meiosis. PMID:26319516

  11. The Interferon Consensus Sequence Binding Protein (Icsbp/Irf8) Is Required for Termination of Emergency Granulopoiesis.

    PubMed

    Hu, Liping; Huang, Weiqi; Hjort, Elizabeth E; Bei, Ling; Platanias, Leonidas C; Eklund, Elizabeth A

    2016-02-19

    Emergency granulopoiesis occurs in response to infectious or inflammatory challenge and is a component of the innate immune response. Some molecular events involved in initiating emergency granulopoiesis are known, but termination of this process is less well defined. In this study, we found that the interferon consensus sequence binding protein (Icsbp/Irf8) was required to terminate emergency granulopoiesis. Icsbp is an interferon regulatory transcription factor with leukemia suppressor activity. Expression of Icsbp is decreased in chronic myeloid leukemia, and Icsbp(-/-) mice exhibit progressive granulocytosis with evolution to blast crisis, similar to the course of human chronic myeloid leukemia. In this study, we found aberrantly sustained granulocyte production in Icsbp(-/-) mice after stimulation of an emergency granulopoiesis response. Icsbp represses transcription of the genes encoding Fas-associated phosphatase 1 (Fap1) and growth arrest-specific 2 (Gas2) and activates genes encoding Fanconi C and F. After stimulation of emergency granulopoiesis, we found increased and sustained expression of Fap1 and Gas2 in bone marrow myeloid progenitor cells from Icsbp(-/-) mice in comparison with the wild type. This was associated with resistance to Fas-induced apoptosis and increased β-catenin activity in these cells. We also found that repeated episodes of emergency granulopoiesis accelerated progression to acute myeloid leukemia in Icsbp(-/-) mice. This was associated with impaired Fanconi C and F expression and increased sensitivity to DNA damage in bone marrow myeloid progenitors. Our results suggest that impaired Icsbp expression enhances leukemogenesis by deregulating processes that normally limit granulocyte expansion during the innate immune response. PMID:26683374

  12. A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti–hepatitis C target

    PubMed Central

    Wang, Shao-Ru; Min, Yuan-Qin; Wang, Jia-Qi; Liu, Chao-Xing; Fu, Bo-Shi; Wu, Fan; Wu, Ling-Yu; Qiao, Zhi-Xian; Song, Yan-Yan; Xu, Guo-Hua; Wu, Zhi-Guo; Huang, Gai; Peng, Nan-Fang; Huang, Rong; Mao, Wu-Xiang; Peng, Shuang; Chen, Yu-Qi; Zhu, Ying; Tian, Tian; Zhang, Xiao-Lian; Zhou, Xiang

    2016-01-01

    G-quadruplex (G4) is one of the most important secondary structures in nucleic acids. Until recently, G4 RNAs have not been reported in any ribovirus, such as the hepatitis C virus. Our bioinformatics analysis reveals highly conserved guanine-rich consensus sequences within the core gene of hepatitis C despite the high genetic variability of this ribovirus; we further show using various methods that such consensus sequences can fold into unimolecular G4 RNA structures, both in vitro and under physiological conditions. Furthermore, we provide direct evidences that small molecules specifically targeting G4 can stabilize this structure to reduce RNA replication and inhibit protein translation of intracellular hepatitis C. Ultimately, the stabilization of G4 RNA in the genome of hepatitis C represents a promising new strategy for anti–hepatitis C drug development. PMID:27051880

  13. A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target.

    PubMed

    Wang, Shao-Ru; Min, Yuan-Qin; Wang, Jia-Qi; Liu, Chao-Xing; Fu, Bo-Shi; Wu, Fan; Wu, Ling-Yu; Qiao, Zhi-Xian; Song, Yan-Yan; Xu, Guo-Hua; Wu, Zhi-Guo; Huang, Gai; Peng, Nan-Fang; Huang, Rong; Mao, Wu-Xiang; Peng, Shuang; Chen, Yu-Qi; Zhu, Ying; Tian, Tian; Zhang, Xiao-Lian; Zhou, Xiang

    2016-04-01

    G-quadruplex (G4) is one of the most important secondary structures in nucleic acids. Until recently, G4 RNAs have not been reported in any ribovirus, such as the hepatitis C virus. Our bioinformatics analysis reveals highly conserved guanine-rich consensus sequences within the core gene of hepatitis C despite the high genetic variability of this ribovirus; we further show using various methods that such consensus sequences can fold into unimolecular G4 RNA structures, both in vitro and under physiological conditions. Furthermore, we provide direct evidences that small molecules specifically targeting G4 can stabilize this structure to reduce RNA replication and inhibit protein translation of intracellular hepatitis C. Ultimately, the stabilization of G4 RNA in the genome of hepatitis C represents a promising new strategy for anti-hepatitis C drug development. PMID:27051880

  14. First full-length genome sequence of the polerovirus luffa aphid-borne yellows virus (LABYV) reveals the presence of at least two consensus sequences in an isolate from Thailand.

    PubMed

    Knierim, Dennis; Maiss, Edgar; Kenyon, Lawrence; Winter, Stephan; Menzel, Wulf

    2015-10-01

    Luffa aphid-borne yellows virus (LABYV) was proposed as the name for a previously undescribed polerovirus based on partial genome sequences obtained from samples of cucurbit plants collected in Thailand between 2008 and 2013. In this study, we determined the first full-length genome sequence of LABYV. Based on phylogenetic analysis and genome properties, it is clear that this virus represents a distinct species in the genus Polerovirus. Analysis of sequences from sample TH24, which was collected in 2010 from a luffa plant in Thailand, reveals the presence of two different full-length genome consensus sequences. PMID:26195192

  15. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE) Consensus Sequence Repeats in the Viral Genome

    PubMed Central

    Kumar, Ashutosh; Singh, Himanshu N.; Pareek, Vikas; Raza, Khursheed; Dantham, Subrahamanyam; Kumar, Pavan; Mochan, Sankat; Faiq, Muneeb A.

    2016-01-01

    Owing to the reports of microcephaly as a consistent outcome in the fetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV)—microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favor of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1) sequence homology between ZIKV genome and the response element of an early neural tube developmental marker “retinoic acid” in human DNA and (2) comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE) consensus sequence (5′–AGGTCA–3′) in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly) and other viruses available in National Institute of Health genetic sequence database (GenBank) for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause fetal brain defects (for which maternal-fetal transmission during developing stage may be required). The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although, bioinformatic evidence and

  16. Measuring consensus

    SciTech Connect

    Kurstedt, H.A. Jr.; Brubaker, D.M.; Doss, A.R.; Koelling, C.P.

    1989-10-01

    For this paper, I wanted to compare mathematical techniques against group interaction in generating consensus for a ranking decision. I convened a group to come to consensus on ranking items needed for survival on the moon. I chose this problem because NASA has an approved solution. I solicited the group's individual rankings before and after discussion. I used Kendall's coefficient of concordance to measure the level of consensus before and after discussion and compared the results against individual qualitative responses to a questionnaire designed to also measure consensus. The approved solution allowed me to see if group felt more or less in agreement as they moved closer or farther from the approved solution. As background for this experiment, I researched the existing knowledge on measuring consensus. I make a distinction between consensus and successful consensus, define them, and operationalize them for the purposes of this study. I define different levels of consensus which can be reached regardless of the success of the consensus. In this experiment, I determined the interactive discussion produced consensus, but not successful consensus. The mathematical technique produced a ranking closer to the accepted answer than the group discussion did. 15 refs., 1 tab.

  17. Consensus protein design.

    PubMed

    Porebski, Benjamin T; Buckle, Ashley M

    2016-07-01

    A popular and successful strategy in semi-rational design of protein stability is the use of evolutionary information encapsulated in homologous protein sequences. Consensus design is based on the hypothesis that at a given position, the respective consensus amino acid contributes more than average to the stability of the protein than non-conserved amino acids. Here, we review the consensus design approach, its theoretical underpinnings, successes, limitations and challenges, as well as providing a detailed guide to its application in protein engineering. PMID:27274091

  18. Consensus protein design

    PubMed Central

    Porebski, Benjamin T.; Buckle, Ashley M.

    2016-01-01

    A popular and successful strategy in semi-rational design of protein stability is the use of evolutionary information encapsulated in homologous protein sequences. Consensus design is based on the hypothesis that at a given position, the respective consensus amino acid contributes more than average to the stability of the protein than non-conserved amino acids. Here, we review the consensus design approach, its theoretical underpinnings, successes, limitations and challenges, as well as providing a detailed guide to its application in protein engineering. PMID:27274091

  19. Predicting the functional consequences of non-synonymous DNA sequence variants--evaluation of bioinformatics tools and development of a consensus strategy.

    PubMed

    Frousios, Kimon; Iliopoulos, Costas S; Schlitt, Thomas; Simpson, Michael A

    2013-10-01

    The study of DNA sequence variation has been transformed by recent advances in DNA sequencing technologies. Determination of the functional consequences of sequence variant alleles offers potential insight as to how genotype may influence phenotype. Even within protein coding regions of the genome, establishing the consequences of variation on gene and protein function is challenging and requires substantial laboratory investigation. However, a series of bioinformatics tools have been developed to predict whether non-synonymous variants are neutral or disease-causing. In this study we evaluate the performance of nine such methods (SIFT, PolyPhen2, SNPs&GO, PhD-SNP, PANTHER, Mutation Assessor, MutPred, Condel and CAROL) and developed CoVEC (Consensus Variant Effect Classification), a tool that integrates the prediction results from four of these methods. We demonstrate that the CoVEC approach outperforms most individual methods and highlights the benefit of combining results from multiple tools. PMID:23831115

  20. Animal Protection and Structural Studies of a Consensus Sequence VaccineTargeting the Receptor Binding Domain of the Type IV Pilus of Pseudomonas aeruginosa

    PubMed Central

    Kao, Daniel J.; Churchill, Mair E. A.; Irvin, Randall T.; Hodges, Robert S.

    2010-01-01

    One of the main obstacles in the development of a vaccine against Pseudomonas aeruginosa is the requirement that it is protective against a wide range of virulent strains. We have developed a synthetic-peptide consensus-sequence vaccine (Cs1) that targets the host receptor-binding domain (RBD) of the type IV pilus of P. aeruginosa. Here, we show that this vaccine provides increased protection against challenge by the four piliated strains that we have examined (PAK, PAO, KB7 and P1) in the A.BY/SnJ mouse model of acute P. aeruginosa infection. To further characterize the consensus sequence, we engineered Cs1 into the PAK monomeric pilin protein and determined the crystal structure of the chimeric Cs1 pilin to 1.35 Å resolution. The substitutions (T130K and E135P) used to create Cs1 do not disrupt the conserved backbone conformation of the pilin RBD. In fact, based on the Cs1 pilin structure, we hypothesize that the E135P substitution bolsters the conserved backbone conformation and may partially explain the immunological activity of Cs1. Structural analysis of Cs1, PAK and K122-4 pilins reveal substitutions of non-conserved residues in the RBD are compensated for by complementary changes in the rest of the pilin monomer. Thus, the interactions between the RBD and the rest of the pilin can either be mediated by polar interactions of a hydrogen bond network in some strains or by hydrophobic interactions in others. Both configurations maintain a conserved backbone conformation of the RBD. Thus, the backbone conformation is critical in our consensus-sequence vaccine design and that cross-reactivity of the antibody response may be modulated by the composition of exposed side-chains on the surface of the RBD. This structure will guide our future vaccine design by focusing our investigation on the four variable residue positions that are exposed on the RBD surface. PMID:17936788

  1. Animal Protection and Structural Studies of a Consensus Sequence Vaccine Targeting the Receptor Binding Domain of the Type IV Pilus of Pseudomonas aeruginosa

    SciTech Connect

    Kao, Daniel J.; Churchill, Mair E.A.; Irvin, Randall T.; Hodges, Robert S.

    2008-09-23

    One of the main obstacles in the development of a vaccine against Pseudomonas aeruginosa is the requirement that it is protective against a wide range of virulent strains. We have developed a synthetic-peptide consensus-sequence vaccine (Cs1) that targets the host receptor-binding domain (RBD) of the type IV pilus of P. aeruginosa. Here, we show that this vaccine provides increased protection against challenge by the four piliated strains that we have examined (PAK, PAO, KB7 and P1) in the A.BY/SnJ mouse model of acute P. aeruginosa infection. To further characterize the consensus sequence, we engineered Cs1 into the PAK monomeric pilin protein and determined the crystal structure of the chimeric Cs1 pilin to 1.35 {angstrom} resolution. The substitutions (T130K and E135P) used to create Cs1 do not disrupt the conserved backbone conformation of the pilin RBD. In fact, based on the Cs1 pilin structure, we hypothesize that the E135P substitution bolsters the conserved backbone conformation and may partially explain the immunological activity of Cs1. Structural analysis of Cs1, PAK and K122-4 pilins reveal substitutions of non-conserved residues in the RBD are compensated for by complementary changes in the rest of the pilin monomer. Thus, the interactions between the RBD and the rest of the pilin can either be mediated by polar interactions of a hydrogen bond network in some strains or by hydrophobic interactions in others. Both configurations maintain a conserved backbone conformation of the RBD. Thus, the backbone conformation is critical in our consensus-sequence vaccine design and that cross-reactivity of the antibody response may be modulated by the composition of exposed side-chains on the surface of the RBD. This structure will guide our future vaccine design by focusing our investigation on the four variable residue positions that are exposed on the RBD surface.

  2. easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences

    PubMed Central

    Rosenkranz, David

    2012-01-01

    The PCR-amplification of unknown homologous or paralogous genes generally relies on PCR primers predicted from multi sequence alignments. But increasing sequence divergence can induce the need to use degenerate primers which entails the problem of testing the characteristics, unwanted interactions and potential mispriming of degenerate primers. Here I introduce easyPAC, a new software for the prediction of degenerate primers from multi sequence alignments or single consensus sequences. As a major innovation, easyPAC allows to apply all customary primer test procedures to degenerate primer sequences including fast mapping to reference files. Thus, easyPAC simplifies and expedites the designing of specific degenerate primers enormously. Degenerate primers suggested by easyPAC were used in PCR amplification with subsequent de novo sequencing of TDRD1 exon 11 homologs from several representatives of the haplorrhine primate phylogeny. The results demonstrate the efficient performance of the suggested primers and therefore show that easyPAC can advance upcoming comparative genetic studies.

  3. beta-Cyclodextrin derivatives as carriers to enhance the antiviral activity of an antisense oligonucleotide directed toward a coronavirus intergenic consensus sequence.

    PubMed

    Abdou, S; Collomb, J; Sallas, F; Marsura, A; Finance, C

    1997-01-01

    The ability of cyclodextrins to enhance the antiviral activity of a phosphodiester oligodeoxynucleotide has been investigated. A 18-mer oligodeoxynucleotide complementary to the initiation region of the mRNA coding for the spike protein and containing the intergenic consensus sequence of an enteric coronavirus has been tested for antiviral action against virus growth in human adenocarcinoma cells. The phosphodiester oligodeoxynucleotide only showed a limited effect on virus growth rate (from 12 to 34% viral inhibition in cells treated with 7.5 to 25 microM oligodeoxynucleotide, respectively, at a multiplicity of infection of 0.1 infectious particle per cell). In the same conditions, the phosphorothioate analogue exhibited stronger antiviral activity, the inhibition increased from 56 to 90%. The inhibitory effect of this analogue was antisense and sequence-specific. Northern blot analysis showed that the sequence-dependent mechanism of action appears to be the inhibition of mRNA transcription. We conclude that the coronavirus intergenic consensus sequence is a good target for an antisense oligonucleotide antiviral action. The properties of the phosphodiester oligonucleotide was improved after its complexation with cyclodextrins. The most important increase of the antiviral activity (90% inhibition) was obtained with only 7.5 microM oligonucleotide complexed to a cyclodextrin derivative, 6-deoxy-6-S-beta-D-galactopyranosyl-6-thio-cyclomalto-heptaose+ ++ in a molar ratio of 1:100. These studies suggest that the use of cyclodextrin derivatives as carrier for phosphodiester oligonucleotides delivery may be an effective method for increasing the therapeutic potential of these compounds in viral infections. PMID:9672621

  4. Chicken interferon consensus sequence-binding protein (ICSBP) and interferon regulatory factor (IRF) 1 genes reveal evolutionary conservation in the IRF gene family.

    PubMed Central

    Jungwirth, C; Rebbert, M; Ozato, K; Degen, H J; Schultz, U; Dawid, I B

    1995-01-01

    Members of the IRF family mediate transcriptional responses to interferons (IFNs) and to virus infection. So far, proteins of this family have been studied only among mammalian species. Here we report the isolation of cDNA clones encoding two members of this family from chicken, interferon consensus sequence-binding protein (ICSBP) and IRF-1. The predicted chicken ICSBP and IRF-1 proteins show high levels of sequence similarity to their corresponding human and mouse counterparts. Sequence identities in the putative DNA-binding domains of chicken and human ICSBP and IRF-1 were 97% and 89%, respectively, whereas the C-terminal regions showed identities of 64% and 51%; sequence relationships with mouse ICSBP and IRF-1 are very similar. Chicken ICSBP was found to be expressed in several embryonic tissues, and both chicken IRF-1 and ICSBP were strongly induced in chicken fibroblasts by IFN treatment, supporting the involvement of these factors in IFN-regulated gene expression. The presence of proteins homologous to mammalian IRF family members, together with earlier observations on the occurrence of functionally homologous IFN-responsive elements in chicken and mammalian genes, highlights the conservation of transcriptional mechanisms in the IFN system, a finding that contrasts with the extensive sequence and functional divergence of the IFNs. Images Fig. 3 Fig. 4 Fig. 5 PMID:7536924

  5. Towards a consensus Y-chromosomal phylogeny and Y-SNP set in forensics in the next-generation sequencing era.

    PubMed

    Larmuseau, Maarten H D; Van Geystelen, Anneleen; Kayser, Manfred; van Oven, Mannis; Decorte, Ronny

    2015-03-01

    Currently, several different Y-chromosomal phylogenies and haplogroup nomenclatures are presented in scientific literature and at conferences demonstrating the present diversity in Y-chromosomal phylogenetic trees and Y-SNP sets used within forensic and anthropological research. This situation can be ascribed to the exponential growth of the number of Y-SNPs discovered due to mostly next-generation sequencing (NGS) studies. As Y-SNPs and their respective phylogenetic positions are important in forensics, such as for male lineage characterization and paternal bio-geographic ancestry inference, there is a need for forensic geneticists to know how to deal with these newly identified Y-SNPs and phylogenies, especially since these phylogenies are often created with other aims than to carry out forensic genetic research. Therefore, we give here an overview of four categories of currently used Y-chromosomal phylogenies and the associated Y-SNP sets in scientific research in the current NGS era. We compare these categories based on the construction method, their advantages and disadvantages, the disciplines wherein the phylogenetic tree can be used, and their specific relevance for forensic geneticists. Based on this overview, it is clear that an up-to-date reduced tree with a consensus Y-SNP set and a stable nomenclature will be the most appropriate reference resource for forensic research. Initiatives to reach such an international consensus are therefore highly recommended. PMID:25488610

  6. A Screen for Dominant Negative Mutants of SEC18 Reveals a Role for the AAA Protein Consensus Sequence in ATP Hydrolysis

    PubMed Central

    Steel, Gregor J.; Harley, Carol; Boyd, Alan; Morgan, Alan

    2000-01-01

    An evolutionarily ancient mechanism is used for intracellular membrane fusion events ranging from endoplasmic reticulum–Golgi traffic in yeast to synaptic vesicle exocytosis in the human brain. At the heart of this mechanism is the core complex of N-ethylmaleimide-sensitive fusion protein (NSF), soluble NSF attachment proteins (SNAPs), and SNAP receptors (SNAREs). Although these proteins are accepted as key players in vesicular traffic, their molecular mechanisms of action remain unclear. To illuminate important structure–function relationships in NSF, a screen for dominant negative mutants of yeast NSF (Sec18p) was undertaken. This involved random mutagenesis of a GAL1-regulated SEC18 yeast expression plasmid. Several dominant negative alleles were identified on the basis of galactose-inducible growth arrest, of which one, sec18-109, was characterized in detail. The sec18-109 phenotype (abnormal membrane trafficking through the biosynthetic pathway, accumulation of a membranous tubular network, growth suppression, increased cell density) is due to a single A-G substitution in SEC18 resulting in a missense mutation in Sec18p (Thr394→Pro). Thr394 is conserved in most AAA proteins and indeed forms part of the minimal AAA consensus sequence that serves as a signature of this large protein family. Analysis of recombinant Sec18-109p indicates that the mutation does not prevent hexamerization or interaction with yeast α-SNAP (Sec17p), but instead results in undetectable ATPase activity that cannot be stimulated by Sec17p. This suggests a role for the AAA protein consensus sequence in regulating ATP hydrolysis. Furthermore, this approach of screening for dominant negative mutants in yeast can be applied to other conserved proteins so as to highlight important functional domains in their mammalian counterparts. PMID:10749934

  7. [Creation of DNA vaccine vector based on codon-optimized gene of rabies virus glycoprotein (G protein) with consensus amino acid sequence].

    PubMed

    Starodubova, E S; Kuzmenko, Y V; Latanova, A A; Preobrazhenskaya, O V; Karpov, V L

    2016-01-01

    An optimized design of the rabies virus glycoprotein (G protein) for use within DNA vaccines has been suggested. The design represents a territorially adapted antigen constructed taking into account glycoprotein amino acid sequences of the rabies viruses registered in the Russian Federation and the vaccine Vnukovo-32 strain. Based on the created consensus amino acid sequence, the nucleotide codon-optimized sequence of this modified glycoprotein was obtained and cloned into the pVAX1 plasmid (a vector of the last generation used in the creation of DNA vaccines). A twofold increase in this gene expression compared to the expression of the Vnukovo-32 strain viral glycoprotein gene in a similar vector was registered in the transfected cell culture. It has been demonstrated that the accumulation of modified G protein exceeds the number of the control protein synthesized using the plasmid with the Vnukovo-32 strain viral glycoprotein gene by 20 times. Thus, the obtained modified rabies virus glycoprotein can be considered to be a promising DNA vaccine antigen. PMID:27239860

  8. Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information

    PubMed Central

    Pollastri, Gianluca; Martin, Alberto JM; Mooney, Catherine; Vullo, Alessandro

    2007-01-01

    Background Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to known structures is available. Structural properties are also routinely used in protein analysis even when homology is available, largely because homology modelling is lower throughput than, say, secondary structure prediction. Nonetheless, predictors of secondary structure and solvent accessibility are virtually always ab initio. Results Here we develop high-throughput machine learning systems for the prediction of protein secondary structure and solvent accessibility that exploit homology to proteins of known structure, where available, in the form of simple structural frequency profiles extracted from sets of PDB templates. We compare these systems to their state-of-the-art ab initio counterparts, and with a number of baselines in which secondary structures and solvent accessibilities are extracted directly from the templates. We show that structural information from templates greatly improves secondary structure and solvent accessibility prediction quality, and that, on average, the systems significantly enrich the information contained in the templates. For sequence similarity exceeding 30%, secondary structure prediction quality is approximately 90%, close to its theoretical maximum, and 2-class solvent accessibility roughly 85%. Gains are robust with respect to template selection noise, and significant for marginal sequence similarity and for short alignments, supporting the claim that these improved predictions may prove beneficial beyond the case in which clear homology is available. Conclusion The predictive system are publicly available at the address . PMID:17570843

  9. The N-X-S/T consensus sequence is required but not sufficient for bacterial N-linked protein glycosylation.

    PubMed

    Nita-Lazar, Mihai; Wacker, Michael; Schegg, Belinda; Amber, Saba; Aebi, Markus

    2005-04-01

    In the Gram-negative bacterium Campylobacter jejuni there is a pgl (protein glycosylation) locus-dependent general N-glycosylation system of proteins. One of the proteins encoded by pgl locus, PglB, a homolog of the eukaryotic oligosaccharyltransferase component Stt3p, is proposed to function as an oligosaccharyltransferase in this prokaryotic system. The sequence requirements of the acceptor polypeptide for N-glycosylation were analyzed by reverse genetics using the reconstituted glycosylation of the model protein AcrA in Escherichia coli. As in eukaryotes, the N-X-S/T sequon is an essential but not a sufficient determinant for N-linked protein glycosylation. This conclusion was supported by the analysis of a novel C. jejuni glycoprotein, HisJ. Export of the polypeptide to the periplasm was required for glycosylation. Our data support the hypothesis that eukaryotic and bacterial N-linked protein glycosylation are homologous processes. PMID:15574802

  10. Interaction of the Heparin-Binding Consensus Sequence of β-Amyloid Peptides with Heparin and Heparin-Derived Oligosaccharides.

    PubMed

    Nguyen, Khanh; Rabenstein, Dallas L

    2016-03-10

    Alzheimer's disease (AD) is characterized by the presence of amyloid plaques in the AD brain. Comprised primarily of the 40- and 42-residue β-amyloid (Aβ) peptides, there is evidence that the heparan sulfate (HS) of heparan sulfate proteoglycans (HSPGs) plays a role in amyloid plaque formation and stability; however, details of the interaction of Aβ peptides with HS are not known. We have characterized the interaction of heparin and heparin-derived oligosaccharides with a model peptide for the heparin- and HS-binding domain of Aβ peptides (Ac-VHHQKLV-NH2; Aβ(12-18)), with mutants of Aβ(12-18), and with additional histidine-containing peptides. The nature of the binding interaction was characterized by NMR, binding constants and other thermodynamic parameters were determined by isothermal titration calorimetry (ITC), and relative binding affinities were determined by heparin affinity chromatography. The binding of Aβ(12-18) by heparin and heparin-derived oligosaccharides is pH-dependent, with the imidazolium groups of the histidine side chains interacting site-specifically within a cleft created by a trisaccharide sequence of heparin, the binding is mediated by electrostatic interactions, and there is a significant entropic contribution to the binding free energy as a result of displacement of Na(+) ions from heparin upon binding of cationic Aβ(12-18). The binding constant decreases as the size of the heparin-derived oligosaccharide decreases and as the concentration of Na(+) ion in the bulk solution increases. Structure-binding relationships characterized in this study are analyzed and discussed in terms of the counterion condensation theory of the binding of cationic peptides by anionic polyelectrolytes. PMID:26872053

  11. Minimal residual disease quantification using consensus primers and high-throughput IGH sequencing predicts post-transplant relapse in chronic lymphocytic leukemia

    PubMed Central

    Logan, A C; Zhang, B; Narasimhan, B; Carlton, V; Zheng, J; Moorhead, M; Krampf, M R; Jones, C D; Waqar, A N; Faham, M; Zehnder, J L; Miklos, D B

    2013-01-01

    Quantification of minimal residual disease (MRD) following allogeneic hematopoietic cell transplantation (allo-HCT) predicts post-transplant relapse in patients with chronic lymphocytic leukemia (CLL). We utilized an MRD-quantification method that amplifies immunoglobulin heavy chain (IGH) loci using consensus V and J segment primers followed by high-throughput sequencing (HTS), enabling quantification with a detection limit of one CLL cell per million mononuclear cells. Using this IGH–HTS approach, we analyzed MRD patterns in over 400 samples from 40 CLL patients who underwent reduced-intensity allo-HCT. Nine patients relapsed within 12 months post-HCT. Of the 31 patients in remission at 12 months post-HCT, disease-free survival was 86% in patients with MRD <10−4 and 20% in those with MRD ⩾10−4 (relapse hazard ratio (HR) 9.0; 95% confidence interval (CI) 2.5–32; P<0.0001), with median follow-up of 36 months. Additionally, MRD predicted relapse at other time points, including 9, 18 and 24 months post-HCT. MRD doubling time <12 months with disease burden ⩾10−5 was associated with relapse within 12 months of MRD assessment in 50% of patients, and within 24 months in 90% of patients. This IGH–HTS method may facilitate routine MRD quantification in clinical trials. PMID:23419792

  12. A Research and Discussion Note: The Macrostructure of Consensus Statements

    ERIC Educational Resources Information Center

    Mungra, Philippa

    2007-01-01

    This research note presents a preliminary study of the structure of consensus statements (CSs). The consensus statement is released by a medical association after calling a consensus development conference on a pertinent medical issue. Using a very small corpus, this note attempts to characterize consensus statements by identifying the sequence of…

  13. Interferon Consensus Sequence Binding Protein–deficient Mice Display Impaired Resistance to Intracellular Infection Due to a Primary Defect in Interleukin 12 p40 Induction

    PubMed Central

    Scharton-Kersten, Tanya; Contursi, Cristina; Masumi, Atsuko; Sher, Alan; Ozato, Keiko

    1997-01-01

    Mice lacking the transcription factor interferon consensus sequence binding protein (ICSBP), a member of the interferon regulatory factor family of transcription proteins, were infected with the intracellular protozoan, Toxoplasma gondii. ICSBP-deficient mice exhibited unchecked parasite replication in vivo and rapidly succumbed within 14 d after inoculation with an avirulent Toxoplasma strain. In contrast, few intracellular parasites were observed in wild-type littermates and these animals survived for at least 60 d after infection. Analysis of cytokine synthesis in vitro and in vivo revealed a major deficiency in the expression of both interferon (IFN)-γ and interleukin (IL)-12 p40 in the T. gondii exposed ICSBP−/− animals. In related experiments, macrophages from uninfected ICSBP−/− mice were shown to display a selective impairment in the mRNA expression of IL-12 p40 but not IL-1α, IL-1β, IL-1Ra, IL-6, IL-10, or TNF-α in response to live parasites, parasite antigen, lipopolysaccharide, or Staphylococcus aureus. This selective defect in IL-12 p40 production was observed regardless of whether the macrophages had been primed with IFN-γ. We hypothesize that the impaired synthesis of IL-12 p40 in ICSBP−/− animals is the primary lesion responsible for the loss in resistance to T. gondii because IFN-γ–induced parasite killing was unimpaired in vitro and, more importantly, administration of exogenous IL-12 in vivo significantly prolonged survival of the infected mice. Together these findings implicate ICSBP as a major transcription factor which directly or indirectly regulates IL-12 p40 gene activation and, as a consequence, IFN-γ–dependent host resistance. PMID:9348310

  14. Interferon (IFN) Consensus Sequence-binding Protein, a Transcription Factor of the IFN Regulatory Factor Family, Regulates Immune Responses In Vivo through Control of Interleukin 12 Expression

    PubMed Central

    Giese, Nathalia A.; Gabriele, Lucia; Doherty, T. Mark; Klinman, Dennis M.; Tadesse-Heath, Lekidelu; Contursi, Christina; Epstein, Suzanne L.; Morse, Herbert C.

    1997-01-01

    Mice with a null mutation of the gene encoding interferon consensus sequence-binding protein (ICSBP) develop a chronic myelogenous leukemia-like syndrome and mount impaired responses to certain viral and bacterial infections. To gain a mechanistic understanding of the contributions of ICSBP to humoral and cellular immunity, we characterized the responses of control and ICSBP−/− mice to infection with influenza A (flu) and Leishmania major (L. major). Mice of both genotypes survived infections with flu, but differed markedly in the isotype distribution of antiflu antibodies. In sera of normal mice, immunoglobulin (Ig)G2a antibodies were dominant over IgG1 antibodies, a pattern indicative of a T helper cell type 1 (Th1)-driven response. In sera of ICSBP−/− mice, however, IgG1 antibodies dominated over IgG2a antibodies, a pattern indicative of a Th2-driven response. The dominance of IgG1 and IgE over IgG2a was detected in the sera of uninfected mice as well. A seeming Th2 bias of ICSBP-deficient mice was also uncovered in their inability to control infection with L. major, where resistance is known to be dependent on IL-12 and IFN-γ as components of a Th1 response. Infected ICSBP-deficient mice developed fulminant, disseminated leishmaniasis as a result of failure to mount a Th1-mediated curative response, although T cells remained capable of secreting IFN-γ and macrophages of producing nitric oxide. Compromised Th1 differentiation in ICSBP−/− mice could not be attributed to hyporesponsiveness of CD4+ T cells to interleukin (IL)-12; however, the ability of uninfected and infected ICSBP-deficient mice to produce IL-12 was markedly impaired. This indicates that ICSBP is a deciding factor in Th responses governing humoral and cellular immunity through its role in regulating IL-12 expression. PMID:9348311

  15. Consensus among Economists Revisited.

    ERIC Educational Resources Information Center

    Fuller, Dan; Geide-Stevenson, Doris

    2003-01-01

    Explores consensus among economists on specific propositions on the basis of a fall 2000 survey of American Economic Association members. Finds consensus generally within the profession, although the degree of consensus varies among propositions that are international, macroeconomic, and microeconomic in nature. States the profession displays…

  16. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

    PubMed

    Richards, Sue; Aziz, Nazneen; Bale, Sherri; Bick, David; Das, Soma; Gastier-Foster, Julie; Grody, Wayne W; Hegde, Madhuri; Lyon, Elaine; Spector, Elaine; Voelkerding, Karl; Rehm, Heidi L

    2015-05-01

    The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic testing spanning genotyping, single genes, gene panels, exomes, genomes, transcriptomes, and epigenetic assays for genetic disorders. By virtue of increased complexity, this shift in genetic testing has been accompanied by new challenges in sequence interpretation. In this context the ACMG convened a workgroup in 2013 comprising representatives from the ACMG, the Association for Molecular Pathology (AMP), and the College of American Pathologists to revisit and revise the standards and guidelines for the interpretation of sequence variants. The group consisted of clinical laboratory directors and clinicians. This report represents expert opinion of the workgroup with input from ACMG, AMP, and College of American Pathologists stakeholders. These recommendations primarily apply to the breadth of genetic tests used in clinical laboratories, including genotyping, single genes, panels, exomes, and genomes. This report recommends the use of specific standard terminology-"pathogenic," "likely pathogenic," "uncertain significance," "likely benign," and "benign"-to describe variants identified in genes that cause Mendelian disorders. Moreover, this recommendation describes a process for classifying variants into these five categories based on criteria using typical types of variant evidence (e.g., population data, computational data, functional data, segregation data). Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends that clinical molecular genetic testing should be performed in a

  17. Vaccination of Cattle Persistently Infected with BVDV Does Not Cause a Change in the Consensus Sequence of the Structural Proteins of the Quasispecies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine viral diarrhea virus (BVDV) is a ubiquitous viral pathogen of cattle worldwide. An interesting aspect of these viruses is the great amount of sequence diversity that exists amongst strains in circulation in livestock herds that can impact diagnostic testing. The driving force behind change in...

  18. The Lactobacillus acidophilus S-layer protein gene expression site comprises two consensus promoter sequences, one of which directs transcription of stable mRNA.

    PubMed Central

    Boot, H J; Kolen, C P; Andreadaki, F J; Leer, R J; Pouwels, P H

    1996-01-01

    S-proteins are proteins which form a regular structure (S-layer) on the outside of the cell walls of many bacteria. Two S-protein-encoding genes are located in opposite directions on a 6.0-kb segment of the chromosome of Lactobacillus acidophilus ATCC 4356 bacteria. Inversion of this chromosomal segment occurs through recombination between two regions with identical sequences, thereby interchanging the expressed and the silent genes. In this study, we show that the region involved in recombination also has a function in efficient S-protein production. Two promoter sequences are present in the S-protein gene expression site, although only the most downstream promoter (P-1) is used to direct mRNA synthesis. S-protein mRNA directed by this promoter has a half-life of 15 min. Its untranslated leader can form a stable secondary structure in which the 5' end is base paired, whereas the ribosome-binding site is exposed. Truncation of this leader sequence results in a reduction in protein production, as shown by reporter gene analysis of Lactobacillus casei. The results obtained indicate that the untranslated leader sequence of S-protein mRNA is involved in efficient S-protein production. PMID:8808926

  19. Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria

    PubMed Central

    Harari, Oscar; Park, Sun-Yang; Huang, Henry; Groisman, Eduardo A.; Zwir, Igor

    2010-01-01

    Transcriptional regulators recognize specific DNA sequences. Because these sequences are embedded in the background of genomic DNA, it is hard to identify the key cis-regulatory elements that determine disparate patterns of gene expression. The detection of the intra- and inter-species differences among these sequences is crucial for understanding the molecular basis of both differential gene expression and evolution. Here, we address this problem by investigating the target promoters controlled by the DNA-binding PhoP protein, which governs virulence and Mg2+ homeostasis in several bacterial species. PhoP is particularly interesting; it is highly conserved in different gamma/enterobacteria, regulating not only ancestral genes but also governing the expression of dozens of horizontally acquired genes that differ from species to species. Our approach consists of decomposing the DNA binding site sequences for a given regulator into families of motifs (i.e., termed submotifs) using a machine learning method inspired by the “Divide & Conquer” strategy. By partitioning a motif into sub-patterns, computational advantages for classification were produced, resulting in the discovery of new members of a regulon, and alleviating the problem of distinguishing functional sites in chromatin immunoprecipitation and DNA microarray genome-wide analysis. Moreover, we found that certain partitions were useful in revealing biological properties of binding site sequences, including modular gains and losses of PhoP binding sites through evolutionary turnover events, as well as conservation in distant species. The high conservation of PhoP submotifs within gamma/enterobacteria, as well as the regulatory protein that recognizes them, suggests that the major cause of divergence between related species is not due to the binding sites, as was previously suggested for other regulators. Instead, the divergence may be attributed to the fast evolution of orthologous target genes and/or the

  20. Working toward Consensus.

    ERIC Educational Resources Information Center

    Brown, Harold

    1998-01-01

    A California high school English teacher uses, with students, a culturally sensitive process of facilitating classroom decision making through consensus. He correlates communication and language skills with consensus building, the facilitation of which is a slow process implemented in small portions over the school year. Sidebar provides a…

  1. 7-Benzylamino-6-chloro-2-piperazino-4-pyrrolidino-pteridine, a potent inhibitor of cAMP-specific phosphodiesterase, enhancing nuclear protein binding to the CRE consensus sequence in human tumour cells.

    PubMed

    Wagner, Barbara; Jakobs, Sandra; Habermeyer, Michael; Hippe, Frankie; Cho-Chung, Yoon Sang; Eisenbrand, Gerhard; Marko, Doris

    2002-02-15

    The cAMP-specific phosphodiesterase isoenzyme family PDE4 represents the highest cAMP-hydrolysing activity in many human cancer cell lines including the human large cell lung carcinoma cell line LXFL529L. Treatment of LXFL529L cells with the potent PDE4 inhibitor 7-benzylamino-6-chloro-2-piperazino-4-pyrrolidino-pteridine (DC-TA-46) induces dose-dependent growth inhibition. Cells are arrested in the G(1)-phase of the cell cycle and the induction of apoptosis is observed. In this study, we investigated the effect of DC-TA-46 on downstream elements of the cAMP-pathway. DC-TA-46 mediated inhibition of PDE4 activity in LXFL529L cells resulted in an increase of the intracellular cAMP level and significant induction of the activity of protein kinase A (PKA). The regulatory PKA subunit RIalpha was predominantly expressed in LXFL529L cells. In contrast to effects induced by cAMP analogues like 8-Cl-cAMP, the expression of the regulatory subunits of PKA remained unaffected by DC-TA-46. Treatment of LXFL529L cells with DC-TA-46 enhanced the binding of nuclear proteins to the cAMP-responsive element (CRE) consensus sequence TGACGTCA in a time- and dose-dependent manner, indicating the activation of transcription factors by PKA phosphorylation. PMID:11992633

  2. Molecular diagnosis of mucopolysaccharidosis type II (Hunter syndrome) by automated sequencing and computer-assisted interpretation: toward mutation mapping of the iduronate-2-sulfatase gene.

    PubMed Central

    Jonsson, J J; Aronovich, E L; Braun, S E; Whitley, C B

    1995-01-01

    Virtually all mutations causing Hunter syndrome (mucopolysaccharidosis type II) are expected to be new mutations. Therefore, as a means of molecular diagnosis, we developed a rapid method to sequence the entire iduronate-2-sulfatase (IDS) coding region. PCR amplicons representing the IDS cDNA were sequenced with an automatic instrument, and output was analyzed by computer-assisted interpretation of tracings, using Staden programs on a Sun computer. Mutations were found in 10 of 11 patients studied. Unique missense mutations were identified in five patients: H229Y (685C-->T, severe phenotype); P358R (1073C-->G, severe); R468W (1402C-->T, mild); P469H (1406C-->A, mild); and Y523C (1568A-->G, mild). Non-sense mutations were identified in two patients: R172X (514C-->T, severe) and Q389X (1165C-->T, severe). Two other patients with severe disease had insertions of 1 and 14 bp, in exons 3 and 6, respectively. In another patient with severe disease, the predominant (> 95%) IDS message resulted from aberrant splicing, which skipped exon 3. In this last case, consensus sequences for splice sites in exon 3 were intact, but a 395 C-->G mutation was identified 24 bp upstream from the 3' splice site of exon 3. This mutation created a cryptic 5' splice site with a better consensus sequence for 5' splice sites than the natural 5' splice site of intron 3. A minor population of the IDS message was processed by using this cryptic splice site; however, no correctly spliced message was detected in leukocytes from this patient. The mutational topology of the IDS gene is presented. Images Figure 2 PMID:7887413

  3. Phosphorylation of Simian Cytomegalovirus Assembly Protein Precursor (pAPNG.5) and Proteinase Precursor (pAPNG1): Multiple Attachment Sites Identified, Including Two Adjacent Serines in a Casein Kinase II Consensus Sequence

    PubMed Central

    Plafker, Scott M.; Woods, Amina S.; Gibson, Wade

    1999-01-01

    The assembly protein precursor (pAP) of cytomegalovirus (CMV), and its homologs in other herpesviruses, functions at several key steps during the process of capsid formation. This protein, and the genetically related maturational proteinase, is distinguished from the other capsid proteins by posttranslational modifications, including phosphorylation. The objective of this study was to identify sites at which pAP is phosphorylated so that the functional significance of this modification and the enzyme(s) responsible for it can be determined. In the work reported here, we used peptide mapping, mass spectrometry, and site-directed mutagenesis to identify two sets of pAP phosphorylation sites. One is a casein kinase II (CKII) consensus sequence that contains two adjacent serines, both of which are phosphorylated. The other site(s) is in a different domain of the protein, is phosphorylated less frequently than the CKII site, does not require preceding CKII-site phosphorylation, and causes an electrophoretic mobility shift when phosphorylated. Transfection/expression assays for proteolytic activity showed no gross effect of CKII-site phosphorylation on the enzymatic activity of the proteinase or on the substrate behavior of pAP. Evidence is presented that both the CKII sites and the secondary sites are phosphorylated in virus-infected cells and plasmid-transfected cells, indicating that these modifications can be made by a cellular enzyme(s). Apparent compartmental differences in phosphorylation of the CKII-site (cytoplasmic) and secondary-site (nuclear) serines suggest the involvement of more that one enzyme in these modifications. PMID:10516011

  4. Expression of Interferon Consensus Sequence Binding Protein (ICSBP) Is Downregulated in Bcr-Abl-Induced Murine Chronic Myelogenous Leukemia-Like Disease, and Forced Coexpression of ICSBP Inhibits Bcr-Abl-Induced Myeloproliferative Disorder

    PubMed Central

    Hao, Sheryl X.; Ren, Ruibao

    2000-01-01

    Chronic myelogenous leukemia (CML) is a clonal myeloproliferative disorder resulting from the neoplastic transformation of a hematopoietic stem cell. The majority of cases of CML are associated with the (9;22) chromosome translocation that generates the bcr-abl chimeric gene. Alpha interferon (IFN-α) treatment induces hematological remission and prolongs life in 75% of CML patients in the chronic phase. It has been shown that mice deficient in interferon consensus sequence binding protein (ICSBP), a member of the interferon regulatory factor family, manifest a CML-like syndrome. We have shown that expression of Bcr-Abl in bone marrow (BM) cells from 5-fluorouracil (5-FU)-treated mice by retroviral transduction efficiently induces a myeloproliferative disease in mice resembling human CML. To directly test whether icsbp can function as a tumor suppressor gene, we examined the effect of ICSBP on Bcr-Abl-induced CML-like disease using this murine model for CML. We found that expression of the ICSBP protein was significantly decreased in Bcr-Abl-induced CML-like disease. Forced coexpression of ICSBP inhibited the Bcr-Abl-induced colony formation of BM cells from 5-FU-treated mice in vitro and Bcr-Abl-induced CML-like disease in vivo. Interestingly, coexpression of ICSBP and Bcr-Abl induced a transient B-lymphoproliferative disorder in the murine model of Bcr-Abl-induced CML-like disease. Overexpression of ICSBP consistently promotes rather than inhibits Bcr-Abl-induced B lymphoproliferation in a murine model where BM cells from non-5-FU-treated donors were used, indicating that ICSBP has a specific antitumor activity toward myeloid neoplasms. We also found that overexpression of ICSBP negatively regulated normal hematopoiesis. These data provide direct evidence that ICSBP can act as a tumor suppressor that regulates normal and neoplastic proliferation of hematopoietic cells. PMID:10648600

  5. Towards Consensus Gene Ages

    PubMed Central

    Liebeskind, Benjamin J.; McWhite, Claire D.; Marcotte, Edward M.

    2016-01-01

    Correctly estimating the age of a gene or gene family is important for a variety of fields, including molecular evolution, comparative genomics, and phylogenetics, and increasingly for systems biology and disease genetics. However, most studies use only a point estimate of a gene’s age, neglecting the substantial uncertainty involved in this estimation. Here, we characterize this uncertainty by investigating the effect of algorithm choice on gene-age inference and calculate consensus gene ages with attendant error distributions for a variety of model eukaryotes. We use 13 orthology inference algorithms to create gene-age datasets and then characterize the error around each age-call on a per-gene and per-algorithm basis. Systematic error was found to be a large factor in estimating gene age, suggesting that simple consensus algorithms are not enough to give a reliable point estimate. We also found that different sources of error can affect downstream analyses, such as gene ontology enrichment. Our consensus gene-age datasets, with associated error terms, are made fully available at so that researchers can propagate this uncertainty through their analyses (geneages.org). PMID:27259914

  6. Spanish Consensus Statement

    PubMed Central

    Rey, Guillermo Álvarez; Cuesta, Jordi Ardevol; Loureda, Rafael Arriaza; España, Fernando Ávila; Matas, Ramón Balius; Pazos, Fernando Baró; de Dios Beas Jiménez, Juan; Rosell, Jorge Candel; Fernandez, César Cobián; Ros, Francisco Esparza; Colmenero, Josefina Espejo; de Prado, Jorge Fernández; Cota, Juan José García; González, Jose Ignacio Garrido; Santander, Manuela González; Munilla, Miguel Ángel Herrador; Ruiz, Francisco Ivorra; Díaz, Fernando Jiménez; Marqueta, Pedro Manonelles; Fernandez, Antonio Maestro; Benito, Juan José Muñoz; Vilás, Ramón Olivé; Teres, Xavier Peirau; Amaro, José Peña; Roque, Juan Pérez San; Parenteu, Christophe Ramírez; Serna, Juan Ribas; Álvarez, Mikel Sánchez; Marchori, Carlos Sanchez; Soto, Miguel del Valle; Alonso, José María Villalón; García, Pedro Guillen; de la Iglesia, Nicolas Hugo; Alcorocho, Juan Manuel Lopez

    2016-01-01

    On the 21st of March, 2015, experts met at Clínica CEMTRO in Madrid, Spain, under the patronage of The Spanish Society for Sports Traumatology (SETRADE), The Spanish Federation of Sports Medicine (FEMEDE), The Spanish Association of Medical Services for Football Clubs (AEMEF), and The Spanish Association of Medical Services for Basketball Clubs (AEMB) with the aim of establishing a round table that would allow specialists to consider the most appropriate current general actions to be taken when treating muscle tears in sport, based on proven scientific data described in the medical literature. Each expert received a questionnaire prior to the aforementioned meeting comprising a set of questions concerning therapeutic indications generally applied in the different stages present during muscle repair. The present Consensus Document is the result of the answers to the questionnaire and resulting discussion and consensus over which are the best current indications in the treatment of muscle tears in sport. Avoiding immobilization, not taking nonsteroidal anti-inflammatory drugs (NSAIDs) randomly, fostering early mobilization, increasing vascularization of injured, site and regulating inflammatory mechanisms—without inhibiting these from the early stages of the recovery period—all stood out as main points of the Consensus Document. Additionally, there is controversy concerning cell stimulation techniques and the use of growth factors or cell inhibitors. The decision concerning discharge was unanimous, as was the criteria considered when it came to performing sport techniques without pain. PMID:27213161

  7. Towards Consensus Gene Ages.

    PubMed

    Liebeskind, Benjamin J; McWhite, Claire D; Marcotte, Edward M

    2016-01-01

    Correctly estimating the age of a gene or gene family is important for a variety of fields, including molecular evolution, comparative genomics, and phylogenetics, and increasingly for systems biology and disease genetics. However, most studies use only a point estimate of a gene's age, neglecting the substantial uncertainty involved in this estimation. Here, we characterize this uncertainty by investigating the effect of algorithm choice on gene-age inference and calculate consensus gene ages with attendant error distributions for a variety of model eukaryotes. We use 13 orthology inference algorithms to create gene-age datasets and then characterize the error around each age-call on a per-gene and per-algorithm basis. Systematic error was found to be a large factor in estimating gene age, suggesting that simple consensus algorithms are not enough to give a reliable point estimate. We also found that different sources of error can affect downstream analyses, such as gene ontology enrichment. Our consensus gene-age datasets, with associated error terms, are made fully available at so that researchers can propagate this uncertainty through their analyses (geneages.org). PMID:27259914

  8. Achieving consensus in environmental programs

    SciTech Connect

    Kurstedt, Jr., H. A.; Jones, R. M.; Walker, J. A.; Middleman, L. I.

    1989-01-01

    In this paper, we describe a new research effort on consensus tied to the Environmental Restoration Program (ERP) within the US Department of Energy's Office of Defense Waste and Transportation Management (DWTM). We define consensus and explain why consensus decisions are not merely desirable but necessary in furthering ERP activities. As examples of our planned applied research, we first discuss Nominal Group Technique as a representative consensus-generating tool, and we conclude by describing the consensus-related mission of the Waste Management Review Group, established at Virginia Tech to conduct independent, third-party review of DWTM/ERP plans and activities. 10 refs.

  9. Microscopic enteritis: Bucharest consensus.

    PubMed

    Rostami, Kamran; Aldulaimi, David; Holmes, Geoffrey; Johnson, Matt W; Robert, Marie; Srivastava, Amitabh; Fléjou, Jean-François; Sanders, David S; Volta, Umberto; Derakhshan, Mohammad H; Going, James J; Becheanu, Gabriel; Catassi, Carlo; Danciu, Mihai; Materacki, Luke; Ghafarzadegan, Kamran; Ishaq, Sauid; Rostami-Nejad, Mohammad; Peña, A Salvador; Bassotti, Gabrio; Marsh, Michael N; Villanacci, Vincenzo

    2015-03-01

    Microscopic enteritis (ME) is an inflammatory condition of the small bowel that leads to gastrointestinal symptoms, nutrient and micronutrient deficiency. It is characterised by microscopic or sub-microscopic abnormalities such as microvillus changes and enterocytic alterations in the absence of definite macroscopic changes using standard modern endoscopy. This work recognises a need to characterize disorders with microscopic and submicroscopic features, currently regarded as functional or non-specific entities, to obtain further understanding of their clinical relevance. The consensus working party reviewed statements about the aetiology, diagnosis and symptoms associated with ME and proposes an algorithm for its investigation and treatment. Following the 5(th) International Course in Digestive Pathology in Bucharest in November 2012, an international group of 21 interested pathologists and gastroenterologists formed a working party with a view to formulating a consensus statement on ME. A five-step agreement scale (from strong agreement to strong disagreement) was used to score 21 statements, independently. There was strong agreement on all statements about ME histology (95%-100%). Statements concerning diagnosis achieved 85% to 100% agreement. A statement on the management of ME elicited agreement from the lowest rate (60%) up to 100%. The remaining two categories showed general agreement between experts on clinical presentation (75%-95%) and pathogenesis (80%-90%) of ME. There was strong agreement on the histological definition of ME. Weaker agreement on management indicates a need for further investigations, better definitions and clinical trials to produce quality guidelines for management. This ME consensus is a step toward greater recognition of a significant entity affecting symptomatic patients previously labelled as non-specific or functional enteropathy. PMID:25759526

  10. Microscopic enteritis: Bucharest consensus

    PubMed Central

    Rostami, Kamran; Aldulaimi, David; Holmes, Geoffrey; Johnson, Matt W; Robert, Marie; Srivastava, Amitabh; Fléjou, Jean-François; Sanders, David S; Volta, Umberto; Derakhshan, Mohammad H; Going, James J; Becheanu, Gabriel; Catassi, Carlo; Danciu, Mihai; Materacki, Luke; Ghafarzadegan, Kamran; Ishaq, Sauid; Rostami-Nejad, Mohammad; Peña, A Salvador; Bassotti, Gabrio; Marsh, Michael N; Villanacci, Vincenzo

    2015-01-01

    Microscopic enteritis (ME) is an inflammatory condition of the small bowel that leads to gastrointestinal symptoms, nutrient and micronutrient deficiency. It is characterised by microscopic or sub-microscopic abnormalities such as microvillus changes and enterocytic alterations in the absence of definite macroscopic changes using standard modern endoscopy. This work recognises a need to characterize disorders with microscopic and submicroscopic features, currently regarded as functional or non-specific entities, to obtain further understanding of their clinical relevance. The consensus working party reviewed statements about the aetiology, diagnosis and symptoms associated with ME and proposes an algorithm for its investigation and treatment. Following the 5th International Course in Digestive Pathology in Bucharest in November 2012, an international group of 21 interested pathologists and gastroenterologists formed a working party with a view to formulating a consensus statement on ME. A five-step agreement scale (from strong agreement to strong disagreement) was used to score 21 statements, independently. There was strong agreement on all statements about ME histology (95%-100%). Statements concerning diagnosis achieved 85% to 100% agreement. A statement on the management of ME elicited agreement from the lowest rate (60%) up to 100%. The remaining two categories showed general agreement between experts on clinical presentation (75%-95%) and pathogenesis (80%-90%) of ME. There was strong agreement on the histological definition of ME. Weaker agreement on management indicates a need for further investigations, better definitions and clinical trials to produce quality guidelines for management. This ME consensus is a step toward greater recognition of a significant entity affecting symptomatic patients previously labelled as non-specific or functional enteropathy. PMID:25759526

  11. Surface Hopping by Consensus.

    PubMed

    Martens, Craig C

    2016-07-01

    We present a new stochastic surface hopping method for modeling molecular dynamics with electronic transitions. The approach, consensus surface hopping (CSH), is a numerical framework for solving the semiclassical limit Liouville equation describing nuclear dynamics on coupled electronic surfaces using ensembles of trajectories. In contrast to existing techniques based on propagating independent classical trajectories that undergo stochastic hops between the electronic states, the present method determines the probabilities of transition of each trajectory collectively with input from the entire ensemble. The full coherent dynamics of the coupled system arise naturally at the ensemble level and ad hoc corrections, such as momentum rescaling to impose strict trajectory energy conservation and artificial decoherence to avoid the overcoherence of the quantum states associated with independent trajectories, are avoided. PMID:27345103

  12. Multipolar consensus for phylogenetic trees.

    PubMed

    Bonnard, Cécile; Berry, Vincent; Lartillot, Nicolas

    2006-10-01

    Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection. However, in the case of heterogeneous collections of trees, the resulting consensus may be poorly resolved (strict consensus, majority-rule consensus, ...), or may perform arbitrary choices among mutually incompatible clades, or splits (greedy consensus). Here, we propose an alternative method, which we call the multipolar consensus (MPC). Its aim is to display all the splits having a support above a predefined threshold, in a minimum number of consensus trees, or poles. We show that the problem is equivalent to a graph-coloring problem, and propose an implementation of the method. Finally, we apply the MPC to real data sets. Our results indicate that, typically, all the splits down to a weight of 10% can be displayed in no more than 4 trees. In addition, in some cases, biologically relevant secondary signals, which would not have been present in any of the classical consensus trees, are indeed captured by our method, indicating that the MPC provides a convenient exploratory method for phylogenetic analysis. The method was implemented in a package freely available at http://www.lirmm.fr/~cbonnard/MPC.html PMID:17060203

  13. Brazilian Consensus on Photoprotection

    PubMed Central

    Schalka, Sérgio; Steiner, Denise; Ravelli, Flávia Naranjo; Steiner, Tatiana; Terena, Aripuanã Cobério; Marçon, Carolina Reato; Ayres, Eloisa Leis; Addor, Flávia Alvim Sant'anna; Miot, Helio Amante; Ponzio, Humberto; Duarte, Ida; Neffá, Jane; da Cunha, José Antônio Jabur; Boza, Juliana Catucci; Samorano, Luciana de Paula; Corrêa, Marcelo de Paula; Maia, Marcus; Nasser, Nilton; Leite, Olga Maria Rodrigues Ribeiro; Lopes, Otávio Sergio; Oliveira, Pedro Dantas; Meyer, Renata Leal Bregunci; Cestari, Tânia; dos Reis, Vitor Manoel Silva; Rego, Vitória Regina Pedreira de Almeida

    2014-01-01

    Brazil is a country of continental dimensions with a large heterogeneity of climates and massive mixing of the population. Almost the entire national territory is located between the Equator and the Tropic of Capricorn, and the Earth axial tilt to the south certainly makes Brazil one of the countries of the world with greater extent of land in proximity to the sun. The Brazilian coastline, where most of its population lives, is more than 8,500 km long. Due to geographic characteristics and cultural trends, Brazilians are among the peoples with the highest annual exposure to the sun. Epidemiological data show a continuing increase in the incidence of non-melanoma and melanoma skin cancers. Photoprotection can be understood as a set of measures aimed at reducing sun exposure and at preventing the development of acute and chronic actinic damage. Due to the peculiarities of Brazilian territory and culture, it would not be advisable to replicate the concepts of photoprotection from other developed countries, places with completely different climates and populations. Thus the Brazilian Society of Dermatology has developed the Brazilian Consensus on Photoprotection, the first official document on photoprotection developed in Brazil for Brazilians, with recommendations on matters involving photoprotection. PMID:25761256

  14. Between consensus and contestation.

    PubMed

    Weale, Albert

    2016-08-15

    Purpose - Noting that discussions of public participation and priority setting typically presuppose certain political theories of democracy, the purpose of this paper is to discuss two theories: the consensual and the agonistic. The distinction is illuminating when considering the difference between institutionalized public participation and contestatory participation. Design/methodology/approach - The approach is a theoretical reconstruction of two ways of thinking about public participation in relation to priority setting in health care, drawing on the work of Habermas, a deliberative theorist, and Mouffe, a theorist of agonism. Findings - The different theoretical approaches can be associated with different ways of understanding priority setting. In particular, agonistic democratic theory would understand priority setting as system of inclusions and exclusions rather than the determination of a consensus of social values, which is the typical deliberative way of thinking about the issues. Originality/value - The paper shows the value of drawing out explicitly the tacit assumptions of practices of political participation in order to reveal their scope and limitations. It suggests that making such theoretical presuppositions explicit has value for health services management in recognizing these implicit choices. PMID:27468774

  15. Hohenheim consensus workshop: copper.

    PubMed

    Schümann, K; Classen, H G; Dieter, H H; König, J; Multhaup, G; Rükgauer, M; Summer, K H; Bernhardt, J; Biesalski, H K

    2002-06-01

    Copper (Cu) is an essential trace element with many physiological functions. Homeostatic mechanisms exist to allow Cu to act as a cofactor in enzymatic processes and to prevent accumulation of Cu to toxic levels. The aim of this commentary is to better understand the role of dietary Cu supply in deficiency and under physiological and pathological conditions. The essentiality of Cu can be attributed to its role as a cofactor in a number of enzymes that are involved in the defence against oxidative stress. Cu, however, has a second face, that of a toxic compound as it is observed with accumulating evidence in hepatic, neurodegenerative and cardiovascular diseases. The destructive potential of Cu can be attributed to inherent physico-chemical properties. The main property is its ability to take part in Fenton-like reactions in which the highly reactive and extremely deleterious hydroxyl radical is formed. Diseases caused by dietary Cu overload could be based on a genetic predisposition. Thus, an assessment of risk-groups, such as infants with impaired mechanisms of Cu homeostasis regarding detoxification, is of special interest, as their Cu intake with resuspended formula milk may be very high. This implies the need for reliable diagnostic markers to determine the Cu status. These topics were introduced at the workshop by the participants followed by extensive group discussion. The consensus statements were agreed on by all members. One of the conclusions is that a re-assessment of published data is necessary and future research is required. PMID:12032645

  16. Consensus on consensus: a synthesis of consensus estimates on human-caused global warming

    NASA Astrophysics Data System (ADS)

    Cook, John; Oreskes, Naomi; Doran, Peter T.; Anderegg, William R. L.; Verheggen, Bart; Maibach, Ed W.; Carlton, J. Stuart; Lewandowsky, Stephan; Skuce, Andrew G.; Green, Sarah A.; Nuccitelli, Dana; Jacobs, Peter; Richardson, Mark; Winkler, Bärbel; Painting, Rob; Rice, Ken

    2016-04-01

    The consensus that humans are causing recent global warming is shared by 90%–100% of publishing climate scientists according to six independent studies by co-authors of this paper. Those results are consistent with the 97% consensus reported by Cook et al (Environ. Res. Lett. 8 024024) based on 11 944 abstracts of research papers, of which 4014 took a position on the cause of recent global warming. A survey of authors of those papers (N = 2412 papers) also supported a 97% consensus. Tol (2016 Environ. Res. Lett. 11 048001) comes to a different conclusion using results from surveys of non-experts such as economic geologists and a self-selected group of those who reject the consensus. We demonstrate that this outcome is not unexpected because the level of consensus correlates with expertise in climate science. At one point, Tol also reduces the apparent consensus by assuming that abstracts that do not explicitly state the cause of global warming (‘no position’) represent non-endorsement, an approach that if applied elsewhere would reject consensus on well-established theories such as plate tectonics. We examine the available studies and conclude that the finding of 97% consensus in published climate research is robust and consistent with other surveys of climate scientists and peer-reviewed studies.

  17. Consensus development for healthcare professionals

    PubMed Central

    Kea, Bory; Sun, Benjamin C.

    2015-01-01

    Consensus development sprang from a desire to synthesize clinician and expert opinions on clinical practice and research agendas in the 1950s. And since the American Institute of Medicine formally defined “guidelines” in 1990, there has been a proliferation of clinical practice guidelines (CPG) both formally and informally. This modern decision making tool used by both physicians and patients, requires extensive planning to meet the challenges of consensus development while reaping its rewards. Consensus allows for a group approach with multiple experts sharing ideas to form consensus on topics ranging from appropriateness of procedures to research agenda development. Disagreements can shed light on areas of controversy and launch further discussions. It has five main components: three inputs (defining the task, participant identification and recruitment, and information synthesis), the approach (consensus development by explicit or implicit means), and the output (dissemination of results). Each aspect requires extensive planning a priori as they influence the entire process, from how information will be interpreted, the interaction of participants, the resulting judgment, to whether there will be uptake of results. Implicit approaches utilize qualitative methods and/or a simple voting structure of majority wins, and are used in informal consensus development methods and consensus development conferences. Explicit approaches aggregate results or judgments using explicit rules set a priori with definitions of “agreement” or consensus. Because the implicit process can be more opaque, unforeseen challenges can emerge such as the undue influence of a minority. And yet, the logistics of explicit approaches may be more time consuming and not appropriate when speed is a priority. In determining which method to use, it is important to understand the pros and cons of the different approaches and how it will affect the overall input, approach, and outcome. PMID

  18. Distributed consensus on camera pose.

    PubMed

    Jorstad, Anne; DeMenthon, Daniel; Wang, I-Jeng; Burlina, Philippe

    2010-09-01

    Our work addresses pose estimation in a distributed camera framework. We examine how processing cameras can best reach a consensus about the pose of an object when they are each given a model of the object, defined by a set of point coordinates in the object frame of reference. The cameras can only see a subset of the object feature points in the midst of background clutter points, not knowing which image points match with which object points, nor which points are object points or background points. The cameras individually recover a prediction of the object's pose using their knowledge of the model, and then exchange information with their neighbors, performing consensus updates locally to obtain a single estimate consistent across all cameras, without requiring a common centralized processor. Our main contributions are: 1) we present a novel algorithm performing consensus updates in 3-D world coordinates penalized by a 3-D model, and 2) we perform a thorough comparison of our method with other current consensus methods. Our method is consistently the most accurate, and we confirm that the existing consensus method based upon calculating the Karcher mean of rotations is also reliable and fast. Experiments on simulated and real imagery are reported. PMID:20363678

  19. C3 glomerulopathy: consensus report

    PubMed Central

    Pickering, Matthew C; D'Agati, Vivette D; Nester, Carla M; Smith, Richard J; Haas, Mark; Appel, Gerald B; Alpers, Charles E; Bajema, Ingeborg M; Bedrosian, Camille; Braun, Michael; Doyle, Mittie; Fakhouri, Fadi; Fervenza, Fernando C; Fogo, Agnes B; Frémeaux-Bacchi, Véronique; Gale, Daniel P; Goicoechea de Jorge, Elena; Griffin, Gene; Harris, Claire L; Holers, V Michael; Johnson, Sally; Lavin, Peter J; Medjeral-Thomas, Nicholas; Paul Morgan, B; Nast, Cynthia C; Noel, Laure-Hélène; Peters, D Keith; Rodríguez de Córdoba, Santiago; Servais, Aude; Sethi, Sanjeev; Song, Wen-Chao; Tamburini, Paul; Thurman, Joshua M; Zavros, Michael; Cook, H Terence

    2013-01-01

    C3 glomerulopathy is a recently introduced pathological entity whose original definition was glomerular pathology characterized by C3 accumulation with absent or scanty immunoglobulin deposition. In August 2012, an invited group of experts (comprising the authors of this document) in renal pathology, nephrology, complement biology, and complement therapeutics met to discuss C3 glomerulopathy in the first C3 Glomerulopathy Meeting. The objectives were to reach a consensus on: the definition of C3 glomerulopathy, appropriate complement investigations that should be performed in these patients, and how complement therapeutics should be explored in the condition. This meeting report represents the current consensus view of the group. PMID:24172683

  20. Evolutionary origin of asymptotically stable consensus.

    PubMed

    Tang, Chang-Bing; Wu, Bin; Wang, Jian-Bo; Li, Xiang

    2014-01-01

    Consensus is widely observed in nature as well as in society. Up to now, many works have focused on what kind of (and how) isolated single structures lead to consensus, while the dynamics of consensus in interdependent populations remains unclear, although interactive structures are everywhere. For such consensus in interdependent populations, we refer that the fraction of population adopting a specified strategy is the same across different interactive structures. A two-strategy game as a conflict is adopted to explore how natural selection affects the consensus in such interdependent populations. It is shown that when selection is absent, all the consensus states are stable, but none are evolutionarily stable. In other words, the final consensus state can go back and forth from one to another. When selection is present, there is only a small number of stable consensus state which are evolutionarily stable. Our study highlights the importance of evolution on stabilizing consensus in interdependent populations. PMID:24699444

  1. International consensus on allergy immunotherapy.

    PubMed

    Jutel, Marek; Agache, Ioana; Bonini, Sergio; Burks, A Wesley; Calderon, Moises; Canonica, Walter; Cox, Linda; Demoly, Pascal; Frew, Antony J; O'Hehir, Robin; Kleine-Tebbe, Jörg; Muraro, Antonella; Lack, Gideon; Larenas, Désirée; Levin, Michael; Nelson, Harald; Pawankar, Ruby; Pfaar, Oliver; van Ree, Ronald; Sampson, Hugh; Santos, Alexandra F; Du Toit, George; Werfel, Thomas; Gerth van Wijk, Roy; Zhang, Luo; Akdis, Cezmi A

    2015-09-01

    Allergen immunotherapy (AIT) has been used to treat allergic disease since the early 1900s. Despite numerous clinical trials and meta-analyses proving AIT efficacious, it remains underused and is estimated to be used in less than 10% of patients with allergic rhinitis or asthma worldwide. In addition, there are large differences between regions, which are not only due to socioeconomic status. There is practically no controversy about the use of AIT in the treatment of allergic rhinitis and allergic asthma, but for atopic dermatitis or food allergy, the indications for AIT are not well defined. The elaboration of a wider consensus is of utmost importance because AIT is the only treatment that can change the course of allergic disease by preventing the development of asthma and new allergen sensitizations and by inducing allergen-specific immune tolerance. Safer and more effective AIT strategies are being continuously developed both through elaboration of new allergen preparations and adjuvants and alternate routes of administration. A number of guidelines, consensus documents, or both are available on both the international and national levels. The international community of allergy specialists recognizes the need to develop a comprehensive consensus report to harmonize, disseminate, and implement the best AIT practice. Consequently, the International Collaboration in Asthma, Allergy and Immunology, formed by the European Academy of Allergy and Clinical Immunology; the American Academy of Allergy, Asthma & Immunology; the American College of Allergy, Asthma & Immunology; and the World Allergy Organization, has decided to issue an international consensus on AIT. PMID:26162571

  2. Consensus algorithms in decentralized networks

    NASA Astrophysics Data System (ADS)

    Coduti, Leonardo Phillip

    We consider a decentralized network with the following goal: the state at each node of the network iteratively converges to the same value. Ensuring that this goal is achieved requires certain properties of the topology of the network and the function describing the evolution of the network. We will present these properties for deterministic systems, extending current results in the literature. As an additional contribution, we will show how the convergence results for stochastic systems are direct consequences of the corresponding deterministic systems, drastically simplifying many other current results. In general, these consensus systems can be both time invariant and time varying, and we will extend all our deterministic and stochastic results to include time varying systems as well. We will then consider a more complex consensus problem, the resource allocation problem. In this situation each node of the network has both a state and a capacity. The capacity is a monotone increasing function of the state, and the goal is for the nodes to exchange capacity in a decentralized manner in order to drive all of the states to the same value. Conditions ensuring consensus in the deterministic setting will be presented, and we will show how convergence in this system also comes from the fundamental deterministic result for consensus algorithms. The main results will again be extended to stochastic and time varying systems. The linear consensus system requires the construction of a matrix of weighting parameters with specific properties. We present an iterative algorithm for determining the weighting parameters in a decentralized fashion; the weighting parameters are specified by the nodes and each node only specifies the weighting parameters as sociated with that node. The results assume that the communication graph of the network is directed, and we consider both synchronous communication, and stochastic asynchronous networks.

  3. Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins.

    PubMed

    Risso, Valeria A; Gavira, Jose A; Gaucher, Eric A; Sanchez-Ruiz, Jose M

    2014-06-01

    Consensus-sequence engineering has generated protein variants with enhanced stability, and sometimes, with modulated biological function. Consensus mutations are often interpreted as the introduction of ancestral amino acid residues. However, the precise relationship between consensus engineering and ancestral protein resurrection is not fully understood. Here, we report the properties of proteins encoded by consensus sequences derived from a multiple sequence alignment of extant, class A β-lactamases, as compared with the properties of ancient Precambrian β-lactamases resurrected in the laboratory. These comparisons considered primary sequence, secondary, and tertiary structure, as well as stability and catalysis against different antibiotics. Out of the three consensus variants generated, one could not be expressed and purified (likely due to misfolding and/or low stability) and only one displayed substantial stability having substrate promiscuity, although to a lower extent than ancient β-lactamases. These results: (i) highlight the phenotypic differences between consensus variants and laboratory resurrections of ancestral proteins; (ii) question interpretations of consensus proteins as phenotypic proxies of ancestral proteins; and (iii) support the notion that ancient proteins provide a robust approach toward the preparation of protein variants having large numbers of mutational changes while possessing unique biomolecular properties. PMID:24710963

  4. New consensus nomenclature for mammalian keratins

    PubMed Central

    Schweizer, Jürgen; Bowden, Paul E.; Coulombe, Pierre A.; Langbein, Lutz; Lane, E. Birgitte; Magin, Thomas M.; Maltais, Lois; Omary, M. Bishr; Parry, David A.D.; Rogers, Michael A.; Wright, Mathew W.

    2006-01-01

    Keratins are intermediate filament–forming proteins that provide mechanical support and fulfill a variety of additional functions in epithelial cells. In 1982, a nomenclature was devised to name the keratin proteins that were known at that point. The systematic sequencing of the human genome in recent years uncovered the existence of several novel keratin genes and their encoded proteins. Their naming could not be adequately handled in the context of the original system. We propose a new consensus nomenclature for keratin genes and proteins that relies upon and extends the 1982 system and adheres to the guidelines issued by the Human and Mouse Genome Nomenclature Committees. This revised nomenclature accommodates functional genes and pseudogenes, and although designed specifically for the full complement of human keratins, it offers the flexibility needed to incorporate additional keratins from other mammalian species. PMID:16831889

  5. Using Consensus Groups in Online Learning

    ERIC Educational Resources Information Center

    Smith, Regina O.; Dirkx, John M.

    2007-01-01

    This chapter describes online consensus group work, a form of collaborative learning. It discusses collaborative learning, small group work, and consensus learning, with recommendations for their use in online contexts.

  6. Energy strategy: Roadmap to consensus

    SciTech Connect

    Not Available

    1990-11-01

    The United States lacks a comprehensive approach to policy-making in the energy realm. Today, as in the past, individual constituency groups tend to focus on their particular aspect of the energy challenge. Many employ a ``decide-announce-defend`` approach to policy-making, setting out to secure a unilateral advantage for themselves. By so doing, they inevitably pit interest against interest. The result is a polarization of constituencies, and shortsighted policies designed to address the issue of the moment. The American Energy Assurance Council (AEAC) is a non-profit organization founded in 1987 for the sole purpose of facilitating progress toward a fair efficient wise, stable, and consensus-based national energy strategy. AEAC does not have a substantive policy agencies. Rather, we are committed to supporting a process whereby the many stakeholders and policy makers concerned with energy-related issues can come together in productive discourse, thereby overcoming ignorance of each other`s positions. The Council seeks to act as a facilitative body, providing a ``safe`` context for inventive and creative thinking. We attempt to build a store of common knowledge, and to build on that store according to mutually agreed-upon groundrules, and employing sophisticated approaches to facilitation and mediation. This report, the National Energy Consensus Experiment (NECE), was an ambitious experiment in consensus-building. We learned a great deal from it, both in terms of substance and process, and we are convinced that it holds important lessons for others who may seek to build consensus in the public policy realm.

  7. Energy strategy: Roadmap to consensus

    SciTech Connect

    Not Available

    1990-11-01

    The United States lacks a comprehensive approach to policy-making in the energy realm. Today, as in the past, individual constituency groups tend to focus on their particular aspect of the energy challenge. Many employ a decide-announce-defend'' approach to policy-making, setting out to secure a unilateral advantage for themselves. By so doing, they inevitably pit interest against interest. The result is a polarization of constituencies, and shortsighted policies designed to address the issue of the moment. The American Energy Assurance Council (AEAC) is a non-profit organization founded in 1987 for the sole purpose of facilitating progress toward a fair efficient wise, stable, and consensus-based national energy strategy. AEAC does not have a substantive policy agencies. Rather, we are committed to supporting a process whereby the many stakeholders and policy makers concerned with energy-related issues can come together in productive discourse, thereby overcoming ignorance of each other's positions. The Council seeks to act as a facilitative body, providing a safe'' context for inventive and creative thinking. We attempt to build a store of common knowledge, and to build on that store according to mutually agreed-upon groundrules, and employing sophisticated approaches to facilitation and mediation. This report, the National Energy Consensus Experiment (NECE), was an ambitious experiment in consensus-building. We learned a great deal from it, both in terms of substance and process, and we are convinced that it holds important lessons for others who may seek to build consensus in the public policy realm.

  8. Liberal Education: An Overlapping Pragmatic Consensus.

    ERIC Educational Resources Information Center

    Paris, David C.; Kimball, Bruce A.

    2000-01-01

    Suggests in Bruce Kimball's thesis that a pragmatic consensus was emerging about the understanding of liberal education offers that it might be best understood by comparing it to J. Rawl's idea of an "overlapping consensus." States that by comparing and contrasting these ideas that the emerging consensus is pragmatic in nature. (CMK)

  9. A consensus procedure for predicting the location of alpha-helical transmembrane segments in proteins.

    PubMed

    Parodi, L A; Granatir, C A; Maggiora, G M

    1994-09-01

    To aid in the development of three-dimensional models of membrane-bound proteins, a consensus procedure for predicting alpha-helical transmembrane segments from amino acid sequence is presented. The algorithm combines the results of six individual prediction methods and some basic properties of membrane-spanning helices to obtain a final consensus prediction. Comparison with experiment and several other recently developed methods shows that the consensus procedure performs quite well in comparison to other recent methods. A FORTRAN program has been developed which takes an input file containing an amino acid sequence in one-letter code and outputs a list of the alpha-helical transmembrane segments predicted by the consensus algorithm. PMID:7828069

  10. Canadian asthma consensus report, 1999

    PubMed Central

    Boulet, L P; Becker, A; Bérubé, D; Beveridge, R; Ernst, P

    1999-01-01

    OBJECTIVES: To provide physicians with current guidelines for the diagnosis and optimal management of asthma in children and adults, including pregnant women and the elderly, in office, emergency department, hospital and clinic settings. OPTIONS: The consensus group considered the roles of education, avoidance of provocative environmental and other factors, diverse pharmacotherapies, delivery devices and emergency and in-hospital management of asthma. OUTCOMES: Provision of the best control of asthma by confirmation of the diagnosis using objective measures, rapid achievement and maintenance of control and regular follow-up. EVIDENCE: The key diagnostic and therapeutic recommendations are based on the 1995 Canadian guidelines and a critical review of the literature by small groups before a full meeting of the consensus group. Recommendations are graded according to 5 levels of evidence. Differences of opinion were resolved by consensus following discussion. VALUES: Respirologists, immunoallergists, pediatricians and emergency and family physicians gave prime consideration to the achievement and maintenance of optimal control of asthma through avoidance of environmental inciters, education of patients and the lowest effective regime of pharmacotherapy to reduce morbidity and mortality. BENEFITS, HARMS AND COSTS: Adherence to the guidelines should be accompanied by significant reduction in patients' symptoms, reduced morbidity and mortality, fewer emergency and hospital admissions, fewer adverse side-effects from medications, better quality of life for patients and reduced costs. RECOMMENDATIONS: Recommendations are included in each section of the report. In summary, after a diagnosis of asthma is made based on clinical evaluation, including demonstration of variable airflow obstruction, and contributing factors are identified, a treatment plan is established to obtain and maintain optimal asthma control. The main components of treatment are patient education

  11. Learning consensus in adversarial environments

    NASA Astrophysics Data System (ADS)

    Vamvoudakis, Kyriakos G.; García Carrillo, Luis R.; Hespanha, João. P.

    2013-05-01

    This work presents a game theory-based consensus problem for leaderless multi-agent systems in the presence of adversarial inputs that are introducing disturbance to the dynamics. Given the presence of enemy components and the possibility of malicious cyber attacks compromising the security of networked teams, a position agreement must be reached by the networked mobile team based on environmental changes. The problem is addressed under a distributed decision making framework that is robust to possible cyber attacks, which has an advantage over centralized decision making in the sense that a decision maker is not required to access information from all the other decision makers. The proposed framework derives three tuning laws for every agent; one associated with the cost, one associated with the controller, and one with the adversarial input.

  12. Subclinical hypothyroidism: Controversies to consensus

    PubMed Central

    Raza, Syed Abbas; Mahmood, Nasir

    2013-01-01

    Diagnoses of subclinicaal hypothyroidism (SCH) is biochemically made, when serum thyroid stimulating hormone (TSH) levels is elevated while free thyroid hormone levels are within normal reference range. SCH is diagnosed after excluding all other causes of elevated TSH levels. Symptoms of SCH may vary from being asymptomatic to having mild nonspecific symptoms. The risk of progression to overt hypothyroidism is related to number of factors including initial serum TSH concentration, presence of auto antibodies, family history and presence goiter. Various screening recommendations for thyroid function assessment are in practice. There are still controversies surrounding SCH and associated risk of various cardiovascular diseases (CVDs), pregnancy outcomes, neuropsychiatric issues, metabolic syndrome, and dyslipidemia. Consensus will require more large randomized clinical studies involving various age groups and medical condition, especially in developing countries. All these efforts will definitely improve our understanding of disease and ultimately patient outcomes. PMID:24910826

  13. Consensus in a Precambrian garden

    NASA Astrophysics Data System (ADS)

    Maggs, William Ward

    At the Precambrian-Cambrian boundary, the course of life on Earth underwent a dramatic change that culminated in the rise of predators and other complex animals, a group of paleontologists agreed at a conferece last week.Just prior to 590 million years ago, the ecology of life in the oceans was very simple; soft-shelled multicellular animals called Ediacara lived in apparent harmony with vast mats o f bacteria and algae that covered the seafloor, dependent on the photosynthesis or chemosynthesis of their one-celled hosts for their existence. According to the consensus reached by the scientists, this symbiotic and apparently global “Garden of Ediacara” fell early in the Cambrian Period, as the mats declined and food chains multiplied with new animals that, for the first time in Earth's history, preyed on other living things.

  14. Data publication consensus and controversies

    PubMed Central

    Kratz, John; Strasser, Carly

    2014-01-01

    The movement to bring datasets into the scholarly record as first class research products (validated, preserved, cited, and credited) has been inching forward for some time, but now the pace is quickening. As data publication venues proliferate, significant debate continues over formats, processes, and terminology. Here, we present an overview of data publication initiatives underway and the current conversation, highlighting points of consensus and issues still in contention. Data publication implementations differ in a variety of factors, including the kind of documentation, the location of the documentation relative to the data, and how the data is validated. Publishers may present data as supplemental material to a journal article, with a descriptive “data paper,” or independently. Complicating the situation, different initiatives and communities use the same terms to refer to distinct but overlapping concepts. For instance, the term published means that the data is publicly available and citable to virtually everyone, but it may or may not imply that the data has been peer-reviewed. In turn, what is meant by data peer review is far from defined; standards and processes encompass the full range employed in reviewing the literature, plus some novel variations. Basic data citation is a point of consensus, but the general agreement on the core elements of a dataset citation frays if the data is dynamic or part of a larger set. Even as data publication is being defined, some are looking past publication to other metaphors, notably “data as software,” for solutions to the more stubborn problems. PMID:25075301

  15. Hilar Cholangiocarcinoma: expert consensus statement

    PubMed Central

    Mansour, John C; Aloia, Thomas A; Crane, Christopher H; Heimbach, Julie K; Nagino, Masato; Vauthey, Jean-Nicolas

    2015-01-01

    An American Hepato-Pancreato-Biliary Association (AHPBA)-sponsored consensus meeting of expert panellists met on 15 January 2014 to review current evidence on the management of hilar cholangiocarcinoma in order to establish practice guidelines and to agree consensus statements. It was established that the treatment of patients with hilar cholangiocarcinoma requires a coordinated, multidisciplinary approach to optimize the chances for both durable survival and effective palliation. An adequate diagnostic and staging work-up includes high-quality cross-sectional imaging; however, pathologic confirmation is not required prior to resection or initiation of a liver transplant trimodal treatment protocol. The ideal treatment for suitable patients with resectable hilar malignancy is resection of the intra- and extrahepatic bile ducts, as well as resection of the involved ipsilateral liver. Preoperative biliary drainage is best achieved with percutaneous transhepatic approaches and may be indicated for patients with cholangitis, malnutrition or hepatic insufficiency. Portal vein embolization is a safe and effective strategy for increasing the future liver remnant (FLR) and is particularly useful for patients with an FLR of <30%. Selected patients with unresectable hilar cholangiocarcinoma should be evaluated for a standard trimodal protocol incorporating external beam and endoluminal radiation therapy, systemic chemotherapy and liver transplantation. Post-resection chemoradiation should be offered to patients who show high-risk features on surgical pathology. Chemoradiation is also recommended for patients with locally advanced, unresectable hilar cancers. For patients with locally recurrent or metastatic hilar cholangiocarcinoma, first-line chemotherapy with gemcitabine and cisplatin is recommended based on multiple Phase II trials and a large randomized controlled trial including a heterogeneous population of patients with biliary cancers. PMID:26172136

  16. Hilar cholangiocarcinoma: expert consensus statement.

    PubMed

    Mansour, John C; Aloia, Thomas A; Crane, Christopher H; Heimbach, Julie K; Nagino, Masato; Vauthey, Jean-Nicolas

    2015-08-01

    An American Hepato-Pancreato-Biliary Association (AHPBA)-sponsored consensus meeting of expert panellists met on 15 January 2014 to review current evidence on the management of hilar cholangiocarcinoma in order to establish practice guidelines and to agree consensus statements. It was established that the treatment of patients with hilar cholangiocarcinoma requires a coordinated, multidisciplinary approach to optimize the chances for both durable survival and effective palliation. An adequate diagnostic and staging work-up includes high-quality cross-sectional imaging; however, pathologic confirmation is not required prior to resection or initiation of a liver transplant trimodal treatment protocol. The ideal treatment for suitable patients with resectable hilar malignancy is resection of the intra- and extrahepatic bile ducts, as well as resection of the involved ipsilateral liver. Preoperative biliary drainage is best achieved with percutaneous transhepatic approaches and may be indicated for patients with cholangitis, malnutrition or hepatic insufficiency. Portal vein embolization is a safe and effective strategy for increasing the future liver remnant (FLR) and is particularly useful for patients with an FLR of <30%. Selected patients with unresectable hilar cholangiocarcinoma should be evaluated for a standard trimodal protocol incorporating external beam and endoluminal radiation therapy, systemic chemotherapy and liver transplantation. Post-resection chemoradiation should be offered to patients who show high-risk features on surgical pathology. Chemoradiation is also recommended for patients with locally advanced, unresectable hilar cancers. For patients with locally recurrent or metastatic hilar cholangiocarcinoma, first-line chemotherapy with gemcitabine and cisplatin is recommended based on multiple Phase II trials and a large randomized controlled trial including a heterogeneous population of patients with biliary cancers. PMID:26172136

  17. Intrahepatic cholangiocarcinoma: expert consensus statement.

    PubMed

    Weber, Sharon M; Ribero, Dario; O'Reilly, Eileen M; Kokudo, Norihiro; Miyazaki, Masaru; Pawlik, Timothy M

    2015-08-01

    An American Hepato-Pancreato-Biliary Association (AHPBA)-sponsored consensus meeting of expert panellists met on 15 January 2014 to review current evidence on the management of intrahepatic cholangiocarcinoma (ICC) in order to establish practice guidelines and to agree on consensus statements. The treatment of ICC requires a coordinated, multidisciplinary approach to optimize survival. Biopsy is not necessary if the surgeon suspects ICC and is planning curative resection, although biopsy should be obtained before systemic or locoregional therapies are initiated. Assessment of resectability is best accomplished using cross-sectional imaging [computed tomography (CT) or magnetic resonance imaging (MRI)], but the role of positron emission tomography (PET) is unclear. Resectability in ICC is defined by the ability to completely remove the disease while leaving an adequate liver remnant. Extrahepatic disease, multiple bilobar or multicentric tumours, and lymph node metastases beyond the primary echelon are contraindications to resection. Regional lymphadenectomy should be considered a standard part of surgical therapy. In patients with high-risk features, the routine use of diagnostic laparoscopy is recommended. The preoperative diagnosis of combined hepatocellular carcinoma and cholangiocarcinoma (cHCC-CC) by imaging studies is extremely difficult. Surgical resection remains the mainstay of treatment, but survival is worse than in HCC alone. There are no adequately powered, randomized Phase III trials that can provide definitive recommendations for adjuvant therapy for ICC. Patients with high-risk features (lymphovascular invasion, multicentricity or satellitosis, large tumours) should be encouraged to enrol in clinical trials and to consider adjuvant therapy. Cisplatin plus gemcitabine represents the standard-of-care, front-line systemic therapy for metastatic ICC. Genomic analyses of biliary cancers support the development of targeted therapeutic interventions. PMID

  18. International Consensus on drug allergy.

    PubMed

    Demoly, P; Adkinson, N F; Brockow, K; Castells, M; Chiriac, A M; Greenberger, P A; Khan, D A; Lang, D M; Park, H-S; Pichler, W; Sanchez-Borges, M; Shiohara, T; Thong, B Y- H

    2014-04-01

    When drug reactions resembling allergy occur, they are called drug hypersensitivity reactions (DHRs) before showing the evidence of either drug-specific antibodies or T cells. DHRs may be allergic or nonallergic in nature, with drug allergies being immunologically mediated DHRs. These reactions are typically unpredictable. They can be life-threatening, may require or prolong hospitalization, and may necessitate changes in subsequent therapy. Both underdiagnosis (due to under-reporting) and overdiagnosis (due to an overuse of the term ‘allergy’) are common. A definitive diagnosis of such reactions is required in order to institute adequate treatment options and proper preventive measures. Misclassification based solely on the DHR history without further testing may affect treatment options, result in adverse consequences, and lead to the use of more-expensive or less-effective drugs, in contrast to patients who had undergone a complete drug allergy workup. Several guidelines and/or consensus documents on general or specific drug class-induced DHRs are available to support the medical decision process. The use of standardized systematic approaches for the diagnosis and management of DHRs carries the potential to improve outcomes and should thus be disseminated and implemented. Consequently, the International Collaboration in Asthma, Allergy and Immunology (iCAALL), formed by the European Academy of Allergy and Clinical Immunology (EAACI), the American Academy of Allergy, Asthma and Immunology (AAAAI), the American College of Allergy, Asthma and Immunology (ACAAI), and the World Allergy Organization (WAO), has decided to issue an International CONsensus (ICON) on drug allergy. The purpose of this document is to highlight the key messages that are common to many of the existing guidelines, while critically reviewing and commenting on any differences and deficiencies of evidence, thus providing a comprehensive reference document for the diagnosis and management of

  19. Eastern Canadian Gastrointestinal Cancer Consensus Conference 2014

    PubMed Central

    Tsvetkova, E.; Sud, S.; Aucoin, N.; Biagi, J.; Burkes, R.; Samson, B.; Brule, S.; Cripps, C.; Colwell, B.; Falkson, C.; Dorreen, M.; Goel, R.; Halwani, F.; Maroun, J.; Michaud, N.; Tehfe, M.; Thirlwell, M.; Vickers, M.; Asmis, T.

    2015-01-01

    The annual Eastern Canadian Colorectal Cancer Consensus Conference was held in Montreal, Quebec, 23–25 October 2014. Expert radiation, medical, and surgical oncologists and pathologists involved in the management of patients with gastrointestinal malignancies participated in presentations and discussions resulting in consensus statements on such hot topics as management of neuroendocrine tumours, advanced and metastatic pancreatic cancer, and metastatic colorectal cancer. PMID:26300681

  20. Posterior Probabilities for a Consensus Ordering.

    ERIC Educational Resources Information Center

    Fligner, Michael A.; Verducci, Joseph S.

    1990-01-01

    The concept of consensus ordering is defined, and formulas for exact and approximate posterior probabilities for consensus ordering are developed under the assumption of a generalized Mallows' model with a diffuse conjugate prior. These methods are applied to a data set concerning 98 college students. (SLD)

  1. Myalgic encephalomyelitis: International Consensus Criteria

    PubMed Central

    Carruthers, B M; van de Sande, M I; De Meirleir, K L; Klimas, N G; Broderick, G; Mitchell, T; Staines, D; Powles, A C P; Speight, N; Vallings, R; Bateman, L; Baumgarten-Austrheim, B; Bell, D S; Carlo-Stella, N; Chia, J; Darragh, A; Jo, D; Lewis, D; Light, A R; Marshall-Gradisbik, S; Mena, I; Mikovits, J A; Miwa, K; Murovska, M; Pall, M L; Stevens, S

    2011-01-01

    , Japan; A. Kirchenstein Institute of Microbiology and Virology, Riga Stradins University, Riga, Latvia; Department of Biochemistry & Basic Medical Sciences, Washington State University, Portland, OR; Department of Sports Sciences, University of the Pacific, Stockton, CA USA). Myalgic encephalomyelitis: International Consensus Criteria (Review). J Intern Med 2011; 270: 327–338. The label ‘chronic fatigue syndrome’ (CFS) has persisted for many years because of the lack of knowledge of the aetiological agents and the disease process. In view of more recent research and clinical experience that strongly point to widespread inflammation and multisystemic neuropathology, it is more appropriate and correct to use the term ‘myalgic encephalomyelitis’ (ME) because it indicates an underlying pathophysiology. It is also consistent with the neurological classification of ME in the World Health Organization’s International Classification of Diseases (ICD G93.3). Consequently, an International Consensus Panel consisting of clinicians, researchers, teaching faculty and an independent patient advocate was formed with the purpose of developing criteria based on current knowledge. Thirteen countries and a wide range of specialties were represented. Collectively, members have approximately 400 years of both clinical and teaching experience, authored hundreds of peer-reviewed publications, diagnosed or treated approximately 50 000 patients with ME, and several members coauthored previous criteria. The expertise and experience of the panel members as well as PubMed and other medical sources were utilized in a progression of suggestions/drafts/reviews/revisions. The authors, free of any sponsoring organization, achieved 100% consensus through a Delphi-type process. The scope of this paper is limited to criteria of ME and their application. Accordingly, the criteria reflect the complex symptomatology. Operational notes enhance clarity and specificity by providing guidance in the

  2. [GEITDAH consensus on attention deficit hyperactivity disorder].

    PubMed

    Montañés-Rada, F; Gastaminza-Pérez, X; Catalá, M A; Ruiz-Sanz, F; Ruiz-Lázaro, P M; Herreros-Rodríguez, O; García-Giral, M; Ortiz-Guerra, J; Alda-Díez, J A; Mojarro-Práxedes, D; Cantó-Díez, T; Mardomingo-Sanz, M J; Sasot-Llevadot, J; Pàmias, M; Rey-Sánchez, F

    2010-11-16

    In this article, the GEITDAH -the Spanish abbreviation of the Special Interest Group on Attention Deficit Hyper-activity Disorder (ADHD)- presents a consensus reached by experts in the management of ADHD from all over Spain. The consensus concerns fundamental aspects that should be the starting point for future local or regional consensus guides. Another aim of this consensus is also to reduce the amount of variability that occurs in the health care offered to patients with ADHD in our country, as well as to act as a stimulus in educational matters. That fact that it is not very long will make it more popular among greater numbers of people and this will allow these goals to be reached more effectively. The conclusions in the consensus guide have been constructed around an introduction dealing with basic aspects and recommendations for diagnosis, treatment (both pharmacological and psychotherapeutic), patient flow and organisational aspects. PMID:21069642

  3. [Mexican consensus on portal hypertension].

    PubMed

    Narváez-Rivera, R M; Cortez-Hernández, C A; González-González, J A; Tamayo-de la Cuesta, J L; Zamarripa-Dorsey, F; Torre-Delgadillo, A; Rivera-Ramos, J F J; Vinageras-Barroso, J I; Muneta-Kishigami, J E; Blancas-Valencia, J M; Antonio-Manrique, M; Valdovinos-Andraca, F; Brito-Lugo, P; Hernández-Guerrero, A; Bernal-Reyes, R; Sobrino-Cossío, S; Aceves-Tavares, G R; Huerta-Guerrero, H M; Moreno-Gómez, N; Bosques-Padilla, F J

    2013-01-01

    The aim of the Mexican Consensus on Portal Hypertension was to develop documented guidelines to facilitate clinical practice when dealing with key events of the patient presenting with portal hypertension and variceal bleeding. The panel of experts was made up of Mexican gastroenterologists, hepatologists, and endoscopists, all distinguished professionals. The document analyzes themes of interest in the following modules: preprimary and primary prophylaxis, acute variceal hemorrhage, and secondary prophylaxis. The management of variceal bleeding has improved considerably in recent years. Current information indicates that the general management of the cirrhotic patient presenting with variceal bleeding should be carried out by a multidisciplinary team, with such an approach playing a major role in the final outcome. The combination of drug and endoscopic therapies is recommended for initial management; vasoactive drugs should be started as soon as variceal bleeding is suspected and maintained for 5 days. After the patient is stabilized, urgent diagnostic endoscopy should be carried out by a qualified endoscopist, who then performs the corresponding endoscopic variceal treatment. Antibiotic prophylaxis should be regarded as an integral part of treatment, started upon hospital admittance and continued for 5 days. If there is treatment failure, rescue therapies should be carried out immediately, taking into account that interventional radiology therapies are very effective in controlling refractory variceal bleeding. These guidelines have been developed for the purpose of achieving greater clinical efficacy and are based on the best evidence of portal hypertension that is presently available. PMID:23664429

  4. Sampled-Data Consensus Over Random Networks

    NASA Astrophysics Data System (ADS)

    Wu, Junfeng; Meng, Ziyang; Yang, Tao; Shi, Guodong; Johansson, Karl Henrik

    2016-09-01

    This paper considers the consensus problem for a network of nodes with random interactions and sampled-data control actions. We first show that consensus in expectation, in mean square, and almost surely are equivalent for a general random network model when the inter-sampling interval and network size satisfy a simple relation. The three types of consensus are shown to be simultaneously achieved over an independent or a Markovian random network defined on an underlying graph with a directed spanning tree. For both independent and Markovian random network models, necessary and sufficient conditions for mean-square consensus are derived in terms of the spectral radius of the corresponding state transition matrix. These conditions are then interpreted as the existence of critical value on the inter-sampling interval, below which global mean-square consensus is achieved and above which the system diverges in mean-square sense for some initial states. Finally, we establish an upper bound on the inter-sampling interval below which almost sure consensus is reached, and a lower bound on the inter-sampling interval above which almost sure divergence is reached. Some numerical simulations are given to validate the theoretical results and some discussions on the critical value of the inter-sampling intervals for the mean-square consensus are provided.

  5. Gallbladder cancer: expert consensus statement.

    PubMed

    Aloia, Thomas A; Járufe, Nicolas; Javle, Milind; Maithel, Shishir K; Roa, Juan C; Adsay, Volkan; Coimbra, Felipe J F; Jarnagin, William R

    2015-08-01

    An American Hepato-Pancreato-Biliary Association (AHPBA)-sponsored consensus meeting of expert panellists was convened on 15 January 2014 to review current evidence on the management of gallbladder carcinoma in order to establish practice guidelines. In summary, within high incidence areas, the assessment of routine gallbladder specimens should include the microscopic evaluation of a minimum of three sections and the cystic duct margin; specimens with dysplasia or proven cancer should be extensively sampled. Provided the patient is medically fit for surgery, data support the resection of all gallbladder polyps of >1.0 cm in diameter and those with imaging evidence of vascular stalks. The minimum staging evaluation of patients with suspected or proven gallbladder cancer includes contrasted cross-sectional imaging and diagnostic laparoscopy. Adequate lymphadenectomy includes assessment of any suspicious regional nodes, evaluation of the aortocaval nodal basin, and a goal recovery of at least six nodes. Patients with confirmed metastases to N2 nodal stations do not benefit from radical resection and should receive systemic and/or palliative treatments. Primary resection of patients with early T-stage (T1b-2) disease should include en bloc resection of adjacent liver parenchyma. Patients with T1b, T2 or T3 disease that is incidentally identified in a cholecystectomy specimen should undergo re-resection unless this is contraindicated by advanced disease or poor performance status. Re-resection should include complete portal lymphadenectomy and bile duct resection only when needed to achieve a negative margin (R0) resection. Patients with preoperatively staged T3 or T4 N1 disease should be considered for clinical trials of neoadjuvant chemotherapy. Following R0 resection of T2-4 disease in N1 gallbladder cancer, patients should be considered for adjuvant systemic chemotherapy and/or chemoradiotherapy. PMID:26172135

  6. Polyphasic taxonomy, a consensus approach to bacterial systematics.

    PubMed Central

    Vandamme, P; Pot, B; Gillis, M; de Vos, P; Kersters, K; Swings, J

    1996-01-01

    Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question. PMID

  7. Comparing and Contrasting Consensus versus Empirical Domains

    PubMed Central

    Jason, Leonard A.; Kot, Bobby; Sunnquist, Madison; Brown, Abigail; Reed, Jordan; Furst, Jacob; Newton, Julia L.; Strand, Elin Bolle; Vernon, Suzanne D.

    2015-01-01

    Background Since the publication of the CFS case definition [1], there have been a number of other criteria proposed including the Canadian Consensus Criteria [2] and the Myalgic Encephalomyelitis: International Consensus Criteria. [3] Purpose The current study compared these domains that were developed through consensus methods to one obtained through more empirical approaches using factor analysis. Methods Using data mining, we compared and contrasted fundamental features of consensus-based criteria versus empirical latent factors. In general, these approaches found the domain of Fatigue/Post-exertional malaise as best differentiating patients from controls. Results Findings indicated that the Fukuda et al. criteria had the worst sensitivity and specificity. Conclusions These outcomes might help both theorists and researchers better determine which fundamental domains to be used for the case definition. PMID:26977374

  8. Examining the Scientific Consensus on Climate Change

    NASA Astrophysics Data System (ADS)

    Doran, Peter T.; Kendall Zimmerman, Maggie

    2009-01-01

    Fifty-two percent of Americans think most climate scientists agree that the Earth has been warming in recent years, and 47% think climate scientists agree (i.e., that there is a scientific consensus) that human activities are a major cause of that warming, according to recent polling (see http://www.pollingreport.com/enviro.htm). However, attempts to quantify the scientific consensus on anthropogenic warming have met with criticism. For instance, Oreskes [2004] reviewed 928 abstracts from peer-reviewed research papers and found that more than 75% either explicitly or implicitly accepted the consensus view that Earth's climate is being affected by human activities. Yet Oreskes's approach has been criticized for overstating the level of consensus acceptance within the examined abstracts [Peiser, 2005] and for not capturing the full diversity of scientific opinion [Pielke, 2005]. A review of previous attempts at quantifying the consensus and criticisms is provided by Kendall Zimmerman [2008]. The objective of our study presented here is to assess the scientific consensus on climate change through an unbiased survey of a large and broad group of Earth scientists.

  9. High-affinity consensus binding of target RNAs by the STAR/GSG proteins GLD-1, STAR-2 and Quaking

    PubMed Central

    2010-01-01

    Background STAR/GSG proteins regulate gene expression in metazoans by binding consensus sites in the 5' or 3' UTRs of target mRNA transcripts. Owing to the high degree of homology across the STAR domain, most STAR proteins recognize similar RNA consensus sequences. Previously, the consensus for a number of well-characterized STAR proteins was defined as a hexameric sequence, referred to as the SBE, for STAR protein binding element. C. elegans GLD-1 and mouse Quaking (Qk-1) are two representative STAR proteins that bind similar consensus hexamers, which differ only in the preferred nucleotide identities at certain positions. Earlier reports also identified partial consensus elements located upstream or downstream of a canonical consensus hexamer in target RNAs, although the relative contribution of these sequences to the overall binding energy remains less well understood. Additionally, a recently identified STAR protein called STAR-2 from C. elegans is thought to bind target RNA consensus sites similar to that of GLD-1 and Qk-1. Results Here, a combination of fluorescence-polarization and gel mobility shift assays was used to demonstrate that STAR-2 binds to a similar RNA consensus as GLD-1 and Qk-1. These assays were also used to further delineate the contributions of each hexamer consensus nucleotide to high-affinity binding by GLD-1, Qk-1 and STAR-2 in a variety of RNA contexts. In addition, the effects of inserting additional full or partial consensus elements upstream or downstream of a canonical hexamer in target RNAs were also measured to better define the sequence elements and RNA architecture recognized by different STAR proteins. Conclusions The results presented here indicate that a single hexameric consensus is sufficient for high-affinity RNA binding by STAR proteins, and that upstream or downstream partial consensus elements may alter binding affinities depending on the sequence and spacing. The general requirements determined for high-affinity RNA

  10. Asian Consensus Report on Functional Dyspepsia

    PubMed Central

    Miwa, Hiroto; Ghoshal, Uday C; Gonlachanvit, Sutep; Gwee, Kok-Ann; Ang, Tiing-Leong; Chang, Full-Young; Fock, Kwong Ming; Hongo, Michio; Hou, Xiaohua; Kachintorn, Udom; Ke, Meiyun; Lai, Kwok-Hung; Lee, Kwang Jae; Lu, Ching-Liang; Mahadeva, Sanjiv; Miura, Soichiro; Park, Hyojin; Rhee, Poong-Lyul; Sugano, Kentaro; Vilaichone, Ratha-korn; Wong, Benjamin CY

    2012-01-01

    Background/Aims Environmental factors such as food, lifestyle and prevalence of Helicobacter pylori infection are widely different in Asian countries compared to the West, and physiological functions and genetic factors of Asians may also be different from those of Westerners. Establishing an Asian consensus for functional dyspepsia is crucial in order to attract attention to such data from Asian countries, to articulate the experience and views of Asian experts, and to provide a relevant guide on management of functional dyspepsia for primary care physicians working in Asia. Methods Consensus team members were selected from Asian experts and consensus development was carried out using a modified Delphi method. Consensus teams collected published papers on functional dyspepsia especially from Asia and developed candidate consensus statements based on the generated clinical questions. At the first face-to-face meeting, each statement was reviewed and e-mail voting was done twice. At the second face-to-face meeting, final voting on each statement was done using keypad voting system. A grade of evidence and a strength of recommendation were applied to each statement according to the method of the GRADE Working Group. Results Twenty-nine consensus statements were finalized, including 7 for definition and diagnosis, 5 for epidemiology, 9 for pathophysiology and 8 for management. Algorithms for diagnosis and management of functional dyspepsia were added. Conclusions This consensus developed by Asian experts shows distinctive features of functional dyspepsia in Asia and will provide a guide to the diagnosis and management of functional dyspepsia for Asian primary care physicians. PMID:22523724

  11. A 24-base-pair sequence 3' to the human erythropoietin gene contains a hypoxia-responsive transcriptional enhancer.

    PubMed Central

    Madan, A; Curtin, P T

    1993-01-01

    Erythropoietin (Epo) synthesis increases in response to hypoxia. The hepatoma cell line Hep 3B produces low basal levels of Epo mRNA which increase markedly with hypoxia. To define the sequences necessary for this response, we linked fragments of the human Epo gene to a luciferase vector, introduced these plasmids into Hep 3B cells and assayed for luciferase activity after growth in 1% or 21% oxygen. A 621-bp Epo promoter fragment resulted in a 2.4-fold increase in luciferase activity with hypoxia. We tested several Epo gene fragments upstream of this Epo promoter fragment and found that a 613-bp Bgl II-Pvu II 3' fragment had a 10-fold increase in activity with hypoxia regardless of orientation. This fragment had a similar level of activity when linked to a simian virus 40 promoter. Portions of this fragment retained activity, including a 38-bp Apa I-Taq I fragment that had a 17-fold increase in activity with hypoxia. Deletion of nt 4-13 or 19-28 from this 38-bp fragment resulted in a loss of activity. The 24-bp upstream portion of the 38-bp fragment showed an 8-fold increase in activity with hypoxia. However, deletion of nt 19-24 or mutagenesis of nt 21 or 22 in this 24-bp fragment resulted in loss of activity. Our studies indicate that the transcriptional response of the human Epo gene to hypoxia is mediated in part by promoter sequences and to a greater degree by an enhancer element located in a 24-bp portion of the 3' flanking sequence of the gene. PMID:8387202

  12. A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An ultra-dense consensus (UDC) genetic map of tetraploid cotton was constructed using six high-density component maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cut...

  13. Reaching Consensus by Allowing Moments of Indecision.

    PubMed

    Svenkeson, A; Swami, A

    2015-01-01

    Group decision-making processes often turn into a drawn out and costly battle between two opposing subgroups. Using analytical arguments based on a master equation description of the opinion dynamics occurring in a three-state model of cooperatively interacting units, we show how the capability of a social group to reach consensus can be enhanced when there is an intermediate state for indecisive individuals to pass through. The time spent in the intermediate state must be relatively short compared to that of the two polar states in order to create the beneficial effect. Furthermore, the cooperation between individuals must not be too low, as the benefit to consensus is possible only when the cooperation level exceeds a specific threshold. We also discuss how zealots, agents that remain in one state forever, can affect the consensus among the rest of the population by counteracting the benefit of the intermediate state or making it virtually impossible for an opposition to form. PMID:26439503

  14. Reaching Consensus by Allowing Moments of Indecision

    NASA Astrophysics Data System (ADS)

    Svenkeson, A.; Swami, A.

    2015-10-01

    Group decision-making processes often turn into a drawn out and costly battle between two opposing subgroups. Using analytical arguments based on a master equation description of the opinion dynamics occurring in a three-state model of cooperatively interacting units, we show how the capability of a social group to reach consensus can be enhanced when there is an intermediate state for indecisive individuals to pass through. The time spent in the intermediate state must be relatively short compared to that of the two polar states in order to create the beneficial effect. Furthermore, the cooperation between individuals must not be too low, as the benefit to consensus is possible only when the cooperation level exceeds a specific threshold. We also discuss how zealots, agents that remain in one state forever, can affect the consensus among the rest of the population by counteracting the benefit of the intermediate state or making it virtually impossible for an opposition to form.

  15. Lack of consensus in social systems

    NASA Astrophysics Data System (ADS)

    Benczik, I. J.; Benczik, S. Z.; Schmittmann, B.; Zia, R. K. P.

    2008-05-01

    We propose an exactly solvable model for the dynamics of voters in a two-party system. The opinion formation process is modeled on a random network of agents. The dynamical nature of interpersonal relations is also reflected in the model, as the connections in the network evolve with the dynamics of the voters. In the infinite time limit, an exact solution predicts the emergence of consensus, for arbitrary initial conditions. However, before consensus is reached, two different metastable states can persist for exponentially long times. One state reflects a perfect balancing of opinions, the other reflects a completely static situation. An estimate of the associated lifetimes suggests that lack of consensus is typical for large systems.

  16. Trust method for multi-agent consensus

    NASA Astrophysics Data System (ADS)

    Mikulski, Dariusz G.; Lewis, Frank L.; Gu, Edward Y.; Hudas, Greg R.

    2012-06-01

    The consensus problem in multi-agent systems often assumes that all agents are equally trustworthy to seek agreement. But for multi-agent military applications - particularly those that deal with sensor fusion or multi-robot formation control - this assumption may create the potential for compromised network security or poor cooperative performance. As such, we present a trust-based solution for the discrete-time multi-agent consensus problem and prove its asymptotic convergence in strongly connected digraphs. The novelty of the paper is a new trust algorithm called RoboTrust, which is used to calculate trustworthiness in agents using observations and statistical inferences from various historical perspectives. The performance of RoboTrust is evaluated within the trust-based consensus protocol under different conditions of tolerance and confirmation.

  17. Consensus in personality judgments at zero acquaintance.

    PubMed

    Albright, L; Kenny, D A; Malloy, T E

    1988-09-01

    This research focused on the target effect on a perceiver's judgments of personality when the perceiver and the target are unacquainted. The perceiver was given no opportunity to interact with the target, a condition we refer to as zero acquaintance. We reasoned that in order to make personality judgments, perceivers would use the information available to them (physical appearance). Consensus in personality judgments would result, then, from shared stereotypes about particular physical appearance characteristics. Results from three separate studies with 259 subjects supported this hypothesis. On two of the five dimensions (extraversion and conscientiousness) on which subjects rated each other, a significant proportion of variance was due to the stimulus target. Consensus on judgments of extraversion appears to have been largely mediated by judgments of physical attractiveness. Across the three studies there was also evidence that the consensus in judgments on these two dimensions had some validity, in that they correlated with self-judgments on those two dimensions. PMID:3171912

  18. Reaching Consensus by Allowing Moments of Indecision

    PubMed Central

    Svenkeson, A.; Swami, A.

    2015-01-01

    Group decision-making processes often turn into a drawn out and costly battle between two opposing subgroups. Using analytical arguments based on a master equation description of the opinion dynamics occurring in a three-state model of cooperatively interacting units, we show how the capability of a social group to reach consensus can be enhanced when there is an intermediate state for indecisive individuals to pass through. The time spent in the intermediate state must be relatively short compared to that of the two polar states in order to create the beneficial effect. Furthermore, the cooperation between individuals must not be too low, as the benefit to consensus is possible only when the cooperation level exceeds a specific threshold. We also discuss how zealots, agents that remain in one state forever, can affect the consensus among the rest of the population by counteracting the benefit of the intermediate state or making it virtually impossible for an opposition to form. PMID:26439503

  19. [SECOT consensus on medial femorotibial osteoarthritis].

    PubMed

    Moreno, A; Silvestre, A; Carpintero, P

    2013-01-01

    A consensus, prepared by SECOT, is presented on the management of medial knee compartment osteoarthritis, in order to establish clinical criteria and recommendations directed at unifying the criteria in its management, dealing with the factors involved in the pathogenesis of medial femorotibial knee osteoarthritis, the usefulness of diagnostic imaging techniques, and the usefulness of arthroscopy. Conservative and surgical treatments are also analysed. The experts consulted showed a consensus (agreed or disagreed) in 65.8% of the items considered, leaving 14items where no consensus was found, which included the aetiopathogenesis of the osteoarthritis, the value of NMR in degenerative disease, the usefulness of COX-2 and the chondroprotective drugs, as well as on the ideal valgus tibial osteotomy technique. PMID:24169227

  20. Consensus methods: characteristics and guidelines for use.

    PubMed Central

    Fink, A; Kosecoff, J; Chassin, M; Brook, R H

    1984-01-01

    Consensus methods are being used increasingly to solve problems in medicine and health. Their main purpose is to define levels of agreement on controversial subjects. Advocates suggest that, when properly employed, consensus strategies can create structured environments in which experts are given the best available information, allowing their solutions to problems to be more justifiable and credible than otherwise. This paper surveys the characteristics of several major methods (Delphi, Nominal Group, and models developed by the National Institutes of Health and Glaser) and provides guidelines for those who want to use the techniques. Among the concerns these guidelines address are selecting problems, choosing members for consensus panels, specifying acceptable levels of agreement, properly using empirical data, obtaining professional and political support, and disseminating results. PMID:6380323

  1. Event-triggered consensus tracking of multi-agent systems with Lur'e nonlinear dynamics

    NASA Astrophysics Data System (ADS)

    Huang, Na; Duan, Zhisheng; Wen, Guanghui; Zhao, Yu

    2016-05-01

    In this paper, distributed consensus tracking problem for networked Lur'e systems is investigated based on event-triggered information interactions. An event-triggered control algorithm is designed with the advantages of reducing controller update frequency and sensor energy consumption. By using tools of ?-procedure and Lyapunov functional method, some sufficient conditions are derived to guarantee that consensus tracking is achieved under a directed communication topology. Meanwhile, it is shown that Zeno behaviour of triggering time sequences is excluded for the proposed event-triggered rule. Finally, some numerical simulations on coupled Chua's circuits are performed to illustrate the effectiveness of the theoretical algorithms.

  2. RNA sequence analysis using covariance models.

    PubMed Central

    Eddy, S R; Durbin, R

    1994-01-01

    We describe a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family. We call these models 'covariance models'. A covariance model of tRNA sequences is an extremely sensitive and discriminative tool for searching for additional tRNAs and tRNA-related sequences in sequence databases. A model can be built automatically from an existing sequence alignment. We also describe an algorithm for learning a model and hence a consensus secondary structure from initially unaligned example sequences and no prior structural information. Models trained on unaligned tRNA examples correctly predict tRNA secondary structure and produce high-quality multiple alignments. The approach may be applied to any family of small RNA sequences. Images PMID:8029015

  3. Consensus dynamics on random rectangular graphs

    NASA Astrophysics Data System (ADS)

    Estrada, Ernesto; Sheerin, Matthew

    2016-06-01

    A random rectangular graph (RRG) is a generalization of the random geometric graph (RGG) in which the nodes are embedded into a rectangle with side lengths a and b = 1 / a, instead of on a unit square [ 0 , 1 ] 2. Two nodes are then connected if and only if they are separated at a Euclidean distance smaller than or equal to a certain threshold radius r. When a = 1 the RRG is identical to the RGG. Here we apply the consensus dynamics model to the RRG. Our main result is a lower bound for the time of consensus, i.e., the time at which the network reaches a global consensus state. To prove this result we need first to find an upper bound for the algebraic connectivity of the RRG, i.e., the second smallest eigenvalue of the combinatorial Laplacian of the graph. This bound is based on a tight lower bound found for the graph diameter. Our results prove that as the rectangle in which the nodes are embedded becomes more elongated, the RRG becomes a 'large-world', i.e., the diameter grows to infinity, and a poorly-connected graph, i.e., the algebraic connectivity decays to zero. The main consequence of these findings is the proof that the time of consensus in RRGs grows to infinity as the rectangle becomes more elongated. In closing, consensus dynamics in RRGs strongly depend on the geometric characteristics of the embedding space, and reaching the consensus state becomes more difficult as the rectangle is more elongated.

  4. Identification of consensus binding sites clarifies FMRP binding determinants.

    PubMed

    Anderson, Bart R; Chopra, Pankaj; Suhl, Joshua A; Warren, Stephen T; Bassell, Gary J

    2016-08-19

    Fragile X mental retardation protein (FMRP) is a multifunctional RNA-binding protein with crucial roles in neuronal development and function. Efforts aimed at elucidating how FMRP target mRNAs are selected have produced divergent sets of target mRNA and putative FMRP-bound motifs, and a clear understanding of FMRP's binding determinants has been lacking. To clarify FMRP's binding to its target mRNAs, we produced a shared dataset of FMRP consensus binding sequences (FCBS), which were reproducibly identified in two published FMRP CLIP sequencing datasets. This comparative dataset revealed that of the various sequence and structural motifs that have been proposed to specify FMRP binding, the short sequence motifs TGGA and GAC were corroborated, and a novel TAY motif was identified. In addition, the distribution of the FCBS set demonstrates that FMRP preferentially binds to the coding region of its targets but also revealed binding along 3' UTRs in a subset of target mRNAs. Beyond probing these putative motifs, the FCBS dataset of reproducibly identified FMRP binding sites is a valuable tool for investigating FMRP targets and function. PMID:27378784

  5. The human minisatellite consensus at breakpoints of oncogene translocations.

    PubMed Central

    Krowczynska, A M; Rudders, R A; Krontiris, T G

    1990-01-01

    A reexamination of human minisatellite (hypervariable) regions following the cloning and sequencing of the new minisatellite, VTR1.1, revealed that many of these structures possessed a strongly conserved copy of the chi-like octamer, GC[A/T]GG[A/T]GG. In oncogene translocations apparently created by aberrant VDJ recombinase activity, this VTR octamer was often found within a few bases of the breakpoint (p less than 10(-10)). Three bcl2 rearrangements which occurred within 2 bp of one another were located precisely adjacent to this consensus; it defined the 5' border of that oncogene's major breakpoint cluster. Several c-myc translocations also occurred within 2 bp of this sequence. While the appearance of a chi-like element in polymorphic minisatellite sequences is consistent with a role promoting either recombination or replication slippage, the existence of such elements at sites of somatic translocations suggests chi function in site-specific recombination, perhaps as a subsidiary recognition signal in immunoglobulin gene rearrangement. We discuss the implications of these observations for mechanisms by which oncogene translocations and minisatellite sequences are generated. Images PMID:1969618

  6. Teaching Persuasion as Consensus in Business Communication.

    ERIC Educational Resources Information Center

    Blyler, Nancy Roundy

    1993-01-01

    Suggests that understanding the "tools of rhetorical analysis" in relation to persuasion can help business communication teachers better incorporate the concept of consensus building into their courses. Discusses incorporating rhetorical techniques (using metaphors, calling on readers' schemata, and using narratives) into a business communication…

  7. The Future of Education's Liberal Consensus.

    ERIC Educational Resources Information Center

    Finn, Chester E., Jr.

    1980-01-01

    The liberal consensus that has shaped national education policy is seen as succumbing to dubious ideas and undesirable practices. Issues discussed include: educational equity, equality and quality; measures of educational achievement; accountability; "need" and ability; statism and monoply, pluralism and diversity; federal role; and quota systems…

  8. Consensus among Economists--An Update

    ERIC Educational Resources Information Center

    Fuller, Dan; Geide-Stevenson, Doris

    2014-01-01

    In this article, the authors explore consensus among economists on specific propositions based on a fall 2011 survey of American Economic Association members. Results are based on 568 responses and provide evidence of changes in opinion over time by including propositions from earlier studies in 2000 (Fuller and Geide-Stevenson 2003) and 1992…

  9. Teacher Effectiveness in Physical Education--Consensus?

    ERIC Educational Resources Information Center

    Rink, Judith

    2014-01-01

    This article synthesizes the series of manuscripts on teacher effectiveness in physical education recently published by the "Research Quarterly for Exercise and Sport" and highlights both the consensus and points of disagreement. Although there is much agreement as to the mission to develop a physically active lifestyle, there is a great…

  10. Self-Directed Learning: Consensus & Conflict.

    ERIC Educational Resources Information Center

    Long, Huey B.; And Others

    The following papers are presented in this book: "Self-Directed Learning: Consensus and Conflict" (Long); "Challenges in the Study and Practice of Self-Directed Learning" (Long); "A Conceptual Model of Autodidactism" (Tremblay, Theil); "Functional and Dysfunctional Uses of Self-Directedness in Adult Learning" (Bonham); "Relationship between Scores…

  11. Health Promoting Schools: Consensus, Strategies, and Potential

    ERIC Educational Resources Information Center

    Macnab, Andrew J.; Gagnon, Faith A.; Stewart, Donald

    2014-01-01

    Purpose: The purpose of this paper is to summarize a consensus statement generated on the current challenges, strategies, and potential of health promoting schools (HPS) at a 2011 colloquium at the Stellenbosch Institute for Advanced Study where 40 people from five continents came together to share their global and regional experience surrounding…

  12. Report on the Consensus Workshop on Formaldehyde.

    PubMed Central

    1984-01-01

    The Consensus Workshop on Formaldehyde consisted of bringing together scientists from academia, government, industry and public interest groups to address some important toxicological questions concerning the health effects of formaldehyde. The participants in the workshop, the Executive Panel which coordinated the meeting, and the questions posed, all were chosen through a broadly based nomination process in order to achieve as comprehensive a consensus as possible. The subcommittees considered the toxicological problems associated with formaldehyde in the areas of exposure, epidemiology, carcinogenicity/histology/genotoxicity, immunology/sensitization/irritation, structure activity/biochemistry/metabolism, reproduction/teratology, behavior/neurotoxicity/psychology and risk estimation. Some questions considered included the possible human carcinogenicity of formaldehyde, as well as other human health effects, and the interpretation of pathology induced by formaldehyde. These reports, plus introductory material on the procedures used in setting up the Consensus Workshop are presented here. Additionally, there is included a listing of the data base that was made available to the panel chairmen prior to the meeting and was readily accessible to the participants during their deliberations in the meeting. This data base, since it was computerized, was also capable of being searched for important terms. These materials were supplemented by information brought by the panelists. The workshop has defined the consensus concerning a number of major points in formaldehyde toxicology and has identified a number of major deficits in understanding which are important guides to future research. PMID:6525992

  13. Report on the Consensus Workshop on Formaldehyde.

    PubMed

    1984-12-01

    The Consensus Workshop on Formaldehyde consisted of bringing together scientists from academia, government, industry and public interest groups to address some important toxicological questions concerning the health effects of formaldehyde. The participants in the workshop, the Executive Panel which coordinated the meeting, and the questions posed, all were chosen through a broadly based nomination process in order to achieve as comprehensive a consensus as possible. The subcommittees considered the toxicological problems associated with formaldehyde in the areas of exposure, epidemiology, carcinogenicity/histology/genotoxicity, immunology/sensitization/irritation, structure activity/biochemistry/metabolism, reproduction/teratology, behavior/neurotoxicity/psychology and risk estimation. Some questions considered included the possible human carcinogenicity of formaldehyde, as well as other human health effects, and the interpretation of pathology induced by formaldehyde. These reports, plus introductory material on the procedures used in setting up the Consensus Workshop are presented here. Additionally, there is included a listing of the data base that was made available to the panel chairmen prior to the meeting and was readily accessible to the participants during their deliberations in the meeting. This data base, since it was computerized, was also capable of being searched for important terms. These materials were supplemented by information brought by the panelists. The workshop has defined the consensus concerning a number of major points in formaldehyde toxicology and has identified a number of major deficits in understanding which are important guides to future research. PMID:6525992

  14. Quorum responses and consensus decision making

    PubMed Central

    Sumpter, David J.T.; Pratt, Stephen C.

    2008-01-01

    Animal groups are said to make consensus decisions when group members come to agree on the same option. Consensus decisions are taxonomically widespread and potentially offer three key benefits: maintenance of group cohesion, enhancement of decision accuracy compared with lone individuals and improvement in decision speed. In the absence of centralized control, arriving at a consensus depends on local interactions in which each individual's likelihood of choosing an option increases with the number of others already committed to that option. The resulting positive feedback can effectively direct most or all group members to the best available choice. In this paper, we examine the functional form of the individual response to others' behaviour that lies at the heart of this process. We review recent theoretical and empirical work on consensus decisions, and we develop a simple mathematical model to show the central importance to speedy and accurate decisions of quorum responses, in which an animal's probability of exhibiting a behaviour is a sharply nonlinear function of the number of other individuals already performing this behaviour. We argue that systems relying on such quorum rules can achieve cohesive choice of the best option while also permitting adaptive tuning of the trade-off between decision speed and accuracy. PMID:19073480

  15. Epistemic Iterations and Consensus Definitions of Validity

    ERIC Educational Resources Information Center

    Engelhard, George, Jr.; Behizadeh, Nadia

    2012-01-01

    In his article, Paul E. Newton has conducted a review of selected perspectives on validity theory with the goal of disambiguating the definition of validity and describing a consensus definition of validity. Newton provides a nuanced discussion of the evolution of the concept of validity over the years. His Focus article has two major goals: (1)…

  16. Consensus among Economics Teachers from Transition Economies

    ERIC Educational Resources Information Center

    Leet, Don R.; Lang, Nancy A.

    2010-01-01

    The authors analyze the economic opinions of teachers and economists from the former Soviet Union who participated in economic education programs sponsored by the U.S. Department of Education under the auspices of the National Council on Economic Education from 1995-2001. They sought to determine the level of consensus on economic topics among the…

  17. Multi-Attribute Consensus Building Tool

    ERIC Educational Resources Information Center

    Shyyan, Vitaliy; Christensen, Laurene; Thurlow, Martha; Lazarus, Sheryl

    2013-01-01

    The Multi-Attribute Consensus Building (MACB) method is a quantitative approach for determining a group's opinion about the importance of each item (strategy, decision, recommendation, policy, priority, etc.) on a list (Vanderwood, & Erickson, 1994). This process enables a small or large group of participants to generate and discuss a set…

  18. Genome Sequence Databases (Overview): Sequencing and Assembly

    SciTech Connect

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  19. Cloning and deliberation: Korean consensus conference.

    PubMed

    Kim, Myung-Sik

    2002-12-01

    This article addresses the 2nd Korean consensus conference on cloning that was held by the Korean National commission for UNESCO in 1999. It notes that the citizens participated directly and handled the important social agenda through deliberative process. The consensus conference is another democratic form derived from preference aggregative democracy in the sense that it basically depends on public judgment of the citizens. Compared to other models (elitist or preference aggregative), it has some advantages: 1. It can solve the problem of political legitimacy. 2. It can check the partiality of expert groups in biotechnology and ethics. 3. It enables us to make informed, responsible decisions. 4. It results in education of citizens' preference. However, we need to expand the deliberative model. First, we need institutional efforts on behalf of future generations because cloning relates to them. Second, we should not include the value of life which cannot be expressed in the form of argument or discourse. PMID:12870502

  20. Management of chronic hepatitis C: Consensus guidelines

    PubMed Central

    Sherman, Morris; Shafran, Stephen; Burak, Kelly; Doucette, Karen; Wong, Winnie; Girgrah, Nigel; Yoshida, Eric; Renner, Eberhard; Wong, Philip; Deschênes, Marc

    2007-01-01

    Since the last consensus conference on the management of chronic viral hepatitis, a number of studies looking at modifications of the standard course of treatment have been published. These changes have been sufficiently substantive to warrant review to determine whether any changes in the recommended treatment algorithms are needed. A consensus development conference was held in January 2007, and the present document highlights the results of the presentations and discussion about these issues. It reviews the epidemiology of hepatitis C in Canada, treatment of acute hepatitis C and new algorithms in chronic hepatitis C, including retreatment of previous treatment failures. In addition, sections on management of hepatitis C in special populations have been updated. There is also a section on the use of hematopoietic growth factors to help manage patients on therapy. The document should be read in conjunction with the previous document to identify changes. Some recommendations made in the previous document remain and are not discussed here. PMID:17568824

  1. The Temporal Structure of Scientific Consensus Formation

    PubMed Central

    Shwed, Uri; Bearman, Peter S.

    2011-01-01

    This article engages with problems that are usually opaque: What trajectories do scientific debates assume, when does a scientific community consider a proposition to be a fact, and how can we know that? We develop a strategy for evaluating the state of scientific contestation on issues. The analysis builds from Latour’s black box imagery, which we observe in scientific citation networks. We show that as consensus forms, the importance of internal divisions to the overall network structure declines. We consider substantive cases that are now considered facts, such as the carcinogenicity of smoking and the non-carcinogenicity of coffee. We then employ the same analysis to currently contested cases: the suspected carcinogenicity of cellular phones, and the relationship between vaccines and autism. Extracting meaning from the internal structure of scientific knowledge carves a niche for renewed sociological commentary on science, revealing a typology of trajectories that scientific propositions may experience en route to consensus. PMID:21886269

  2. Melanocortin 1 receptor (MC1R) gene sequence variation and melanism in the gray (Sciurus carolinensis), fox (Sciurus niger), and red (Sciurus vulgaris) squirrel.

    PubMed

    McRobie, Helen R; King, Linda M; Fanutti, Cristina; Coussons, Peter J; Moncrief, Nancy D; Thomas, Alison P M

    2014-01-01

    Sequence variations in the melanocortin 1 receptor (MC1R) gene are associated with melanism in many different species of mammals, birds, and reptiles. The gray squirrel (Sciurus carolinensis), found in the British Isles, was introduced from North America in the late 19th century. Melanism in the British gray squirrel is associated with a 24-bp deletion in the MC1R. To investigate the origin of this mutation, we sequenced the MC1R of 95 individuals including 44 melanic gray squirrels from both the British Isles and North America. Melanic gray squirrels of both populations had the same 24-bp deletion associated with melanism. Given the significant deletion associated with melanism in the gray squirrel, we sequenced the MC1R of both wild-type and melanic fox squirrels (Sciurus niger) (9 individuals) and red squirrels (Sciurus vulgaris) (39 individuals). Unlike the gray squirrel, no association between sequence variation in the MC1R and melanism was found in these 2 species. We conclude that the melanic gray squirrel found in the British Isles originated from one or more introductions of melanic gray squirrels from North America. We also conclude that variations in the MC1R are not associated with melanism in the fox and red squirrels. PMID:24534267

  3. After seven years, where's the consensus

    SciTech Connect

    Norman, M.R.

    1993-04-01

    It has been 7 years since the discovery of copper oxide superconductors, yet there is no consensus on the correct theory for this phenomenon. The theory can be divided into 3 groups: ordinary (phonons), exotic (AF spin fluctuations, nested Fermi liquid, excitons, spin bags, odd frequency pairing), and revolutionary (Luttinger liquid, spin-charge separation, gauge theories, anyons, marginal Fermi liquid). C-axis dispersion, dHvA, and magneto-oscillations are also discussed.

  4. 43 CFR 46.110 - Incorporating consensus-based management.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Incorporating consensus-based management... § 46.110 Incorporating consensus-based management. (a) Consensus-based management incorporates direct community involvement in consideration of bureau activities subject to NEPA analyses, from initial...

  5. A Self-Categorization Explanation for Opinion Consensus Perceptions

    ERIC Educational Resources Information Center

    Zhang, Jinguang; Reid, Scott A.

    2013-01-01

    The public expression of opinions (and related communicative activities) hinges upon the perception of opinion consensus. Current explanations for opinion consensus perceptions typically focus on egocentric and other biases, rather than functional cognitions. Using self-categorization theory we showed that opinion consensus perceptions flow from…

  6. Advertising, Consensus, and Aging in Multilayer Sznajd Model

    NASA Astrophysics Data System (ADS)

    Schulze, Christian

    In the Sznajd consensus model on the square lattice, two people who agree in their opinions convince their neighbors of this opinion. We generalize it to many layers representing many age levels, and check if a consensus among all layers is possible. Advertising sometimes, but not always, produces a consensus on the advertised opinion.

  7. 43 CFR 46.110 - Incorporating consensus-based management.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 1 2013-10-01 2013-10-01 false Incorporating consensus-based management... OF THE NATIONAL ENVIRONMENTAL POLICY ACT OF 1969 Protection and Enhancement of Environmental Quality § 46.110 Incorporating consensus-based management. (a) Consensus-based management incorporates...

  8. 43 CFR 46.110 - Incorporating consensus-based management.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 1 2014-10-01 2014-10-01 false Incorporating consensus-based management... OF THE NATIONAL ENVIRONMENTAL POLICY ACT OF 1969 Protection and Enhancement of Environmental Quality § 46.110 Incorporating consensus-based management. (a) Consensus-based management incorporates...

  9. 43 CFR 46.110 - Incorporating consensus-based management.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 1 2012-10-01 2011-10-01 true Incorporating consensus-based management... OF THE NATIONAL ENVIRONMENTAL POLICY ACT OF 1969 Protection and Enhancement of Environmental Quality § 46.110 Incorporating consensus-based management. (a) Consensus-based management incorporates...

  10. Group-consensus method and results

    SciTech Connect

    Meyer, M.A.; Peaslee, A.T. Jr.; Booker, J.M.

    1982-11-01

    This report focuses on the group consensus method, its application, results, and recommendations for future use. The method involves a group of qualified individuals who reach agreement on one answer after discussing the options in a face-to-face situation. The group method was used to elicit estimates on the relevance of weapon-related components to certain military threats or needs. In this study, the group consensus method was chosen from four possible methods to provide input data for a decision analysis model being tested for weapons-planning use. The major goal of the weapons-planning project was to determine the applicability of the decision anlaysis model, a modified linear utility model. This report examines whether the estimates (also referred to as weights) properly reflected the relationships between the components being judged. Statistical analysis (chi-square tests) indicated that the estimates were largely assigned according to the relationships between the components. Behavioral and cognitive factors could not be found to correlate to the assignment of the estimates. In sum, the group consensus method was judged suitable for situations in which a single estimate must be obtained from many estimates and stringent controls over the estimating process would be unacceptably burdensome.

  11. International consensus on ANA patterns (ICAP): the bumpy road towards a consensus on reporting ANA results.

    PubMed

    Damoiseaux, Jan; von Mühlen, Carlos A; Garcia-De La Torre, Ignacio; Carballo, Orlando Gabriel; de Melo Cruvinel, Wilson; Francescantonio, Paulo Luiz Carvalho; Fritzler, Marvin J; Herold, Manfred; Mimori, Tsuneyo; Satoh, Minoru; Andrade, Luis E C; Chan, Edward K L; Conrad, Karsten

    2016-12-01

    The International Consensus on ANA Patterns (ICAP) was initiated as a workshop aiming to thoroughly discuss and achieve consensus regarding the morphological patterns observed in the indirect immunofluorescence assay on HEp-2 cells. One of the topics discussed at the second ICAP workshop, and addressed in this paper, was the harmonization of reporting ANA test results. This discussion centered on the issue if cytoplasmic and mitotic patterns should be reported as positive or negative. This report outlines the issues that impact on two major different reporting methods. Although it was appreciated by all participants that cytoplasmic and mitotic patterns are clinically relevant, implications for existing diagnostic/classification criteria for ANA-associated diseases in particular hampered a final consensus on this topic. Evidently, a more concerted action of all relevant stakeholders is required. Future ICAP workshops may help to facilitate this action. PMID:26831867

  12. Deep sequencing of immune repertoires during bovine development and in response to respiratory pathogen challenge

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vertebrate immune systems generate diverse repertoires of antibodies capable of mediating response to a variety of antigens. Single-molecule circular consensus sequencing permits the sequencing of expressed antibody repertoires at previously unattainable depths of coverage and accuracy. We examined...

  13. Developing consensus criteria for sarcopenia: an update.

    PubMed

    McLean, Robert R; Kiel, Douglas P

    2015-04-01

    Sarcopenia, the age-related loss of muscle mass and strength, is a major cause of impaired physical function, which contributes to mobility disability, falls and hospitalizations in older adults. Lower muscle mass and strength are also associated with lower bone mineral density and greater risk for osteoporotic fractures. Thus, identification of sarcopenia could be important for fracture prevention as it may help improve fracture risk assessment, and muscle mass and strength can be improved with exercise, even among the frailest older adults. Unfortunately, there are no consensus diagnostic criteria for sarcopenia. Consequently there is no guidance to help clinicians identify older adults with clinically meaningful low muscle mass or weakness. Further, development of novel sarcopenia therapies is hindered not only due to the difficulty in identifying participants for clinical trials, and but also because there are no validated, clinically appropriate endpoints for assessment of treatment efficacy. There is currently a major push to establish a consensus definition of sarcopenia, and recent work holds promise that this goal may be within reach. This article discusses the evolution of the definition of sarcopenia, and focuses on the latest recommended diagnostic criteria proposed by the Foundation for the National Institutes of Health (FNIH) Sarcopenia Project. While these empirically-based cut-points for clinically important low muscle mass and weakness are a significant step forward for the sarcopenia field, important questions remain to be answered before consensus diagnostic criteria can be definitively established. Ongoing work to refine sarcopenia criteria will further advance the field and bring this important contributor to falls, fractures and disability into the mainstream of clinical care and ultimately lead to better quality of life with aging. PMID:25735999

  14. Pan-Serotype Diagnostic for Foot-and-Mouth Disease Using the Consensus Antigen of Nonstructural Protein 3B

    PubMed Central

    Van Dreumel, Alyssa K.; Michalski, Wojtek P.; McNabb, Leanne M.; Shiell, Brian J.; Singanallur, Nagendrakumar B.

    2015-01-01

    An amino acid consensus sequence for the seven serotypes of foot-and-mouth disease virus (FMDV) nonstructural protein 3B, including all three contiguous repeats, and its use in the development of a pan-serotype diagnostic test for all seven FMDV serotypes are described. The amino acid consensus sequence of the 3B protein was determined from a multiple-sequence alignment of 125 sequences of 3B. The consensus 3B (c3B) protein was expressed as a soluble recombinant fusion protein with maltose-binding protein (MBP) using a bacterial expression system and was affinity purified using amylose resin. The MBP-c3B protein was used as the antigen in the development of a competition enzyme-linked immunosorbent assay (cELISA) for detection of anti-3B antibodies in bovine sera. The comparative diagnostic sensitivity and specificity at 47% inhibition were estimated to be 87.22% and 93.15%, respectively. Reactivity of c3B with bovine sera representing the seven FMDV serotypes demonstrated the pan-serotype diagnostic capability of this bioreagent. The consensus antigen and competition ELISA are described here as candidates for a pan-serotype diagnostic test for FMDV infection. PMID:25788546

  15. Multiple chemical sensitivity: a 1999 consensus.

    PubMed

    1999-01-01

    Consensus criteria for the definition of multiple chemical sensitivity (MCS) were first identified in a 1989 multidisciplinary survey of 89 clinicians and researchers with extensive experience in, but widely differing views of, MCS. A decade later, their top 5 consensus criteria (i.e., defining MCS as [1] a chronic condition [2] with symptoms that recur reproducibly [3] in response to low levels of exposure [4] to multiple unrelated chemicals and [5] improve or resolve when incitants are removed) are still unrefuted in published literature. Along with a 6th criterion that we now propose adding (i.e., requiring that symptoms occur in multiple organ systems), these criteria are all commonly encompassed by research definitions of MCS. Nonetheless, their standardized use in clinical settings is still lacking, long overdue, and greatly needed--especially in light of government studies in the United States, United Kingdom, and Canada that revealed 2-4 times as many cases of chemical sensitivity among Gulf War veterans than undeployed controls. In addition, state health department surveys of civilians in New Mexico and California showed that 2-6%, respectively, already had been diagnosed with MCS and that 16% of the civilians reported an "unusual sensitivity" to common everyday chemicals. Given this high prevalence, as well as the 1994 consensus of the American Lung Association, American Medical Association, U.S. Environmental Protection Agency, and the U.S. Consumer Product Safety Commission that "complaints [of MCS] should not be dismissed as psychogenic, and a thorough workup is essential," we recommend that MCS be formally diagnosed--in addition to any other disorders that may be present--in all cases in which the 6 aforementioned consensus criteria are met and no single other organic disorder (e.g., mastocytosis) can account for all the signs and symptoms associated with chemical exposure. The millions of civilians and tens of thousands of Gulf War veterans who

  16. Consensus Paper: Neuroimmune Mechanisms of Cerebellar Ataxias.

    PubMed

    Mitoma, Hiroshi; Adhikari, Keya; Aeschlimann, Daniel; Chattopadhyay, Partha; Hadjivassiliou, Marios; Hampe, Christiane S; Honnorat, Jérôme; Joubert, Bastien; Kakei, Shinji; Lee, Jongho; Manto, Mario; Matsunaga, Akiko; Mizusawa, Hidehiro; Nanri, Kazunori; Shanmugarajah, Priya; Yoneda, Makoto; Yuki, Nobuhiro

    2016-04-01

    In the last few years, a lot of publications suggested that disabling cerebellar ataxias may develop through immune-mediated mechanisms. In this consensus paper, we discuss the clinical features of the main described immune-mediated cerebellar ataxias and address their presumed pathogenesis. Immune-mediated cerebellar ataxias include cerebellar ataxia associated with anti-GAD antibodies, the cerebellar type of Hashimoto's encephalopathy, primary autoimmune cerebellar ataxia, gluten ataxia, Miller Fisher syndrome, ataxia associated with systemic lupus erythematosus, and paraneoplastic cerebellar degeneration. Humoral mechanisms, cell-mediated immunity, inflammation, and vascular injuries contribute to the cerebellar deficits in immune-mediated cerebellar ataxias. PMID:25823827

  17. Anticoagulants: Major Advances Without Clear Consensus.

    PubMed

    Hohl, R J

    2016-08-01

    Therapeutics for thrombosis were discovered because of observations made nearly one hundred years ago. The mainstays of these treatments have been either heparin or warfarin, with the latter being preferred for long-term anticoagulation. In the last six years, newer agents with antigoagulant activities have been approved for clinical use. These agents have advantages and disadvantages over warfarin and consensus for their use is still being formed, as is the manner in which the more traditional agents, such as warfarin, should be used and monitored. PMID:27393187

  18. Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.).

    PubMed

    Cloutier, Sylvie; Ragupathy, Raja; Miranda, Evelyn; Radovanovic, Natasa; Reimer, Elsa; Walichnowski, Andrzej; Ward, Kerry; Rowland, Gordon; Duguid, Scott; Banik, Mitali

    2012-12-01

    Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1-52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence. PMID:22890805

  19. Consensus on biomarkers for neuroendocrine tumour disease

    PubMed Central

    Oberg, Kjell; Modlin, Irvin M; De Herder, Wouter; Pavel, Marianne; Klimstra, David; Frilling, Andrea; Metz, David C; Heaney, Anthony; Kwekkeboom, Dik; Strosberg, Jonathan; Meyer, Timothy; Moss, Steven F; Washington, Kay; Wolin, Edward; Liu, Eric; Goldenring, James

    2016-01-01

    Management of neuroendocrine neoplasia represents a clinical challenge because of its late presentation, lack of treatment options, and limitations in present imaging modalities and biomarkers to guide management. Monoanalyte biomarkers have poor sensitivity, specificity, and predictive ability. A National Cancer Institute summit, held in 2007, on neuroendocrine tumours noted biomarker limitations to be a crucial unmet need in the management of neuroendocrine tumours. A multinational consensus meeting of multidisciplinary experts in neuroendocrine tumours assessed the use of current biomarkers and defined the perquisites for novel biomarkers via the Delphi method. Consensus (at >75%) was achieved for 88 (82%) of 107 assessment questions. The panel concluded that circulating multianalyte biomarkers provide the highest sensitivity and specificity necessary for minimum disease detection and that this type of biomarker had sufficient information to predict treatment effectiveness and prognosis. The panel also concluded that no monoanalyte biomarker of neuroendocrine tumours has yet fulfilled these criteria and there is insufficient information to support the clinical use of miRNA or circulating tumour cells as useful prognostic markers for this disease. The panel considered that trials measuring multianalytes (eg, neuroendocrine gene transcripts) should also identify how such information can optimise the management of patients with neuroendocrine tumours. PMID:26370353

  20. Consensus physical activity guidelines for Asian Indians.

    PubMed

    Misra, Anoop; Nigam, Priyanka; Hills, Andrew P; Chadha, Davinder S; Sharma, Vineeta; Deepak, K K; Vikram, Naval K; Joshi, Shashank; Chauhan, Ashish; Khanna, Kumud; Sharma, Rekha; Mittal, Kanchan; Passi, Santosh Jain; Seth, Veenu; Puri, Seema; Devi, Ratna; Dubey, A P; Gupta, Sunita

    2012-01-01

    India is currently undergoing rapid economic, demographic, and lifestyle transformations. A key feature of the latter transformation has been inappropriate and inadequate diets and decreases in physical activity. Data from various parts of India have shown a steady increase in the prevalence of lifestyle-related diseases such as type 2 diabetes mellitus (T2DM), the metabolic syndrome, hypertension, coronary heart disease (CHD), etc., frequently in association with overweight or obesity. Comparative data show that Asian Indians are more sedentary than white Caucasians. In this review, the Consensus Group considered the available physical activity guidelines from international and Indian studies and formulated India-specific guidelines. A total of 60 min of physical activity is recommended every day for healthy Asian Indians in view of the high predisposition to develop T2DM and CHD. This should include at least 30 min of moderate-intensity aerobic activity, 15 min of work-related activity, and 15 min of muscle-strengthening exercises. For children, moderate-intensity physical activity for 60 min daily should be in the form of sport and physical activity. This consensus statement also includes physical activity guidelines for pregnant women, the elderly, and those suffering from obesity, T2DM, CHD, etc. Proper application of guidelines is likely to have a significant impact on the prevalence and management of obesity, the metabolic syndrome, T2DM, and CHD in Asian Indians. PMID:21988275

  1. International Consensus On (ICON) Pediatric Asthma

    PubMed Central

    Papadopoulos, N. G.; Arakawa, H.; Carlsen, K.-H.; Custovic, A.; Gern, J.; Lemanske, R.; Le Souef, P.; Makela, M.; Roberts, G.; Wong, G.; Zar, H.; Akdis, C. A.; Bacharier, L. B.; Baraldi, E.; van Bever, H. P.; de Blic, J.; Boner, A.; Burks, W.; Casale, T. B.; Castro-Rodriguez, J. A.; Chen, Y. Z.; El-Gamal, Y. M.; Everard, M. L.; Frischer, T.; Geller, M.; Gereda, J.; Goh, D. Y.; Guilbert, T. W.; Hedlin, G.; Heymann, P. W.; Hong, S. J.; Hossny, E. M.; Huang, J. L.; Jackson, D. J.; de Jongste, J. C.; Kalayci, O.; Khaled, N.; Kling, S.; Kuna, P.; Lau, S.; Ledford, D. K.; Lee, S. I.; Liu, A. H.; Lockey, R. F.; Lodrup-Carlsen, K.; Lotvall, J.; Morikawa, A.; Nieto, A.; Paramesh, H.; Pawankar, R.; Pohunek, P.; Pongracic, J.; Price, D.; Robertson, C.; Rosario, N.; Rossenwasser, L. J.; Sly, P. D.; Stein, R.; Stick, S.; Szefler, S.; Taussig, L. M.; Valovirta, E.; Vichyanond, P.; Wallace, D.; Weinberg, E.; Wennergren, G.; Wildhaber, J.; Zeiger, R. S.

    2015-01-01

    Asthma is the most common chronic lower respiratory disease in childhood throughout the world. Several guidelines and/or consensus documents are available to support medical decisions on pediatric asthma. Although there is no doubt that the use of common systematic approaches for management can considerably improve outcomes, dissemination and implementation of these are still major challenges. Consequently, the International Collaboration in Asthma, Allergy and Immunology (iCAALL), recently formed by the EAACI, AAAAI, ACAAI and WAO, has decided to propose an International Consensus on (ICON) Pediatric Asthma. The purpose of this document is to highlight the key messages that are common to many of the existing guidelines, while critically reviewing and commenting on any differences, thus providing a concise reference. The principles of pediatric asthma management are generally accepted. Overall, the treatment goal is disease control. In order to achieve this, patients and their parents should be educated to optimally manage the disease, in collaboration with health care professionals. Identification and avoidance of triggers is also of significant importance. Assessment and monitoring should be performed regularly to re-evaluate and fine-tune treatment. Pharmacotherapy is the cornerstone of treatment. The optimal use of medication can, in most cases, help patients control symptoms and reduce the risk for future morbidity. The management of exacerbations is a major consideration, independent from chronic treatment. There is a trend towards considering phenotype specific treatment choices; however this goal has not yet been achieved. PMID:22702533

  2. Global consensus on ADHD/HKD.

    PubMed

    Remschmidt, Helmut

    2005-05-01

    A Global ADHD Working Group of experienced clinicians and researchers was gathered to review the latest evidence, discuss current best practice in the treatment of attention-deficit/hyperactivity disorder (ADHD), and make a statement based on consensus. The statement aims to re-affirm ADHD as a valid disorder that exists across different cultures, has a significant global impact, and should be diagnosed and effectively treated wherever it occurs. ADHD is one of the most common neurobehavioural disorders of childhood and impacts on many aspects of development, including social, emotional and cognitive functioning, in the home and school environment. Although these findings are from developed countries, the impact in developing countries is likely to be similar. There is strong supportive evidence for the validity of ADHD as a syndrome with neurobiological aspects, and complex genetic factors are primarily implicated in the aetiology. Accurate diagnosis and measurement of impairment is important to enable appropriate and successful management of symptoms. ADHD is a persistent condition that needs to be treated and monitored over time. The evidence supporting medication-based interventions (such as methylphenidate) is strong and consensus treatment algorithms to guide the multimodal treatment of ADHD, alone and in combination with common comorbidities, are suggested. PMID:15959658

  3. Consensus Paper: Management of Degenerative Cerebellar Disorders

    PubMed Central

    Ilg, W.; Bastian, A. J.; Boesch, S.; Burciu, R. G.; Celnik, P.; Claaßen, J.; Feil, K.; Kalla, R.; Miyai, I.; Nachbauer, W.; Schöls, L.; Strupp, M.; Synofzik, M.; Teufel, J.

    2015-01-01

    Treatment of motor symptoms of degenerative cerebellar ataxia remains difficult. Yet there are recent developments that are likely to lead to significant improvements in the future. Most desirable would be a causative treatment of the underlying cerebellar disease. This is currently available only for a very small subset of cerebellar ataxias with known metabolic dysfunction. However, increasing knowledge of the pathophysiology of hereditary ataxia should lead to an increasing number of medically sensible drug trials. In this paper, data from recent drug trials in patients with recessive and dominant cerebellar ataxias will be summarized. There is consensus that up to date, no medication has been proven effective. Aminopyridines and acetazolamide are the only exception, which are beneficial in patients with episodic ataxia type 2. Aminopyridines are also effective in a subset of patients presenting with downbeat nystagmus. As such, all authors agreed that the mainstays of treatment of degenerative cerebellar ataxia are currently physiotherapy, occupational therapy, and speech therapy. For many years, well-controlled rehabilitation studies in patients with cerebellar ataxia were lacking. Data of recently published studies show that coordinative training improves motor function in both adult and juvenile patients with cerebellar degeneration. Given the well-known contribution of the cerebellum to motor learning, possible mechanisms underlying improvement will be outlined. There is consensus that evidence-based guidelines for the physiotherapy of degenerative cerebellar ataxia need to be developed. Future developments in physiotherapeutical interventions will be discussed including application of non-invasive brain stimulation. PMID:24222635

  4. Consensus in networks of mobile communicating agents

    NASA Astrophysics Data System (ADS)

    Baronchelli, Andrea; Díaz-Guilera, Albert

    2012-01-01

    Populations of mobile and communicating agents describe a vast array of technological and natural systems, ranging from sensor networks to animal groups. Here, we investigate how a group-level agreement may emerge in the continuously evolving network defined by the local interactions of the moving individuals. We adopt a general scheme of motion in two dimensions and we let the individuals interact through the minimal naming game, a prototypical scheme to investigate social consensus. We distinguish different regimes of convergence determined by the emission range of the agents and by their mobility, and we identify the corresponding scaling behaviors of the consensus time. In the same way, we rationalize also the behavior of the maximum memory used during the convergence process, which determines the minimum cognitive/storage capacity needed by the individuals. Overall, we believe that the simple and general model presented in this paper can represent a helpful reference for a better understanding of the behavior of populations of mobile agents.

  5. Consensus in evolving networks of mobile agents

    NASA Astrophysics Data System (ADS)

    Baronchelli, Andrea; Díaz-Guilera, Albert

    2012-02-01

    Populations of mobile and communicating agents describe a vast array of technological and natural systems, ranging from sensor networks to animal groups. Here, we investigate how a group-level agreement may emerge in the continuously evolving networks defined by the local interactions of the moving individuals. We adopt a general scheme of motion in two dimensions and we let the individuals interact through the minimal naming game, a prototypical scheme to investigate social consensus. We distinguish different regimes of convergence determined by the emission range of the agents and by their mobility, and we identify the corresponding scaling behaviors of the consensus time. In the same way, we rationalize also the behavior of the maximum memory used during the convergence process, which determines the minimum cognitive/storage capacity needed by the individuals. Overall, we believe that the simple and general model presented in this talk can represent a helpful reference for a better understanding of the behavior of populations of mobile agents.

  6. Consensus and ordering in language dynamics

    NASA Astrophysics Data System (ADS)

    Castelló, X.; Baronchelli, A.; Loreto, V.

    2009-10-01

    We consider two social consensus models, the AB-model and the Naming Game restricted to two conventions, which describe a population of interacting agents that can be in either of two equivalent states (A or B) or in a third mixed (AB) state. Proposed in the context of language competition and emergence, the AB state was associated with bilingualism and synonymy respectively. We show that the two models are equivalent in the mean field approximation, though the differences at the microscopic level have non-trivial consequences. To point them out, we investigate an extension of these dynamics in which confidence/trust is considered, focusing on the case of an underlying fully connected graph, and we show that the consensus-polarization phase transition taking place in the Naming Game is not observed in the AB model. We then consider the interface motion in regular lattices. Qualitatively, both models show the same behavior: a diffusive interface motion in a one-dimensional lattice, and a curvature driven dynamics with diffusing stripe-like metastable states in a two-dimensional one. However, in comparison to the Naming Game, the AB-model dynamics is shown to slow down the diffusion of such configurations.

  7. Military consensus behind Soviet arms control proposals

    SciTech Connect

    Weickhardt, G.C.

    1987-09-01

    For nearly two years General Secretary Mikhail Gorbachev has tried to entice the West with a spectacular array of arms control proposals and initiatives. On issues such as on-site inspections and European missile reductions, he has made such significant concessions over previous Soviet positions that questions have been raised, and not satisfactorily answered, about how much support Gorbachev's diplomacy enjoys among the Soviet military. For example, have Gorbachev's proposals been a bold personal gamble to achieve agreement without the prior approval of the Soviet military bureaucracy. Or does his arms control diplomacy represent a broad consensus among the military leadership and a realignment of Soviet military doctrine and grand strategy. A careful examination of recent Soviet military thought shows that such a consensus exists. A broad and stable coalition of key military leaders supports the General Secretary's policies. Moreover, recent Soviet concessions are not, as commonly argued, a stopgap ploy to halt the US Strategic Defense Initiative or Star Wars. Rather, the military's support for Gorbachev's arms-control diplomacy is based on some serious strategic analysis and stems from broad, fundamental, and enduring changes in Soviet national security policy.

  8. Consensus of expertise: the role of consensus of experts in formulating public policy and estimating facts.

    PubMed

    Veatch, R M

    1991-08-01

    For years analysts have recognized the error of assuming that experts in medical science are also experts in deciding the clinically correct course for patients. This paper extends the analysis of the use of the consensus of experts to their use in public policy groups such as NIH Consensus Development panels. After arguing that technical experts cannot be expected to be expert on public policy decisions, the author extends the criticism to the use of the consensus of experts in estimating facts to provide a basis for policy decisions. It is argued that to the extent that (a) experts' views regarding a body of facts can be expected to correlate with their values relevant to those facts; and (b) the values of experts differ from the values of lay people, even the estimates of the facts given by the consensus of expert panels can be expected to differ from the estimates lay people would have given had they had the relevant scientific expertise. PMID:1895026

  9. Consensus statement on palliative lung radiotherapy: third international consensus workshop on palliative radiotherapy and symptom control.

    PubMed

    Rodrigues, George; Macbeth, Fergus; Burmeister, Bryan; Kelly, Karie-Lynn; Bezjak, Andrea; Langer, Corey; Hahn, Carol; Movsas, Benjamin

    2012-01-01

    The purpose of this work is to disseminate a consensus statement on palliative radiotherapy (RT) of lung cancer created in conjunction with the Third International Lung Cancer Consensus Workshop. The palliative lung RT workshop committee agreed on 5 questions relating to (1) patient selection, (2) thoracic external-beam radiation therapy (XRT) fractionation, (3) endobronchial brachytherapy (EBB), (4) concurrent chemotherapy (CC), and (5) palliative endpoint definitions. A PubMed search for primary/cross-referenced practice guidelines, consensus statements, meta-analyses, and/or systematic reviews was conducted. Final consensus statements were created after review and discussion of the available evidence. The following summary statements reflect the consensus of the international working group. 1. Key factors involved in the decision to deliver palliative RT include performance status, tumor stage, pulmonary function, XRT volume, symptomatology, weight loss, and patient preference. 2. Palliative thoracic XRT is generally indicated for patients with stage IV disease with current/impending symptoms and for patients with stage III disease treated for palliative intent. 3. There is no evidence to routinely recommend EBB alone or in conjunction with other palliative maneuvers in the initial palliative management of endobronchial obstruction resulting from lung cancer. 4. There is currently no evidence to routinely recommend CC with palliative-intent RT. 5. Standard assessment of symptoms and health-related quality of life (QOL) using validated questionnaires should be carried out in palliative RT lung cancer trials. Despite an expanding literature, continued prospective randomized investigations to better define the role of XRT, EBB, and CC in the context of thoracic palliation of patients with lung cancer is needed. PMID:21729656

  10. Comparing Whole-Genome Sequencing with Sanger Sequencing for spa Typing of Methicillin-Resistant Staphylococcus aureus

    PubMed Central

    Petersen, Andreas; Worning, Peder; Nielsen, Jesper Boye; Larner-Svensson, Hanna; Johansen, Helle Krogh; Andersen, Leif Percival; Jarløv, Jens Otto; Boye, Kit; Larsen, Anders Rhod; Westh, Henrik

    2014-01-01

    spa typing of methicillin-resistant Staphylococcus aureus (MRSA) has traditionally been done by PCR amplification and Sanger sequencing of the spa repeat region. At Hvidovre Hospital, Denmark, whole-genome sequencing (WGS) of all MRSA isolates has been performed routinely since January 2013, and an in-house analysis pipeline determines the spa types. Due to national surveillance, all MRSA isolates are sent to Statens Serum Institut, where the spa type is determined by PCR and Sanger sequencing. The purpose of this study was to evaluate the reliability of the spa types obtained by 150-bp paired-end Illumina WGS. MRSA isolates from new MRSA patients in 2013 (n = 699) in the capital region of Denmark were included. We found a 97% agreement between spa types obtained by the two methods. All isolates achieved a spa type by both methods. Nineteen isolates differed in spa types by the two methods, in most cases due to the lack of 24-bp repeats in the whole-genome-sequenced isolates. These related but incorrect spa types should have no consequence in outbreak investigations, since all epidemiologically linked isolates, regardless of spa type, will be included in the single nucleotide polymorphism (SNP) analysis. This will reveal the close relatedness of the spa types. In conclusion, our data show that WGS is a reliable method to determine the spa type of MRSA. PMID:25297335

  11. Consensus, clinical decision making, and unsettled cases.

    PubMed

    Adams, David M; Winslade, William J

    2011-01-01

    The model of clinical ethics consultation (CEC) defended in the ASBH Core Competencies report has gained significant traction among scholars and healthcare providers. On this model, the aim of CEC is to facilitate deliberative reflection and thereby resolve conflicts and clarify value uncertainty by invoking and pursuing a process of consensus building. It is central to the model that the facilitated consensus falls within a range of allowable options, defined by societal values: prevailing legal requirements, widely endorsed organizational policies, and professional standards of practice and codes of conduct. Moreover, the model stipulates that ethics consultants must refrain from giving substantive recommendations regarding how parties to a moral disagreement in the clinic should evaluate their options. We argue that this model of CEC is incomplete, because it wrongly assumes that what counts as the proper set of allowable options among which the parties are to deliberate will itself always be clearly discernible. We illustrate this problem with a recent case on which one of us consulted-a neonate born with trisomy 18 (T18). We try to show that law, policy, and standards of practice reveal no clear answer to the question posed by the case: namely, whether forgoing gastrostomy tube feedings for a baby with T18 is allowable. We suggest there may be other kinds of cases in which it may simply be unsettled whether a given choice falls within the set of allowable options within which consensus is to be facilitated. What should an ethicist do when confronting such unsettled cases? We agree with the facilitation model that an ethicist should remain neutral among the allowable options, when it is clear what the allowable options are. But, in unsettled cases, the role of a consultant should be expanded to include a process of moral inquiry into what the allowable options should be. We end by raising the issue of whether this means an ethicist should share his or her own

  12. Consensus statements for screening and assessment tools.

    PubMed

    Bédard, Michel; Dickerson, Anne E

    2014-04-01

    Occupational therapists, both generalists and specialists, have a critical role in providing services to senior drivers. These services include evaluating fitness-to-drive, developing interventions to support community mobility, and facilitating the transition from driving to non-driving when necessary for personal and community safety. The evaluation component and decision-making process about fitness-to-drive are highly dependent on the use of screening and assessment tools. The purpose of this paper is to briefly present the rationale and context for 12 consensus statements about the usefulness and appropriateness of screening and assessment tools to determine fitness-to-drive, within the occupational therapy clinical setting, and their implications on community mobility. PMID:24754760

  13. The Consensus Molecular Subtypes of Colorectal Cancer

    PubMed Central

    Guinney, Justin; Dienstmann, Rodrigo; Wang, Xin; de Reyniès, Aurélien; Schlicker, Andreas; Soneson, Charlotte; Marisa, Laetitia; Roepman, Paul; Nyamundanda, Gift; Angelino, Paolo; Bot, Brian M.; Morris, Jeffrey S.; Simon, Iris M.; Gerster, Sarah; Fessler, Evelyn; de Sousa e Melo, Felipe; Missiaglia, Edoardo; Ramay, Hena; Barras, David; Homicsko, Krisztian; Maru, Dipen; Manyam, Ganiraju C.; Broom, Bradley; Boige, Valerie; Perez-Villamil, Beatriz; Laderas, Ted; Salazar, Ramon; Gray, Joe W.; Hanahan, Douglas; Tabernero, Josep; Bernards, Rene; Friend, Stephen H.; Laurent-Puig, Pierre; Medema, Jan Paul; Sadanandam, Anguraj; Wessels, Lodewyk; Delorenzi, Mauro; Kopetz, Scott; Vermeulen, Louis; Tejpar, Sabine

    2015-01-01

    Colorectal cancer (CRC) is a frequently lethal disease with heterogeneous outcomes and drug responses. To resolve inconsistencies among the reported gene expression–based CRC classifications and facilitate clinical translation, we formed an international consortium dedicated to large-scale data sharing and analytics across expert groups. We show marked interconnectivity between six independent classification systems coalescing into four consensus molecular subtypes (CMS) with distinguishing features: CMS1 (MSI Immune, 14%), hypermutated, microsatellite unstable, strong immune activation; CMS2 (Canonical, 37%), epithelial, chromosomally unstable, marked WNT and MYC signaling activation; CMS3 (Metabolic, 13%), epithelial, evident metabolic dysregulation; and CMS4 (Mesenchymal, 23%), prominent transforming growth factor β activation, stromal invasion, and angiogenesis. Samples with mixed features (13%) possibly represent a transition phenotype or intra-tumoral heterogeneity. We consider the CMS groups the most robust classification system currently available for CRC – with clear biological interpretability – and the basis for future clinical stratification and subtype–based targeted interventions. PMID:26457759

  14. Building a consensus about energy technologies

    NASA Astrophysics Data System (ADS)

    Wilbanks, T. J.

    1981-09-01

    The making and sustaining of major energy policy decisions are considered. The major policy alternatives for making energy decision-making more effective are outlined. The focus is on relatively large decisions about energy technologies. The policy alternatives are characterized as being either focused on technology or on social action. Technology focused options include technology choices and improvements. Social action focused options include information, incentives, legitimacy, and institutional changes. But it is clear that they pose several basic philosophical questions, such as whether to base decisions on strong central leadership or on broad consensus formation. And it is clear that the options vary in being best suited for business as usual situations or emergency decision making situations.

  15. Using Network Dynamical Influence to Drive Consensus

    NASA Astrophysics Data System (ADS)

    Punzo, Giuliano; Young, George F.; MacDonald, Malcolm; Leonard, Naomi E.

    2016-05-01

    Consensus and decision-making are often analysed in the context of networks, with many studies focusing attention on ranking the nodes of a network depending on their relative importance to information routing. Dynamical influence ranks the nodes with respect to their ability to influence the evolution of the associated network dynamical system. In this study it is shown that dynamical influence not only ranks the nodes, but also provides a naturally optimised distribution of effort to steer a network from one state to another. An example is provided where the “steering” refers to the physical change in velocity of self-propelled agents interacting through a network. Distinct from other works on this subject, this study looks at directed and hence more general graphs. The findings are presented with a theoretical angle, without targeting particular applications or networked systems; however, the framework and results offer parallels with biological flocks and swarms and opportunities for design of technological networks.

  16. Using Network Dynamical Influence to Drive Consensus.

    PubMed

    Punzo, Giuliano; Young, George F; Macdonald, Malcolm; Leonard, Naomi E

    2016-01-01

    Consensus and decision-making are often analysed in the context of networks, with many studies focusing attention on ranking the nodes of a network depending on their relative importance to information routing. Dynamical influence ranks the nodes with respect to their ability to influence the evolution of the associated network dynamical system. In this study it is shown that dynamical influence not only ranks the nodes, but also provides a naturally optimised distribution of effort to steer a network from one state to another. An example is provided where the "steering" refers to the physical change in velocity of self-propelled agents interacting through a network. Distinct from other works on this subject, this study looks at directed and hence more general graphs. The findings are presented with a theoretical angle, without targeting particular applications or networked systems; however, the framework and results offer parallels with biological flocks and swarms and opportunities for design of technological networks. PMID:27210291

  17. American National Standards: The Consensus Process

    NASA Technical Reports Server (NTRS)

    Schafer, Thom

    2000-01-01

    Since the early 20th Century, technical and professional societies have developed standards within their areas of expertise addressing aspects of their industries which they feel would benefit from a degree of standardization. From the beginning, the use of these standards was strictly voluntary. It did not take jurisdictional authorities long, however, to recognize that application of these voluntary standards enhanced public safety, as well as leveling the playing field in trade. Hence, laws were passed mandating their use. Purchasers of goods and services also recognized the advantages of standardization, and began requiring the use of standards in their procurement contracts. But how do jurisdictions and purchasers know that the standard they are mandating is a broad-based industry standard, or a narrowly focused set of rules which only apply to one company or institution, thereby giving them an unfair advantage? The answer is "consensus", and a unified approach in achieving it.

  18. Child abuser stereotypes: consensus among clinicians.

    PubMed

    Krowchuk, H V

    1989-02-01

    This article reports the results of an investigation of nurses' stereotypes of child abusers. Ninety-four registered nurses completed a questionnaire that measured subjects' knowledge of child abuse; professional contact with perpetrators and victims of abuse; knowledge of the causes of child abuse; and child abuser stereotypes. Results reveal a consensus among the subjects as to the stereotypes associated with child abusers. This study supports the notion that nurses stereotype individuals on the basis of demographic characteristics. This study also raises questions regarding the bias that may result from the use of child abuser stereotypes. Clinical decision-making processes could become compromised if biased judgements are used in planning nursing care for clients diagnosed as child abusers. PMID:2930179

  19. Using Network Dynamical Influence to Drive Consensus

    PubMed Central

    Punzo, Giuliano; Young, George F.; Macdonald, Malcolm; Leonard, Naomi E.

    2016-01-01

    Consensus and decision-making are often analysed in the context of networks, with many studies focusing attention on ranking the nodes of a network depending on their relative importance to information routing. Dynamical influence ranks the nodes with respect to their ability to influence the evolution of the associated network dynamical system. In this study it is shown that dynamical influence not only ranks the nodes, but also provides a naturally optimised distribution of effort to steer a network from one state to another. An example is provided where the “steering” refers to the physical change in velocity of self-propelled agents interacting through a network. Distinct from other works on this subject, this study looks at directed and hence more general graphs. The findings are presented with a theoretical angle, without targeting particular applications or networked systems; however, the framework and results offer parallels with biological flocks and swarms and opportunities for design of technological networks. PMID:27210291

  20. Robust point matching via vector field consensus.

    PubMed

    Jiayi Ma; Ji Zhao; Jinwen Tian; Yuille, Alan L; Zhuowen Tu

    2014-04-01

    In this paper, we propose an efficient algorithm, called vector field consensus, for establishing robust point correspondences between two sets of points. Our algorithm starts by creating a set of putative correspondences which can contain a very large number of false correspondences, or outliers, in addition to a limited number of true correspondences (inliers). Next, we solve for correspondence by interpolating a vector field between the two point sets, which involves estimating a consensus of inlier points whose matching follows a nonparametric geometrical constraint. We formulate this a maximum a posteriori (MAP) estimation of a Bayesian model with hidden/latent variables indicating whether matches in the putative set are outliers or inliers. We impose nonparametric geometrical constraints on the correspondence, as a prior distribution, using Tikhonov regularizers in a reproducing kernel Hilbert space. MAP estimation is performed by the EM algorithm which by also estimating the variance of the prior model (initialized to a large value) is able to obtain good estimates very quickly (e.g., avoiding many of the local minima inherent in this formulation). We illustrate this method on data sets in 2D and 3D and demonstrate that it is robust to a very large number of outliers (even up to 90%). We also show that in the special case where there is an underlying parametric geometrical model (e.g., the epipolar line constraint) that we obtain better results than standard alternatives like RANSAC if a large number of outliers are present. This suggests a two-stage strategy, where we use our nonparametric model to reduce the size of the putative set and then apply a parametric variant of our approach to estimate the geometric parameters. Our algorithm is computationally efficient and we provide code for others to use it. In addition, our approach is general and can be applied to other problems, such as learning with a badly corrupted training data set. PMID:24808341

  1. A healthy bladder: a consensus statement

    PubMed Central

    Lukacz, E S; Sampselle, C; Gray, M; MacDiarmid, S; Rosenberg, M; Ellsworth, P; Palmer, M H

    2011-01-01

    A panel of experts in urology, urogynecology, nursing, and behavioral therapy convened in 2010 to discuss the importance of a healthy bladder on overall health. They determined that a consensus statement was necessary to raise awareness among the general public, healthcare providers, payors, and policymakers, with the goals of minimizing the impact of poor bladder health and stimulating primary prevention of bladder conditions. In this statement, ‘healthy’ bladder function is described, as well as internal and external factors that influence bladder health. It is suggested that primary prevention strategies should be aimed at providing education regarding normal lower urinary tract structures and functioning to the public, including patients and healthcare providers. This education may promote the achievement of optimal bladder health by increasing healthy bladder habits and behaviors, awareness of risk factors, healthcare seeking, and clinician engagement and reducing stigma and other barriers to treatment. Promoting optimal bladder health may reduce the personal, societal and economic impact of bladder conditions, including anxiety and depression and costs associated with conditions or diseases and their treatment. While adopting healthy bladder habits and behaviors and behaviors may improve or maintain bladder health, it is important to recognize that certain symptoms may indicate the presence of conditions that require medical attention; many bladder conditions are treatable with a range of options for most bladder conditions. Lastly, the authors propose clinical directives based on persuasive and convergent research to improve and maintain bladder health. The authors hope that this statement will lead to promotion and achievement of optimal bladder health, which may improve overall health and help minimize the effects of bladder conditions on the public, healthcare professionals, educators, employers, and payors. The advisors are in consensus regarding the

  2. Consensus on precision medicine for metastatic cancers: a report from the MAP conference.

    PubMed

    Swanton, C; Soria, J-C; Bardelli, A; Biankin, A; Caldas, C; Chandarlapaty, S; de Koning, L; Dive, C; Feunteun, J; Leung, S-Y; Marais, R; Mardis, E R; McGranahan, N; Middleton, G; Quezada, S A; Rodón, J; Rosenfeld, N; Sotiriou, C; André, F

    2016-08-01

    Recent advances in biotechnologies have led to the development of multiplex genomic and proteomic analyses for clinical use. Nevertheless, guidelines are currently lacking to determine which molecular assays should be implemented in metastatic cancers. The first MAP conference was dedicated to exploring the use of genomics to better select therapies in the treatment of metastatic cancers. Sixteen consensus items were covered. There was a consensus that new technologies like next-generation sequencing of tumors and ddPCR on circulating free DNA have convincing analytical validity. Further work needs to be undertaken to establish the clinical utility of liquid biopsies and the added clinical value of expanding from individual gene tests into large gene panels. Experts agreed that standardized bioinformatics methods for biological interpretation of genomic data are needed and that precision medicine trials should be stratified based on the level of evidence available for the genomic alterations identified. PMID:27143638

  3. Detection and analysis of diverse herpesviral species by consensus primer PCR.

    PubMed Central

    VanDevanter, D R; Warrener, P; Bennett, L; Schultz, E R; Coulter, S; Garber, R L; Rose, T M

    1996-01-01

    A consensus primer PCR method which amplifies a region of herpesviral DNA-directed DNA polymerase (EC 2.7.7.7) and which uses degenerate primers in a nested format was developed. Primers were designed to target sequences coding for highly conserved amino acid motifs covering a region of approximately 800 bp. The assay was applied to 22 species of herpesviruses (8 human and 14 animal viruses), with PCR products obtained for 21 of 22 viruses. In the process, 14 previously unreported amino acid-coding sequences from herpesviral DNA polymerases were obtained, including regions of human herpesviruses 7 and 8. The 50 to 60 amino acid-coding sequences recovered in the present study were determined to be unique to each viral species studied, with very little sequence variation between strains of a single species when studied. Template dilution studies in the presence of human carrier DNA demonstrated that six human herpesviruses (herpesviruses 1, 2, 3, 4, 5, and 6B) could be detected at levels at or below 100 genome equivalents per 100 ng of carrier DNA. These data suggest that consensus primer PCR targeted to herpesviral DNA polymerase may prove to be useful in the detection and identification of known herpesviruses in clinical samples and the initial characterization of new herpesviral genomes. PMID:8784566

  4. Identification of DVA Interneuron Regulatory Sequences in Caenorhabditis elegans

    PubMed Central

    Puckett Robinson, Carmie; Schwarz, Erich M.; Sternberg, Paul W.

    2013-01-01

    Background The identity of each neuron is determined by the expression of a distinct group of genes comprising its terminal gene battery. The regulatory sequences that control the expression of such terminal gene batteries in individual neurons is largely unknown. The existence of a complete genome sequence for C. elegans and draft genomes of other nematodes let us use comparative genomics to identify regulatory sequences directing expression in the DVA interneuron. Methodology/Principal Findings Using phylogenetic comparisons of multiple Caenorhabditis species, we identified conserved non-coding sequences in 3 of 10 genes (fax-1, nmr-1, and twk-16) that direct expression of reporter transgenes in DVA and other neurons. The conserved region and flanking sequences in an 85-bp intronic region of the twk-16 gene directs highly restricted expression in DVA. Mutagenesis of this 85 bp region shows that it has at least four regions. The central 53 bp region contains a 29 bp region that represses expression and a 24 bp region that drives broad neuronal expression. Two short flanking regions restrict expression of the twk-16 gene to DVA. A shared GA-rich motif was identified in three of these genes but had opposite effects on expression when mutated in the nmr-1 and twk-16 DVA regulatory elements. Conclusions/Significance We identified by multi-species conservation regulatory regions within three genes that direct expression in the DVA neuron. We identified four contiguous regions of sequence of the twk-16 gene enhancer with positive and negative effects on expression, which combined to restrict expression to the DVA neuron. For this neuron a single binding site may thus not achieve sufficient specificity for cell specific expression. One of the positive elements, an 8-bp sequence required for expression was identified in silico by sequence comparisons of seven nematode species, demonstrating the potential resolution of expanded multi-species phylogenetic comparisons. PMID

  5. Definition of a consensus transportin-specific nucleocytoplasmic transport signal.

    PubMed

    Bogerd, H P; Benson, R E; Truant, R; Herold, A; Phingbodhipakkiya, M; Cullen, B R

    1999-04-01

    The low cytoplasmic and high nuclear concentration of the GTP-bound form of Ran provides directionality for both nuclear protein import and export. Both import and export factors bind RanGTP directly, yet this interaction produces opposite effects; in the former case, RanGTP binding induces nuclear cargo release, whereas in the latter, RanGTP binding induces nuclear cargo assembly. Therefore, nuclear import and export receptors and their protein recognition sites are predicted to be distinct. Nevertheless, the approximately 38-amino acid M9 sequence present in heterogeneous nuclear ribonucleoprotein A1 has been reported to serve as both a nuclear localization signal and a nuclear export signal, even though only one protein, the nuclear import factor transportin, has been shown to bind M9 directly. We have used a combination of mutational randomization followed by selection for transportin binding to exhaustively define amino acids in M9 that are critical for transportin binding in vivo. As expected, the resultant approximately 12-amino acid transportin-binding consensus sequence is also predictive of nuclear localization signal activity. Surprisingly, however, this extensive mutational analysis failed to dissect M9 nuclear localization signal and nuclear export signal function. Nevertheless, transportin appears unlikely to be the M9 export receptor, as RanGTP can be shown to block M9 binding by transportin not only in vitro, but also in the nucleus in vivo. This analysis therefore predicts the existence of a nuclear export receptor distinct from transportin that nevertheless shares a common protein-binding site on heterogeneous nuclear ribonucleoprotein A1. PMID:10092666

  6. Ensemble distribution models in conservation prioritization: from consensus predictions to consensus reserve networks

    PubMed Central

    Meller, Laura; Cabeza, Mar; Pironon, Samuel; Barbet-Massin, Morgane; Maiorano, Luigi; Georges, Damien; Thuiller, Wilfried

    2014-01-01

    Aim Conservation planning exercises increasingly rely on species distributions predicted either from one particular statistical model or, more recently, from an ensemble of models (i.e. ensemble forecasting). However, it has not yet been explored how different ways of summarizing ensemble predictions affect conservation planning outcomes. We evaluate these effects and compare commonplace consensus methods, applied before the conservation prioritization phase, to a novel method that applies consensus after reserve selection. Location Europe. Methods We used an ensemble of predicted distributions of 146 Western Palaearctic bird species in alternative ways: four different consensus methods, as well as distributions discounted with variability, were used to produce inputs for spatial conservation prioritization. In addition, we developed and tested a novel method, in which we built 100 datasets by sampling the ensemble of predicted distributions, ran a conservation prioritization analysis on each of them and averaged the resulting priority ranks. We evaluated the conservation outcome against three controls: (i) a null control, based on random ranking of cells; (2) the reference solution, based on an expert-refined dataset; and (3) the independent solution, based on an independent dataset. Results Networks based on predicted distributions were more representative of rare species than randomly selected networks. Alternative methods to summarize ensemble predictions differed in representativeness of resulting reserve networks. Our novel method resulted in better representation of rare species than pre-selection consensus methods. Main conclusions Retaining information about the variation in the predicted distributions throughout the conservation prioritization seems to provide better results than summarizing the predictions before conservation prioritization. Our results highlight the need to understand and consider model-based uncertainty when using predicted

  7. Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions

    PubMed Central

    Thanaraj, T. A.; Clark, Francis

    2001-01-01

    It has been previously observed that the intrinsically weak variant GC donor sites, in order to be recognized by the U2-type spliceosome, possess strong consensus sequences maximized for base pair formation with U1 and U5/U6 snRNAs. However, variability in signal strength is a fundamental mechanism for splice site selection in alternative splicing. Here we report human alternative GC-AG introns (for the first time from any species), and show that while constitutive GC-AG introns do possess strong signals at their donor sites, a large subset of alternative GC-AG introns possess weak consensus sequences at their donor sites. Surprisingly, this subset of alternative isoforms shows strong consensus at acceptor exon positions 1 and 2. The improved consensus at the acceptor exon can facilitate a strong interaction with U5 snRNA, which tethers the two exons for ligation during the second step of splicing. Further, these isoforms nearly always possess alternative acceptor sites and exhibit particularly weak polypyrimidine tracts characteristic of AG-dependent introns. The acceptor exon nucleotides are part of the consensus required for the U2AF35-mediated recognition of AG in such introns. Such improved consensus at acceptor exons is not found in either normal or alternative GT-AG introns having weak donor sites or weak polypyrimidine tracts. The changes probably reflect mechanisms that allow GC-AG alternative intron isoforms to cope with two conflicting requirements, namely an apparent need for differential splice strength to direct the choice of alternative sites and a need for improved donor signals to compensate for the central mismatch base pair (C-A) in the RNA duplex of U1 snRNA and the pre-mRNA. The other important findings include (i) one in every twenty alternative introns is a GC-AG intron, and (ii) three of every five observed GC-AG introns are alternative isoforms. PMID:11410667

  8. Is Liberalism Strong Enough for a Moral Consensus?

    ERIC Educational Resources Information Center

    Wilson, John

    1990-01-01

    Argues that liberalism is strong enough to sustain a moral consensus if its logic and psychological bases are understood. Rejects ideological positions, emphasizing the value of rational discourse for reaching consensus. Encourages liberal educators to make clear their commitment to a liberalism that avoids both authoritarianism and paranoia. (CH)

  9. Part Two: Infantile Spasms--The New Consensus

    ERIC Educational Resources Information Center

    Pellock, John M.; O'Hara, Kathryn

    2011-01-01

    This article presents the conclusion made by the consensus group regarding infantile spasms. The consensus group concluded that "infantile spasms are a major form of severe epileptic encephalopathy of early childhood that results in neurodevelopmental regression and imposes a significant health burden." The entire group agrees that the best…

  10. The Consensus Definition Redefined from a Representational Perspective

    ERIC Educational Resources Information Center

    Zand Scholten, Annemarie

    2012-01-01

    This paper presents the author's critique to Paul E. Newton's article titled "Clarifying the consensus definition of validity." In his article, Newton not only clarifies but also redefines the consensus definition of validity. In this redefinition he omits the term "construct" and introduces the term "measurement." Both omission and introduction…

  11. Consensus networks with time-delays over finite fields

    NASA Astrophysics Data System (ADS)

    Li, Xiuxian; Su, Housheng; Chen, Michael Z. Q.

    2016-05-01

    In this paper, we investigate the consensus problem in networks with time-delays over finite fields. The delays are categorised into three cases: single constant delay, multiple constant delays, and time-varying bounded delays. For all cases, some sufficient and necessary conditions for consensus are derived. Furthermore, assuming that the communication graph is strongly connected, some of the obtained necessary conditions reveal that the conditions for consensus with time-delays over finite fields depend not only on the diagonal entries but also on the off-diagonal entries, something that is intrinsically distinct from the case over real numbers (where having at least one nonzero diagonal entry is a sufficient and necessary condition to guarantee consensus). In addition, it is shown that delayed networks cannot achieve consensus when the interaction graph is a tree if the corresponding delay-free networks cannot reach consensus, which is consistent with the result over real numbers. As for average consensus, we show that it can never be achieved for delayed networks over finite fields, although it indeed can be reached under several conditions for delay-free networks over finite fields. Finally, networks with time-varying delays are discussed and one sufficient condition for consensus is presented by graph-theoretic method.

  12. Rural/Urban Elderly and Siblings: Their Value Consensus.

    ERIC Educational Resources Information Center

    Suggs, Patricia K.; Kivett, Vira R.

    Consensus has been identified as a dimension of family solidarity with important implications for the family network. To investigate the factors contributing to consensus between older adults and their sibling of most contact, 275 adults (173 females, 102 males), with a mean age of 74 years, were interviewed using a questionnaire covering work and…

  13. 77 FR 24251 - Consensus Standards, Light-Sport Aircraft

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-23

    ... Federal Aviation Administration Consensus Standards, Light-Sport Aircraft AGENCY: Federal Aviation... availability of three new and three revised consensus standards relating to the provisions of the Sport Pilot and Light-Sport Aircraft rule issued July 16, 2004, and effective September 1, 2004....

  14. 78 FR 35085 - Consensus Standards, Light-Sport Aircraft

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-11

    ... Federal Aviation Administration Consensus Standards, Light-Sport Aircraft AGENCY: Federal Aviation... availability of one new and seven revised consensus standards relating to the provisions of the Sport Pilot and Light-Sport Aircraft rule issued July 16, 2004, and effective September 1, 2004. ASTM...

  15. Fast second-order consensus via predictive mechanisms

    NASA Astrophysics Data System (ADS)

    Wu, Jie; Zhang, Li-Yi; Bai, Yu

    2015-01-01

    In this paper, we discuss second-order consensus problems for multi-agent systems with dynamic agents and fixed topologies. A new second-order consensus protocol incorporating the predictive mechanism is proposed and a convergence analysis related to the real and imaginary parts of the eigenvalues of the Laplacian matrix of the corresponding network is provided. We establish a direct connection between the eigenvalues of the Laplacian matrix and parameters of the proposed second-order consensus model, and we compute a lower bound for the sum of parameters. It is proved under general conditions related to the second-order consensus protocol and the network topology that the asymptotic consensus is achieved and the convergence speed is increased via designing a state predictor. Finally, simulation results are provided to verify the effectiveness of the proposed protocol and the analytical claims.

  16. Joining consensus of networked multi-agent systems with nonlinear couplings and weighting constraints

    NASA Astrophysics Data System (ADS)

    Wang, Bohui; Wang, Jingcheng; Zhang, Langwen; Ge, Yang

    2016-04-01

    This paper studies the joining consensus of networked multi-agent systems subject to nonlinear couplings and weighted directed graphs via pinning control. A weighted-average consensus protocol is proposed to achieve the collective decision by interacting with the local information of some pinned agents. By proposing a novel joining consensus protocol, average consensus and general consensus strategies are joined to achieve an agreement for the weighting networked system. Furthermore, by calculating a proper consensus gain and using finite control Lyapunov controllers, an efficient joining consensus protocol is presented to improve the consensus speed. Sufficient conditions for achieving the consensuses asymptotically are proved. Finally, theoretical results are validated via simulations.

  17. The role of fanatics in consensus formation

    NASA Astrophysics Data System (ADS)

    Gündüç, Semra

    2015-08-01

    A model of opinion dynamics with two types of agents as social actors are presented, using the Ising thermodynamic model as the dynamics template. The agents are considered as opportunists which live at sites and interact with the neighbors, or fanatics/missionaries which move from site to site randomly in persuasion of converting agents of opposite opinion with the help of opportunists. Here, the moving agents act as an external influence on the opportunists to convert them to the opposite opinion. It is shown by numerical simulations that such dynamics of opinion formation may explain some details of consensus formation even when one of the opinions are held by a minority. Regardless the distribution of the opinion, different size societies exhibit different opinion formation behavior and time scales. In order to understand general behavior, the scaling relations obtained by comparing opinion formation processes observed in societies with varying population and number of randomly moving agents are studied. For the proposed model two types of scaling relations are observed. In fixed size societies, increasing the number of randomly moving agents give a scaling relation for the time scale of the opinion formation process. The second type of scaling relation is due to the size dependent information propagation in finite but large systems, namely finite-size scaling.

  18. Managing Carious Lesions: Consensus Recommendations on Terminology.

    PubMed

    Innes, N P T; Frencken, J E; Bjørndal, L; Maltz, M; Manton, D J; Ricketts, D; Van Landuyt, K; Banerjee, A; Campus, G; Doméjean, S; Fontana, M; Leal, S; Lo, E; Machiulskiene, V; Schulte, A; Splieth, C; Zandona, A; Schwendicke, F

    2016-05-01

    Variation in the terminology used to describe clinical management of carious lesions has contributed to a lack of clarity in the scientific literature and beyond. In this article, the International Caries Consensus Collaboration presents 1) issues around terminology, a scoping review of current words used in the literature for caries removal techniques, and 2) agreed terms and definitions, explaining how these were decided.Dental cariesis the name of the disease, and thecarious lesionis the consequence and manifestation of the disease-the signs or symptoms of the disease. The termdental caries managementshould be limited to situations involving control of the disease through preventive and noninvasive means at a patient level, whereascarious lesion managementcontrols the disease symptoms at the tooth level. While it is not possible to directly relate the visual appearance of carious lesions' clinical manifestations to the histopathology, we have based the terminology around the clinical consequences of disease (soft, leathery, firm, and hard dentine). Approaches to carious tissue removal are defined: 1)selective removal of carious tissue-includingselective removal to soft dentineandselective removal to firm dentine; 2)stepwise removal-including stage 1,selective removal to soft dentine, and stage 2,selective removal to firm dentine6 to 12 mo later; and 3)nonselective removal to hard dentine-formerly known ascomplete caries removal(technique no longer recommended). Adoption of these terms, around managing dental caries and its sequelae, will facilitate improved understanding and communication among researchers and within dental educators and the wider clinical dentistry community. PMID:27099357

  19. Parma consensus statement on metabolic disruptors.

    PubMed

    Heindel, Jerrold J; vom Saal, Frederick S; Blumberg, Bruce; Bovolin, Patrizia; Calamandrei, Gemma; Ceresini, Graziano; Cohn, Barbara A; Fabbri, Elena; Gioiosa, Laura; Kassotis, Christopher; Legler, Juliette; La Merrill, Michele; Rizzir, Laura; Machtinger, Ronit; Mantovani, Alberto; Mendez, Michelle A; Montanini, Luisa; Molteni, Laura; Nagel, Susan C; Parmigiani, Stefano; Panzica, Giancarlo; Paterlini, Silvia; Pomatto, Valentina; Ruzzin, Jérôme; Sartor, Giorgio; Schug, Thaddeus T; Street, Maria E; Suvorov, Alexander; Volpi, Riccardo; Zoeller, R Thomas; Palanza, Paola

    2015-01-01

    A multidisciplinary group of experts gathered in Parma Italy for a workshop hosted by the University of Parma, May 16-18, 2014 to address concerns about the potential relationship between environmental metabolic disrupting chemicals, obesity and related metabolic disorders. The objectives of the workshop were to: 1. Review findings related to the role of environmental chemicals, referred to as "metabolic disruptors", in obesity and metabolic syndrome with special attention to recent discoveries from animal model and epidemiology studies; 2. Identify conclusions that could be drawn with confidence from existing animal and human data; 3. Develop predictions based on current data; and 4. Identify critical knowledge gaps and areas of uncertainty. The consensus statements are intended to aid in expanding understanding of the role of metabolic disruptors in the obesity and metabolic disease epidemics, to move the field forward by assessing the current state of the science and to identify research needs on the role of environmental chemical exposures in these diseases. We propose broadening the definition of obesogens to that of metabolic disruptors, to encompass chemicals that play a role in altered susceptibility to obesity, diabetes and related metabolic disorders including metabolic syndrome. PMID:26092037

  20. Bleeding Avoidance Strategies: Consensus and Controversy

    PubMed Central

    Dauerman, Harold L.; Rao, Sunil V.; Resnic, Frederic S.; Applegate, Robert J.

    2011-01-01

    Bleeding complications after coronary intervention are associated with prolonged hospitalization, increased hospital costs, patient dissatisfaction, morbidity and one year mortality. Bleeding Avoidance Strategies represent a term incorporating multiple modalities that aim to reduce bleeding and vascular complications after cardiovascular catheterization. Recent improvements in the rates of bleeding complications after invasive cardiovascular procedures suggests that the clinical community has successfully embraced specific strategies and improved patient care in this area. There remains controversy regarding the efficacy, safety and/or practicality of 3 key bleeding avoidance strategies for cardiac catheterization and coronary intervention: procedural (radial artery approach, safezone arteriotomy), pharmacologic (multiple agents) and technological (vascular closure devices) approaches to improved access. In this article, we address areas of consensus with respect to selected modalities in order to define the role of each strategy in current practice. Furthermore, we focus on areas of controversy for selected modalities in order to define key areas warranting cautious clinical approaches and the need for future randomized clinical trials in this area. PMID:21700085

  1. Prediction of collective opinion in consensus formation

    NASA Astrophysics Data System (ADS)

    Hou, Lei; Liu, Jianguo; Pan, Xue; Song, Wen-Jun; Li, Xu-Dong

    2014-12-01

    In the consensus formation dynamics, the effect of leaders and interventions have been widely studied for it has many applications such as in politics and commerce. However, the problem is how to know if it is necessary for one to make an intervention. In this paper, we theoretically propose a method for predicting the tendency and final state of collective opinion. By giving each agent a conviction ci which measures the ability to insist on his opinion, we present an opinion formation model in which agents with high convictions naturally show up properties of the opinion leaders. Results reveal that, although each agent initially gets an opinion evenly distributed in the range [-1, 1], the collective opinion of the steady-state may deviate to the positive or negative direction because of the initial bias of the leaders' opinions. We further get the correlation coefficient of the linear relationship between the collective opinion and the initial bias according to both the experimental and theoretical analysis. Thus, we could predict the final state at the very beginning of the dynamic only if we get the opinions of a small portion of the population. The prediction would afford us more time and opportunities to make reactions and interventions.

  2. [New argentine consensus of respiratory rehabilitation 2008].

    PubMed

    Sívori, Martín; Almeida, Marta; Benzo, Roberto; Boim, Clarisa; Brassesco, Marisa; Callejas, Osvaldo; Capparelli, Ignacio; Conti, Ernesto; Díaz, Mariano; Draghi, Jorge; Franco, Javier; Gando, Sebastián; Giuliano, Germán; Guida, Roxana; Jolly, Enrique; Pessolano, Fernando; Rabinovich, Roberto; Ratto, Patricia; Rhodius, Edgardo; Saadia, Marcela; Salvado, Alejandro; Sobrino, Edgardo; Victorio, Carlos

    2008-01-01

    Respiratory rehabilitation (RR) is a multidisciplinary program of care for patients with chronic respiratory impairment, individually tailored, designed to optimize physical and social performance and patient autonomy. It is particularly indicated in chronic obstructive pulmonary disease (COPD) patients with exercise intolerance. The objectives of respiratory rehabilitation are: reduction in symptoms and exercise intolerance, improvement of health-related quality of life, and reduction of health costs. A group of neumonologists, nutritionists and physical therapists performed a systematic review of the evidence in RR to update previous local guidelines. Inclusion and exclusion criteria, guidelines for initial evaluation and follow up and resources needed are defined. Training characteristics are recommended regarding frequency of the visits, intensity, progression and duration of the exercise training. Aerobic training was recommended for lower limb (1A), upper limb (1B). Strength training must be added (1B). Respiratory muscle training and other physiotherapy techniques were recommended only for specific patients (1C). In addition recommendations have been made for educational objectives of the program including smoking cessation, nutritional and psychological support. The positive impact of RR on reductions of health care costs and reductions on hospitalizations (Evidence A) and mortality (Evidence B) were analized. Respiratory rehabilitation is a key component in the modern treatment of COPD patients. This consensus statement was prepared based on the most recent scientific evidence and adjusted to the local environment with the aim of being implemented nationally. PMID:18786894

  3. Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions

    PubMed Central

    Tang, Rongying; Prosser, Debra O.; Love, Donald R.

    2016-01-01

    The increasing diagnostic use of gene sequencing has led to an expanding dataset of novel variants that lie within consensus splice junctions. The challenge for diagnostic laboratories is the evaluation of these variants in order to determine if they affect splicing or are merely benign. A common evaluation strategy is to use in silico analysis, and it is here that a number of programmes are available online; however, currently, there are no consensus guidelines on the selection of programmes or protocols to interpret the prediction results. Using a collection of 222 pathogenic mutations and 50 benign polymorphisms, we evaluated the sensitivity and specificity of four in silico programmes in predicting the effect of each variant on splicing. The programmes comprised Human Splice Finder (HSF), Max Entropy Scan (MES), NNSplice, and ASSP. The MES and ASSP programmes gave the highest performance based on Receiver Operator Curve analysis, with an optimal cut-off of score reduction of 10%. The study also showed that the sensitivity of prediction is affected by the level of conservation of individual positions, with in silico predictions for variants at positions −4 and +7 within consensus splice sites being largely uninformative. PMID:27313609

  4. Consensus definitions of 14 severe acute toxic effects for childhood lymphoblastic leukaemia treatment: a Delphi consensus.

    PubMed

    Schmiegelow, Kjeld; Attarbaschi, Andishe; Barzilai, Shlomit; Escherich, Gabriele; Frandsen, Thomas Leth; Halsey, Christina; Hough, Rachael; Jeha, Sima; Kato, Motohiro; Liang, Der-Cherng; Mikkelsen, Torben Stamm; Möricke, Anja; Niinimäki, Riitta; Piette, Caroline; Putti, Maria Caterina; Raetz, Elizabeth; Silverman, Lewis B; Skinner, Roderick; Tuckuviene, Ruta; van der Sluis, Inge; Zapotocka, Ester

    2016-06-01

    Although there are high survival rates for children with acute lymphoblastic leukaemia, their outcome is often counterbalanced by the burden of toxic effects. This is because reported frequencies vary widely across studies, partly because of diverse definitions of toxic effects. Using the Delphi method, 15 international childhood acute lymphoblastic leukaemia study groups assessed acute lymphoblastic leukaemia protocols to address toxic effects that were to be considered by the Ponte di Legno working group. 14 acute toxic effects (hypersensitivity to asparaginase, hyperlipidaemia, osteonecrosis, asparaginase-associated pancreatitis, arterial hypertension, posterior reversible encephalopathy syndrome, seizures, depressed level of consciousness, methotrexate-related stroke-like syndrome, peripheral neuropathy, high-dose methotrexate-related nephrotoxicity, sinusoidal obstructive syndrome, thromboembolism, and Pneumocystis jirovecii pneumonia) that are serious but too rare to be addressed comprehensively within any single group, or are deemed to need consensus definitions for reliable incidence comparisons, were selected for assessment. Our results showed that none of the protocols addressed all 14 toxic effects, that no two protocols shared identical definitions of all toxic effects, and that no toxic effect definition was shared by all protocols. Using the Delphi method over three face-to-face plenary meetings, consensus definitions were obtained for all 14 toxic effects. In the overall assessment of outcome of acute lymphoblastic leukaemia treatment, these expert opinion-based definitions will allow reliable comparisons of frequencies and severities of acute toxic effects across treatment protocols, and facilitate international research on cause, guidelines for treatment adaptation, preventive strategies, and development of consensus algorithms for reporting on acute lymphoblastic leukaemia treatment. PMID:27299279

  5. Status of conversion of NE standards to national consensus standards

    SciTech Connect

    Jennings, S.D.

    1991-07-01

    One major goal of the Nuclear Standards Program is to convert existing Nuclear Energy (NE) standards into national consensus standards (where possible). This means that an NE standard may form the basis for a standards-writing committee to produce a standard in the same subject area using the national consensus process. This report is a summary of the activities that have evolved to effect conversion of NE standards to national consensus standards, and the status of current conversion activities. In some cases, all requirements in an NE standard will not be incorporated into the published national consensus standard because these requirements may be considered too restrictive or too specific for broader applications by the nuclear industry. If these requirements are considered necessary for nuclear reactor program applications, the program standard will be revised and issued as a supplement to the national consensus standard. The supplement program standard will contain only those necessary requirements not reflected by the national consensus standard. Therefore, while complete conversion of program standards may not always be realized, the standards policy has been fully supported in attempting to make maximum use of the national consensus standard. 1 tab.

  6. Status of conversion of NE standards to national consensus standards

    SciTech Connect

    Jennings, S.D.

    1990-06-01

    One major goal of the Nuclear Standards Program is to convert existing NE standards into national consensus standards (where possible). This means that an NE standard in the same subject area using the national consensus process. This report is a summary of the activities that have evolved to effect conversion of NE standards to national consensus standards, and the status of current conversion activities. In some cases, all requirements in an NE standard will not be incorporated into the published national consensus standard because these requirements may be considered too restrictive or too specific for broader application by the nuclear industry. If these requirements are considered necessary for nuclear reactor program applications, the program standard will be revised and issued as a supplement to the national consensus standard. The supplemental program standard will contain only those necessary requirements not reflected by the national consensus standard. Therefore, while complete conversion of program standards may not always be realized, the standards policy has been fully supported in attempting to make maximum use of the national consensus standard. 1 tab.

  7. A collaborative platform for consensus sessions in pathology over Internet.

    PubMed

    Zapletal, Eric; Le Bozec, Christel; Degoulet, Patrice; Jaulent, Marie-Christine

    2003-01-01

    The design of valid databases in pathology faces the problem of diagnostic disagreement between pathologists. Organizing consensus sessions between experts to reduce the variability is a difficult task. The TRIDEM platform addresses the issue to organize consensus sessions in pathology over the Internet. In this paper, we present the basis to achieve such collaborative platform. On the one hand, the platform integrates the functionalities of the IDEM consensus module that alleviates the consensus task by presenting to pathologists preliminary computed consensus through ergonomic interfaces (automatic step). On the other hand, a set of lightweight interaction tools such as vocal annotations are implemented to ease the communication between experts as they discuss a case (interactive step). The architecture of the TRIDEM platform is based on a Java-Server-Page web server that communicate with the ObjectStore PSE/PRO database used for the object storage. The HTML pages generated by the web server run Java applets to perform the different steps (automatic and interactive) of the consensus. The current limitations of the platform is to only handle a synchronous process. Moreover, improvements like re-writing the consensus workflow with a protocol such as BPML are already forecast. PMID:14663991

  8. Developing syndrome definitions based on consensus and current use

    PubMed Central

    Dowling, John N; Baer, Atar; Buckeridge, David L; Cochrane, Dennis; Conway, Michael A; Elkin, Peter; Espino, Jeremy; Gunn, Julia E; Hales, Craig M; Hutwagner, Lori; Keller, Mikaela; Larson, Catherine; Noe, Rebecca; Okhmatovskaia, Anya; Olson, Karen; Paladini, Marc; Scholer, Matthew; Sniegoski, Carol; Thompson, David; Lober, Bill

    2010-01-01

    Objective Standardized surveillance syndromes do not exist but would facilitate sharing data among surveillance systems and comparing the accuracy of existing systems. The objective of this study was to create reference syndrome definitions from a consensus of investigators who currently have or are building syndromic surveillance systems. Design Clinical condition–syndrome pairs were catalogued for 10 surveillance systems across the United States and the representatives of these systems were brought together for a workshop to discuss consensus syndrome definitions. Results Consensus syndrome definitions were generated for the four syndromes monitored by the majority of the 10 participating surveillance systems: Respiratory, gastrointestinal, constitutional, and influenza-like illness (ILI). An important element in coming to consensus quickly was the development of a sensitive and specific definition for respiratory and gastrointestinal syndromes. After the workshop, the definitions were refined and supplemented with keywords and regular expressions, the keywords were mapped to standard vocabularies, and a web ontology language (OWL) ontology was created. Limitations The consensus definitions have not yet been validated through implementation. Conclusion The consensus definitions provide an explicit description of the current state-of-the-art syndromes used in automated surveillance, which can subsequently be systematically evaluated against real data to improve the definitions. The method for creating consensus definitions could be applied to other domains that have diverse existing definitions. PMID:20819870

  9. 5S rRNA sequences from four marine invertebrates and implications for base pairing models of metazoan sequences.

    PubMed

    Walker, W F; Doolittle, W F

    1983-08-11

    The nucleotide sequences of 5S rRNAs from the starfish Asterias vulgaris, the squid Illex illecebrosus, the sipunculid Phascolopsis gouldii and the jellyfish Aurelia aurita were determined. The sequence from Asterias lends support for one of two previous base pairing models for helix E in metazoan sequences. The Aurelia sequence differs by five nucleotides from that previously reported and does not violate the consensus secondary structure model for eukaryotic 5S rRNA. PMID:6136024

  10. [Preliminary evaluation of Chile's First Citizen Consensus Conference].

    PubMed

    Pellegrini Filho, Alberto; Zurita, Laura

    2004-05-01

    This piece provides an initial assessment of the First Citizen Consensus Conference, an event held in the city of Santiago, Chile, from 22-24 November 2003, on the subject of "The Management of My Medical Record." This conference was the first citizen consensus conference that has been held in Chile as well as the first such conference in Latin America. Consensus conferences were devised by the Danish Board of Technology in 1987 as a way to assess science and technology issues through discussions between experts and a panel of lay persons. At the end of a consensus conference, the lay persons express their opinions and recommendations in a consensus report that is directed at policymakers, decision-makers, and the public in general. The objective of a consensus conference is to bridge the gaps that routinely exist among the general public, experts, and elected officials. So far, the Danish Board of Technology has organized more than 20 of these conferences, using a methodology that has become established as a model. Taking into account the changes that have occurred in the relationship between science and society at large, the Pan American Health Organization has decided to support the holding of consensus conferences in Latin America and the Caribbean. The First Citizen Consensus Conference adapted the Danish methodology to conditions in Chile, and this piece assesses the modifications that were made. In addition, some 6 to 12 months after the conference, there will be an external evaluation of the outcomes and impact of the conference, especially in the communications media, public debate, decision-making, and perceptions of the persons who were involved. Despite the criticisms made in this piece and some shortcomings that are pointed out, the First Citizen Consensus Conference achieved all of its objectives and will serve as an excellent model for similar conferences in other countries of the Americas. PMID:15231085

  11. Deep sequencing increases hepatitis C virus phylogenetic cluster detection compared to Sanger sequencing.

    PubMed

    Montoya, Vincent; Olmstead, Andrea; Tang, Patrick; Cook, Darrel; Janjua, Naveed; Grebely, Jason; Jacka, Brendan; Poon, Art F Y; Krajden, Mel

    2016-09-01

    Effective surveillance and treatment strategies are required to control the hepatitis C virus (HCV) epidemic. Phylogenetic analyses are powerful tools for reconstructing the evolutionary history of viral outbreaks and identifying transmission clusters. These studies often rely on Sanger sequencing which typically generates a single consensus sequence for each infected individual. For rapidly mutating viruses such as HCV, consensus sequencing underestimates the complexity of the viral quasispecies population and could therefore generate different phylogenetic tree topologies. Although deep sequencing provides a more detailed quasispecies characterization, in-depth phylogenetic analyses are challenging due to dataset complexity and computational limitations. Here, we apply deep sequencing to a characterized population to assess its ability to identify phylogenetic clusters compared with consensus Sanger sequencing. For deep sequencing, a sample specific threshold determined by the 50th percentile of the patristic distance distribution for all variants within each individual was used to identify clusters. Among seven patristic distance thresholds tested for the Sanger sequence phylogeny ranging from 0.005-0.06, a threshold of 0.03 was found to provide the maximum balance between positive agreement (samples in a cluster) and negative agreement (samples not in a cluster) relative to the deep sequencing dataset. From 77 HCV seroconverters, 10 individuals were identified in phylogenetic clusters using both methods. Deep sequencing analysis identified an additional 4 individuals and excluded 8 other individuals relative to Sanger sequencing. The application of this deep sequencing approach could be a more effective tool to understand onward HCV transmission dynamics compared with Sanger sequencing, since the incorporation of minority sequence variants improves the discrimination of phylogenetically linked clusters. PMID:27282472

  12. Promoter sequences and algorithmical methods for identifying them.

    PubMed

    Vanet, A; Marsan, L; Sagot, M F

    1999-01-01

    This paper presents a survey of currently available mathematical models and algorithmical methods for trying to identify promoter sequences. The methods concern both searching in a genome for a previously defined consensus and extracting a consensus from a set of sequences. Such methods were often tailored for either eukaryotes or prokaryotes although this does not preclude use of the same method for both types of organisms. The survey therefore covers all methods; however, emphasis is placed on prokaryotic promoter sequence identification. Illustrative applications of the main extracting algorithms are given for three bacteria. PMID:10673015

  13. Sarcopenia: European consensus on definition and diagnosis

    PubMed Central

    Cruz-Jentoft, Alfonso J.; Baeyens, Jean Pierre; Bauer, Jürgen M.; Boirie, Yves; Cederholm, Tommy; Landi, Francesco; Martin, Finbarr C.; Michel, Jean-Pierre; Rolland, Yves; Schneider, Stéphane M.; Topinková, Eva; Vandewoude, Maurits; Zamboni, Mauro

    2010-01-01

    The European Working Group on Sarcopenia in Older People (EWGSOP) developed a practical clinical definition and consensus diagnostic criteria for age-related sarcopenia. EWGSOP included representatives from four participant organisations, i.e. the European Geriatric Medicine Society, the European Society for Clinical Nutrition and Metabolism, the International Association of Gerontology and Geriatrics—European Region and the International Association of Nutrition and Aging. These organisations endorsed the findings in the final document. The group met and addressed the following questions, using the medical literature to build evidence-based answers: (i) What is sarcopenia? (ii) What parameters define sarcopenia? (iii) What variables reflect these parameters, and what measurement tools and cut-off points can be used? (iv) How does sarcopenia relate to cachexia, frailty and sarcopenic obesity? For the diagnosis of sarcopenia, EWGSOP recommends using the presence of both low muscle mass + low muscle function (strength or performance). EWGSOP variously applies these characteristics to further define conceptual stages as ‘presarcopenia’, ‘sarcopenia’ and ‘severe sarcopenia’. EWGSOP reviewed a wide range of tools that can be used to measure the specific variables of muscle mass, muscle strength and physical performance. Our paper summarises currently available data defining sarcopenia cut-off points by age and gender; suggests an algorithm for sarcopenia case finding in older individuals based on measurements of gait speed, grip strength and muscle mass; and presents a list of suggested primary and secondary outcome domains for research. Once an operational definition of sarcopenia is adopted and included in the mainstream of comprehensive geriatric assessment, the next steps are to define the natural course of sarcopenia and to develop and define effective treatment. PMID:20392703

  14. Consensus statement on diabetes in children

    PubMed Central

    Prasanna Kumar, K. M.; Dev, N. Prabhu; Raman, K. V.; Desai, Rajnanda; Prasadini, T. Geetha; Das, A. K.; Ramoul, Soraya

    2014-01-01

    While T1DM has been traditionally seen as a minor concern in the larger picture of pediatric ailments, new data reveals that the incidence of T1DM has assumed alarming proportions. It has long been clear that while the disease may be diagnosed at an early age, its impact is not isolated to afflicted children. The direct impact of the disease on the patient is debilitating due to the nature of the disease and lack of proper access to treatment in India. But this impact is further compounded by the utter apathy and often times antipathy, which patients withT1DM have to face. Lack of awareness of the issue in all stakeholders, low access to quality healthcare, patient, physician, and system level barriers to the delivery of optimal diabetes care are some of the factors which hinder successful management of T1DM. The first international consensus meet on diabetes in children was convened with the aim of providing a common platform to all the stakeholders in the management of T1DM, to discuss the academic, administrative and healthcare system related issues. The ultimate aim was to articulate the problems faced by children with diabetes in a way that centralized their position and focused on creating modalities of management sensitive to their needs and aspirations. It was conceptualized to raise a strong voice of advocacy for improving the management of T1DM and ensuring that “No child should die of diabetes”. The unique clinical presentations of T1DM coupled with ignorance on the part of the medical community and society in general results in outcomes that are far worse than that seen with T2DM. So there is a need to substantially improve training of HCPs at all levels on this neglected aspect of healthcare. PMID:24944917

  15. In control? IQC consensus and statutory regulation.

    PubMed

    Lee, Graham R; Fitzgibbon, Maria C; O'Shea, Paula

    2016-06-13

    have provided a template to potentially harmonise IQC practice nationally. Given the central and critical role that IQC practice plays in ensuring the quality of patient results' importance, the authors contend that the time has come for international consensus and statutory regulation regarding the minimally acceptable criteria for its implementation, monitoring and review. PMID:27256773

  16. 1st International consensus guidelines for advanced breast cancer (ABC 1).

    PubMed

    Cardoso, F; Costa, A; Norton, L; Cameron, D; Cufer, T; Fallowfield, L; Francis, P; Gligorov, J; Kyriakides, S; Lin, N; Pagani, O; Senkus, E; Thomssen, C; Aapro, M; Bergh, J; Di Leo, A; El Saghir, N; Ganz, P A; Gelmon, K; Goldhirsch, A; Harbeck, N; Houssami, N; Hudis, C; Kaufman, B; Leadbeater, M; Mayer, M; Rodger, A; Rugo, H; Sacchini, V; Sledge, G; van't Veer, L; Viale, G; Krop, I; Winer, E

    2012-06-01

    The 1st international Consensus Conference for Advanced Breast Cancer (ABC 1) took place on November 2011, in Lisbon. Consensus guidelines for the management of this disease were developed. This manuscript summarizes these international consensus guidelines. PMID:22425534

  17. Weighted Average Consensus-Based Unscented Kalman Filtering.

    PubMed

    Li, Wangyan; Wei, Guoliang; Han, Fei; Liu, Yurong

    2016-02-01

    In this paper, we are devoted to investigate the consensus-based distributed state estimation problems for a class of sensor networks within the unscented Kalman filter (UKF) framework. The communication status among sensors is represented by a connected undirected graph. Moreover, a weighted average consensus-based UKF algorithm is developed for the purpose of estimating the true state of interest, and its estimation error is bounded in mean square which has been proven in the following section. Finally, the effectiveness of the proposed consensus-based UKF algorithm is validated through a simulation example. PMID:26168453

  18. Admissible consensus for heterogeneous descriptor multi-agent systems

    NASA Astrophysics Data System (ADS)

    Yang, Xin-Rong; Liu, Guo-Ping

    2016-09-01

    This paper focuses on the admissible consensus problem for heterogeneous descriptor multi-agent systems. Based on algebra, graph and descriptor system theory, the necessary and sufficient conditions are proposed for heterogeneous descriptor multi-agent systems achieving admissible consensus. The provided conditions depend on not only the structure properties of each agent dynamics but also the topologies within the descriptor multi-agent systems. Moreover, an algorithm is given to design the novel consensus protocol. A numerical example demonstrates the effectiveness of the proposed design approach.

  19. GENERAL: Consensus protocol for multi-agent continuous systems

    NASA Astrophysics Data System (ADS)

    Tan, Fu-Xiao; Guan, Xin-Ping; Liu, De-Rong

    2008-10-01

    Based on the algebraic graph theory, the networked multi-agent continuous systems are investigated. Firstly, the digraph (directed graph) represents the topology of a networked system, and then a consensus convergence criterion of system is proposed. Secondly, the issue of stability of multi-agent systems and the consensus convergence problem of information states are all analysed. Furthermore, the consensus equilibrium point of system is proved to be global and asymptotically reach the convex combination of initial states. Finally, two examples are taken to show the effectiveness of the results obtained in this paper.

  20. Complete Genome Sequence of Vaccinia Virus Strain L-IVP.

    PubMed

    Shvalov, Alexander N; Sivolobova, Galina F; Kuligina, Elena V; Kochneva, Galina V

    2016-01-01

    Most of the live vaccine doses of vaccinia virus donated to the Intensified Smallpox Eradication Programme after 1971 were prepared using the L-IVP strain. A mixture of three clones of the L-IVP strain was sequenced using MySEQ. Consensus sequence similarity with the vaccinia virus Lister strain is 99.5%. PMID:27174282

  1. Complete Genome Sequence of Vaccinia Virus Strain L-IVP

    PubMed Central

    Shvalov, Alexander N.; Sivolobova, Galina F.; Kuligina, Elena V.

    2016-01-01

    Most of the live vaccine doses of vaccinia virus donated to the Intensified Smallpox Eradication Programme after 1971 were prepared using the L-IVP strain. A mixture of three clones of the L-IVP strain was sequenced using MySEQ. Consensus sequence similarity with the vaccinia virus Lister strain is 99.5%. PMID:27174282

  2. Consensus statement: the 16th Annual Western Canadian Gastrointestinal Cancer Consensus Conference; Saskatoon, Saskatchewan; September 5–6, 2014

    PubMed Central

    Ahmed, S.; Bathe, O.; Berry, S.; Buie, D.; Davies, J.; Doll, C.; Dowden, S.; Gill, S.; Gordon, V.; Hebbard, P.; Jones, E.; Kennecke, H.; Koski, S.; Krahn, M.; Le, D.; Lim, H.; Lund, C.; Luo, Y.; Mcffadden, A.; Mcghie, J.; Mulder, K.; Park, J.; Rashidi, F.; Sami, A.; Tan, K.T.; Wong, R.

    2015-01-01

    The 16th annual Western Canadian Gastrointestinal Cancer Consensus Conference was held in Saskatoon, Saskatchewan, September 4–5, 2014. The Consensus Conference is an interactive, multidisciplinary event attended by health care professionals from across western Canada (British Columbia, Alberta, Saskatchewan, and Manitoba) involved in the care of gastrointestinal cancer. Surgical, medical, and radiation oncologists; pathologists; radiologists; and allied health care professionals participated in presentation and discussion sessions for the purposes of developing the recommendations presented here. This consensus statement addresses current issues in the management of colorectal cancer. PMID:25908916

  3. NIH Blood and Marrow Transplant Late Effects Consensus Conference

    Cancer.gov

    This day and a half symposium will bring together experts in blood and marrow transplantation, late effects, and health care delivery to discuss current evidence and knowledge gaps, develop consensus guidelines, and inform future research in the BMT survivor population.

  4. Forecasting to Consensus Gathering, Delphi Grows Up to College Needs

    ERIC Educational Resources Information Center

    Judd, Robert C.

    1972-01-01

    What began as a hypothetical approach to educational forecasting is now gaining momentum as a workable consensus gathering technique for all phases of educational administration and planning. (Editor/HS)

  5. Climate science, character, and the "hard-won" consensus.

    PubMed

    Ranalli, Brent

    2012-06-01

    What makes a consensus among scientists credible and convincing? This paper introduces the notion of a "hard-won" consensus and uses examples from recent debates over climate change science to show that this heuristic standard for evaluating the quality of a consensus is widely shared. The extent to which a consensus is "hard won" can be understood to depend on the personal qualities of the participating experts; the article demonstrates the continuing utility of the norms of modern science introduced by Robert K. Merton by showing that individuals on both sides of the climate science debate rely intuitively on Mertonian ideas--interpreted in terms of character--to frame their arguments. PMID:23002583

  6. Consensus statement on standard of care for congenital muscular dystrophies.

    PubMed

    Wang, Ching H; Bonnemann, Carsten G; Rutkowski, Anne; Sejersen, Thomas; Bellini, Jonathan; Battista, Vanessa; Florence, Julaine M; Schara, Ulrike; Schuler, Pamela M; Wahbi, Karim; Aloysius, Annie; Bash, Robert O; Béroud, Christophe; Bertini, Enrico; Bushby, Kate; Cohn, Ronald D; Connolly, Anne M; Deconinck, Nicolas; Desguerre, Isabelle; Eagle, Michelle; Estournet-Mathiaud, Brigitte; Ferreiro, Ana; Fujak, Albert; Goemans, Nathalie; Iannaccone, Susan T; Jouinot, Patricia; Main, Marion; Melacini, Paola; Mueller-Felber, Wolfgang; Muntoni, Francesco; Nelson, Leslie L; Rahbek, Jes; Quijano-Roy, Susana; Sewry, Caroline; Storhaug, Kari; Simonds, Anita; Tseng, Brian; Vajsar, Jiri; Vianello, Andrea; Zeller, Reinhard

    2010-12-01

    Congenital muscular dystrophies are a group of rare neuromuscular disorders with a wide spectrum of clinical phenotypes. Recent advances in understanding the molecular pathogenesis of congenital muscular dystrophy have enabled better diagnosis. However, medical care for patients with congenital muscular dystrophy remains very diverse. Advances in many areas of medical technology have not been adopted in clinical practice. The International Standard of Care Committee for Congenital Muscular Dystrophy was established to identify current care issues, review literature for evidence-based practice, and achieve consensus on care recommendations in 7 areas: diagnosis, neurology, pulmonology, orthopedics/rehabilitation, gastroenterology/ nutrition/speech/oral care, cardiology, and palliative care. To achieve consensus on the care recommendations, 2 separate online surveys were conducted to poll opinions from experts in the field and from congenital muscular dystrophy families. The final consensus was achieved in a 3-day workshop conducted in Brussels, Belgium, in November 2009. This consensus statement describes the care recommendations from this committee. PMID:21078917

  7. Defensive pride and consensus: strength in imaginary numbers.

    PubMed

    McGregor, Ian; Nail, Paul R; Marigold, Denise C; Kang, So-Jin

    2005-12-01

    Failure (Study 1) and attachment separation thoughts (Study 2) caused exaggerated consensus estimates for personal beliefs about unrelated social issues. This compensatory consensus effect was most pronounced among defensively proud individuals, that is, among those with the combination of high explicit and low implicit self-esteem (Study 1) and the combination of high attachment avoidance and low attachment anxiety (Study 2). In Study 3, another form of defensive pride, narcissism, was associated with exaggerated consensual worldview defense after a system-injustice threat. In Study 4, imagined consensus reduced subjective salience of proud individuals' troubling thoughts. Compensatory consensus is seen as a kind of defensive self-affirmation that defensively proud people turn to for insulation from distressing thoughts. PMID:16393029

  8. Adaptive neural network consensus based control of robot formations

    NASA Astrophysics Data System (ADS)

    Guzey, H. M.; Sarangapani, Jagannathan

    2013-05-01

    In this paper, adaptive consensus based formation control scheme is derived for mobile robots in a pre-defined formation when full dynamics of the robots which include inertia, Corolis, and friction vector are considered. It is shown that dynamic uncertainties of robots can make overall formation unstable when traditional consensus scheme is utilized. In order to estimate the affine nonlinear robot dynamics, a NN based adaptive scheme is utilized. In addition to this adaptive feedback control input, an additional control input is introduced based on the consensus approach to make the robots keep their desired formation. Subsequently, the outer consensus loop is redesigned for reduced communication. Lyapunov theory is used to show the stability of overall system. Simulation results are included at the end.

  9. Scientific consensus, the law, and same sex parenting outcomes.

    PubMed

    adams, Jimi; Light, Ryan

    2015-09-01

    While the US Supreme Court was considering two related cases involving the constitutionality of same-sex marriage, one major question informing that decision was whether scientific research had achieved consensus regarding how children of same-sex couples fare. Determining the extent of consensus has become a key aspect of how social science evidence and testimony is accepted by the courts. Here, we show how a method of analyzing temporal patterns in citation networks can be used to assess the state of social scientific literature as a means to inform just such a question. Patterns of clustering within these citation networks reveal whether and when consensus arises within a scientific field. We find that the literature on outcomes for children of same-sex parents is marked by scientific consensus that they experience "no differences" compared to children from other parental configurations. PMID:26188455

  10. ESMO-ESGO-ESTRO Consensus Conference on Endometrial Cancer

    PubMed Central

    Colombo, Nicoletta; Creutzberg, Carien; Amant, Frederic; Bosse, Tjalling; González-Martín, Antonio; Ledermann, Jonathan; Marth, Christian; Nout, Remi; Querleu, Denis; Mirza, Mansoor Raza; Sessa, Cristiana

    2016-01-01

    Abstract The first joint European Society for Medical Oncology (ESMO), European SocieTy for Radiotherapy & Oncology (ESTRO) and European Society of Gynaecological Oncology (ESGO) consensus conference on endometrial cancer was held on 11–13 December 2014 in Milan, Italy, and comprised a multidisciplinary panel of 40 leading experts in the management of endometrial cancer. Before the conference, the expert panel prepared three clinically-relevant questions about endometrial cancer relating to the following four areas: prevention and screening, surgery, adjuvant treatment and advanced and recurrent disease. All relevant scientific literature, as identified by the experts, was reviewed in advance. During the consensus conference, the panel developed recommendations for each specific question and a consensus was reached. Results of this consensus conference, together with a summary of evidence supporting each recommendation, are detailed in this article. All participants have approved this final article. PMID:26645990

  11. A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences

    NASA Technical Reports Server (NTRS)

    Ho, P. S.; Ellison, M. J.; Quigley, G. J.; Rich, A.

    1986-01-01

    The ease with which a particular DNA segment adopts the left-handed Z-conformation depends largely on the sequence and on the degree of negative supercoiling to which it is subjected. We describe a computer program (Z-hunt) that is designed to search long sequences of naturally occurring DNA and retrieve those nucleotide combinations of up to 24 bp in length which show a strong propensity for Z-DNA formation. Incorporated into Z-hunt is a statistical mechanical model based on empirically determined energetic parameters for the B to Z transition accumulated to date. The Z-forming potential of a sequence is assessed by ranking its behavior as a function of negative superhelicity relative to the behavior of similar sized randomly generated nucleotide sequences assembled from over 80,000 combinations. The program makes it possible to compare directly the Z-forming potential of sequences with different base compositions and different sequence lengths. Using Z-hunt, we have analyzed the DNA sequences of the bacteriophage phi X174, plasmid pBR322, the animal virus SV40 and the replicative form of the eukaryotic adenovirus-2. The results are compared with those previously obtained by others from experiments designed to locate Z-DNA forming regions in these sequences using probes which show specificity for the left-handed DNA conformation.

  12. Next generation sequencing of viral RNA genomes

    PubMed Central

    2013-01-01

    Background With the advent of Next Generation Sequencing (NGS) technologies, the ability to generate large amounts of sequence data has revolutionized the genomics field. Most RNA viruses have relatively small genomes in comparison to other organisms and as such, would appear to be an obvious success story for the use of NGS technologies. However, due to the relatively low abundance of viral RNA in relation to host RNA, RNA viruses have proved relatively difficult to sequence using NGS technologies. Here we detail a simple, robust methodology, without the use of ultra-centrifugation, filtration or viral enrichment protocols, to prepare RNA from diagnostic clinical tissue samples, cell monolayers and tissue culture supernatant, for subsequent sequencing on the Roche 454 platform. Results As representative RNA viruses, full genome sequence was successfully obtained from known lyssaviruses belonging to recognized species and a novel lyssavirus species using these protocols and assembling the reads using de novo algorithms. Furthermore, genome sequences were generated from considerably less than 200 ng RNA, indicating that manufacturers’ minimum template guidance is conservative. In addition to obtaining genome consensus sequence, a high proportion of SNPs (Single Nucleotide Polymorphisms) were identified in the majority of samples analyzed. Conclusions The approaches reported clearly facilitate successful full genome lyssavirus sequencing and can be universally applied to discovering and obtaining consensus genome sequences of RNA viruses from a variety of sources. PMID:23822119

  13. Globular glial tauopathies (GGT): consensus recommendations.

    PubMed

    Ahmed, Zeshan; Bigio, Eileen H; Budka, Herbert; Dickson, Dennis W; Ferrer, Isidro; Ghetti, Bernardino; Giaccone, Giorgio; Hatanpaa, Kimmo J; Holton, Janice L; Josephs, Keith A; Powers, James; Spina, Salvatore; Takahashi, Hitoshi; White, Charles L; Revesz, Tamas; Kovacs, Gabor G

    2013-10-01

    Recent studies have highlighted a group of 4-repeat (4R) tauopathies that are characterised neuropathologically by widespread, globular glial inclusions (GGIs). Tau immunohistochemistry reveals 4R immunoreactive globular oligodendroglial and astrocytic inclusions and the latter are predominantly negative for Gallyas silver staining. These cases are associated with a range of clinical presentations, which correlate with the severity and distribution of underlying tau pathology and neurodegeneration. Their heterogeneous clinicopathological features combined with their rarity and under-recognition have led to cases characterised by GGIs being described in the literature using various and redundant terminologies. In this report, a group of neuropathologists form a consensus on the terminology and classification of cases with GGIs. After studying microscopic images from previously reported cases with suspected GGIs (n = 22), this panel of neuropathologists with extensive experience in the diagnosis of neurodegenerative diseases and a documented record of previous experience with at least one case with GGIs, agreed that (1) GGIs were present in all the cases reviewed; (2) the morphology of globular astrocytic inclusions was different to tufted astrocytes and finally that (3) the cases represented a number of different neuropathological subtypes. They also agreed that the different morphological subtypes are likely to be part of a spectrum of a distinct disease entity, for which they recommend that the overarching term globular glial tauopathy (GGT) should be used. Type I cases typically present with frontotemporal dementia, which correlates with the fronto-temporal distribution of pathology. Type II cases are characterised by pyramidal features reflecting motor cortex involvement and corticospinal tract degeneration. Type III cases can present with a combination of frontotemporal dementia and motor neuron disease with fronto-temporal cortex, motor cortex and

  14. Globular glial tauopathies (GGT): consensus recommendations

    PubMed Central

    Bigio, Eileen H.; Budka, Herbert; Dickson, Dennis W.; Ferrer, Isidro; Ghetti, Bernardino; Giaccone, Giorgio; Hatanpaa, Kimmo J.; Holton, Janice L.; Josephs, Keith A.; Powers, James; Spina, Salvatore; Takahashi, Hitoshi; White, Charles L.; Revesz, Tamas

    2014-01-01

    Rrecent studies have highlighted a group of 4-repeat (4R) tauopathies that are characterised neuropathologically by widespread, globular glial inclusions (GGIs). Tau immunohistochemistry reveals 4R immunore-active globular oligodendroglial and astrocytic inclusions and the latter are predominantly negative for Gallyas silver staining. These cases are associated with a range of clinical presentations, which correlate with the severity and distribution of underlying tau pathology and neurodegeneration. Their heterogeneous clinicopathological features combined with their rarity and under-recognition have led to cases characterised by GGIs being described in the literature using various and redundant terminologies. In this report, a group of neuropathologists form a consensus on the terminology and classification of cases with GGIs. After studying microscopic images from previously reported cases with suspected GGIs (n = 22), this panel of neuropathologists with extensive experience in the diagnosis of neurodegenerative diseases and a documented record of previous experience with at least one case with GGIs, agreed that (1) GGIs were present in all the cases reviewed; (2) the morphology of globular astrocytic inclusions was different to tufted astrocytes and finally that (3) the cases represented a number of different neuropathological subtypes. They also agreed that the different morphological subtypes are likely to be part of a spectrum of a distinct disease entity, for which they recommend that the overarching term globular glial tauopathy (GGT) should be used. Type I cases typically present with frontotemporal dementia, which correlates with the fronto-temporal distribution of pathology. Type II cases are characterised by pyramidal features reflecting motor cortex involvement and corticospinal tract degeneration. Type III cases can present with a combination of frontotemporal dementia and motor neuron disease with fronto-temporal cortex, motor cortex and

  15. Consensus time and conformity in the adaptive voter model

    NASA Astrophysics Data System (ADS)

    Rogers, Tim; Gross, Thilo

    2013-09-01

    The adaptive voter model is a paradigmatic model in the study of opinion formation. Here we propose an extension for this model, in which conflicts are resolved by obtaining another opinion, and analytically study the time required for consensus to emerge. Our results shed light on the rich phenomenology of both the original and extended adaptive voter models, including a dynamical phase transition in the scaling behavior of the mean time to consensus.

  16. ABC3 Consensus: Assessment by a German Group of Experts.

    PubMed

    Thomssen, Christoph; Augustin, Doris; Ettl, Johannes; Haidinger, Renate; Lück, Hans-Joachim; Lüftner, Diana; Marmé, Frederik; Marschner, Norbert; Müller, Lothar; Overkamp, Friedrich; Ruckhäberle, Eugen; Thill, Marc; Untch, Michael; Wuerstlein, Rachel; Harbeck, Nadia

    2016-02-01

    The Advanced Breast Cancer Third International Consensus Conference on the diagnosis and treatment of advanced breast cancer took place in Lisbon, Portugal, on November 5-7, 2015. This year's conference (ABC3) was focused on the treatment of metastatic breast cancer (stage IV), as it was 4 years ago at the first consensus meeting (ABC1). A matter of particular interest was the patients' perspective. Thus, patient-relevant issues were addressed by the consensus discussions, such as those on treatment goals, quality of life, care of long-term survivors ('survivorship issues'), and coping with disease-related symptoms and the side effects of treatment. Further important issues on the agenda were the use of standardized instruments for the assessment of individual treatment success ('patient-reported outcome measures') and the evaluation of the benefit of novel drugs (e.g. the European Society for Medical Oncology (ESMO) Magnitude of Clinical Benefit Scale). Diagnosis and treatment of inoperable locally advanced breast cancer had already been discussed 2 years earlier at the ABC2 Consensus and were not dealt with in the framework of this year's ABC3 Consensus. With regard to country-specific peculiarities, which unavoidably found their way into the ABC Consensus, a working group of German breast cancer experts commented on the voting results of the ABC panelists. As for the past consensus, the group specially considered the German guidelines for the diagnosis and treatment of breast cancer (AGO (Gyneco-Oncology Working Group), S3, DGHO (German Society of Hematology and Medical Oncology)) in order to adapt the ABC3 consensus for everyday therapy in Germany. PMID:27051399

  17. Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks.

    PubMed

    Kennedy, Martyn; Holland, Barbara R; Gray, Russell D; Spencer, Hamish G

    2005-08-01

    Long-branch attraction is a well-known source of systematic error that can mislead phylogenetic methods; it is frequently invoked post hoc, upon recovering a different tree from the one expected based on prior evidence. We demonstrate that methods that do not force the data onto a single tree, such as spectral analysis, Neighbor-Net, and consensus networks, can be used to detect conflicting signals within the data, including those caused by long-branch attraction. We illustrate this approach using a set of taxa from three unambiguously monophyletic families within the Pelecaniformes: the darters, the cormorants and shags, and the gannets and boobies. These three families are universally acknowledged as forming a monophyletic group, but the relationship between the families remains contentious. Using sequence data from three mitochondrial genes (12S, ATPase 6, and ATPase 8) we demonstrate that the relationship between these three families is difficult to resolve because they are separated by a short internal branch and there are conflicting signals due to long-branch attraction, which are confounded with nonhomogeneous sequence evolution across the different genes. Spectral analysis, Neighbor-Net, and consensus networks reveal conflicting signals regarding the placement of one of the darters, with support found for darter monophyly, but also support for a conflicting grouping with the outgroup, pelicans. Furthermore, parsimony and maximum-likelihood analyses produced different trees, with one of the two most parsimonious trees not supporting the monophyly of the darters. Monte Carlo simulations, however, were not sensitive enough to reveal long-branch attraction unless the branches are longer than those actually observed. These results indicate that spectral analysis, Neighbor-Net, and consensus networks offer a powerful approach to detecting and understanding the source of conflicting signals within phylogenetic data. PMID:16109705

  18. Building of multilevel stakeholder consensus in radioactive waste repository siting

    SciTech Connect

    Dreimanis, A.

    2007-07-01

    This report considers the problem of multilevel consensus building for siting and construction of shared multinational/regional repositories for radioactive waste (RW) deep disposal. In the siting of a multinational repository there appears an essential innovative component of stakeholder consensus building, namely: to reach consent - political, social, economic, ecological - among international partners, in addition to solving the whole set of intra-national consensus building items. An entire partnering country is considered as a higher-level stakeholder - the national stakeholder, represented by the national government, being faced to simultaneous seeking an upward (international) and a downward (intra-national) consensus in a psychologically stressed environment, possibly being characterized by diverse political, economic and social interests. The following theses as a possible interdisciplinary approach towards building of shared understanding and stakeholder consensus on the international scale of RW disposal are forwarded and developed: a) building of international stakeholder consensus would be promoted by activating and diversifying on the international scale multilateral interactions between intra- and international stakeholders, including web-based networks of the RW disposal site investigations and decision-making, as well as networks for international cooperation among government authorities in nuclear safety, b) gradual progress in intergovernmental consensus and reaching multilateral agreements on shared deep repositories will be the result of democratic dialogue, via observing the whole set of various interests and common resolving of emerged controversies by using advanced synergetic approaches of conflict resolution, c) cross-cultural thinking and world perception, mental flexibility, creativity and knowledge are considered as basic prerogatives for gaining a higher level of mutual understanding and consensus for seeking further consensus, for

  19. Oligonucleotide Sequence Motifs as Nucleosome Positioning Signals

    PubMed Central

    Collings, Clayton K.; Fernandez, Alfonso G.; Pitschka, Chad G.; Hawkins, Troy B.; Anderson, John N.

    2010-01-01

    To gain a better understanding of the sequence patterns that characterize positioned nucleosomes, we first performed an analysis of the periodicities of the 256 tetranucleotides in a yeast genome-wide library of nucleosomal DNA sequences that was prepared by in vitro reconstitution. The approach entailed the identification and analysis of 24 unique tetranucleotides that were defined by 8 consensus sequences. These consensus sequences were shown to be responsible for most if not all of the tetranucleotide and dinucleotide periodicities displayed by the entire library, demonstrating that the periodicities of dinucleotides that characterize the yeast genome are, in actuality, due primarily to the 8 consensus sequences. A novel combination of experimental and bioinformatic approaches was then used to show that these tetranucleotides are important for preferred formation of nucleosomes at specific sites along DNA in vitro. These results were then compared to tetranucleotide patterns in genome-wide in vivo libraries from yeast and C. elegans in order to assess the contributions of DNA sequence in the control of nucleosome residency in the cell. These comparisons revealed striking similarities in the tetranucleotide occurrence profiles that are likely to be involved in nucleosome positioning in both in vitro and in vivo libraries, suggesting that DNA sequence is an important factor in the control of nucleosome placement in vivo. However, the strengths of the tetranucleotide periodicities were 3–4 fold higher in the in vitro as compared to the in vivo libraries, which implies that DNA sequence plays less of a role in dictating nucleosome positions in vivo. The results of this study have important implications for models of sequence-dependent positioning since they suggest that a defined subset of tetranucleotides is involved in preferred nucleosome occupancy and that these tetranucleotides are the major source of the dinucleotide periodicities that are characteristic of

  20. Rhesus macaques vaccinated with consensus envelopes elicit partially protective immune responses against SHIV SF162p4 challenge

    PubMed Central

    2013-01-01

    The development of a preventative HIV/AIDS vaccine is challenging due to the diversity of viral genome sequences, especially in the viral envelope (Env160). Since it is not possible to directly match the vaccine strain to the vast number of circulating HIV-1 strains, it is necessary to develop an HIV-1 vaccine that can protect against a heterologous viral challenge. Previous studies from our group demonstrated that a mixture of wild type clade B Envgp160s were able to protect against a heterologous clade B challenge more effectively than a consensus clade B Envgp160 vaccine. In order to broaden the immune response to other clades of HIV, in this study rhesus macaques were vaccinated with a polyvalent mixture of purified HIV-1 trimerized consensus Envgp140 proteins representing clades A, B, C, and E. The elicited immune responses were compared to a single consensus Envgp140 representing all isolates in group M (Con M). Both vaccines elicited anti- Envgp140 IgG antibodies that bound an equal number of HIV-1 Envgp160 proteins representing clades A, B and C. In addition, both vaccines elicited antibodies that neutralized the HIV-1SF162 isolate. However, the vaccinated monkeys were not protected against SHIVSF162p4 challenge. These results indicate that consensus Envgp160 vaccines, administered as purified Envgp140 trimers, elicit antibodies that bind to Envgp160s from strains representing multiple clades of HIV-1, but these vaccines did not protect against heterologous SHIV challenge. PMID:23548077

  1. Quantitative application of the primary progressive aphasia consensus criteria

    PubMed Central

    Wicklund, Meredith R.; Duffy, Joseph R.; Strand, Edythe A.; Machulda, Mary M.; Whitwell, Jennifer L.

    2014-01-01

    Objective: To determine how well the consensus criteria could classify subjects with primary progressive aphasia (PPA) using a quantitative speech and language battery that matches the test descriptions provided by the consensus criteria. Methods: A total of 105 participants with a neurodegenerative speech and language disorder were prospectively recruited and underwent neurologic, neuropsychological, and speech and language testing and MRI in this case-control study. Twenty-one participants with apraxia of speech without aphasia served as controls. Select tests from the speech and language battery were chosen for application of consensus criteria and cutoffs were employed to determine syndromic classification. Hierarchical cluster analysis was used to examine participants who could not be classified. Results: Of the 84 participants, 58 (69%) could be classified as agrammatic (27%), semantic (7%), or logopenic (35%) variants of PPA. The remaining 31% of participants could not be classified. Of the unclassifiable participants, 2 clusters were identified. The speech and language profile of the first cluster resembled mild logopenic PPA and the second cluster semantic PPA. Gray matter patterns of loss of these 2 clusters of unclassified participants also resembled mild logopenic and semantic variants. Conclusions: Quantitative application of consensus PPA criteria yields the 3 syndromic variants but leaves a large proportion unclassified. Therefore, the current consensus criteria need to be modified in order to improve sensitivity. PMID:24598709

  2. Weighted voting-based consensus clustering for chemical structure databases.

    PubMed

    Saeed, Faisal; Ahmed, Ali; Shamsir, Mohd Shahir; Salim, Naomie

    2014-06-01

    The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures. PMID:24830925

  3. Expert Consensus Panel Guidelines on Geriatric Assessment in Oncology

    PubMed Central

    O'Donovan, A.; Mohile, S.G.; Leech, M.

    2015-01-01

    Introduction Despite consensus guidelines on best practice in the care of older patients with cancer, geriatric assessment (GA) has yet to be optimally integrated into the field of oncology in most countries. There is a relative lack of consensus in the published literature as to the best approach to take, and there is a degree of uncertainty as to how integration of geriatric medicine principles might optimally predict patient outcomes. The aim of the current study was to obtain consensus on GA in oncology to inform the implementation of a geriatric oncology programme. Methods A four round Delphi process was employed. The Delphi method is a structured group facilitation process, using multiple iterations in order to gain consensus on a given topic Results Consensus was reached on the optimal assessment method and interventions required for the commonly employed domains of GA. Other aspects of GA, such as screening methods and age cutoff for assessment represented a higher degree of disagreement. Discussion The expert panel employed in this study clearly identified the criteria that should be included in a clinical geriatric oncology programme. In the absence of evidence-based guidelines, this may prove useful in the care of older cancer patients. PMID:25757457

  4. Repetitive Sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Repetitive sequences, or repeats, account for a substantial portion of the eukaryotic genomes. These sequences include very different types of DNA with respect to mode of origin, function, structure, and genomic distribution. Two large families of repetitive sequences can be readily recognized, ta...

  5. Cultural Consensus Theory: Aggregating Continuous Responses in a Finite Interval

    NASA Astrophysics Data System (ADS)

    Batchelder, William H.; Strashny, Alex; Romney, A. Kimball

    Cultural consensus theory (CCT) consists of cognitive models for aggregating responses of "informants" to test items about some domain of their shared cultural knowledge. This paper develops a CCT model for items requiring bounded numerical responses, e.g. probability estimates, confidence judgments, or similarity judgments. The model assumes that each item generates a latent random representation in each informant, with mean equal to the consensus answer and variance depending jointly on the informant and the location of the consensus answer. The manifest responses may reflect biases of the informants. Markov Chain Monte Carlo (MCMC) methods were used to estimate the model, and simulation studies validated the approach. The model was applied to an existing cross-cultural dataset involving native Japanese and English speakers judging the similarity of emotion terms. The results sharpened earlier studies that showed that both cultures appear to have very similar cognitive representations of emotion terms.

  6. APASL consensus statements and recommendation on treatment of hepatitis C.

    PubMed

    Omata, Masao; Kanda, Tatsuo; Wei, Lai; Yu, Ming-Lung; Chuang, Wang-Long; Ibrahim, Alaaeldin; Lesmana, Cosmas Rinaldi Adithya; Sollano, Jose; Kumar, Manoj; Jindal, Ankur; Sharma, Barjesh Chander; Hamid, Saeed S; Dokmeci, A Kadir; Mamun-Al-Mahtab; McCaughan, Geofferey W; Wasim, Jafri; Crawford, Darrell H G; Kao, Jia-Horng; Yokosuka, Osamu; Lau, George K K; Sarin, Shiv Kumar

    2016-09-01

    The Asian-Pacific Association for the Study of the Liver (APASL) convened an international working party on the "APASL consensus statements and recommendation on management of hepatitis C" in March, 2015, in order to revise "APASL consensus statements and management algorithms for hepatitis C virus infection (Hepatol Int 6:409-435, 2012)". The working party consisted of expert hepatologists from the Asian-Pacific region gathered at Istanbul Congress Center, Istanbul, Turkey on 13 March 2015. New data were presented, discussed and debated to draft a revision. Participants of the consensus meeting assessed the quality of cited studies. Finalized recommendations on treatment of hepatitis C are presented in this review. PMID:27130427

  7. Social and strategic imitation: the way to consensus

    PubMed Central

    Vilone, Daniele; Ramasco, José J.; Sánchez, Angel; Miguel, Maxi San

    2012-01-01

    Humans do not always make rational choices, a fact that experimental economics is putting on solid grounds. The social context plays an important role in determining our actions, and often we imitate friends or acquaintances without any strategic consideration. We explore here the interplay between strategic and social imitative behavior in a coordination problem on a social network. We observe that for interactions on 1D and 2D lattices any amount of social imitation prevents the freezing of the network in domains with different conventions, thus leading to global consensus. For interactions on complex networks, the interplay of social and strategic imitation also drives the system towards global consensus while neither dynamics alone does. We find an optimum value for the combination of imitative behaviors to reach consensus in a minimum time, and two different dynamical regimes to approach it: exponential when social imitation predominates, power-law when strategic considerations prevail. PMID:23008751

  8. Quantised consensus of multi-agent systems with nonlinear dynamics

    NASA Astrophysics Data System (ADS)

    Zhu, Yunru; Zheng, Yuanshi; Wang, Long

    2015-08-01

    This paper studies the consensus problem of first-order and second-order multi-agent systems with nonlinear dynamics and quantised interactions. Continuous-time and impulsive control inputs are designed for the multi-agent systems on the logarithmic quantised relative state measurements of agents, respectively. By using nonsmooth analysis tools, we get some sufficient conditions for the consensus of multi-agent systems under the continuous-time inputs. Compared with continuous-time control inputs, impulsive distributed control inputs just use the state variables of the systems at discrete-time instances. Based on impulsive control theory, we prove that the multi-agent systems can reach consensus by choosing proper control gains and impulsive intervals. The simulation results are given to verify the effectiveness of the theoretical results.

  9. Consensus and stratification in the affective meaning of human sociality

    PubMed Central

    Ambrasat, Jens; von Scheve, Christian; Conrad, Markus; Schauenburg, Gesche; Schröder, Tobias

    2014-01-01

    We investigate intrasocietal consensus and variation in affective meanings of concepts related to authority and community, two elementary forms of human sociality. Survey participants (n = 2,849) from different socioeconomic status (SES) groups in German society provided ratings of 909 social concepts along three basic dimensions of affective meaning. Results show widespread consensus on these meanings within society and demonstrate that a meaningful structure of socially shared knowledge emerges from organizing concepts according to their affective similarity. The consensus finding is further qualified by evidence for subtle systematic variation along SES differences. In relation to affectively neutral words, high-status individuals evaluate intimacy-related and socially desirable concepts as less positive and powerful than middle- or low-status individuals, while perceiving antisocial concepts as relatively more threatening. This systematic variation across SES groups suggests that the affective meaning of sociality is to some degree a function of social stratification. PMID:24843121

  10. Committees and consensus: how many heads are better than one?

    PubMed

    Caws, P

    1991-08-01

    The first section of this paper asks why the notion of consensus has recently come to the fore in the medical humanities, and suggests that the answer is a function of growing technological and professional complexity. The next two sections examine the concept of consensus analytically, citing some of the recent philosophical literature. The fourth section looks at committee deliberations and their desirable outcomes, and questions the degree to which consensus serves those outcomes. In the fifth and last section it is suggested that if I am to subscribe to a consensual outcome responsibly I must be personally committed to it, and that this requires a form of knowledge I call 'fiduciary', in this case knowledge of the competence and trustworthiness of other participants in deliberation whose expertise may have influenced my agreement. PMID:1895023

  11. Climate Consensus and `Misinformation': A Rejoinder to Agnotology, Scientific Consensus, and the Teaching and Learning of Climate Change

    NASA Astrophysics Data System (ADS)

    Legates, David R.; Soon, Willie; Briggs, William M.; Monckton of Brenchley, Christopher

    2015-04-01

    Agnotology is the study of how ignorance arises via circulation of misinformation calculated to mislead. Legates et al. (Sci Educ 22:2007-2017, 2013) had questioned the applicability of agnotology to politically-charged debates. In their reply, Bedford and Cook (Sci Educ 22:2019-2030, 2013), seeking to apply agnotology to climate science, asserted that fossil-fuel interests had promoted doubt about a climate consensus. Their definition of climate `misinformation' was contingent upon the post-modernist assumptions that scientific truth is discernible by measuring a consensus among experts, and that a near unanimous consensus exists. However, inspection of a claim by Cook et al. (Environ Res Lett 8:024024, 2013) of 97.1 % consensus, heavily relied upon by Bedford and Cook, shows just 0.3 % endorsement of the standard definition of consensus: that most warming since 1950 is anthropogenic. Agnotology, then, is a two-edged sword since either side in a debate may claim that general ignorance arises from misinformation allegedly circulated by the other. Significant questions about anthropogenic influences on climate remain. Therefore, Legates et al. appropriately asserted that partisan presentations of controversies stifle debate and have no place in education.

  12. Consensus Conference on North American Training in Hepatopancreaticobiliary Surgery: A Review of the Conference and Presentation of Consensus Statements.

    PubMed

    Jeyarajah, D R; Berman, R S; Doyle, M B; Geevarghese, S K; Posner, M C; Farmer, D; Minter, R M

    2016-04-01

    The findings and recommendations of the North American consensus conference on training in hepatopancreaticobiliary (HPB) surgery held in October 2014 are presented. The conference was hosted by the Society for Surgical Oncology (SSO), the Americas Hepato-Pancreatico-Biliary Association (AHPBA), and the American Society of Transplant Surgeons (ASTS). The current state of training in HPB surgery in North America was defined through three pathways-HPB, surgical oncology, and solid organ transplant fellowships. Consensus regarding programmatic requirements included establishment of minimum case volumes and inclusion of quality metrics. Formative assessment, using milestones as a framework and inclusive of both operative and nonoperative skills, must be present. Specific core HPB cases should be defined and used for evaluation of operative skills. The conference concluded with a focus on the optimal means to perform summative assessment to evaluate the individual fellow completing a fellowship in HPB surgery. Presentations from the hospital perspective and the American Board of Surgery led to consensus that summative assessment was desired by the public and the hospital systems and should occur in a uniform but possibly modular manner for all HPB fellowship pathways. A task force composed of representatives of the SSO, AHPBA, and ASTS are charged with implementation of the consensus statements emanating from this consensus conference. PMID:26928942

  13. Kyoto global consensus report on Helicobacter pylori gastritis

    PubMed Central

    Sugano, Kentaro; Tack, Jan; Kuipers, Ernst J; Graham, David Y; El-Omar, Emad M; Miura, Soichiro; Haruma, Ken; Asaka, Masahiro; Uemura, Naomi; Malfertheiner, Peter

    2015-01-01

    Objective To present results of the Kyoto Global Consensus Meeting, which was convened to develop global consensus on (1) classification of chronic gastritis and duodenitis, (2) clinical distinction of dyspepsia caused by Helicobacter pylori from functional dyspepsia, (3) appropriate diagnostic assessment of gastritis and (4) when, whom and how to treat H. pylori gastritis. Design Twenty-three clinical questions addressing the above-mentioned four domains were drafted for which expert panels were asked to formulate relevant statements. A Delphi method using an anonymous electronic system was adopted to develop the consensus, the level of which was predefined as ≥80%. Final modifications of clinical questions and consensus were achieved at the face-to-face meeting in Kyoto. Results All 24 statements for 22 clinical questions after extensive modifications and omission of one clinical question were achieved with a consensus level of >80%. To better organise classification of gastritis and duodenitis based on aetiology, a new classification of gastritis and duodenitis is recommended for the 11th international classification. A new category of H. pylori-associated dyspepsia together with a diagnostic algorithm was proposed. The adoption of grading systems for gastric cancer risk stratification, and modern image-enhancing endoscopy for the diagnosis of gastritis, were recommended. Treatment to eradicate H. pylori infection before preneoplastic changes develop, if feasible, was recommended to minimise the risk of more serious complications of the infection. Conclusions A global consensus for gastritis was developed for the first time, which will be the basis for an international classification system and for further research on the subject. PMID:26187502

  14. IncobotulinumtoxinA in aesthetics: Russian multidisciplinary expert consensus recommendations

    PubMed Central

    Yutskovskaya, Yana; Gubanova, Elena; Khrustaleva, Irina; Atamanov, Vasiliy; Saybel, Anastasiya; Parsagashvili, Elena; Dmitrieva, Irina; Sanchez, Elena; Lapatina, Natalia; Korolkova, Tatiana; Saromytskaya, Alena; Goltsova, Elena; Satardinova, Elmira

    2015-01-01

    Background Although there are various international consensus recommendations on the use of botulinum neurotoxin type A (BoNT/A) in facial aesthetics, there are no global or Russian guidelines on the optimal dose of incobotulinumtoxinA, free from complexing proteins, within specific aesthetic indications. This article reports the outcomes of two expert consensus meetings, conducted to review and analyze efficacy and tolerability data for incobotulinumtoxinA in various facial aesthetic indications and to give expert consensus recommendations to ensure best clinical practice among Russian clinicians. Methods Thirteen dermatology and/or plastic surgery experts attended meetings held in Paris, France (November 2013), and Moscow, Russia (March 2014). The expert group reviewed and analyzed the existing evidence, consensus recommendations, and Russian experts’ extensive practical experience of incobotulinumtoxinA in aesthetics to reach consensus on optimal doses, potential dose adjustments, and injection sites of incobotulinumtoxinA for facial aesthetics. Results All experts developed guidance on the optimal doses for incobotulinumtoxinA treatment of different regions of the upper and lower face. The expert panel agreed that there are no differences in the efficacy and duration of the effect between the four BoNT/As that are commercially available for facial aesthetic indications in Russia and that, when administered correctly, all BoNT/As can achieve optimal results. Experts also agreed that nonresponse to BoNT/A can be caused by neutralizing antibodies. Conclusion On the basis of the scientific and clinical evidence available for incobotulinumtoxinA, coupled with the extensive clinical experience of the consensus group, experts recommended the optimal doses of incobotulinumtoxinA effective for treatment of wrinkles of the upper and lower face to achieve the expected aesthetic outcome. These first Russian guidelines on the optimal use of incobotulinumtoxinA for

  15. Expert consensus document: European Consensus Statement on congenital hypogonadotropic hypogonadism--pathogenesis, diagnosis and treatment.

    PubMed

    Boehm, Ulrich; Bouloux, Pierre-Marc; Dattani, Mehul T; de Roux, Nicolas; Dodé, Catherine; Dunkel, Leo; Dwyer, Andrew A; Giacobini, Paolo; Hardelin, Jean-Pierre; Juul, Anders; Maghnie, Mohamad; Pitteloud, Nelly; Prevot, Vincent; Raivio, Taneli; Tena-Sempere, Manuel; Quinton, Richard; Young, Jacques

    2015-09-01

    Congenital hypogonadotropic hypogonadism (CHH) is a rare disorder caused by the deficient production, secretion or action of gonadotropin-releasing hormone (GnRH), which is the master hormone regulating the reproductive axis. CHH is clinically and genetically heterogeneous, with >25 different causal genes identified to date. Clinically, the disorder is characterized by an absence of puberty and infertility. The association of CHH with a defective sense of smell (anosmia or hyposmia), which is found in ∼50% of patients with CHH is termed Kallmann syndrome and results from incomplete embryonic migration of GnRH-synthesizing neurons. CHH can be challenging to diagnose, particularly when attempting to differentiate it from constitutional delay of puberty. A timely diagnosis and treatment to induce puberty can be beneficial for sexual, bone and metabolic health, and might help minimize some of the psychological effects of CHH. In most cases, fertility can be induced using specialized treatment regimens and several predictors of outcome have been identified. Patients typically require lifelong treatment, yet ∼10-20% of patients exhibit a spontaneous recovery of reproductive function. This Consensus Statement summarizes approaches for the diagnosis and treatment of CHH and discusses important unanswered questions in the field. PMID:26194704

  16. Eating Disorders: Cultural Model and Consensus Regarding Food.

    PubMed

    Manochio-Pina, Marina; Dos Santos, José Ernesto; Dressler, William W; Pessa Ribeiro, Rosane Pilot

    2015-01-01

    The cultural model of food was applied to 112 adult patients with eating disorders (PG) and 36 healthy adult women (CG) of similar age. The Free List and Ranking of Foods was used to group foods and verify consensus and cultural aspects. Calories, health, and taste were the dimensions used by the participants to group the foods, and strong consensus was achieved in regard to calories and health. There were, however, inter- and intra-group divergences in regard to these ideas, especially in the PG. The CG used distinct criteria, showing a more complex model. PMID:25874647

  17. Consensus gene regulatory networks: combining multiple microarray gene expression datasets

    NASA Astrophysics Data System (ADS)

    Peeling, Emma; Tucker, Allan

    2007-09-01

    In this paper we present a method for modelling gene regulatory networks by forming a consensus Bayesian network model from multiple microarray gene expression datasets. Our method is based on combining Bayesian network graph topologies and does not require any special pre-processing of the datasets, such as re-normalisation. We evaluate our method on a synthetic regulatory network and part of the yeast heat-shock response regulatory network using publicly available yeast microarray datasets. Results are promising; the consensus networks formed provide a broader view of the potential underlying network, obtaining an increased true positive rate over networks constructed from a single data source.

  18. Exploring community structure in networks by consensus dynamics

    NASA Astrophysics Data System (ADS)

    He, He; Yang, Bo; Hu, Xiaoming

    2016-05-01

    This paper investigates the relationship between community structure and consensus dynamics in complex networks. We analyze the dynamical process towards consensus and show that those sets of densely interconnected nodes corresponding to well-defined communities appear in different time scales. In order to reveal such topological scales, two algorithms built around the idea of visualizing the evolution of different measured quantities are proposed. Then we test our algorithms on a few benchmark graphs whose community structures are already known. Numeric simulations are given to demonstrate the effectiveness and reliability of our methods.

  19. Genomics and Machine Learning for Taxonomy Consensus: The Mycobacterium tuberculosis Complex Paradigm

    PubMed Central

    Azé, Jérôme; Sola, Christophe; Zhang, Jian; Lafosse-Marin, Florian; Yasmin, Memona; Siddiqui, Rubina; Kremer, Kristin; van Soolingen, Dick; Refrégier, Guislaine

    2015-01-01

    Infra-species taxonomy is a prerequisite to compare features such as virulence in different pathogen lineages. Mycobacterium tuberculosis complex taxonomy has rapidly evolved in the last 20 years through intensive clinical isolation, advances in sequencing and in the description of fast-evolving loci (CRISPR and MIRU-VNTR). On-line tools to describe new isolates have been set up based on known diversity either on CRISPRs (also known as spoligotypes) or on MIRU-VNTR profiles. The underlying taxonomies are largely concordant but use different names and offer different depths. The objectives of this study were 1) to explicit the consensus that exists between the alternative taxonomies, and 2) to provide an on-line tool to ease classification of new isolates. Genotyping (24-VNTR, 43-spacers spoligotypes, IS6110-RFLP) was undertaken for 3,454 clinical isolates from the Netherlands (2004-2008). The resulting database was enlarged with African isolates to include most human tuberculosis diversity. Assignations were obtained using TB-Lineage, MIRU-VNTRPlus, SITVITWEB and an algorithm from Borile et al. By identifying the recurrent concordances between the alternative taxonomies, we proposed a consensus including 22 sublineages. Original and consensus assignations of the all isolates from the database were subsequently implemented into an ensemble learning approach based on Machine Learning tool Weka to derive a classification scheme. All assignations were reproduced with very good sensibilities and specificities. When applied to independent datasets, it was able to suggest new sublineages such as pseudo-Beijing. This Lineage Prediction tool, efficient on 15-MIRU, 24-VNTR and spoligotype data is available on the web interface “TBminer.” Another section of this website helps summarizing key molecular epidemiological data, easing tuberculosis surveillance. Altogether, we successfully used Machine Learning on a large dataset to set up and make available the first

  20. Laryngeal examination in thyroid and parathyroid surgery: An American Head and Neck Society consensus statement: AHNS Consensus Statement.

    PubMed

    Sinclair, Catherine F; Bumpous, Jeffrey M; Haugen, Bryan R; Chala, Andres; Meltzer, Daniel; Miller, Barbra S; Tolley, Neil S; Shin, Jennifer J; Woodson, Gayle; Randolph, Gregory W

    2016-06-01

    This American Head and Neck Society (AHNS) consensus statement discusses the techniques of laryngeal examination for patients undergoing thyroidectomy and parathyroidectomy. It is intended to help guide all clinicians who diagnose or manage adult patients with thyroid disease for whom surgery is indicated, contemplated, or has been performed. This consensus statement concludes that flexible transnasal laryngoscopy is the optimal laryngeal examination technique, with other techniques including laryngeal ultrasound and stroboscopy being useful in selected scenarios. © 2016 Wiley Periodicals, Inc. Head Neck 38: 811-819, 2016. PMID:26970554

  1. A Consensus Method for the Prediction of ‘Aggregation-Prone’ Peptides in Globular Proteins

    PubMed Central

    Tsolis, Antonios C.; Papandreou, Nikos C.; Iconomidou, Vassiliki A.; Hamodrakas, Stavros J.

    2013-01-01

    The purpose of this work was to construct a consensus prediction algorithm of ‘aggregation-prone’ peptides in globular proteins, combining existing tools. This allows comparison of the different algorithms and the production of more objective and accurate results. Eleven (11) individual methods are combined and produce AMYLPRED2, a publicly, freely available web tool to academic users (http://biophysics.biol.uoa.gr/AMYLPRED2), for the consensus prediction of amyloidogenic determinants/‘aggregation-prone’ peptides in proteins, from sequence alone. The performance of AMYLPRED2 indicates that it functions better than individual aggregation-prediction algorithms, as perhaps expected. AMYLPRED2 is a useful tool for identifying amyloid-forming regions in proteins that are associated with several conformational diseases, called amyloidoses, such as Altzheimer's, Parkinson's, prion diseases and type II diabetes. It may also be useful for understanding the properties of protein folding and misfolding and for helping to the control of protein aggregation/solubility in biotechnology (recombinant proteins forming bacterial inclusion bodies) and biotherapeutics (monoclonal antibodies and biopharmaceutical proteins). PMID:23326595

  2. A High-Density SNP and SSR Consensus Map Reveals Segregation Distortion Regions in Wheat

    PubMed Central

    Li, Chunlian; Bai, Guihua; Chao, Shiaoman; Wang, Zhonghua

    2015-01-01

    Segregation distortion is a widespread phenomenon in plant and animal genomes and significantly affects linkage map construction and identification of quantitative trait loci (QTLs). To study segregation distortion in wheat, a high-density consensus map was constructed using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers by merging two genetic maps developed from two recombinant-inbred line (RIL) populations, Ning7840 × Clark and Heyne × Lakin. Chromosome regions with obvious segregation distortion were identified in the map. A total of 3541 SNPs and 145 SSRs were mapped, and the map covered 3258.7 cM in genetic distance with an average interval of 0.88 cM. The number of markers that showed distorted segregation was 490 (18.5%) in the Ning7840 × Clark population and 225 (10.4%) in the Heyne × Lakin population. Most of the distorted markers (630) were mapped in the consensus map, which accounted for 17.1% of mapped markers. The majority of the distorted markers clustered in the segregation distortion regions (SDRs) on chromosomes 1B, 2A, 2B, 3A, 3B, 4B, 5A, 5B, 5D, 6B, 7A, and 7D. All of the markers in a given SDR skewed toward one of the parents, suggesting that gametophytic competition during zygote formation was most likely one of the causes for segregation distortion in the populations. PMID:26601111

  3. International consensus guidance for management of myasthenia gravis

    PubMed Central

    Wolfe, Gil I.; Benatar, Michael; Evoli, Amelia; Gilhus, Nils E.; Illa, Isabel; Kuntz, Nancy; Massey, Janice M.; Melms, Arthur; Murai, Hiroyuki; Nicolle, Michael; Palace, Jacqueline; Richman, David P.; Verschuuren, Jan; Narayanaswami, Pushpa

    2016-01-01

    Objective: To develop formal consensus-based guidance for the management of myasthenia gravis (MG). Methods: In October 2013, the Myasthenia Gravis Foundation of America appointed a Task Force to develop treatment guidance for MG, and a panel of 15 international experts was convened. The RAND/UCLA appropriateness methodology was used to develop consensus guidance statements. Definitions were developed for goals of treatment, minimal manifestations, remission, ocular MG, impending crisis, crisis, and refractory MG. An in-person panel meeting then determined 7 treatment topics to be addressed. Initial guidance statements were developed from literature summaries. Three rounds of anonymous e-mail votes were used to attain consensus on guidance statements modified on the basis of panel input. Results: Guidance statements were developed for symptomatic and immunosuppressive treatments, IV immunoglobulin and plasma exchange, management of impending and manifest myasthenic crisis, thymectomy, juvenile MG, MG associated with antibodies to muscle-specific tyrosine kinase, and MG in pregnancy. Conclusion: This is an international formal consensus of MG experts intended to be a guide for clinicians caring for patients with MG worldwide. PMID:27358333

  4. When goals diverge: Staff consensus and the organizational climate.

    PubMed

    Melnick, Gerald; Ulaszek, Wendy R; Lin, Hsiu-Ju; Wexler, Harry K

    2009-08-01

    A sample of correctional officers and prison substance abuse treatment staff collected by the National Criminal Justice Treatment Practices Survey is used to provide an exploratory study of an aspect of organizational culture consisting of consensus (agreement) among prison personnel regarding their beliefs about rehabilitation in the presence of conflicting organizational goals and aspects of the organizational climate important to change. Findings show that among those staff members responding to the survey, the belief in rehabilitation scale mean score was associated with higher levels of organizational commitment, and interdepartmental coordination. However, an hierarchical linear modeling (HLM) analysis that used an index score derived from the standard deviation for staff consensus regarding these same beliefs about rehabilitation produced a different pattern of results, showing that high levels of consensus were associated with job frustration, cynicism towards the ability of the institution to change, and lower levels of organizational commitment. The authors conclude that, although the sample may not express the beliefs of corrections officers or prison-based treatment staff at large, within the sample, consensus appeared to play a unique role in evaluating the effect of divergent goals on organizational climate as it relates to change, and warrants consideration when considering the effects of organizational climate. PMID:19097709

  5. What Happened to the Consensus on Higher Still? CES Briefing.

    ERIC Educational Resources Information Center

    Raffe, David; Howieson, Cathy; Tinklin, Teresa

    The Scottish "exam results crisis" of August 2000 appeared to reveal widespread dissatisfaction with the Higher Still reforms introduced the previous year. For a time the future of the reform seemed to hang in the balance. Yet Higher Still was the product of the consensus which emerged from the "Howie debates" of the early 1990s. It involved a…

  6. Ethics & Agenda 21: Moral Implications of a Global Consensus.

    ERIC Educational Resources Information Center

    Brown, Noel J., Ed.; Quiblier, Pierre, Ed.

    At the Earth Summit held at Rio in June 1992, the leaders of more than 170 countries were able to adopt by consensus a common global strategy, an agenda for action, namely Agenda 21, that envisions a future that will be prosperous, equitable, and sustainable. This book contains a collection of essays by leading environmental philosophers,…

  7. ISPMD consensus on the management of premenstrual disorders

    PubMed Central

    O’Brien, Patrick Michael Shaughn; Bäckström, Torbjorn; Brown, Candace; Dennerstein, Lorraine; Endicott, Jean; Epperson, C. Neill; Eriksson, Elias; Freeman, Ellen W.; Halbreich, Uriel; Ismail, Khalid; Panay, Nicholas; Pearlstein, Teri; Rapkin, Andrea; Reid, Robert; Rubinow, David; Schmidt, Peter; Steiner, Meir; Studd, John; Sundström-Poromaa, Inger; Yonkers, Kimberly

    2014-01-01

    The second consensus meeting of the International Society for Premenstrual Disorders (ISPMD) took place in London during March 2011. The primary goal was to evaluate the published evidence and consider the expert opinions of the ISPMD members to reach a consensus on advice for the management of premenstrual disorders. Gynaecologists, psychiatrists, psychologists and pharmacologists each formally presented the evidence within their area of expertise; this was followed by an in-depth discussion leading to consensus recommendations. This article provides a comprehensive review of the outcomes from the meeting. The group discussed and agreed that careful diagnosis based on the recommendations and classification derived from the first ISPMD consensus conference is essential and should underlie the appropriate management strategy. Options for the management of premenstrual disorders fall under two broad categories, (a) those influencing central nervous activity, particularly the modulation of the neurotransmitter serotonin and (b) those that suppress ovulation. Psychotropic medication, such as selective serotonin reuptake inhibitors, probably acts by dampening the influence of sex steroids on the brain. Oral contraceptives, gonadotropin-releasing hormone agonists, danazol and estradiol all most likely function by ovulation suppression. The role of oophorectomy was also considered in this respect. Alternative therapies are also addressed, with, e.g. cognitive behavioural therapy, calcium supplements and Vitex agnus castus warranting further exploration. PMID:23624686

  8. Demographic Homogeneity and Spousal Consensus: A Methodological Perspective

    ERIC Educational Resources Information Center

    Jaco, Daniel E.; Shepard, Jon M.

    1975-01-01

    The findings in this study were generally inconsistent and nonsupportive of a relationship between demographic homogeneity and spousal response consensus within or across the two areas of sex knowledge and family planning attitudes. Consideration of the limitations, implications, and future directions of this research are presented. (Author/PC)

  9. Unavoidable pressure injury: state of the science and consensus outcomes.

    PubMed

    Edsberg, Laura E; Langemo, Diane; Baharestani, Mona Mylene; Posthauer, Mary Ellen; Goldberg, Margaret

    2014-01-01

    In the vast majority of cases, appropriate identification and mitigation of risk factors can prevent or minimize pressure ulcer (PU) formation. However, some PUs are unavoidable. Based on the importance of this topic and the lack of literature focused on PU unavoidability, the National Pressure Ulcer Advisory Panel hosted a multidisciplinary conference in 2014 to explore the issue of PU unavoidability within an organ system framework, which considered the complexities of nonmodifiable intrinsic and extrinsic risk factors. Prior to the conference, an extensive literature review was conducted to analyze and summarize the state of the science in the area of unavoidable PU development and items were developed. An interactive process was used to gain consensus based on these items among stakeholders of various organizations and audience members. Consensus was reached when 80% agreement was obtained. The group reached consensus that unavoidable PUs do occur. Consensus was also obtained in areas related to cardiopulmonary status, hemodynamic stability, impact of head-of-bed elevation, septic shock, body edema, burns, immobility, medical devices, spinal cord injury, terminal illness, and nutrition. PMID:24901936

  10. Position Statements, Issue Briefs, Resolutions and Consensus Statements. Revised

    ERIC Educational Resources Information Center

    National Association of School Nurses (NJ1), 2012

    2012-01-01

    This article presents position statements, issue briefs, and resolutions and consensus statements of the National Association of School Nurses (NASN). The Position Statements include: (1) Allergy/Anaphylaxis Management in the School Setting; (2) Caseload Assignments; (3) Child Mortality in the School Setting; (4) Chronic Health Conditions, Managed…

  11. Functional Analysis of HIV/AIDS Stigma: Consensus or Divergence?

    ERIC Educational Resources Information Center

    Hosseinzadeh, Hassan; Hossain, Syeda Zakia

    2011-01-01

    Functional theory proposes that attitudes may serve a variety of purposes for individuals. This study aimed to determine whether stigmatized attitudes toward HIV/AIDS serve the same function for all (consensus function) or serve different functions for different individuals (divergence function) by assessing various aspects of HIV/AIDS stigma…

  12. Recommendations for the treatment of migraine attacks - a Brazilian consensus.

    PubMed

    Bordini, Carlos Alberto; Roesler, Célia; Carvalho, Deusvenir de Souza; Macedo, Djacir Dantas P; Piovesan, Élcio; Melhado, Eliana Meire; Dach, Fabiola; Kowacs, Fernando; Silva Júnior, Hilton Mariano da; Souza, Jano Alves de; Maciel, Jayme Antunes; Carvalho, João José de Freitas de; Speciali, José Geraldo; Barea, Liselotte Menke; Queiroz, Luiz Paulo; Ciciarelli, Marcelo Cedrinho; Valença, Marcelo Moraes; Lima, Márcia Maria Ferreira; Vincent, Maurice Borges

    2016-03-01

    In this article, a group of experts in headache management of the Brazilian Headache Society developed through a consensus strategic measurements to treat a migraine attack in both the child and the adult. Particular emphasis was laid on the treatment of migraine in women, including at pregnancy, lactation and perimenstrual period. PMID:27050859

  13. Consensus and Dissent: Teaching English Past, Present, and Future.

    ERIC Educational Resources Information Center

    Farmer, Marjorie N., Ed.

    Published in conjunction with the diamond jubilee of the National Council of Teachers of English, the essays in this yearbook explore the dichotomies characterizing Council debates over the years, such as freedom and discipline, tradition and reform, theory and practice--all reflecting a profession defining itself in a rhythm of consensus and…

  14. The "Beijing Consensus" and the Chinese Model of University Autonomy

    ERIC Educational Resources Information Center

    Zha, Qiang; Hayhoe, Ruth

    2014-01-01

    This paper attempts to address connections between the Chinese model for development or the "Beijing Consensus" and Chinese universities. Chinese universities seem to be caught between serving governmental agendas and pursuing their own goals as an academic community. Up until recently, they had become used to following the lead of the…

  15. Revised global consensus statement on menopausal hormone therapy.

    PubMed

    de Villiers, T J; Hall, J E; Pinkerton, J V; Pérez, S Cerdas; Rees, M; Yang, C; Pierroz, D D

    2016-09-01

    The following Consensus Statement is endorsed by The International Menopause Society, The North American Menopause Society, The Endocrine Society, The European Menopause and Andropause Society, The Asia Pacific Menopause Federation, The International Osteoporosis Foundation and The Federation of Latin American Menopause Societies. PMID:27389038

  16. Groping and Hoping for a Consensus on Calculator Use.

    ERIC Educational Resources Information Center

    Mathematics Education Dialogues, 1999

    1999-01-01

    This issue of Mathematics Education Dialogues focuses on the use of calculators in the mathematics classroom. The eleven articles on this theme include: (1) "Groping and Hoping for a Consensus on Calculator Use" (Zalman Usiskin); (2) "Let's Abolish Pencil-and-Paper Arithmetic" (Anthony Ralston); (3) "Do We Need Calculators?" (Kim Mackey); (4) "How…

  17. Forging Consensus for Implementing Youth Socialization Policy in Northwest China

    ERIC Educational Resources Information Center

    Fairbrother, Gregory P.

    2011-01-01

    The goal of this article is to examine how the provincial education media in China play a role of forging consensus among local actors responsible for the implementation of new centrally-promulgated youth socialization policy. In doing so, it also explores the tension among three of the Chinese state's claims to legitimacy: economic development,…

  18. Expert Consensus on Characteristics of Wisdom: A Delphi Method Study

    ERIC Educational Resources Information Center

    Jeste, Dilip V.; Ardelt, Monika; Blazer, Dan; Kraemer, Helena C.; Vaillant, George; Meeks, Thomas W.

    2010-01-01

    Purpose: Wisdom has received increasing attention in empirical research in recent years, especially in gerontology and psychology, but consistent definitions of wisdom remain elusive. We sought to better characterize this concept via an expert consensus panel using a 2-phase Delphi method. Design and Methods: A survey questionnaire comprised 53…

  19. When Consensus Decision-Making Fails: A Case Study.

    ERIC Educational Resources Information Center

    Savage, Grant T.

    Habermas's theory of dialogue was used to evaluate the process of decision making that occurred in a labor-management committee's meeting to discuss flextime. The study attempted to determine why, at that meeting, the committee's consensus process of decision making failed. W.R. Bion's theory of unconscious group motives was also used to…

  20. Relevance of Web Documents:Ghosts Consensus Method.

    ERIC Educational Resources Information Center

    Gorbunov, Andrey L.

    2002-01-01

    Discusses how to improve the quality of Internet search systems and introduces the Ghosts Consensus Method which is free from the drawbacks of digital democracy algorithms and is based on linear programming tasks. Highlights include vector space models; determining relevant documents; and enriching query terms. (LRW)

  1. Ways To Achieve "Working Consensus": Some Cross-Cultural Considerations.

    ERIC Educational Resources Information Center

    Pearson, Bethyl A.; Xu, Qiang

    A study investigated cultural variations in the ways groups of speakers reach consensus in the face of disagreement or suggestion. Subjects were six graduate students in each of five groups: one composed of native speakers of American English, two of Taiwanese Chinese, and two of mainland Chinese. Each group performed a desert survival exercise,…

  2. Facilitating a Faculty Learning Community: Determining Consensus Using Q Methodology

    ERIC Educational Resources Information Center

    Ramlo, Susan

    2011-01-01

    With plans to improve a Technical Report Writing course, writing faculty and engineering technology faculty formed a faculty learning community (FLC). Although discussions were often productive, it was often difficult to gauge consensus and differing views among the group members. In a previous study, Q methodology, a measure of subjectivity, was…

  3. How to Judge a Science Fair. Use the Consensus Method.

    ERIC Educational Resources Information Center

    Levin, Karen Noel; Levin, Robert E.

    1991-01-01

    Discussed is a method for judging science fair projects considered to be more accurate than just an averaging of scores. The use of many categories so that the number of projects in each is relatively small is proposed. The advantages of using the consensus method are described. (KR)

  4. Scalable and Fault Tolerant Failure Detection and Consensus

    SciTech Connect

    Katti, Amogh; Di Fatta, Giuseppe; Naughton III, Thomas J; Engelmann, Christian

    2015-01-01

    Future extreme-scale high-performance computing systems will be required to work under frequent component failures. The MPI Forum's User Level Failure Mitigation proposal has introduced an operation, MPI_Comm_shrink, to synchronize the alive processes on the list of failed processes, so that applications can continue to execute even in the presence of failures by adopting algorithm-based fault tolerance techniques. This MPI_Comm_shrink operation requires a fault tolerant failure detection and consensus algorithm. This paper presents and compares two novel failure detection and consensus algorithms. The proposed algorithms are based on Gossip protocols and are inherently fault-tolerant and scalable. The proposed algorithms were implemented and tested using the Extreme-scale Simulator. The results show that in both algorithms the number of Gossip cycles to achieve global consensus scales logarithmically with system size. The second algorithm also shows better scalability in terms of memory and network bandwidth usage and a perfect synchronization in achieving global consensus.

  5. Building Consensus and Providing Guidance among Professional Societies?

    ERIC Educational Resources Information Center

    Lott, Johnny W.

    2007-01-01

    Beyond Crossroads has as a stated objective having "two-year college mathematics faculty and institutions collaborate with professional societies, government agencies, and educational institutions to build consensus and provide guidance to practitioners." Issues involving two-year faculty and university faculty members in conversations about…

  6. Using Dynamic Modeling to Scope Environmental Problems and Build Consensus

    PubMed

    Costanza; Ruth

    1998-03-01

    / This paper assesses the changing role of dynamic modeling for understanding and managing complex ecological economic systems. It discusses new modeling tools for problem scoping and consensus building among a broad range of stakeholders and describes four case studies in which dynamic modeling has been used to collect and organize data, synthesize knowledge, and build consensus about the management of complex systems. The case studies range from industrial systems (mining, smelting, and refining of iron and steel in the United States) to ecosystems (Louisiana coastal wetlands, and Fynbos ecosystems in South Africa) to linked ecological economic systems (Maryland's Patuxent River basin in the United States). They illustrate uses of dynamic modeling to include stakeholders in all stages of consensus building, ranging from initial problem scoping to model development. The resultant models are the first stage in a three-stage modeling process that includes research and management models as the later stages.KEY WORDS: Dynamic modeling; Scoping; Consensus building; Environmental management; Ecosystem management; Policy making; Graphical programming languages PMID:9465128

  7. 75 FR 70074 - Consensus Standards, Light-Sport Aircraft

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-16

    ... Federal Aviation Administration Consensus Standards, Light-Sport Aircraft AGENCY: Federal Aviation... provisions of the Sport Pilot and Light-Sport Aircraft rule issued July 16, 2004, and effective September 1, 2004. ASTM International Committee F37 on Light Sport Aircraft developed the revised standards...

  8. 76 FR 45647 - Consensus Standards, Light-Sport Aircraft

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-29

    ... revision process. Background: Under the provisions of the Sport Pilot and Light-Sport Aircraft rule, 69 FR... Federal Aviation Administration Consensus Standards, Light-Sport Aircraft AGENCY: Federal Aviation... to the provisions of the Sport Pilot and Light-Sport Aircraft rule issued July 16, 2004,...

  9. Canadian Athletic Therapists' Association Education Task Force Consensus Statements

    ERIC Educational Resources Information Center

    Lafave, Mark R.; Bergeron, Glen; Klassen, Connie; Parr, Kelly; Valdez, Dennis; Elliott, Jacqueline; Peeler, Jason; Orecchio, Elsa; McKenzie, Kirsty; Streed, Kristin; DeMont, Richard

    2016-01-01

    Context: A published commentary from 2 of the current authors acted as a catalyst for raising some key issues that have arisen in athletic therapy education in Canada over the years. Objective: The purpose of this article is to report on the process followed to establish a number of consensus statements related to postsecondary athletic therapy…

  10. Consensus Problems on Small World Graphs: A Structural Study

    NASA Astrophysics Data System (ADS)

    Hovareshti, Pedram; Baras, John S.

    Consensus problems arise in many instances of collaborative control of multi-agent complex systems; where it is important for the agents to act in coordination with the other agents. To reach coordination, agents need to share information. In large groups of agents the information sharing should be local in some sense, due to energy limitations, reliability, and other constraints. A consensus protocol is an iterative method that provides the group with a common coordination variable. However, local information exchange limits the speed of convergence of such protocols. Therefore, in order to achieve high convergence speed, we should be able to design appropriate network topologies. A reasonable conjecture is that the small world graphs should result in good convergence speed for consensus problems because their low average pairwise path length should speed the diffusion of information in the system. In this paper we address this conjecture by simulations and also by studying the spectral properties of a class of matrices corresponding to consensus problems on small world graphs.

  11. The Consensus Plan: Dutchess Community College, 1984-85.

    ERIC Educational Resources Information Center

    Donsky, Aaron P.; And Others

    This 1984-85 Consensus Plan for Dutchess Community College is the result of a comprehensive planning process characterized by three elements: (1) a cycle of departmental input directed by a voluntary planning committee and finalized by the deans and president; (2) an integrated process in which departmental plans reflect the major thrusts…

  12. Precision of distances and ordering of microsatellite markers in consensus linkage maps of chromosomes 1, 3 and 4 from two reciprocal chicken populations using bootstrap sampling.

    PubMed

    Rosário, M F; Margarido, G R A; Boschiero, C; Moura, A S A M T; Ledur, M C; Coutinho, L L; Garcia, A A F

    2010-01-01

    Some factors complicate comparisons between linkage maps from different studies. This problem can be resolved if measures of precision, such as confidence intervals and frequency distributions, are associated with markers. We examined the precision of distances and ordering of microsatellite markers in the consensus linkage maps of chromosomes 1, 3 and 4 from two F(2) reciprocal Brazilian chicken populations, using bootstrap sampling. Single and consensus maps were constructed. The consensus map was compared with the International Consensus Linkage Map and with the whole genome sequence. Some loci showed segregation distortion and missing data, but this did not affect the analyses negatively. Several inversions and position shifts were detected, based on 95% confidence intervals and frequency distributions of loci. Some discrepancies in distances between loci and in ordering were due to chance, whereas others could be attributed to other effects, including reciprocal crosses, sampling error of the founder animals from the two populations, F(2) population structure, number of and distance between microsatellite markers, number of informative meioses, loci segregation patterns, and sex. In the Brazilian consensus GGA1, locus LEI1038 was in a position closer to the true genome sequence than in the International Consensus Map, whereas for GGA3 and GGA4, no such differences were found. Extending these analyses to the remaining chromosomes should facilitate comparisons and the integration of several available genetic maps, allowing meta-analyses for map construction and quantitative trait loci (QTL) mapping. The precision of the estimates of QTL positions and their effects would be increased with such information. PMID:20645260

  13. Immunogenicity of a novel engineered HIV-1 clade C synthetic consensus-based envelope DNA vaccine.

    PubMed

    Yan, Jian; Corbitt, Natasha; Pankhong, Panyupa; Shin, Thomas; Khan, Amir; Sardesai, Niranjan Y; Weiner, David B

    2011-09-22

    DNA vaccines require significant engineering in order to generate strong CTL responses in both non-human primates and humans. In this study, we designed a clade C env gene (EY3E1-C) to decrease the genetic distances of virus isolates within clade C and focus the induced T cell responses to conserved clade C epitopes. After generating a consensus sequence by analyzing full-length clade C env early transmitter sequences, several modifications were performed to increase the expression of the EY3E1-C, including codon/RNA optimization, addition of Kozak sequence and addition of an IgE leader sequence. We also shortened the V1 and V2 loops to approximate early transmitter isolate sequences and the cytoplasmic tail was truncated to prevent envelope recycling. When studied as a DNA vaccine in Balb/c mice, compared to a primary codon-optimized clade C envelope DNA vaccine (p96ZM651gp140-CD5), this novel construct is up to three times more potent in driving CTL responses. Importantly this construct not only induces stronger cross-reactive cellular responses within clade C, it also induces stronger immune responses against clade B and group M envelope peptide pools than p96ZM651gp140-CD5. Epitope mapping demonstrated that EY3E1-C was able to induce clade C envelope-specific immune responses against 15 peptide pools, clade B envelope-specific immune responses against 19 peptide pools and group M envelope-specific immune responses against 16 peptide pools out of 29, respectively, indicating that a significant increase in the breadth of induced immune responses. The analysis of antibody responses suggested that vaccination of pEY3E1-C could induce a clade C envelope-specific antibody response. The cellular immune responses of pEY3E1-C could be further enhanced when the DNA was delivered by using electroporation (EP). Thus, the synthetic engineered consensus EY3E1-C gene is capable of eliciting stronger and broader CTL responses than primary clade C envelopes. This finding

  14. Detection and analysis of six lizard adenoviruses by consensus primer PCR provides further evidence of a reptilian origin for the atadenoviruses.

    PubMed

    Wellehan, James F X; Johnson, April J; Harrach, Balázs; Benkö, Mária; Pessier, Allan P; Johnson, Calvin M; Garner, Michael M; Childress, April; Jacobson, Elliott R

    2004-12-01

    A consensus nested-PCR method was designed for investigation of the DNA polymerase gene of adenoviruses. Gene fragments were amplified and sequenced from six novel adenoviruses from seven lizard species, including four species from which adenoviruses had not previously been reported. Host species included Gila monster, leopard gecko, fat-tail gecko, blue-tongued skink, Tokay gecko, bearded dragon, and mountain chameleon. This is the first sequence information from lizard adenoviruses. Phylogenetic analysis indicated that these viruses belong to the genus Atadenovirus, supporting the reptilian origin of atadenoviruses. This PCR method may be useful for obtaining templates for initial sequencing of novel adenoviruses. PMID:15542689

  15. Detection and Analysis of Six Lizard Adenoviruses by Consensus Primer PCR Provides Further Evidence of a Reptilian Origin for the Atadenoviruses

    PubMed Central

    Wellehan, James F. X.; Johnson, April J.; Harrach, Balázs; Benkö, Mária; Pessier, Allan P.; Johnson, Calvin M.; Garner, Michael M.; Childress, April; Jacobson, Elliott R.

    2004-01-01

    A consensus nested-PCR method was designed for investigation of the DNA polymerase gene of adenoviruses. Gene fragments were amplified and sequenced from six novel adenoviruses from seven lizard species, including four species from which adenoviruses had not previously been reported. Host species included Gila monster, leopard gecko, fat-tail gecko, blue-tongued skink, Tokay gecko, bearded dragon, and mountain chameleon. This is the first sequence information from lizard adenoviruses. Phylogenetic analysis indicated that these viruses belong to the genus Atadenovirus, supporting the reptilian origin of atadenoviruses. This PCR method may be useful for obtaining templates for initial sequencing of novel adenoviruses. PMID:15542689

  16. Noise and Hearing Loss. NIH Consensus Development Conference Consensus Statement (January 22-24, 1990). Volume 8, Number 1.

    ERIC Educational Resources Information Center

    National Institutes of Health (DHHS), Bethesda, MD.

    This report is the product of a National Institutes of Health Consensus Development Conference on Noise and Hearing Loss which addressed the characteristics of noise-induced hearing loss, acoustic parameters of hazardous noise exposure, individual and age-specific susceptibility, and prevention strategies. The report examines the incidence of…

  17. Direct Chloroplast Sequencing: Comparison of Sequencing Platforms and Analysis Tools for Whole Chloroplast Barcoding

    PubMed Central

    Brozynska, Marta; Furtado, Agnelo; Henry, Robert James

    2014-01-01

    Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina) and Ion Torrent (Life Technology) sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare). Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels) between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis. PMID:25329378

  18. Sequence-specific interaction between HIV-1 matrix protein and viral genomic RNA revealed by in vitro genetic selection.

    PubMed Central

    Purohit, P; Dupont, S; Stevenson, M; Green, M R

    2001-01-01

    The human immunodeficiency virus type-1 matrix protein (HIV-1 MA) is a multifunctional structural protein synthesized as part of the Pr55 gag polyprotein. We have used in vitro genetic selection to identify an RNA consensus sequence that specifically interacts with MA (Kd = 5 x 10(-7) M). This 13-nt MA binding consensus sequence bears a high degree of homology (77%) to a region (nt 1433-1446) within the POL open reading frame of the HIV-1 genome (consensus sequence from 38 HIV-1 strains). Chemical interference experiments identified the nucleotides within the MA binding consensus sequence involved in direct contact with MA. We further demonstrate that this RNA-protein interaction is mediated through a stretch of basic amino acids within MA. Mutations that disrupt the interaction between MA and its RNA binding site within the HIV-1 genome resulted in a measurable decrease in viral replication. PMID:11345436

  19. Consensus Conference on North American Training in Hepatopancreaticobiliary Surgery: A Review of the Conference and Presentation of Consensus Statements.

    PubMed

    Jeyarajah, D Rohan; Berman, Russell S; Doyle, Majella; Geevarghese, Sunil K; Posner, Mitchell C; Farmer, Douglas; Minter, Rebecca M

    2016-07-01

    The findings and recommendations of the North American Consensus Conference on Training in HPB Surgery held October 2014 are presented. The conference was hosted by the Society for Surgical Oncology (SSO), Americas Hepatopancreaticobiliary Association (AHPBA), and the American Society of Transplant Surgeons (ASTS). The current state of training in HPB surgery in North America was defined through three pathways-HPB, Surgical Oncology, and Solid Organ Transplant fellowships. Consensus regarding programmatic requirements included establishment of minimum case volumes and inclusion of quality metrics. Formative assessment, using milestones as a framework and inclusive of both operative and non-operative skills, must be present. Specific core HPB cases should be defined and used for evaluation of operative skills. The conference concluded with a focus on the optimal means to perform summative assessment to evaluate the individual fellow completing a fellowship in HPB surgery. Presentations from the hospital perspective and the American Board of Surgery led to consensus that summative assessment was desired by the public and the hospital systems, and should occur in a uniform but possibly modular manner for all HPB fellowship pathways. A task force comprised of representatives of the SSO, AHPBA, and ASTS are charged with implementation of the consensus statements emanating from this consensus conference.Copyright © 2016 The American Society of Transplantation, the American Society of Transplant Surgeons, and the Society of Surgical Oncology. All rights reserved. No part of this document may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without written permission by The American Society of Transplantation, the American Society of Transplant Surgeons, or the Society of Surgical Oncology. PMID:26932708

  20. Rat beta 1-adrenergic receptor regulatory region containing consensus AP-2 elements recognizes novel transactivator proteins.

    PubMed

    Kirigiti, P; Yang, Y F; Li, X; Li, B; Midson, C N; Machida, C A

    2000-03-01

    beta 1-Adrenergic receptors (beta1-ARs) serve as important regulators of central nervous system (CNS)-mediated behavior and several neural functions, including mood, memory, neuroendocrine control, and stimulation of autonomic function. Using beta 1-AR-luciferase reporter recombinants, we have previously determined that important beta 1-AR genetic elements controlling expression within the C6 glioma cell line are contained within the region -396 to -299, relative to the translational start site. By conducting progressive internal deletions of the rat beta 1-AR 5' flanking region and with the use of beta 1-AR-luciferase recombinants, we have verified that this region contains the primary beta 1-AR promoter and/or major regulatory elements. To begin the identification of protein factors involved in beta 1-AR transcriptional activity conferred by this beta 1-AR region and flanking sequences, we conducted electrophoretic mobility shift assays using defined beta 1-AR DNA subregion probes. One probe (GS-1), encompassing the region -396 to -367, was found to produce two major and two minor mobility shift complexes when bound to nuclear extracts from the beta 1-AR expresser C6 cell line. UV-crosslinking of DNA-protein complexes, coupled with DNase I digestion, indicated that this beta 1-AR region interacts with one major protein of approximately 117 kDa molecular weight and additional minor proteins. GS-1 DNA-protein complexes were observed using beta 1-AR expresser tissues in the CNS, including cortex, hippocampus, and olfactory bulb. No DNA-protein complexes were observed when using nuclear extracts from beta 1-AR nonexpresser tissues; in some cases, using L6 cells, previously characterized to express little or no beta1-ARs, a reduction in intensities of the DNA-protein complexes was observed. Competition experiments indicate that nuclear protein binds to one of two subregions within the GS-1 sequence that contain AP-2-like consensus elements. Recombinant AP-2 protein

  1. A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda.

    PubMed

    Westbrook, Jared W; Chhatre, Vikram E; Wu, Le-Shin; Chamala, Srikar; Neves, Leandro Gomide; Muñoz, Patricio; Martínez-García, Pedro J; Neale, David B; Kirst, Matias; Mockaitis, Keithanne; Nelson, C Dana; Peter, Gary F; Davis, John M; Echt, Craig S

    2015-08-01

    A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.6 cM and total map length was 2305 cM. Functional predictions of mapped genes were improved by aligning expressed sequence tags used for marker discovery to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 3305 scaffold sequences onto 12 linkage groups. The consensus genetic map was used to compare the genome-wide linkage disequilibrium in a population of distantly related P. taeda individuals (ADEPT2) used for association genetic studies and a multiple-family pedigree used for genomic selection (CCLONES). The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations. The average squared correlations, r(2), between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r(2) did not decay substantially with genetic distance. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii. PMID:26068575

  2. A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda

    PubMed Central

    Westbrook, Jared W.; Chhatre, Vikram E.; Wu, Le-Shin; Chamala, Srikar; Neves, Leandro Gomide; Muñoz, Patricio; Martínez-García, Pedro J.; Neale, David B.; Kirst, Matias; Mockaitis, Keithanne; Nelson, C. Dana; Peter, Gary F.; Echt, Craig S.

    2015-01-01

    A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.6 cM and total map length was 2305 cM. Functional predictions of mapped genes were improved by aligning expressed sequence tags used for marker discovery to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 3305 scaffold sequences onto 12 linkage groups. The consensus genetic map was used to compare the genome-wide linkage disequilibrium in a population of distantly related P. taeda individuals (ADEPT2) used for association genetic studies and a multiple-family pedigree used for genomic selection (CCLONES). The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations. The average squared correlations, r2, between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r2 did not decay substantially with genetic distance. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii. PMID:26068575

  3. Revisiting and re-engineering the classical zinc finger peptide: consensus peptide-1 (CP-1).

    PubMed

    Besold, Angelique N; Widger, Leland R; Namuswe, Frances; Michalek, Jamie L; Michel, Sarah L J; Goldberg, David P

    2016-04-22

    Zinc plays key structural and catalytic roles in biology. Structural zinc sites are often referred to as zinc finger (ZF) sites, and the classical ZF contains a Cys2His2 motif that is involved in coordinating Zn(ii). An optimized Cys2His2 ZF, named consensus peptide 1 (CP-1), was identified more than 20 years ago using a limited set of sequenced proteins. We have reexamined the CP-1 sequence, using our current, much larger database of sequenced proteins that have been identified from high-throughput sequencing methods, and found the sequence to be largely unchanged. The CCHH ligand set of CP-1 was then altered to a CAHH motif to impart hydrolytic activity. This ligand set mimics the His2Cys ligand set of peptide deformylase (PDF), a hydrolytically active M(ii)-centered (M = Zn or Fe) protein. The resultant peptide [CP-1(CAHH)] was evaluated for its ability to coordinate Zn(ii) and Co(ii) ions, adopt secondary structure, and promote hydrolysis. CP-1(CAHH) was found to coordinate Co(ii) and Zn(ii) and a pentacoordinate geometry for Co(ii)-CP-1(CAHH) was implicated from UV-vis data. This suggests a His2Cys(H2O)2 environment at the metal center. The Zn(ii)-bound CP-1(CAHH) was shown to adopt partial secondary structure by 1-D (1)H NMR spectroscopy. Both Zn(ii)-CP-1(CAHH) and Co(ii)-CP-1(CAHH) show good hydrolytic activity toward the test substrate 4-nitrophenyl acetate, exhibiting faster rates than most active synthetic Zn(ii) complexes. PMID:26936488

  4. The pivotal role of perceived scientific consensus in acceptance of science

    NASA Astrophysics Data System (ADS)

    Lewandowsky, Stephan; Gignac, Gilles E.; Vaughan, Samuel

    2013-04-01

    Although most experts agree that CO2 emissions are causing anthropogenic global warming (AGW), public concern has been declining. One reason for this decline is the `manufacture of doubt' by political and vested interests, which often challenge the existence of the scientific consensus. The role of perceived consensus in shaping public opinion is therefore of considerable interest: in particular, it is unknown whether consensus determines people's beliefs causally. It is also unclear whether perception of consensus can override people's `worldviews', which are known to foster rejection of AGW. Study 1 shows that acceptance of several scientific propositions--from HIV/AIDS to AGW--is captured by a common factor that is correlated with another factor that captures perceived scientific consensus. Study 2 reveals a causal role of perceived consensus by showing that acceptance of AGW increases when consensus is highlighted. Consensus information also neutralizes the effect of worldview.

  5. Children trust a consensus composed of outgroup members--but do not retain that trust.

    PubMed

    Chen, Eva E; Corriveau, Kathleen H; Harris, Paul L

    2013-01-01

    Children prefer to learn from informants in consensus with one another. However, no research has examined whether this preference exists across cultures, and whether the race of the informants impacts that preference. In 2 studies, one hundred thirty-six 4- to 7-year-old European American and Taiwanese children demonstrated a systematic preference for a consensus. Nevertheless, the initial strength and persistence of that preference depended on the racial composition of the consensus. Children's preference for consensus members belonging to the same race as themselves persisted even when only one consensus member remained to provide information. When the consensus consisted of different-race informants, preference for the consensus was initially apparent but lost when only one member from the consensus remained with the dissenting informant. PMID:22994587

  6. 76 FR 78307 - Manufactured Housing Consensus Committee; Notice Inviting Nominations of Individuals To Serve on...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-16

    ... URBAN DEVELOPMENT Manufactured Housing Consensus Committee; Notice Inviting Nominations of Individuals To Serve on the Committee AGENCY: Office of the Assistant Secretary for Housing--Federal Housing... Housing Consensus Committee (MHCC), a Federal advisory committee established by the National...

  7. Uroncor consensus statement: Management of biochemical recurrence after radical radiotherapy for prostate cancer: From biochemical failure to castration resistance.

    PubMed

    López Torrecilla, José; Hervás, Asunción; Zapatero, Almudena; Gómez Caamaño, Antonio; Macías, Victor; Herruzo, Ismael; Maldonado, Xavier; Gómez Iturriaga, Alfonso; Casas, Francesc; González San Segundo, Carmen

    2015-01-01

    Management of patients who experience biochemical failure after radical radiotherapy with or without hormonal therapy is highly challenging. The clinician must not only choose the type of treatment, but also the timing and optimal sequence of treatment administration. When biochemical failure occurs, numerous treatment scenarios are possible, thus making it more difficult to select the optimal approach. Moreover, rapid and ongoing advances in treatment options require that physicians make decisions that could impact both survival and quality of life. The aim of the present consensus statement, developed by the Urological Tumour Working Group (URONCOR) of the Spanish Society of Radiation Oncology (SEOR), is to provide cancer specialists with the latest, evidence-based information needed to make the best decisions for the patient under all possible treatment scenarios. The structure of this consensus statement follows the typical development of disease progression after biochemical failure, with the most appropriate treatment recommendations given for each stage. The consensus statement is organized into three separate chapters, as follows: biochemical failure with or without local recurrence and/or metastasis; progression after salvage therapy; and treatment of castration-resistant patients. PMID:26109913

  8. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  9. Sequencing Cucumber (Cucumis Sativus L.) Chloroplast Genomes Identifies Differences Between Chilling-Tolerant and-Susceptible Cucumber Lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complete sequencing of cucumber chloroplast (cp)DNA was facilitated by the development of 414 consensus chloroplast sequencing primers (CCSPs) from conserved cpDNA sequences of Arabidopsis (Arabidopsis thaliana L.), spinach (Spinacia oleracea L.), and tobacco (Nicotiana tabacum L.) cpDNAs, using deg...

  10. Engineering large-scale agent-based systems with consensus

    NASA Technical Reports Server (NTRS)

    Bokma, A.; Slade, A.; Kerridge, S.; Johnson, K.

    1994-01-01

    The paper presents the consensus method for the development of large-scale agent-based systems. Systems can be developed as networks of knowledge based agents (KBA) which engage in a collaborative problem solving effort. The method provides a comprehensive and integrated approach to the development of this type of system. This includes a systematic analysis of user requirements as well as a structured approach to generating a system design which exhibits the desired functionality. There is a direct correspondence between system requirements and design components. The benefits of this approach are that requirements are traceable into design components and code thus facilitating verification. The use of the consensus method with two major test applications showed it to be successful and also provided valuable insight into problems typically associated with the development of large systems.

  11. International Consensus on Allergen Immunotherapy II: Mechanisms, standardization, and pharmacoeconomics.

    PubMed

    Jutel, Marek; Agache, Ioana; Bonini, Sergio; Burks, A Wesley; Calderon, Moises; Canonica, Walter; Cox, Linda; Demoly, Pascal; Frew, Antony J; O'Hehir, Robyn; Kleine-Tebbe, Jörg; Muraro, Antonella; Lack, Gideon; Larenas, Désirée; Levin, Michael; Martin, Bryan L; Nelson, Harald; Pawankar, Ruby; Pfaar, Oliver; van Ree, Ronald; Sampson, Hugh; Sublett, James L; Sugita, Kazunari; Du Toit, George; Werfel, Thomas; Gerth van Wijk, Roy; Zhang, Luo; Akdis, Mübeccel; Akdis, Cezmi A

    2016-02-01

    This article continues the comprehensive international consensus (ICON) statement on allergen immunotherapy (AIT). The initial article also recently appeared in the Journal. The conclusions below focus on key mechanisms of AIT-triggered tolerance, requirements in allergen standardization, AIT cost-effectiveness, and regulatory guidance. Potential barriers to and facilitators of the use of AIT are described in addition to future directions. International allergy specialists representing the European Academy of Allergy and Clinical Immunology; the American Academy of Allergy, Asthma & Immunology; the American College of Allergy, Asthma and Immunology; and the World Allergy Organization critically reviewed the existing literature and prepared this summary of recommendations for best AIT practice. The authors contributed equally and reached consensus on the statements presented herein. PMID:26853128

  12. Link-Prediction Enhanced Consensus Clustering for Complex Networks

    PubMed Central

    Burgess, Matthew; Adar, Eytan; Cafarella, Michael

    2016-01-01

    Many real networks that are collected or inferred from data are incomplete due to missing edges. Missing edges can be inherent to the dataset (Facebook friend links will never be complete) or the result of sampling (one may only have access to a portion of the data). The consequence is that downstream analyses that “consume” the network will often yield less accurate results than if the edges were complete. Community detection algorithms, in particular, often suffer when critical intra-community edges are missing. We propose a novel consensus clustering algorithm to enhance community detection on incomplete networks. Our framework utilizes existing community detection algorithms that process networks imputed by our link prediction based sampling algorithm and merges their multiple partitions into a final consensus output. On average our method boosts performance of existing algorithms by 7% on artificial data and 17% on ego networks collected from Facebook. PMID:27203750

  13. Boltzmann-type control of opinion consensus through leaders

    PubMed Central

    Albi, G.; Pareschi, L.; Zanella, M.

    2014-01-01

    The study of formations and dynamics of opinions leading to the so-called opinion consensus is one of the most important areas in mathematical modelling of social sciences. Following the Boltzmann-type control approach recently introduced by the first two authors, we consider a group of opinion leaders who modify their strategy accordingly to an objective functional with the aim of achieving opinion consensus. The main feature of the Boltzmann-type control is that, owing to an instantaneous binary control formulation, it permits the minimization of the cost functional to be embedded into the microscopic leaders’ interactions of the corresponding Boltzmann equation. The related Fokker–Planck asymptotic limits are also derived, which allow one to give explicit expressions of stationary solutions. The results demonstrate the validity of the Boltzmann-type control approach and the capability of the leaders’ control to strategically lead the followers’ opinion. PMID:25288820

  14. A social choice approach to expert consensus panels.

    PubMed

    Gabel, Matthew J; Shipan, Charles R

    2004-05-01

    This study uses recent theoretical work about group decision-making to assess the quality of decision-making by expert consensus panels. We specifically examine (1) when individual members of panels will divulge their private judgments about the decision to the panel, and (2) when the group judgment is superior to the judgment of individual panelists and will lead to better treatment for patients. We conclude that to maximize the chance of an accurate decision, panels should be made as large as possible, adopt the smallest supermajority rule, and attract members with the highest individual competencies. Furthermore, interdependence among panelists and the goal of reaching consensus can reduce the efficacy of these panels. PMID:15120470

  15. Some axiomatic limitations for consensus and supertree functions on hierarchies.

    PubMed

    McMorris, F R; Powers, Robert C

    2016-09-01

    Consensus trees and supertrees are regularly used in systematic biology in order to obtain a summary for the common agreement of the evolutionary relationships among a collection of phylogenetic trees (hierarchies). When every tree is defined on the same set of taxa then consensus functions are used, while if the trees are defined on different sets then supertree functions are used. For both of these situations we will consider some of the limitations that might arise from the placing of singularly reasonable and apparently innocuous conditions on the functions. Previous work is reviewed together with new material. In particular, we consider the impact of axioms requiring that the removal or addition of a tree that contains no, or no new, branching information should not affect the outcome. PMID:27320681

  16. On the accurate construction of consensus genetic maps.

    PubMed

    Wu, Yonghui; Close, Timothy J; Lonardi, Stefano

    2008-01-01

    We study the problem of merging genetic maps, when the individual genetic maps are given as directed acyclic graphs. The problem is to build a consensus map, which includes and is consistent with all (or, the vast majority of) the markers in the individual maps. When markers in the input maps have ordering conflicts, the resulting consensus map will contain cycles. We formulate the problem of resolving cycles in a combinatorial optimization framework, which in turn is expressed as an integer linear program. A faster approximation algorithm is proposed, and an additional speed-up heuristic is developed. According to an extensive set of experimental results, our tool is consistently better than JOINMAP, both in terms of accuracy and running time. PMID:19642288

  17. Consensus perspectives on prophylactic therapy for haemophilia: summary statement.

    PubMed

    Berntorp, E; Astermark, J; Björkman, S; Blanchette, V S; Fischer, K; Giangrande, P L F; Gringeri, A; Ljung, R C; Manco-Johnson, M J; Morfini, M; Kilcoyne, R F; Petrini, P; Rodriguez-Merchan, E C; Schramm, W; Shapiro, A; van den Berg, H M; Hart, C

    2003-05-01

    Participants in an international conference on prophylactic therapy for severe haemophilia developed a consensus summary of the findings and conclusions of the conference. In the consensus, participants agreed upon revised definitions for primary and secondary prophylaxis and also made recommendations concerning the need for an international system of pharmacovigilance. Considerations on starting prophylaxis, monitoring outcomes, and individualizing treatment regimens were discussed. Several research questions were identified as needing further investigation, including when to start and when to stop prophylaxis, optimal dosing and dose interval, and methods for assessment of long-term treatment effects. Such studies should include carefully defined cohorts, validated orthopaedic and quality-of-life assessment instruments, and cost-benefit analyses. PMID:12709030

  18. Efficient Reconstruction of Predictive Consensus Metabolic Network Models

    PubMed Central

    Martins dos Santos, Vitor A. P.; Stelling, Joerg

    2016-01-01

    Understanding cellular function requires accurate, comprehensive representations of metabolism. Genome-scale, constraint-based metabolic models (GSMs) provide such representations, but their usability is often hampered by inconsistencies at various levels, in particular for concurrent models. COMMGEN, our tool for COnsensus Metabolic Model GENeration, automatically identifies inconsistencies between concurrent models and semi-automatically resolves them, thereby contributing to consolidate knowledge of metabolic function. Tests of COMMGEN for four organisms showed that automatically generated consensus models were predictive and that they substantially increased coherence of knowledge representation. COMMGEN ought to be particularly useful for complex scenarios in which manual curation does not scale, such as for eukaryotic organisms, microbial communities, and host-pathogen interactions. PMID:27563720

  19. Bladder Cancer Molecular Taxonomy: Summary from a Consensus Meeting

    PubMed Central

    Lerner, Seth P.; McConkey, David J.; Hoadley, Katherine A.; Chan, Keith S.; Kim, William Y.; Radvanyi, François; Höglund, Mattias; Real, Francisco X.

    2016-01-01

    The advent of Omics technologies has been key to the molecular subclassification of urothelial bladder cancer. Several groups have used different strategies to this aim, with partially overlapping findings. The meeting at the Spanish National Cancer Research Center-CNIO was held to discuss such classifications and reach consensus where appropriate. After updated presentations on the work performed by the teams attending the meeting, a consensus was reached regarding the existence of a group of Basal-Squamous-like tumors – designated BASQ – charaterized the high expression of KRT5/6 and KRT14 and low/undetectable expression of FOXA1 and GATA3. An additional tumor subgroup with urothelial differentiation features was recognized whose optimal molecular definition is required. For other subtypes described, more work is needed to determine how robust they are and how to best define them at the molecular level. PMID:27376123

  20. Canadian student leaders' perspective on interprofessional education: A consensus statement.

    PubMed

    Chicorelli, Jennifer; Dennie, Anik; Heinrich, Christina; Hinchey, Blake; Honarparvar, Faraz; Jennings, Morgan; Keefe, Chad; Metro, Trisha Lee; Peel, Celeste; Snowdon, Cordelia; Tempelman, Justine; Wong, Melody Elise; Forbes, Susan L; Livingston, Lori A

    2016-07-01

    The purpose of this article is to report on the outcomes of an interprofessional education (IPE) consensus-building exercise amongst student leaders enrolled in health science-related degree programs. The 12 participants included undergraduate and graduate students from eight different universities situated in five Canadian provinces. Their areas of study spanned a broad range of professions and disciplines including child and youth care, health promotion, nursing, kinesiology, medicine, physical education, psychology, and social work. A consensus statement regarding IPE and, more specifically, "what we know," "what we don't know," and "where do we go from here" is presented. These insights are unique, and a willingness to embrace them may be critical in building the next generation of improved IPE offerings across the country. PMID:27268765

  1. A failed platform: The Citizen Consensus Conference travels to Chile.

    PubMed

    Ureta, Sebastián

    2016-05-01

    This article starts by reviewing the setbacks that the recent Science and Technology Studies literature has identified in the functioning of technologies of democracy, the different arrangements that look to enact deliberation on technoscientific issues. Putting a focus on the Citizen Consensus Conference, it then proposes that several of these setbacks are related to the kind of "work" that these technologies are expected to do, identifying two kinds of it: performing a laboratory-based experiment and constituting a platform for the dissemination of facts. It then applies this framework to study a Citizen Consensus Conference carried out in Chile in 2003. After a detailed genealogy of the planning, implementation and afterlife of this exercise, the article concludes that several of the limitations experienced are derived from a "successful outcome" conceived as solely running a neat lab-based experiment, arguing for the need to incorporate its functioning as a platform with all the associated transformations and messiness. PMID:25573750

  2. Graph-balancing algorithms for average consensus over directed networks

    NASA Astrophysics Data System (ADS)

    Fan, Yuan; Han, Runzhe; Qiu, Jianbin

    2016-01-01

    Consensus strategies find extensive applications in coordination of robot groups and decision-making of agents. Since balanced graph plays an important role in the average consensus problem and many other coordination problems for directed communication networks, this work explores the conditions and algorithms for the digraph balancing problem. Based on the analysis of graph cycles, we prove that a digraph can be balanced if and only if the null space of its incidence matrix contains positive vectors. Then, based on this result and the corresponding analysis, two weight balance algorithms have been proposed, and the conditions for obtaining a unique balanced solution and a set of analytical results on weight balance problems have been introduced. Then, we point out the relationship between the weight balance problem and the features of the corresponding underlying Markov chain. Finally, two numerical examples are presented to verify the proposed algorithms.

  3. Efficient Reconstruction of Predictive Consensus Metabolic Network Models.

    PubMed

    van Heck, Ruben G A; Ganter, Mathias; Martins Dos Santos, Vitor A P; Stelling, Joerg

    2016-08-01

    Understanding cellular function requires accurate, comprehensive representations of metabolism. Genome-scale, constraint-based metabolic models (GSMs) provide such representations, but their usability is often hampered by inconsistencies at various levels, in particular for concurrent models. COMMGEN, our tool for COnsensus Metabolic Model GENeration, automatically identifies inconsistencies between concurrent models and semi-automatically resolves them, thereby contributing to consolidate knowledge of metabolic function. Tests of COMMGEN for four organisms showed that automatically generated consensus models were predictive and that they substantially increased coherence of knowledge representation. COMMGEN ought to be particularly useful for complex scenarios in which manual curation does not scale, such as for eukaryotic organisms, microbial communities, and host-pathogen interactions. PMID:27563720

  4. [GEITDAH consensus on conduct disorders in children and adolescents].

    PubMed

    Sasot-Llevadot, Jordi; Ibáñez-Bordas, Rosa M; Soto-López, Antonio; Montañés-Rada, Francisco; Gastaminza-Pérez, Xavier; Alda-Díez, José A; Cantó-Díez, Tomás; Catalá, Miguel A; Ferrin-Erdozáin, Maite; García-Giral, Marta; Graell-Bernal, Montserrat; Granada-Jiménez, Olvido; Herreros-Rodríguez, Óscar; Mardomingo-Sanz, María J; Mojarro-Práxedes, Dolores; Morey-Canyelles, Jaume; Ortiz-Guerra, Juan; Pàmies-Massana, Montserrat; Rey-Sánchez, Francisco; Romera-Torrens, María; Rubio-Morell, Belén; Ruiz-Lázaro, Pedro M; Ruiz-Sanz, Francisco

    2015-08-16

    In this paper, the Special Interest Group on Attention Deficit Hyperactivity Disorder (GEITDAH, from its name in Spanish) presents a consensus reached by experts from all over Spain on conduct disorders in children and adolescents. Following the initial work by the team at the Pedopsychiatry Unit at the Quiron-Teknon Hospital in Barcelona, agreements have been reached on a number of basic aspects that could be the starting point for future consensuses. A top priority aim of the work was also to update the criteria in the Diagnostic and statistical manual of mental disorders, fifth edition, for conduct disorders in children and adolescents, together with their comorbidity with attention deficit hyperactivity disorder. PMID:26204088

  5. Children's Hospital Association Consensus Statements for Comorbidities of Childhood Obesity

    PubMed Central

    Eneli, Ihuoma; Hampl, Sarah; Mietus-Snyder, Michele; Mirza, Nazrat; Rhodes, Erinn; Sweeney, Brooke; Tinajero-Deck, Lydia; Woolford, Susan J.; Pont, Stephen J.

    2014-01-01

    Abstract Background: Childhood obesity and overweight affect approximately 30% of US children. Many of these children have obesity-related comorbidities, such as hypertension, dyslipidemia, fatty liver disease, diabetes, polycystic ovary syndrome (PCOS), sleep apnea, psychosocial problems, and others. These children need routine screening and, in many cases, treatment for these conditions. However, because primary care pediatric providers (PCPs) often are underequipped to deal with these comorbidities, they frequently refer these patients to subspecialists. However, as a result of the US pediatric subspecialist shortage and considering that 12.5 million children are obese, access to care by subspecialists is limited. The aim of this article is to provide accessible, user-friendly clinical consensus statements to facilitate the screening, interpretation of results, and early treatment for some of the most common childhood obesity comorbidities. Methods: Members of the Children's Hospital Association (formerly NACHRI) FOCUS on a Fitter Future II (FFFII), a collaboration of 25 US pediatric obesity centers, used a combination of the best available evidence and collective clinical experience to develop consensus statements for pediatric obesity-related comorbidities. FFFII also surveyed the participating pediatric obesity centers regarding their current practices. Results: The work group developed consensus statements for use in the evaluation and treatment of lipids, liver enzymes, and blood pressure abnormalities and PCOS in the child with overweight and obesity. The results of the FFFII survey illustrated the variability in the approach for initial evaluation and treatment as well as pattern of referrals to subspecialists among programs. Conclusions: The consensus statements presented in this article can be a useful tool for PCPs in the management and overall care of children with overweight and obesity. PMID:25019404

  6. [Consensus and action as determinants of psychological consultation].

    PubMed

    Hage, R; Sieland, B

    1984-01-01

    Recent publications in their majority are showing increasing criticism of current counseling concepts, esp. concerning their practical relevance. Therefore a critical revision of counseling models is demanded, with the following essential postulates: more field-oriented, more individual-centered and more evaluative. The model of counseling presented here stresses the importance of consensus and action in order to cope with these postulates. Finally first modes of application are demonstrated. PMID:6730620

  7. After seven years, where`s the consensus?

    SciTech Connect

    Norman, M.R.

    1993-04-01

    It has been 7 years since the discovery of copper oxide superconductors, yet there is no consensus on the correct theory for this phenomenon. The theory can be divided into 3 groups: ordinary (phonons), exotic (AF spin fluctuations, nested Fermi liquid, excitons, spin bags, odd frequency pairing), and revolutionary (Luttinger liquid, spin-charge separation, gauge theories, anyons, marginal Fermi liquid). C-axis dispersion, dHvA, and magneto-oscillations are also discussed.

  8. Global Consensus Recommendations on Prevention and Management of Nutritional Rickets

    PubMed Central

    Munns, Craig F.; Shaw, Nick; Kiely, Mairead; Specker, Bonny L.; Thacher, Tom D.; Ozono, Keiichi; Michigami, Toshimi; Tiosano, Dov; Mughal, M. Zulf; Mäkitie, Outi; Ramos-Abad, Lorna; Ward, Leanne; DiMeglio, Linda A.; Atapattu, Navoda; Cassinelli, Hamilton; Braegger, Christian; Pettifor, John M.; Seth, Anju; Idris, Hafsatu Wasagu; Bhatia, Vijayalakshmi; Fu, Junfen; Goldberg, Gail; Sävendahl, Lars; Khadgawat, Rajesh; Pludowski, Pawel; Maddock, Jane; Hyppönen, Elina; Oduwole, Abiola; Frew, Emma; Aguiar, Magda; Tulchinsky, Ted; Butler, Gary

    2016-01-01

    Background: Vitamin D and calcium deficiencies are common worldwide, causing nutritional rickets and osteomalacia, which have a major impact on health, growth, and development of infants, children, and adolescents; the consequences can be lethal or can last into adulthood. The goals of this evidence-based consensus document are to provide health care professionals with guidance for prevention, diagnosis, and management of nutritional rickets and to provide policy makers with a framework to work toward its eradication. Evidence: A systematic literature search examining the definition, diagnosis, treatment, and prevention of nutritional rickets in children was conducted. Evidence-based recommendations were developed using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) system that describe the strength of the recommendation and the quality of supporting evidence. Process: Thirty-three nominated experts in pediatric endocrinology, pediatrics, nutrition, epidemiology, public health, and health economics evaluated the evidence on specific questions within five working groups. The consensus group, representing 11 international scientific organizations, participated in a multiday conference in May 2014 to reach a global evidence-based consensus. Results: This consensus document defines nutritional rickets and its diagnostic criteria and describes the clinical management of rickets and osteomalacia. Risk factors, particularly in mothers and infants, are ranked, and specific prevention recommendations including food fortification and supplementation are offered for both the clinical and public health contexts. Conclusion: Rickets, osteomalacia, and vitamin D and calcium deficiencies are preventable global public health problems in infants, children, and adolescents. Implementation of international rickets prevention programs, including supplementation and food fortification, is urgently required. PMID:26745253

  9. Food Security: The Elaboration of Contested Claims to a Consensus Frame

    ERIC Educational Resources Information Center

    Mooney, Patrick H.; Hunt, Scott A.

    2009-01-01

    This article demonstrates Gamson's claim that behind the apparent agreement implied by "consensus frames" lies considerable dissensus. Ironically, the very potency of consensus frames may generate contested claims to the ownership of a social problem. Food security is a potent consensus frame that has generated at least three distinct collective…

  10. Dynamic consensus estimation of weighted average on directed graphs

    NASA Astrophysics Data System (ADS)

    Li, Shuai; Guo, Yi

    2015-07-01

    Recent applications call for distributed weighted average estimation over sensor networks, where sensor measurement accuracy or environmental conditions need to be taken into consideration in the final consensused group decision. In this paper, we propose new dynamic consensus filter design to distributed estimate weighted average of sensors' inputs on directed graphs. Based on recent advances in the filed, we modify the existing proportional-integral consensus filter protocol to remove the requirement of bi-directional gain exchange between neighbouring sensors, so that the algorithm works for directed graphs where bi-directional communications are not possible. To compensate for the asymmetric structure of the system introduced by such a removal, sufficient gain conditions are obtained for the filter protocols to guarantee the convergence. It is rigorously proved that the proposed filter protocol converges to the weighted average of constant inputs asymptotically, and to the weighted average of time-varying inputs with a bounded error. Simulations verify the effectiveness of the proposed protocols.

  11. Consensus Statements on the Assessment of Older Drivers

    PubMed Central

    Hogan MD, David B.; Scialfa, Charles T.; Caird, Jeff K.

    2014-01-01

    Background The rapidly increasing number of older drivers is accentuating the challenges in concurrently identifying older drivers posing an unacceptable risk if they continue to drive, while not discriminating against those capable of safely driving. Attendees of an invitational meeting about the assessment of older drivers were asked to participate in a modified Delphi process designed to develop consensus statements on the assessment of older drivers. Methods Forty-one non-student symposium attendees were invited to participate in two rounds of a survey, in which they were asked to indicate their level of agreement (or disagreement) on a five-point Likert scale to a series of statements about the assessment of older drivers. Consensus was defined as 80% + of respondents either agreeing or disagreeing with a statement. Results More than one-half (n = 23) completed the first round of the survey and 12 participated in the second. There was consensus on the need for a modifiable, fair, rational, and widely accessible multi-step approach to the assessment of older drivers. This would require the engagement and support of physicians and other health-care practitioners in identifying and reporting medically at-risk drivers of any age. At a societal level, alternatives to driving a personal motor vehicle should be developed. Conclusions An on-going dialogue about this complex issue is required. Decisions should be based on explicitly stated principles and informed by the best available evidence. PMID:24883166

  12. Word diversity can accelerate consensus in naming game

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-Dan; Wang, Zhen; Zheng, Fei-Fei; Yang, Miao

    2012-03-01

    In this paper, we introduce word diversity that reflects the inhomogeneity of words in a communication into the naming game. Diversity is realized by assigning a weight factor to each word. The weight is determined by three different distributions (uniform, exponential, and power-law distributions). During the communication, the probability that a word is selected from speaker's memory depends on the introduced word diversity. Interestingly, we find that the word diversity following three different distributions can remarkably promote the final convergency, which is of high importance in the self-organized system. In particular, for all the ranges of amplitude of distribution, the power-law distribution enables the fastest consensus, while uniform distribution gives the slowest consensus. We provide an explanation of this effect based on both the number of different names and the number of total names, and find that a wide spread of names induced by the segregation of words is the main promotion factor. Other quantities, including the evolution of the averaging success rate of negotiation and the scaling behavior of consensus time, are also studied. These results are helpful for better understanding the dynamics of the naming game with word diversity.

  13. C1 inhibitor deficiency: 2014 United Kingdom consensus document

    PubMed Central

    Longhurst, H J; Tarzi, M D; Ashworth, F; Bethune, C; Cale, C; Dempster, J; Gompels, M; Jolles, S; Seneviratne, S; Symons, C; Price, A; Edgar, D

    2015-01-01

    C1 inhibitor deficiency is a rare disorder manifesting with recurrent attacks of disabling and potentially life-threatening angioedema. Here we present an updated 2014 United Kingdom consensus document for the management of C1 inhibitor-deficient patients, representing a joint venture between the United Kingdom Primary Immunodeficiency Network and Hereditary Angioedema UK. To develop the consensus, we assembled a multi-disciplinary steering group of clinicians, nurses and a patient representative. This steering group first met in 2012, developing a total of 48 recommendations across 11 themes. The statements were distributed to relevant clinicians and a representative group of patients to be scored for agreement on a Likert scale. All 48 statements achieved a high degree of consensus, indicating strong alignment of opinion. The recommendations have evolved significantly since the 2005 document, with particularly notable developments including an improved evidence base to guide dosing and indications for acute treatment, greater emphasis on home therapy for acute attacks and a strong focus on service organization. PMID:25605519

  14. C1 inhibitor deficiency: 2014 United Kingdom consensus document.

    PubMed

    Longhurst, H J; Tarzi, M D; Ashworth, F; Bethune, C; Cale, C; Dempster, J; Gompels, M; Jolles, S; Seneviratne, S; Symons, C; Price, A; Edgar, D

    2015-06-01

    C1 inhibitor deficiency is a rare disorder manifesting with recurrent attacks of disabling and potentially life-threatening angioedema. Here we present an updated 2014 United Kingdom consensus document for the management of C1 inhibitor-deficient patients, representing a joint venture between the United Kingdom Primary Immunodeficiency Network and Hereditary Angioedema UK. To develop the consensus, we assembled a multi-disciplinary steering group of clinicians, nurses and a patient representative. This steering group first met in 2012, developing a total of 48 recommendations across 11 themes. The statements were distributed to relevant clinicians and a representative group of patients to be scored for agreement on a Likert scale. All 48 statements achieved a high degree of consensus, indicating strong alignment of opinion. The recommendations have evolved significantly since the 2005 document, with particularly notable developments including an improved evidence base to guide dosing and indications for acute treatment, greater emphasis on home therapy for acute attacks and a strong focus on service organization. PMID:25605519

  15. The functional neuroanatomy of bipolar disorder: a consensus model

    PubMed Central

    Strakowski, Stephen M; Adler, Caleb M; Almeida, Jorge; Altshuler, Lori L; Blumberg, Hilary P; Chang, Kiki D; DelBello, Melissa P; Frangou, Sophia; McIntosh, Andrew; Phillips, Mary L; Sussman, Jessika E; Townsend, Jennifer D

    2013-01-01

    Objectives Functional neuroimaging methods have proliferated in recent years, such that functional magnetic resonance imaging, in particular, is now widely used to study bipolar disorder. However, discrepant findings are common. A workgroup was organized by the Department of Psychiatry, University of Cincinnati (Cincinnati, OH, USA) to develop a consensus functional neuroanatomic model of bipolar I disorder based upon the participants’ work as well as that of others. Methods Representatives from several leading bipolar disorder neuroimaging groups were organized to present an overview of their areas of expertise as well as focused reviews of existing data. The workgroup then developed a consensus model of the functional neuroanatomy of bipolar disorder based upon these data. Results Among the participants, a general consensus emerged that bipolar I disorder arises from abnormalities in the structure and function of key emotional control networks in the human brain. Namely, disruption in early development (e.g., white matter connectivity, prefrontal pruning) within brain networks that modulate emotional behavior leads to decreased connectivity among ventral prefrontal networks and limbic brain regions, especially amygdala. This developmental failure to establish healthy ventral prefrontal–limbic modulation underlies the onset of mania and ultimately, with progressive changes throughout these networks over time and with affective episodes, a bipolar course of illness. Conclusions This model provides a potential substrate to guide future investigations and areas needing additional focus are identified. PMID:22631617

  16. Consensus Paper: Pathological Mechanisms Underlying Neurodegeneration in Spinocerebellar Ataxias

    PubMed Central

    Matilla-Dueñas, A.; Ashizawa, T.; Brice, A.; Magri, S.; McFarland, K. N.; Pandolfo, M.; Pulst, S. M.; Riess, O.; Rubinsztein, D. C.; Schmidt, J.; Schmidt, T.; Scoles, D. R.; Stevanin, G.; Taroni, F.; Underwood, B. R.; Sánchez, I.

    2014-01-01

    Intensive scientific research devoted in the recent years to understand the molecular mechanisms or neurodegeneration in spinocerebellar ataxias (SCAs) are identifying new pathways and targets providing new insights and a better understanding of the molecular pathogenesis in these diseases. In this consensus manuscript, the authors discuss their current views on the identified molecular processes causing or modulating the neurodegenerative phenotype in spinocerebellar ataxias with the common opinion of translating the new knowledge acquired into candidate targets for therapy. The following topics are discussed: transcription dysregulation, protein aggregation, autophagy, ion channels, the role of mitochondria, RNA toxicity, modulators of neurodegeneration and current therapeutic approaches. Overall point of consensus includes the common vision of neurodegeneration in SCAs as a multifactorial, progressive and reversible process, at least in early stages. Specific points of consensus include the role of the dysregulation of protein folding, transcription, bioenergetics, calcium handling and eventual cell death with apoptotic features of neurons during SCA disease progression. Unresolved questions include how the dysregulation of these pathways triggers the onset of symptoms and mediates disease progression since this understanding may allow effective treatments of SCAs within the window of reversibility to prevent early neuronal damage. Common opinions also include the need for clinical detection of early neuronal dysfunction, for more basic research to decipher the early neurodegenerative process in SCAs in order to give rise to new concepts for treatment strategies and for the translation of the results to preclinical studies and, thereafter, in clinical practice. PMID:24307138

  17. Per oral cholangiopancreatoscopy in pancreatico biliary diseases - Expert consensus statements

    PubMed Central

    Ramchandani, Mohan; Reddy, Duvvur Nageshwar; Lakhtakia, Sundeep; Tandan, Manu; Maydeo, Amit; Chandrashekhar, Thoguluva Seshadri; Kumar, Ajay; Sud, Randhir; Rerknimitr, Rungsun; Makmun, Dadang; Khor, Christopher

    2015-01-01

    AIM: To provide consensus statements on the use of per-oral cholangiopancreatoscopy (POCPS). METHODS: A workgroup of experts in endoscopic retrograde cholangiopancreatography (ERCP), endosonography, and POCPS generated consensus statements summarizing the utility of POCPS in pancreaticobiliary disease. Recommendation grades used validated evidence ratings of publications from an extensive literature review. RESULTS: Six consensus statements were generated: (1) POCPS is now an important additional tool during ERCP; (2) in patients with indeterminate biliary strictures, POCS and POCS-guided targeted biopsy are useful for establishing a definitive diagnosis; (3) POCS and POCS-guided lithotripsy are recommended for treatment of difficult common bile duct stones when standard techniques fail; (4) in patients with main duct intraductal papillary mucinous neoplasms (IPMN) POPS may be used to assess extent of tumor to assist surgical resection; (5) in difficult pancreatic ductal stones, POPS-guided lithotripsy may be useful in fragmentation and extraction of stones; and (6) additional indications for POCPS include selective guidewire placement, unexplained hemobilia, assessing intraductal biliary ablation therapy, and extracting migrated stents. CONCLUSION: POCPS is important in association with ERCP, particularly for diagnosis of indeterminate biliary strictures and for intra-ductal lithotripsy when other techniques failed, and may be useful for pre-operative assessment of extent of main duct IPMN, for extraction of difficult pancreatic stones, and for unusual indications involving selective guidewire placement, assessing unexplained hemobilia or intraductal biliary ablation therapy, and extracting migrated stents. PMID:25914484

  18. National Cancer Centre Singapore Consensus Guidelines for Hepatocellular Carcinoma

    PubMed Central

    Chow, Pierce K. H.; Choo, Su Pin; Ng, David C. E.; Lo, Richard H. G.; Wang, Michael L. C.; Toh, Han Chong; Tai, David W. M.; Goh, Brian K. P.; Wong, Jen San; Tay, Kiang Hiong; Goh, Anthony S. W.; Yan, Sean X.; Loke, Kelvin S. H.; Thang, Sue Ping; Gogna, Apoorva; Too, Chow Wei; Irani, Farah Gillian; Leong, Sum; Lim, Kiat Hon; Thng, Choon Hua

    2016-01-01

    Hepatocellular carcinoma (HCC) is the 6th most common cancer in the world, but the second most common cause of cancer death. There is no universally accepted consensus practice guidelines for HCC owing to rapid developments in new treatment modalities, the heterogeneous epidemiology and clinical presentation of HCC worldwide. However, a number of regional and national guidelines currently exist which reflect practice relevant to the epidemiology and collective experience of the consensus group. In 2014, clinicians at the multidisciplinary Comprehensive Liver Cancer Clinic (CLCC) at the National Cancer Centre Singapore (NCCS) reviewed the latest published scientific data and existing international and regional practice guidelines, such as those of the National Comprehensive Cancer Network, American Association for the Study of Liver Diseases and the Asian Pacific Association for the Study of the Liver, and modified them to reflect local practice. These would serve as a template by which treatment outcomes can be collated and benchmarked against international data. The NCCS Consensus Guidelines for HCC have been successfully implemented in the CLCC since their publication online on 26th September 2014, and the guidelines allow outcomes of treatment to be compared to international data. These guidelines will be reviewed periodically to incorporate new data. PMID:27386428

  19. Time for a neonatal–specific consensus definition for sepsis

    PubMed Central

    Wynn, James L.; Wong, Hector R.; Shanley, Thomas P.; Bizzarro, Matthew J.; Saiman, Lisa; Polin, Richard A.

    2014-01-01

    Objective To review the accuracy of the pediatric consensus definition of sepsis in term neonates and to determine the definition of neonatal sepsis used. Study selection The review focused primarily on pediatric literature relevant to the topic of interest. Conclusions Neonatal sepsis is variably defined based on a number of clinical and laboratory criteria that make the study of this common and devastating condition very difficult. Diagnostic challenges and uncertain disease epidemiology necessarily result from a variable definition of disease. In 2005, intensivists caring for children recognized that as new drugs became available, children would be increasingly studied and thus, pediatric-specific consensus definitions were needed. Pediatric sepsis criteria are not accurate for term neonates and have not been examined in preterm neonates for whom the developmental stage influences aberrations associated with host immune response. Thus, specific consensus definitions for both term and preterm neonates are needed. Such definitions are critical for the interpretation of observational studies, future training of scientists and practitioners, and implementation of clinical trials in neonates. PMID:24751791

  20. Consequences of the Chicago DSD Consensus: A Personal Perspective.

    PubMed

    Hughes, I A

    2015-05-01

    A decade has passed since the Chicago Consensus meeting was convened to consider how to improve the management of individuals and their families with an intersex disorder. It is apposite to review, from an individual perspective, what impact the Consensus has had on clinical practice and research. Emphasis is placed on nomenclature and DSD classification, multidisciplinary team working, striving to reach a causative diagnosis for DSD, the value of uniformity of collective case registries for rare conditions, and the potential for meaningful clinical outcome studies and basic scientific research. The impact of the Consensus can be gauged objectively by an exponential increase in DSD-related publications in the medical and scientific literature and organisation of numerous national and international meetings. Psychologists and social scientists have embraced the subject area and enhanced the holistic approach to management of DSD. Much needs to be done to improve diagnosis, and to identify measures to predict outcome that can be used both in sex assignment decision-making and to improve the quality of life for young adults with DSD. Though challenging, these goals are attainable through specialist multidisciplinary clinics working at local level and the DSD community at large, collaborating at national and international levels to tap the data resources now being developed. PMID:25750076

  1. National Cancer Centre Singapore Consensus Guidelines for Hepatocellular Carcinoma.

    PubMed

    Chow, Pierce K H; Choo, Su Pin; Ng, David C E; Lo, Richard H G; Wang, Michael L C; Toh, Han Chong; Tai, David W M; Goh, Brian K P; Wong, Jen San; Tay, Kiang Hiong; Goh, Anthony S W; Yan, Sean X; Loke, Kelvin S H; Thang, Sue Ping; Gogna, Apoorva; Too, Chow Wei; Irani, Farah Gillian; Leong, Sum; Lim, Kiat Hon; Thng, Choon Hua

    2016-04-01

    Hepatocellular carcinoma (HCC) is the 6th most common cancer in the world, but the second most common cause of cancer death. There is no universally accepted consensus practice guidelines for HCC owing to rapid developments in new treatment modalities, the heterogeneous epidemiology and clinical presentation of HCC worldwide. However, a number of regional and national guidelines currently exist which reflect practice relevant to the epidemiology and collective experience of the consensus group. In 2014, clinicians at the multidisciplinary Comprehensive Liver Cancer Clinic (CLCC) at the National Cancer Centre Singapore (NCCS) reviewed the latest published scientific data and existing international and regional practice guidelines, such as those of the National Comprehensive Cancer Network, American Association for the Study of Liver Diseases and the Asian Pacific Association for the Study of the Liver, and modified them to reflect local practice. These would serve as a template by which treatment outcomes can be collated and benchmarked against international data. The NCCS Consensus Guidelines for HCC have been successfully implemented in the CLCC since their publication online on 26(th) September 2014, and the guidelines allow outcomes of treatment to be compared to international data. These guidelines will be reviewed periodically to incorporate new data. PMID:27386428

  2. Spanish Consensus Statement: The Treatment of Muscle Tears in Sport.

    PubMed

    Fernandez-Jaén, Tomas F; Rey, Guillermo Álvarez; Cuesta, Jordi Ardevol; Loureda, Rafael Arriaza; España, Fernando Ávila; Matas, Ramón Balius; Pazos, Fernando Baró; de Dios Beas Jiménez, Juan; Rosell, Jorge Candel; Fernandez, César Cobián; Ros, Francisco Esparza; Colmenero, Josefina Espejo; de Prado, Jorge Fernández; Cota, Juan José García; González, Jose Ignacio Garrido; Santander, Manuela González; Munilla, Miguel Ángel Herrador; Ruiz, Francisco Ivorra; Díaz, Fernando Jiménez; Marqueta, Pedro Manonelles; Fernandez, Antonio Maestro; Benito, Juan José Muñoz; Vilás, Ramón Olivé; Teres, Xavier Peirau; Amaro, José Peña; Roque, Juan Pérez San; Parenteu, Christophe Ramírez; Serna, Juan Ribas; Álvarez, Mikel Sánchez; Marchori, Carlos Sanchez; Soto, Miguel Del Valle; Alonso, José María Villalón; García, Pedro Guillen; de la Iglesia, Nicolas Hugo; Alcorocho, Juan Manuel Lopez

    2015-12-01

    On the 21st of March, 2015, experts met at Clínica CEMTRO in Madrid, Spain, under the patronage of The Spanish Society for Sports Traumatology (SETRADE), The Spanish Federation of Sports Medicine (FEMEDE), The Spanish Association of Medical Services for Football Clubs (AEMEF), and The Spanish Association of Medical Services for Basketball Clubs (AEMB) with the aim of establishing a round table that would allow specialists to consider the most appropriate current general actions to be taken when treating muscle tears in sport, based on proven scientific data described in the medical literature. Each expert received a questionnaire prior to the aforementioned meeting comprising a set of questions concerning therapeutic indications generally applied in the different stages present during muscle repair. The present Consensus Document is the result of the answers to the questionnaire and resulting discussion and consensus over which are the best current indications in the treatment of muscle tears in sport. Avoiding immobilization, not taking nonsteroidal anti-inflammatory drugs (NSAIDs) randomly, fostering early mobilization, increasing vascularization of injured, site and regulating inflammatory mechanisms-without inhibiting these from the early stages of the recovery period-all stood out as main points of the Consensus Document. Additionally, there is controversy concerning cell stimulation techniques and the use of growth factors or cell inhibitors. The decision concerning discharge was unanimous, as was the criteria considered when it came to performing sport techniques without pain. PMID:27213161

  3. Brain-specific genes have identifier sequences in their introns.

    PubMed Central

    Milner, R J; Bloom, F E; Lai, C; Lerner, R A; Sutcliffe, J G

    1984-01-01

    The 82-nucleotide identifier (ID) sequence is present in the rat genome in 1-1.5 X 10(5) copies and in cDNA clones of precursors of brain-specific mRNAs. One brain-specific gene contains more than one ID sequence in its introns. There is an excess of ID sequences to brain genes, and some ID sequences appear to have been inserted as mobile elements into other genetic locations. Therefore, brain genes contain ID sequences in their introns, but not all ID sequences are located in brain gene introns. A brain ID consensus sequence has been obtained by comparing 8 ID nucleotide sequences. Images PMID:6583673

  4. Consensus HIV-1 subtype A integrase and its raltegravir-resistant variants: design and characterization of the enzymatic properties.

    PubMed

    Shadrina, Olga; Krotova, Olga; Agapkina, Julia; Knyazhanskaya, Ekaterina; Korolev, Sergey; Starodubova, Elizaveta; Viklund, Alecia; Lukashov, Vladimir; Magnani, Mauro; Medstrand, Patrik; Karpov, Vadim; Gottikh, Marina; Isaguliants, Maria

    2014-07-01

    Model studies of the subtype B and non-subtype B integrases are still required to compare their susceptibility to antiretroviral drugs, evaluate the significance of resistance mutations and identify the impact of natural polymorphisms on the level of enzymatic reactivity. We have therefore designed the consensus integrase of the HIV-1 subtype A strain circulating in the former Soviet Union territory (FSU-A) and two of its variants with mutations of resistance to the strand transfer inhibitor raltegravir. Their genes were synthesized, and expressed in E coli; corresponding His-tagged proteins were purified using the affinity chromatography. The enzymatic properties of the consensus integrases and their sensitivity to raltegravir were examined in a series of standard in vitro reactions and compared to the properties of the integrase of HIV-1 subtype B strain HXB2. The consensus enzyme demonstrated similar DNA-binding properties, but was significantly more active than HXB-2 integrase in the reactions of DNA cleavage and integration. All integrases were equally susceptible to inhibition by raltegravir and elvitegravir, indicating that the sporadic polymorphisms inherent to the HXB-2 enzyme have little effect on its susceptibility to drugs. Insensitivity of the mutated enzymes to the inhibitors of strand transfer occurred at a cost of a 30-90% loss of the efficacies of both 3'-processing and strand transfer. This is the first study to describe the enzymatic properties of the consensus integrase of HIV-1 clade A and the effects of the resistance mutations when the complex actions of sporadic sequence polymorphisms are excluded. PMID:24594066

  5. The Chinese hamster Alu-equivalent sequence: a conserved highly repetitious, interspersed deoxyribonucleic acid sequence in mammals has a structure suggestive of a transposable element.

    PubMed Central

    Haynes, S R; Toomey, T P; Leinwand, L; Jelinek, W R

    1981-01-01

    A consensus sequence has been determined for a major interspersed deoxyribonucleic acid repeat in the genome of Chinese hamster ovary cells (CHO cells). This sequence is extensively homologous to (i) the human Alu sequence (P. L. Deininger et al., J. Mol. Biol., in press), (ii) the mouse B1 interspersed repetitious sequence (Krayev et al., Nucleic Acids Res. 8:1201-1215, 1980) (iii) an interspersed repetitious sequence from African green monkey deoxyribonucleic acid (Dhruva et al., Proc. Natl. Acad. Sci. U.S.A. 77:4514-4518, 1980) and (iv) the CHO and mouse 4.5S ribonucleic acid (this report; F. Harada and N. Kato, Nucleic Acids Res. 8:1273-1285, 1980). Because the CHO consensus sequence shows significant homology to the human Alu sequence it is termed the CHO Alu-equivalent sequence. A conserved structure surrounding CHO Alu-equivalent family members can be recognized. It is similar to that surrounding the human Alu and the mouse B1 sequences, and is represented as follows: direct repeat-CHO-Alu-A-rich sequence-direct repeat. A composite interspersed repetitious sequence has been identified. Its structure is represented as follows: direct repeat-residue 47 to 107 of CHO-Alu-non-Alu repetitious sequence-A-rich sequence-direct repeat. Because the Alu flanking sequences resemble those that flank known transposable elements, we think it likely that the Alu sequence dispersed throughout the mammalian genome by transposition. Images PMID:9279371

  6. Non-consensus Opinion Models on Complex Networks

    NASA Astrophysics Data System (ADS)

    Li, Qian; Braunstein, Lidia A.; Wang, Huijuan; Shao, Jia; Stanley, H. Eugene; Havlin, Shlomo

    2013-04-01

    Social dynamic opinion models have been widely studied to understand how interactions among individuals cause opinions to evolve. Most opinion models that utilize spin interaction models usually produce a consensus steady state in which only one opinion exists. Because in reality different opinions usually coexist, we focus on non-consensus opinion models in which above a certain threshold two opinions coexist in a stable relationship. We revisit and extend the non-consensus opinion (NCO) model introduced by Shao et al. (Phys. Rev. Lett. 103:01870, 2009). The NCO model in random networks displays a second order phase transition that belongs to regular mean field percolation and is characterized by the appearance (above a certain threshold) of a large spanning cluster of the minority opinion. We generalize the NCO model by adding a weight factor W to each individual's original opinion when determining their future opinion (NCO W model). We find that as W increases the minority opinion holders tend to form stable clusters with a smaller initial minority fraction than in the NCO model. We also revisit another non-consensus opinion model based on the NCO model, the inflexible contrarian opinion (ICO) model (Li et al. in Phys. Rev. E 84:066101, 2011), which introduces inflexible contrarians to model the competition between two opinions in a steady state. Inflexible contrarians are individuals that never change their original opinion but may influence the opinions of others. To place the inflexible contrarians in the ICO model we use two different strategies, random placement and one in which high-degree nodes are targeted. The inflexible contrarians effectively decrease the size of the largest rival-opinion cluster in both strategies, but the effect is more pronounced under the targeted method. All of the above models have previously been explored in terms of a single network, but human communities are usually interconnected, not isolated. Because opinions propagate not

  7. List of Predicted Simple Sequence Repeats from Sugar Beet GenBank Accessions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beta vulgaris ESTs from GenBank as of January 2005 collapsed into 13,618 unique clusters (4,023 Tentative Consensus sequences, 9,595 singletons), and 35% were contributed via work partially supported through the BSDF. These sequences were parsed through SSR-Primer software for discovering potential...

  8. Cloning, sequencing and characterization of lipase genes from a polyhydroxyalkanoate- (PHA-) synthesizing Pseudomonas resinovorans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lipase (lip) and lipase-specific foldase (lif) genes of a biodegradable polyhydroxyalkanoate- (PHA-) synthesizing Pseudomonas resinovorans NRRL B-2649 were cloned using primers based on consensus sequences, followed by PCR-based genome walking. Sequence analyses showed a putative Lip gene-product (...

  9. Complete genome sequence of an Argentinean isolate of Solenopsis invicta virus 3

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genome of an Argentinean isolate of Solenopsis invicta virus 3 (SINV-3ArgSF) obtained from the Santa Fe region of Argentina was sequenced in entirety. Assembly of 9 overlapping fragments yielded a consensus genome sequence 10,386 nucleotides long, excluding the poly(A) tail present on the 3' en...

  10. SEQUENCING OF CUCUMBER (CUCUMIS SATIVUS L.) CHLOROPLAST GENOMES IDENTIFIES PUTATIVE CANDIDATE GENES FOR CHILLING TOLERANCE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chilling injury in cucumber (Cucumis sativus L.) is conditioned by maternal factors and the sequencing of its chloroplast (cp) genome could lead to the identification of economically important candidate genes. Complete sequencing of cucumber cpDNA was facilitated by the development of 414 consensus...

  11. Characterization of minisatellites in Arabidopsis thaliana with sequence similarity to the human minisatellite core sequence.

    PubMed

    Tourmente, S; Deragon, J M; Lafleuriel, J; Tutois, S; Pélissier, T; Cuvillier, C; Espagnol, M C; Picard, G

    1994-08-25

    A strategy based on random PCR amplification was used to isolate new repetitive elements of Arabidopsis thaliana. One of the random PCR product analyzed by this approach contained a tandem repetitive minisatellite sequence composed of 33 bp repeated units. The genomic locus corresponding to this PCR product was isolated by screening a lambda genomic library. New related loci were also isolated from the genomic library by screening with a 14 mer oligonucleotide representing a region conserved among the different repeated units. Alignment of the consensus sequence for each minisatellite locus allowed the definition of an Arabidopsis thaliana core sequence that shows strong sequence similarities with the human core sequence and with the generalized recombination signal Chi of Escherichia coli. The minisatellites were tested for their ability to detect polymorphism, and their chromosomal position was established. PMID:8078766

  12. Miz-1 Activates Gene Expression via a Novel Consensus DNA Binding Motif

    PubMed Central

    Barrilleaux, Bonnie L.; Burow, Dana; Lockwood, Sarah H.; Yu, Abigail; Segal, David J.; Knoepfler, Paul S.

    2014-01-01

    The transcription factor Miz-1 can either activate or repress gene expression in concert with binding partners including the Myc oncoprotein. The genomic binding of Miz-1 includes both core promoters and more distal sites, but the preferred DNA binding motif of Miz-1 has been unclear. We used a high-throughput in vitro technique, Bind-n-Seq, to identify two Miz-1 consensus DNA binding motif sequences—ATCGGTAATC and ATCGAT (Mizm1 and Mizm2)—bound by full-length Miz-1 and its zinc finger domain, respectively. We validated these sequences directly as high affinity Miz-1 binding motifs. Competition assays using mutant probes indicated that the binding affinity of Miz-1 for Mizm1 and Mizm2 is highly sequence-specific. Miz-1 strongly activates gene expression through the motifs in a Myc-independent manner. MEME-ChIP analysis of Miz-1 ChIP-seq data in two different cell types reveals a long motif with a central core sequence highly similar to the Mizm1 motif identified by Bind-n-Seq, validating the in vivo relevance of the findings. Miz-1 ChIP-seq peaks containing the long motif are predominantly located outside of proximal promoter regions, in contrast to peaks without the motif, which are highly concentrated within 1.5 kb of the nearest transcription start site. Overall, our results indicate that Miz-1 may be directed in vivo to the novel motif sequences we have identified, where it can recruit its specific binding partners to control gene expression and ultimately regulate cell fate. PMID:24983942

  13. Partial molecular cloning of the JHK retrovirus using gammaretrovirus consensus PCR primers

    PubMed Central

    Halligan, Brian D; Sun, Hai-Yuan; Kushnaryov, Vladimir M; Grossberg, Sidney E

    2013-01-01

    The JHK virus (JHKV) was previously described as a type C retrovirus that has some distinctive ultrastructural features and replicates constitutively in a human B-lymphoblastoid cell line, JHK-3. In order to facilitate the cloning of sequences from JHKV, a series of partially degenerate consensus retroviral PCR primers were created by a data-driven design approach based on an alignment of 14 diverse gammaretroviral genomes. These primers were used in the PCR amplification of purified JHK virion cDNA, and ana lysis of the resulting amplified sequence indicates that the JHKV is in the murine leukemia virus (MLV) family. The JHK sequence is nearly identical to the corresponding region of the Bxv-1 endogenous mouse retrovirus (GenBank accession AC115959) and distinct from XMRV. JHKV gag-specific amplification was demonstrated with nucleic acids from uncultivated, frozen, peripheral blood mononuclear cells (PBMCs) of the index patient, but not in PBMCs from nine healthy blood donors. Unlike earlier reports, in which MLV-like sequences were identified in human source material, which may have been due to murine contamination, budding retrovirions were demonstrated repeatedly by electron microscopy in uncultivated lymphocytes of the index patient that were morphologically identical in their development to the virions in the JHK-3 cells, and immunological evidence was obtained that the index patient produced IgG antibodies that bound to the budding viral particles in patient PBMCs and in the JHK-3 cells. These data indicate that the patient had been infected by JHKV, lending significance to the demonstration of JHKV amplicons in nucleic acids of the patient’s PBMCs. In future studies, the PCR primer sets described herein may expand the detection of an amplifiable subset of viruses related to MLV. PMID:24159361

  14. Mean square average-consensus for multi-agent systems with measurement noise and time delay

    NASA Astrophysics Data System (ADS)

    Sun, Fenglan; Guan, Zhi-Hong; Ding, Li; Wang, Yan-Wu

    2013-06-01

    Mean square average consensus for multi-agent systems with measurement noise and time delay under fixed digraph is studied in this article. The time-varying consensus-gain is introduced to attenuate the measurement noise. By combining the tools of algebraic graph theory, matrix theory and stochastic analysis, consensus protocols for multi-agent systems with measurement noise and time delay are elaborately analysed. The example and simulation results are given to illustrate the effectiveness of the obtained theoretical results. Moreover, the simulations demonstrate that, the proper consensus-gain function in the consensus protocol is the necessary and sufficient condition for the convergence of the multi-agent systems.

  15. "Ditto Heads": Do Conservatives Perceive Greater Consensus Within Their Ranks Than Liberals?

    PubMed

    Stern, Chadly; West, Tessa V; Jost, John T; Rule, Nicholas O

    2014-06-27

    In three studies, we examined (a) whether conservatives possess a stronger desire to share reality than liberals and are therefore more likely to perceive consensus with politically like-minded others even for non-political judgments and, if so, (b) whether motivated perceptions of consensus would give conservatives an edge in progressing toward collective goals. In Study 1, participants estimated ingroup consensus on non-political judgments. Conservatives perceived more ingroup consensus than liberals, regardless of the amount of actual consensus. The desire to share reality mediated the relationship between ideology and perceived ingroup consensus. Study 2 replicated these results and demonstrated that perceiving ingroup consensus predicted a sense of collective efficacy in politics. In Study 3, experimental manipulations of affiliative motives eliminated ideological differences in the desire to share reality. A sense of collective efficacy predicted intentions to vote in a major election. Implications for the attainment of shared goals are discussed. PMID:24972941

  16. Scientists Are from Mars, Laypeople Are from Venus: An Evidence-Based Approach to Consensus Messaging

    NASA Astrophysics Data System (ADS)

    Cook, J.; Jacobs, P.; Nuccitelli, D.

    2014-12-01

    Laypeople use expert opinion as a mental shortcut to form views on complex scientific issues. This heuristic is particularly relevant in the case of climate change, where perception of consensus is one of the main predictors of public support for climate action. A low public perception of consensus (around 60% compared to the actual 97% consensus) is a significant stumbling block to meaningful climate action, underscoring the importance of closing the "consensus gap". However, some scientists question the efficacy or appropriateness of emphasizing consensus in climate communication. I'll summarize the social science research examining the importance and effectiveness of consensus messaging. I'll also present several case studies of consensus messaging employed by the team of communicators at the Skeptical Science website.

  17. A consensus linkage map of oil palm and a major QTL for stem height

    PubMed Central

    Lee, May; Xia, Jun Hong; Zou, Zhongwei; Ye, Jian; Rahmadsyah; Alfiko, Yuzer; Jin, Jingjing; Lieando, Jessica Virginia; Purnamasari, Maria Indah; Lim, Chin Huat; Suwanto, Antonius; Wong, Limsoon; Chua, Nam-Hai; Yue, Gen Hua

    2015-01-01

    Oil palm (Elaeis guinensis Jacquin) is the most important source of vegetable oil and fat. Several linkage maps had been constructed using dominant and co-dominant markers to facilitate mapping of QTL. However, dominant markers are not easily transferable among different laboratories. We constructed a consensus linkage map for oil palm using co-dominant markers (i.e. microsatellite and SNPs) and two F1 breeding populations generated by crossing Dura and Pisifera individuals. Four hundreds and forty-four microsatellites and 36 SNPs were mapped onto 16 linkage groups. The map length was 1565.6 cM, with an average marker space of 3.72 cM. A genome-wide scan of QTL identified a major QTL for stem height on the linkage group 5, which explained 51% of the phenotypic variation. Genes in the QTL were predicted using the palm genome sequence and bioinformatic tools. The linkage map supplies a base for mapping QTL for accelerating the genetic improvement, and will be also useful in the improvement of the assembly of the genome sequences. Markers linked to the QTL may be used in selecting dwarf trees. Genes within the QTL will be characterized to understand the mechanisms underlying dwarfing. PMID:25648560

  18. PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes

    PubMed Central

    Sheu, Shu-Hsien; Lancia, David R.; Clodfelter, Karl H.; Landon, Melissa R.; Vajda, Sandor

    2005-01-01

    PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its ligands (substrate and transition state analogs, cofactors, inhibitors and products). It is available online at http://precise.bu.edu/. In the current version, all information on interactions is extracted from the enzyme–ligand complexes in the Protein Data Bank (PDB) by performing the following steps: (i) clustering homologous enzyme chains such that, in each cluster, the proteins have the same EC number and all sequences are similar; (ii) selecting a representative chain for each cluster; (iii) selecting ligand types; (iv) finding non-bonded interactions and hydrogen bonds; and (v) summing the interactions for all chains within the cluster. The output of the search is the color-coded sequence of the representative. The colors indicate the total number of interactions found at each amino acid position in all chains of the cluster. Clicking on a residue displays a detailed list of interactions for that residue. Optional filters allow restricting the output to selected chains in the cluster, to non-bonded or hydrogen bonding interactions, and to selected ligand types. The binding site information is essential for understanding and altering substrate specificity and for the design of enzyme inhibitors. PMID:15608178

  19. Development of a consensus reverse transcription PCR assay for the specific detection of tortoise picornaviruses.

    PubMed

    Marschang, Rachel E; Ihász, Katalin; Kugler, Renáta; Lengyel, György; Fehér, Enikő; Marton, Szilvia; Bányai, Krisztián; Aqrawi, Tara; Farkas, Szilvia L

    2016-05-01

    Picornaviruses (PVs) of different terrestrial tortoise species, previously designated as Virus "X," have been frequently detected from various tissues by virus isolation in Terrapene heart cell culture as the preferred laboratory method for diagnosis. Here, we describe the development of 2 diagnostic reverse transcription (RT)-PCR-based assays for the identification and characterization of tortoise PVs belonging to the tentative genus Topivirus To test the novel diagnostic systems, PVs were isolated from swab and tissue samples collected in Germany, Italy, and Hungary between 2000 and 2013. All 25 tested isolates gave positive results with both novel consensus primer sets. Sequencing of the amplified products confirmed that all studied viruses were members of the new proposed genus Topivirus Phylogenetic analyses clearly distinguished 2 lineages within the genus. Based on sequence analysis, no association was observed between the geographic distribution and genetic relatedness. Furthermore, no strict host specificity was indicated. The PCR-based diagnosis may provide a time-saving and sensitive method to detect tortoise PVs, and evaluation of PV presence in these animals may help control virus spread. PMID:27034342

  20. Consensus recommendations for a standardized Brain Tumor Imaging Protocol in clinical trials.

    PubMed

    Ellingson, Benjamin M; Bendszus, Martin; Boxerman, Jerrold; Barboriak, Daniel; Erickson, Bradley J; Smits, Marion; Nelson, Sarah J; Gerstner, Elizabeth; Alexander, Brian; Goldmacher, Gregory; Wick, Wolfgang; Vogelbaum, Michael; Weller, Michael; Galanis, Evanthia; Kalpathy-Cramer, Jayashree; Shankar, Lalitha; Jacobs, Paula; Pope, Whitney B; Yang, Dewen; Chung, Caroline; Knopp, Michael V; Cha, Soonme; van den Bent, Martin J; Chang, Susan; Yung, W K Al; Cloughesy, Timothy F; Wen, Patrick Y; Gilbert, Mark R

    2015-09-01

    A recent joint meeting was held on January 30, 2014, with the US Food and Drug Administration (FDA), National Cancer Institute (NCI), clinical scientists, imaging experts, pharmaceutical and biotech companies, clinical trials cooperative groups, and patient advocate groups to discuss imaging endpoints for clinical trials in glioblastoma. This workshop developed a set of priorities and action items including the creation of a standardized MRI protocol for multicenter studies. The current document outlines consensus recommendations for a standardized Brain Tumor Imaging Protocol (BTIP), along with the scientific and practical justifications for these recommendations, resulting from a series of discussions between various experts involved in aspects of neuro-oncology neuroimaging for clinical trials. The minimum recommended sequences include: (i) parameter-matched precontrast and postcontrast inversion recovery-prepared, isotropic 3D T1-weighted gradient-recalled echo; (ii) axial 2D T2-weighted turbo spin-echo acquired after contrast injection and before postcontrast 3D T1-weighted images to control timing of images after contrast administration; (iii) precontrast, axial 2D T2-weighted fluid-attenuated inversion recovery; and (iv) precontrast, axial 2D, 3-directional diffusion-weighted images. Recommended ranges of sequence parameters are provided for both 1.5 T and 3 T MR systems. PMID:26250565

  1. Identification of Novel N-Glycosylation Sites at Noncanonical Protein Consensus Motifs.

    PubMed

    Lowenthal, Mark S; Davis, Kiersta S; Formolo, Trina; Kilpatrick, Lisa E; Phinney, Karen W

    2016-07-01

    N-glycosylation of proteins is well known to occur at asparagine residues that fall within the canonical consensus sequence N-X-S/T but has also been identified at a small number of asparagine residues within N-X-C motifs, including the N491 residue of human serotransferrin. Here we report novel glycosylation sites within noncanonical consensus motifs, in the conformation N-X-C, based on mass spectrometry analysis of partially deglycosylated glycopeptide targets. Alpha-1-acid glycoprotein (A1AG) and serotransferrin (Tf) were observed for the first time to be N-glycosylated on asparagine residues within a total of six unique noncanonical motifs. N-glycosylation was initially predicted in silico based on the evolutionary conservation of the N-X-C motif among related mammalian species and demonstrated experimentally in A1AG from porcine, canine, and feline sources and in human serotransferrin. High-resolution liquid chromatography-tandem mass spectrometry was employed to collect fragmentation data of predicted GlcNAcylated peptides and to assign modification sites within N-X-C motifs. A combination of targeted analytical techniques that includes complementary mass spectrometry platforms, enzymatic digestions, and partial-deglycosylation procedures was developed to confirm the novel observations. Additionally, we found that A1AG in porcine and canine sources is highly N-glycosylated at a noncanonical motif (N-Q-C) based on semiquantitative multiple reaction monitoring analysis-the first report of an N-X-C motif exhibiting substantial N-glycosylation. Although reports of N-X-C motif N-glycosylation are relatively uncommon in the literature, this work adds to a growing list of glycoproteins reported with glycosylation at various forms of noncanonical motifs. PMID:27246700

  2. RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).

    PubMed

    Richardson, Jane S; Schneider, Bohdan; Murray, Laura W; Kapral, Gary J; Immormino, Robert M; Headd, Jeffrey J; Richardson, David C; Ham, Daniela; Hershkovits, Eli; Williams, Loren Dean; Keating, Kevin S; Pyle, Anna Marie; Micallef, David; Westbrook, John; Berman, Helen M

    2008-03-01

    A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a quality-filtered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle delta epsilon zeta alpha beta gamma delta combinations empirically found favorable for the sugar-to-sugar "suite" unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for delta epsilon zeta and a lowercase letter for alpha beta gamma delta, this modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs. PMID:18192612

  3. Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers.

    PubMed

    Van Brabant, Bart; Gray, Tanya; Verslyppe, Bert; Kyrpides, Nikos; Dietrich, Karin; Glöckner, Frank Oliver; Cole, James; Farris, Ryan; Schriml, Lynn M; De Vos, Paul; De Baets, Bernard; Field, Dawn; Dawyndt, Peter

    2008-06-01

    Given the growing wealth of downstream information, the integration of molecular and non-molecular data on a given organism has become a major challenge. For micro-organisms, this information now includes a growing collection of sequenced genes and complete genomes, and for communities of organisms it includes metagenomes. Integration of the data is facilitated by the existence of authoritative, community-recognized, consensus identifiers that may form the heart of so-called information knuckles. The Genomic Standards Consortium (GSC) is building a mapping of identifiers across a group of federated databases with the aim to improve navigation across these resources and to enable the integration of their information in the near future. In particular, this is possible because of the existence of INSDC Genome Project Identifiers (GPIDs) and accession numbers, and the ability of the community to define new consensus identifiers such as the culture identifiers used in the StrainInfo.net bioportal. Here we outline (1) the general design of the Genomic Rosetta Stone project, (2) introduce example linkages between key databases (that cover information about genomes, 16S rRNA gene sequences, and microbial biological resource centers), and (3) make an open call for participation in this project providing a vision for its future use. PMID:18479205

  4. Standard operating procedures for ESPEN guidelines and consensus papers.

    PubMed

    Bischoff, Stephan C; Singer, Pierre; Koller, Michael; Barazzoni, Rocco; Cederholm, Tommy; van Gossum, André

    2015-12-01

    The ESPEN Guideline standard operating procedures (SOP) is based on the methodology provided by the Association of Scientific Medical Societies of Germany (AWMF), the Scottish Intercollegiate Guidelines Network (SIGN), and the Centre for Evidence-based Medicine at the University of Oxford. The SOP is valid and obligatory for all future ESPEN-sponsored guideline projects aiming to generate high-quality guidelines on a regular basis. The SOP aims to facilitate the preparation of guideline projects, to streamline the consensus process, to ensure quality and transparency, and to facilitate the dissemination and publication of ESPEN guidelines. To achieve this goal, the ESPEN Guidelines Editorial board (GEB) has been established headed by two chairmen. The GEB will support and supervise the guideline processes and is responsible for the strategic planning of ESPEN guideline activities. Key elements of the SOP are the generation of well-built clinical questions according to the PICO system, a systemic literature search, a classification of the selected literature according to the SIGN evidence levels providing an evidence table, and a clear and straight-forward consensus procedure consisting of online voting's and a consensus conference. Only experts who meet the obligation to disclosure any potential conflict of interests and who are not employed by the Industry can participate in the guideline process. All recommendations will be graded according to the SIGN grading and novel outcome models besides biomedical endpoints. This approach will further extent the leadership of ESPEN in creating up-to-date and suitable for implementation guidelines and in sharing knowledge on malnutrition and clinical nutrition. PMID:26254807

  5. Tobacco control: consensus report of the National Medical Association.

    PubMed Central

    Marable, Sharon; Crim, Courtney; Dennis, Gary C.; Epps, Roselyn Payne; Freeman, Harold; Mills, Sherry; Coolchan, Eric T.; Robinson, Lawrence; Robinson, Robert; Cole, Lorraine; Payne, Pamela H.

    2002-01-01

    ISSUES: Tobacco Control remains one of the greatest determinants for reducing the morbidity and mortality of African Americans. OBJECTIVE: To examine the scope and consequences of tobacco use among African Americans and characterize its implications for the National Medical Association physician membership and their patients, and identify policy, education, advocacy and research issues in Tobacco Control for the organization. CONSENSUS PROCESS: Literature review using the MEDLINE database from January 1966 to August 1999 Week 1, searching Medical Subject Heading (MeSH) reading combined with text words "Black" or "African American" and "Tobacco" as a search term, identified 130 articles/110 abstracts published between 1988 and February 1999. The panel selected 61 appropriate articles and a paper summarizing the literature review was developed. The summary paper was used as background material for a formal consensus panel discussion on July 16-17, 1999. Consensus among committee members was reached via mail, fax and e-mail using the summary review paper, annotated bibliographies key informant surveys, and previous NMA resolutions on tobacco control. A formal working session was held on July 16-17, 1999 in which four areas of concentration of issues were determined: Policy, Advocacy, Education and Research. All committee members approved the final report. SUMMARY: Because tobacco control issues in African Americans are both complex and poorly understood, the panel views the NMA's role as pivotal in the coordination of resources and capacity-building to address all four areas identified. Stronger partner-ships with traditional federal and nonprofit agencies associated with tobacco control/advocacy in African Americans as well as nontraditional organizations (i.e., churches, academia, marketing and media organizations) also must occur to strengthen the infra-structure needed to assess needs, design appropriate interventions and evaluate the appropriateness

  6. [Sequencing babies?].

    PubMed

    Jordan, Bertrand

    2015-10-01

    An extension of newborn screening to genome sequencing is now feasible but raises a number of scientific, organisational and ethical issues. This is being explored in discussions and in several funded trials, in order to maximize benefits and avoid some identified risks. As some companies are already offering such a service, this is quite an urgent matter. PMID:26481033

  7. Bipartite opinion forming: Towards consensus over coopetition networks

    NASA Astrophysics Data System (ADS)

    Hou, Bo; Chen, Yao; Liu, Guangbin; Sun, Fuchun; Li, Hongbo

    2015-12-01

    Within the framework of signed graph and multi-agent systems, this paper investigates the distributed bipartite opinion forming problem over coopetition networks. Several sufficient algebraic and geometric topology conditions that guarantee consensus, regardless of the magnitudes of individual coupling strengths among the agents, have been derived by exploring the interaction direction patterns. All the criteria presented do not require the global knowledge of the coupling weights of the entire network, and thus are easier to check. The effectiveness of the theoretical results are illustrated by numerical examples.

  8. North American Thrombosis Forum, AF Action Initiative Consensus Document.

    PubMed

    Ruff, Christian T; Ansell, Jack E; Becker, Richard C; Benjamin, Emelia J; Deicicchi, David J; Mark Estes, N A; Ezekowitz, Michael D; Fanikos, John; Fareed, Jawed; Garcia, David; Giugliano, Robert P; Goldhaber, Samuel Z; Granger, Christopher; Healey, Jeff S; Hull, Russell; Hylek, Elaine M; Libby, Peter; Lopes, Renato D; Mahaffey, Kenneth W; Mega, Jessica; Piazza, Gregory; Sasahara, Arthur A; Sorond, Farzaneh A; Spyropoulos, Alex C; Walenga, Jeanine M; Weitz, Jeffrey I

    2016-05-01

    The North American Thrombosis Forum Atrial Fibrillation Action Initiative consensus document is a comprehensive yet practical briefing document focusing on stroke and bleeding risk assessment in patients with atrial fibrillation, as well as recommendations regarding anticoagulation options and management. Despite the breadth of clinical trial data and guideline recommendation updates, many clinicians continue to struggle to synthesize the disparate information available. This problem slows the uptake and utilization of updated risk prediction tools and adoption of new oral anticoagulants. This document serves as a practical and educational reference for the entire medical community involved in the care of patients with atrial fibrillation. PMID:27126598

  9. [3rd Hungarian Breast Cancer Consensus Conference - Surgery Guidelines].

    PubMed

    Lázár, György; Bursics, Attila; Farsang, Zoltán; Harsányi, László; Kósa, Csaba; Maráz, Róbert; Mátrai, Zoltán; Paszt, Attila; Pavlovics, Gábor; Tamás, Róbert

    2016-09-01

    Therapy for breast cancer today is characterised by ever more precise diagnostic methods and ever more effective oncological treatments, a trend which will certainly continue in the future. Breast preservation and the application of oncoplastic principles are increasingly popular. A sentinel lymph node biopsy in the surgical treatment of the axilla is primary, with the indication for axillary block dissection (ABD) narrowing and radiation therapy becoming an alternative to ABD in certain cases. This publication summarises our recommendations on the surgical treatment of breast cancer based on the content of the 2nd Breast Cancer Consensus Conference and considering the latest international studies and professional recommendations. PMID:27579720

  10. Core Outcomes for Colorectal Cancer Surgery: A Consensus Study

    PubMed Central

    Whistance, Robert N.; Forsythe, Rachael O.; Macefield, Rhiannon; Pullyblank, Anne M.; Avery, Kerry N. L.; Brookes, Sara T.; Thomas, Michael G.; Sylvester, Paul A.; Russell, Ann; Oliver, Alfred; Morton, Dion; Kennedy, Robin; Jayne, David G.; Huxtable, Richard; Hackett, Roland; Card, Mia; Brown, Julia; Blazeby, Jane M.

    2016-01-01

    Background Colorectal cancer (CRC) is a major cause of worldwide morbidity and mortality. Surgical treatment is common, and there is a great need to improve the delivery of such care. The gold standard for evaluating surgery is within well-designed randomized controlled trials (RCTs); however, the impact of RCTs is diminished by a lack of coordinated outcome measurement and reporting. A solution to these issues is to develop an agreed standard “core” set of outcomes to be measured in all trials to facilitate cross-study comparisons, meta-analysis, and minimize outcome reporting bias. This study defines a core outcome set for CRC surgery. Methods and Findings The scope of this COS includes clinical effectiveness trials of surgical interventions for colorectal cancer. Excluded were nonsurgical oncological interventions. Potential outcomes of importance to patients and professionals were identified through systematic literature reviews and patient interviews. All outcomes were transcribed verbatim and categorized into domains by two independent researchers. This informed a questionnaire survey that asked stakeholders (patients and professionals) from United Kingdom CRC centers to rate the importance of each domain. Respondents were resurveyed following group feedback (Delphi methods). Outcomes rated as less important were discarded after each survey round according to predefined criteria, and remaining outcomes were considered at three consensus meetings; two involving international professionals and a separate one with patients. A modified nominal group technique was used to gain the final consensus. Data sources identified 1,216 outcomes of CRC surgery that informed a 91 domain questionnaire. First round questionnaires were returned from 63 out of 81 (78%) centers, including 90 professionals, and 97 out of 267 (35%) patients. Second round response rates were high for all stakeholders (>80%). Analysis of responses lead to 45 and 23 outcome domains being retained

  11. The Brazilian health informatics and information policy: building the consensus.

    PubMed

    Leão, Beatriz F; Costa, Cláudio G; Facchini, Luiz Augusto; Bandarra, Ernani B; Gonçalves, Sibele F; Bretas Jr, Nilo; Ferla, Alcindo

    2004-01-01

    This paper describes the construction of the Brazilian Health Information Policy. The Introduction gives an overview of the health informatics scenario in the country and the motivation for the definition of a national policy for the area. The process adopted and the strategies to reach consensus among the different players of the healthcare arena are discussed. The interface with the national health card project and the standards already established are also depicted. The current document and the strategies so far proposed are presented with their respective time table and goals. At the end, a comparison with other national initiatives is drawn. PMID:15361004

  12. [Curative treatment for esophageal cancer: results of a multidisciplinary consensus].

    PubMed

    Allemann, Pierre; Mantziari, Styliani; Wagner, Dorothea; Digklia, Antonia; Ozsahin, Esat; De Bari, Berardino; Dorta, Gian; Godat, Sébastien; Montserrat, Fraga; Sempoux, Christine; Brunel, Christophe; Demartines, Nicolas; Schäfer, Markus

    2016-06-15

    The management of patients with resectable cancer of the esophagus or gastroesophageal junction is currently not standardized. A multi- disciplinary regional consensus has been developed and is presented in this article. The standard workup includes an upper endoscopy, ultrasonography and a CT-scan. For locally advanced tumors, surgery should be associated with either preoperative radiochemotherapy orperioperative chemotherapy after discussion in multidisciplinary tumor board. Before the operation, smoking and alcohol cessation is imperative and nutritional status should be optimized. Nowadays, surgery is well standardized and generally performed minimally invasive accesses. After surgery, clinical and oncological follow-up is necessary. PMID:27487620

  13. SEPAR-ALAT Consensus Document on Antipneumoccal Vaccination in Smokers.

    PubMed

    Jiménez Ruiz, Carlos A; Buljubasich, Daniel; Sansores, Raúl; Riesco Miranda, Juan Antonio; Guerreros Benavides, Alfredo; Luhning, Susana; Chatkin, José Miguel; Zabert, Gustavo; de Granda Orive, José Ignacio; Solano Reina, Segismundo; Casas Herrera, Alejandro; de Lucas Ramos, Pilar

    2015-07-01

    Streptococcus pneumoniae is responsible for several clinical syndromes, such as community-acquired pneumonia, sinusitis, otitis media, and others. The most severe clinical entity caused by this bacteria is undoubtedly invasive pneumococcal disease. Certain factors are known to increase the risk of presenting invasive pneumococcal disease, the most important being smoking habit and underlying concomitant diseases. This article comprises a consensus document on antipneumococcal vaccination in smokers, drawn up by a Smoking Expert Group from the Spanish Society of Pulmonology and Thoracic Surgery and the Latin American Chest Association. PMID:25641351

  14. Optimal benefits for hematopoietic stem cell transplantation: a consensus opinion.

    PubMed

    Maziarz, Richard T; Farnia, Stephanie; Martin, Patricia; Komanduri, Krishna V

    2014-11-01

    Variability in transplantation benefits may directly affect outcomes of individuals undergoing autologous or allogeneic hematopoietic stem cell transplantation procedures. The Financial Working Group of the National Marrow Donor Program-sponsored System Capacity Initiative addressed the issue of variable benefits and reviewed multiple transplantation benefit packages from both public and private payer organizations. On completion of the review, a consensus was obtained on defining a recipient benefit package that avoids major coverage gaps that could negatively influence patient outcomes. The recommendation was to encourage adoption of these benefits at a national level by payers, benefit brokers/consultants, and sales teams. PMID:25020102

  15. BPROMPT: A consensus server for membrane protein prediction.

    PubMed

    Taylor, Paul D; Attwood, Teresa K; Flower, Darren R

    2003-07-01

    Protein structure prediction is a cornerstone of bioinformatics research. Membrane proteins require their own prediction methods due to their intrinsically different composition. A variety of tools exist for topology prediction of membrane proteins, many of them available on the Internet. The server described in this paper, BPROMPT (Bayesian PRediction Of Membrane Protein Topology), uses a Bayesian Belief Network to combine the results of other prediction methods, providing a more accurate consensus prediction. Topology predictions with accuracies of 70% for prokaryotes and 53% for eukaryotes were achieved. BPROMPT can be accessed at http://www.jenner.ac.uk/BPROMPT. PMID:12824397

  16. Is a moral consensus in medical ethics possible?

    PubMed Central

    Mitchell, B.

    1976-01-01

    At the moment in Britain and elsewhere the debate inside and outside of Parliament on various medical issues which are essentially moral never ends. Everybody has his own point of view--or principles. But what emerges for society to adopt can often be called in lay terminology 'compromise'. Professor Mitchell argues in this paper that a moral consensus is possible and indeed ought to be achieved, as today the medical practitioner can no longer make his decision only in accordance with the strict code of ethics of the medical profession. The task of the philosopher, says Professor Mitchell, is to interpret the actions and attitudes demanded by modern medical practice. PMID:957368

  17. Consensus guidelines for the use of ultrasound for diving research.

    PubMed

    Møllerløkken, Andreas; Blogg, S Lesley; Doolette, David J; Nishi, Ronald Y; Pollock, Neal W

    2016-03-01

    The International Meeting on Ultrasound for Diving Research produced expert consensus recommendations for ultrasound detection of vascular gas bubbles and the analysis, interpretation and reporting of such data. Recommendations for standardization of techniques to allow comparison between studies included bubble monitoring site selection, frequency and duration of monitoring, and use of the Spencer, Kisman-Masurel or Eftedal-Brubakk scales. Recommendations for reporting of results included description of subject posture and provocation manoeuvres during monitoring, reporting of untransformed data and the appropriate use of statistics. These guidelines are available from www.dhmjournal.com. PMID:27044459

  18. The Hartford Consensus IV: A Call for Increased National Resilience.

    PubMed

    Jacobs, Lenworth M

    2016-03-01

    National implementation of the Hartford Consensus is a meticulous and incremental process. It consists of many elements that require collaboration and strategic leadership to achieve an efficient, effective, knowledgeable, resilient, and prepared citizenry. We strongly believe the public can and should act as immediate responders to stop bleeding from all hazards, including active shooter and intentional mass casualty events. The ACS has a long history of setting standards and educating responders through its Committee on Trauma and its programs. The ACS is therefore well-positioned to use its national and international networks to implement bleeding control education to improve survival and enhance resilience. PMID:27051933

  19. European consensus statement on leptospirosis in dogs and cats.

    PubMed

    Schuller, S; Francey, T; Hartmann, K; Hugonnard, M; Kohn, B; Nally, J E; Sykes, J

    2015-03-01

    Leptospirosis is a zoonotic disease with a worldwide distribution affecting most mammalian species. Clinical leptospirosis is common in dogs but appears to be rare in cats. Both dogs and cats, however, can shed leptospires in the urine. This is problematic as it can lead to exposure of humans. The control of leptospirosis, therefore, is important not only from an animal but also from a public health perspective. The aim of this consensus statement is to raise awareness of leptospirosis and to outline the current knowledge on the epidemiology, clinical features, diagnostic tools, prevention and treatment measures relevant to canine and feline leptospirosis in Europe. PMID:25754092

  20. Recommendations for Probiotic Use--2015 Update: Proceedings and Consensus Opinion.

    PubMed

    Floch, Martin H; Walker, W Allan; Sanders, Mary Ellen; Nieuwdorp, Max; Kim, Adam S; Brenner, David A; Qamar, Amir A; Miloh, Tamir A; Guarino, Alfredo; Guslandi, Mario; Dieleman, Levinus A; Ringel, Yehuda; Quigley, Eamonn M M; Brandt, Lawrence J

    2015-01-01

    This paper describes the consensus opinion of the participants in the 4th Triennial Yale/Harvard Workshop on Probiotic Recommendations. The recommendations update those of the first 3 meetings that were published in 2006, 2008, and 2011. Recommendations for the use of probiotics in necrotizing enterocolitis, childhood diarrhea, inflammatory bowel disease, irritable bowel syndrome and Clostridium difficile diarrhea are reviewed. In addition, we have added recommendations for liver disease for the first time. As in previous publications, the recommendations are given as A, B, or C ratings. PMID:26447969

  1. Towards a Consensus Annotation System (GSC8 Meeting)

    SciTech Connect

    White, Owen

    2009-09-10

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. "Comparing Annotations: Towards Consensus Annotation" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009

  2. Towards a Consensus Annotation System (GSC8 Meeting)

    ScienceCinema

    White, Owen [University of Maryland

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. "Comparing Annotations: Towards Consensus Annotation" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009

  3. Reaching a consensus: a discrete nonlinear time-varying case

    NASA Astrophysics Data System (ADS)

    Saburov, M.; Saburov, K.

    2016-07-01

    In this paper, we have considered a nonlinear protocol for a structured time-varying and synchronous multi-agent system. By means of cubic triple stochastic matrices, we present an opinion sharing dynamics of the multi-agent system as a trajectory of a non-homogeneous system of cubic triple stochastic matrices. We show that the multi-agent system eventually reaches to a consensus if either of the following two conditions is satisfied: (1) every member of the group people has a positive subjective distribution on the given task after some revision steps or (2) all entries of some cubic triple stochastic matrix are positive.

  4. Archaebacterial rhodopsin sequences: Implications for evolution

    NASA Technical Reports Server (NTRS)

    Lanyi, J. K.

    1991-01-01

    It was proposed over 10 years ago that the archaebacteria represent a separate kingdom which diverged very early from the eubacteria and eukaryotes. It follows that investigations of archaebacterial characteristics might reveal features of early evolution. So far, two genes, one for bacteriorhodopsin and another for halorhodopsin, both from Halobacterium halobium, have been sequenced. We cloned and sequenced the gene coding for the polypeptide of another one of these rhodopsins, a halorhodopsin in Natronobacterium pharaonis. Peptide sequencing of cyanogen bromide fragments, and immuno-reactions of the protein and synthetic peptides derived from the C-terminal gene sequence, confirmed that the open reading frame was the structural gene for the pharaonis halorhodopsin polypeptide. The flanking DNA sequences of this gene, as well as those of other bacterial rhodopsins, were compared to previously proposed archaebacterial consensus sequences. In pairwise comparisons of the open reading frame with DNA sequences for bacterio-opsin and halo-opsin from Halobacterium halobium, silent divergences were calculated. These indicate very considerable evolutionary distance between each pair of genes, even in the dame organism. In spite of this, three protein sequences show extensive similarities, indicating strong selective pressures.

  5. MSLICE Sequencing

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

    2011-01-01

    MSLICE Sequencing is a graphical tool for writing sequences and integrating them into RML files, as well as for producing SCMF files for uplink. When operated in a testbed environment, it also supports uplinking these SCMF files to the testbed via Chill. This software features a free-form textural sequence editor featuring syntax coloring, automatic content assistance (including command and argument completion proposals), complete with types, value ranges, unites, and descriptions from the command dictionary that appear as they are typed. The sequence editor also has a "field mode" that allows tabbing between arguments and displays type/range/units/description for each argument as it is edited. Color-coded error and warning annotations on problematic tokens are included, as well as indications of problems that are not visible in the current scroll range. "Quick Fix" suggestions are made for resolving problems, and all the features afforded by modern source editors are also included such as copy/cut/paste, undo/redo, and a sophisticated find-and-replace system optionally using regular expressions. The software offers a full XML editor for RML files, which features syntax coloring, content assistance and problem annotations as above. There is a form-based, "detail view" that allows structured editing of command arguments and sequence parameters when preferred. The "project view" shows the user s "workspace" as a tree of "resources" (projects, folders, and files) that can subsequently be opened in editors by double-clicking. Files can be added, deleted, dragged-dropped/copied-pasted between folders or projects, and these operations are undoable and redoable. A "problems view" contains a tabular list of all problems in the current workspace. Double-clicking on any row in the table opens an editor for the appropriate sequence, scrolling to the specific line with the problem, and highlighting the problematic characters. From there, one can invoke "quick fix" as described

  6. MISIS-2: A bioinformatics tool for in-depth analysis of small RNAs and representation of consensus master genome in viral quasispecies.

    PubMed

    Seguin, Jonathan; Otten, Patricia; Baerlocher, Loïc; Farinelli, Laurent; Pooggin, Mikhail M

    2016-07-01

    In most eukaryotes, small RNA (sRNA) molecules such as miRNAs, siRNAs and piRNAs regulate gene expression and repress transposons and viruses. AGO/PIWI family proteins sort functional sRNAs based on size, 5'-nucleotide and other sequence features. In plants and some animals, viral sRNAs are extremely diverse and cover the entire viral genome sequences, which allows for de novo reconstruction of a complete viral genome by deep sequencing and bioinformatics analysis of viral sRNAs. Previously, we have developed a tool MISIS to view and analyze sRNA maps of viruses and cellular genome regions which spawn multiple sRNAs. Here we describe a new release of MISIS, MISIS-2, which enables to determine and visualize a consensus sequence and count sRNAs of any chosen sizes and 5'-terminal nucleotide identities. Furthermore we demonstrate the utility of MISIS-2 for identification of single nucleotide polymorphisms (SNPs) at each position of a reference sequence and reconstruction of a consensus master genome in evolving viral quasispecies. MISIS-2 is a Java standalone program. It is freely available along with the source code at the website http://www.fasteris.com/apps. PMID:26994965

  7. Optimizing topical therapies for treating psoriasis: a consensus conference.

    PubMed

    Zeichner, Joshua A; Lebwohl, Mark G; Menter, Alan; Bagel, Jerry; Del Rosso, James Q; Elewski, Boni E; Feldman, Steven R; Kircik, Leon H; Koo, John; Gold, Linda Stein; Tanghetti, Emil

    2010-09-01

    In 2010, an expert committee of physicians and researchers in the field of dermatology working together as the Psoriasis Process of Care Consensus Panel developed consensus guidelines for the treatment of psoriasis. As much as possible, the guidelines were evidence based but also included the extensive clinical experience of the dermatologists. Psoriasis is a lifelong disease that requires long-term treatment and 80% of psoriasis patients have mild to moderate disease. Topical therapies play an important role in the treatment of psoriasis, especially in patients with mild to moderate disease. Patients usually start with monotherapy; however, in more severe cases (> 10% body surface area [BSA], severely impaired quality of life [QOL], or recalcitrant psoriatic lesions), multiple treatment modalities may be used as part of combination, sequential, or rotational therapeutic regimens. Main treatment options include topical steroids, systemic therapies, topical vitamin D treatments such as vitamin D3 ointment, retinoids, phototherapy, and biologic therapies. Other topical therapies include the following steroid-sparing agents: coal tar, anthralin, calcineurin inhibitors, keratolytics, and emollients. Therapeutic considerations also should focus on adherence, improving QOL, and promoting a good patient-physician relationship. PMID:21049712

  8. Starling flock networks manage uncertainty in consensus at low cost.

    PubMed

    Young, George F; Scardovi, Luca; Cavagna, Andrea; Giardina, Irene; Leonard, Naomi E

    2013-01-01

    Flocks of starlings exhibit a remarkable ability to maintain cohesion as a group in highly uncertain environments and with limited, noisy information. Recent work demonstrated that individual starlings within large flocks respond to a fixed number of nearest neighbors, but until now it was not understood why this number is seven. We analyze robustness to uncertainty of consensus in empirical data from multiple starling flocks and show that the flock interaction networks with six or seven neighbors optimize the trade-off between group cohesion and individual effort. We can distinguish these numbers of neighbors from fewer or greater numbers using our systems-theoretic approach to measuring robustness of interaction networks as a function of the network structure, i.e., who is sensing whom. The metric quantifies the disagreement within the network due to disturbances and noise during consensus behavior and can be evaluated over a parameterized family of hypothesized sensing strategies (here the parameter is number of neighbors). We use this approach to further show that for the range of flocks studied the optimal number of neighbors does not depend on the number of birds within a flock; rather, it depends on the shape, notably the thickness, of the flock. The results suggest that robustness to uncertainty may have been a factor in the evolution of flocking for starlings. More generally, our results elucidate the role of the interaction network on uncertainty management in collective behavior, and motivate the application of our approach to other biological networks. PMID:23382667

  9. International consensus for a definition of disease flare in lupus.

    PubMed

    Ruperto, N; Hanrahan, L M; Alarcón, G S; Belmont, H M; Brey, R L; Brunetta, P; Buyon, J P; Costner, M I; Cronin, M E; Dooley, M A; Filocamo, G; Fiorentino, D; Fortin, P R; Franks, A G; Gilkeson, G; Ginzler, E; Gordon, C; Grossman, J; Hahn, B; Isenberg, D A; Kalunian, K C; Petri, M; Sammaritano, L; Sánchez-Guerrero, J; Sontheimer, R D; Strand, V; Urowitz, M; von Feldt, J M; Werth, V P; Merrill, J T

    2011-04-01

    The Lupus Foundation of America (LFA) convened an international working group to obtain a consensus definition of disease flare in lupus. With help from the Paediatric Rheumatology International Trials Organization (PRINTO), two web-based Delphi surveys of physicians were conducted. Subsequently, the LFA held a second consensus conference followed by a third Delphi survey to reach a community-wide agreement for flare definition. Sixty-nine of the 120 (57.5%) polled physicians responded to the first survey. Fifty-nine of the responses were available to draft 12 preliminary statements, which were circulated in the second survey. Eighty-seven of 118 (74%) physicians completed the second survey, with an agreement of 70% for 9/12 (75%) statements. During the second conference, three alternative flare definitions were consolidated and sent back to the international community. One hundred and sixteen of 146 (79.5%) responded, with agreement by 71/116 (61%) for the following definition: "A flare is a measurable increase in disease activity in one or more organ systems involving new or worse clinical signs and symptoms and/or laboratory measurements. It must be considered clinically significant by the assessor and usually there would be at least consideration of a change or an increase in treatment." The LFA proposes this definition for lupus flare on the basis of its high face validity. PMID:21148601

  10. Consensus of Multiagent Systems Using Aperiodic Sampled-Data Control.

    PubMed

    Wu, Yuanqing; Su, Hongye; Shi, Peng; Shu, Zhan; Wu, Zheng-Guang

    2016-09-01

    This paper is concerned with the consensus of multiagent systems with nonlinear dynamics through the use of aperiodic sampled-data controllers, which are more flexible than classical periodic sampled-data controllers. By input delay approach, the resulting sampled-data system is reformulated as a continuous system with time-varying delay in the control input. A continuous Lyapunov functional, which captures the information on sampling pattern, together with the free-weighting matrix method, is then used to establish a sufficient condition for consensusability. For a more general case that the sampled-data controllers are subject to constant input delays, a novel discontinuous Lyapunov functional is introduced on the basis of the vector extension of Wirtinger's inequality. This functional can lead to simplified and efficient stability conditions for computation and optimization. Further results on the estimate of maximal allowable sampling interval upper bound is given as well. Numerical example is provided to show the effectiveness and merits of the proposed protocol. PMID:26316291

  11. Modelling Adaptive Learning Behaviours for Consensus Formation in Human Societies.

    PubMed

    Yu, Chao; Tan, Guozhen; Lv, Hongtao; Wang, Zhen; Meng, Jun; Hao, Jianye; Ren, Fenghui

    2016-01-01

    Learning is an important capability of humans and plays a vital role in human society for forming beliefs and opinions. In this paper, we investigate how learning affects the dynamics of opinion formation in social networks. A novel learning model is proposed, in which agents can dynamically adapt their learning behaviours in order to facilitate the formation of consensus among them, and thus establish a consistent social norm in the whole population more efficiently. In the model, agents adapt their opinions through trail-and-error interactions with others. By exploiting historical interaction experience, a guiding opinion, which is considered to be the most successful opinion in the neighbourhood, can be generated based on the principle of evolutionary game theory. Then, depending on the consistency between its own opinion and the guiding opinion, a focal agent can realize whether its opinion complies with the social norm (i.e., the majority opinion that has been adopted) in the population, and adapt its behaviours accordingly. The highlight of the model lies in that it captures the essential features of people's adaptive learning behaviours during the evolution and formation of opinions. Experimental results show that the proposed model can facilitate the formation of consensus among agents, and some critical factors such as size of opinion space and network topology can have significant influences on opinion dynamics. PMID:27282089

  12. Assessment of the cortisol awakening response: Expert consensus guidelines.

    PubMed

    Stalder, Tobias; Kirschbaum, Clemens; Kudielka, Brigitte M; Adam, Emma K; Pruessner, Jens C; Wüst, Stefan; Dockray, Samantha; Smyth, Nina; Evans, Phil; Hellhammer, Dirk H; Miller, Robert; Wetherell, Mark A; Lupien, Sonia J; Clow, Angela

    2016-01-01

    The cortisol awakening response (CAR), the marked increase in cortisol secretion over the first 30-45 min after morning awakening, has been related to a wide range of psychosocial, physical and mental health parameters, making it a key variable for psychoneuroendocrinological research. The CAR is typically assessed from self-collection of saliva samples within the domestic setting. While this confers ecological validity, it lacks direct researcher oversight which can be problematic as the validity of CAR measurement critically relies on participants closely following a timed sampling schedule, beginning with the moment of awakening. Researchers assessing the CAR thus need to take important steps to maximize and monitor saliva sampling accuracy as well as consider a range of other relevant methodological factors. To promote best practice of future research in this field, the International Society of Psychoneuroendocrinology initiated an expert panel charged with (i) summarizing relevant evidence and collective experience on methodological factors affecting CAR assessment and (ii) formulating clear consensus guidelines for future research. The present report summarizes the results of this undertaking. Consensus guidelines are presented on central aspects of CAR assessment, including objective control of sampling accuracy/adherence, participant instructions, covariate accounting, sampling protocols, quantification strategies as well as reporting and interpreting of CAR data. Meeting these methodological standards in future research will create more powerful research designs, thus yielding more reliable and reproducible results and helping to further advance understanding in this evolving field of research. PMID:26563991

  13. Collective Learning and Optimal Consensus Decisions in Social Animal Groups

    PubMed Central

    Kao, Albert B.; Miller, Noam; Torney, Colin; Hartnett, Andrew; Couzin, Iain D.

    2014-01-01

    Learning has been studied extensively in the context of isolated individuals. However, many organisms are social and consequently make decisions both individually and as part of a collective. Reaching consensus necessarily means that a single option is chosen by the group, even when there are dissenting opinions. This decision-making process decouples the otherwise direct relationship between animals' preferences and their experiences (the outcomes of decisions). Instead, because an individual's learned preferences influence what others experience, and therefore learn about, collective decisions couple the learning processes between social organisms. This introduces a new, and previously unexplored, dynamical relationship between preference, action, experience and learning. Here we model collective learning within animal groups that make consensus decisions. We reveal how learning as part of a collective results in behavior that is fundamentally different from that learned in isolation, allowing grouping organisms to spontaneously (and indirectly) detect correlations between group members' observations of environmental cues, adjust strategy as a function of changing group size (even if that group size is not known to the individual), and achieve a decision accuracy that is very close to that which is provably optimal, regardless of environmental contingencies. Because these properties make minimal cognitive demands on individuals, collective learning, and the capabilities it affords, may be widespread among group-living organisms. Our work emphasizes the importance and need for theoretical and experimental work that considers the mechanism and consequences of learning in a social context. PMID:25101642

  14. Modelling Adaptive Learning Behaviours for Consensus Formation in Human Societies

    PubMed Central

    Yu, Chao; Tan, Guozhen; Lv, Hongtao; Wang, Zhen; Meng, Jun; Hao, Jianye; Ren, Fenghui

    2016-01-01

    Learning is an important capability of humans and plays a vital role in human society for forming beliefs and opinions. In this paper, we investigate how learning affects the dynamics of opinion formation in social networks. A novel learning model is proposed, in which agents can dynamically adapt their learning behaviours in order to facilitate the formation of consensus among them, and thus establish a consistent social norm in the whole population more efficiently. In the model, agents adapt their opinions through trail-and-error interactions with others. By exploiting historical interaction experience, a guiding opinion, which is considered to be the most successful opinion in the neighbourhood, can be generated based on the principle of evolutionary game theory. Then, depending on the consistency between its own opinion and the guiding opinion, a focal agent can realize whether its opinion complies with the social norm (i.e., the majority opinion that has been adopted) in the population, and adapt its behaviours accordingly. The highlight of the model lies in that it captures the essential features of people’s adaptive learning behaviours during the evolution and formation of opinions. Experimental results show that the proposed model can facilitate the formation of consensus among agents, and some critical factors such as size of opinion space and network topology can have significant influences on opinion dynamics. PMID:27282089

  15. A consensus approach to wound care in epidermolysis bullosa

    PubMed Central

    Pope, Elena; Lara-Corrales, Irene; Mellerio, Jemima; Martinez, Anna; Schultz, Gregory; Burrell, Robert; Goodman, Laurie; Coutts, Patricia; Wagner, John; Allen, Upton; Sibbald, Gary

    2013-01-01

    Background Wound care is the cornerstone of treatment for patients with epidermolysis bullosa (EB); however, there are currently no guidelines to help practitioners care for these patients. Objectives The objective of this study was to generate a list of recommendations that will enable practitioners to better care for patients with EB. Methods An expert panel generated a list of recommendations based on the best evidence available. The recommendations were translated into a survey, and sent to other EB experts to generate consensus using an online-based modified Delphi method. The list was refined and grouped into themes and specific recommendations. Results There were15 respondents (45% response rate), with significant experience in the EB field (>10 years [67%]). Respondents included physicians (67%), nurses (17%), and allied health professionals (7%). There was more than 85% agreement for all the proposed items. These were further refined and grouped into 5 main themes (assessment and management of factors that impair healing, patient-centered concerns, local wound care, development of an individualized care plan, and organizational support) and 17 specific recommendations. Limitations There is a paucity of scientific evidence with most recommendations based on expert opinion. Conclusions These recommendations will provide practitioners with a framework for caring for these patients. Additional scientific research including effectiveness studies for everyday practice and expert consensus, may further refine these recommendations. PMID:22387035

  16. Accurate construction of consensus genetic maps via integer linear programming.

    PubMed

    Wu, Yonghui; Close, Timothy J; Lonardi, Stefano

    2011-01-01

    We study the problem of merging genetic maps, when the individual genetic maps are given as directed acyclic graphs. The computational problem is to build a consensus map, which is a directed graph that includes and is consistent with all (or, the vast majority of) the markers in the input maps. However, when markers in the individual maps have ordering conflicts, the resulting consensus map will contain cycles. Here, we formulate the problem of resolving cycles in the context of a parsimonious paradigm that takes into account two types of errors that may be present in the input maps, namely, local reshuffles and global displacements. The resulting combinatorial optimization problem is, in turn, expressed as an integer linear program. A fast approximation algorithm is proposed, and an additional speedup heuristic is developed. Our algorithms were implemented in a software tool named MERGEMAP which is freely available for academic use. An extensive set of experiments shows that MERGEMAP consistently outperforms JOINMAP, which is the most popular tool currently available for this task, both in terms of accuracy and running time. MERGEMAP is available for download at http://www.cs.ucr.edu/~yonghui/mgmap.html. PMID:20479505

  17. [Consensus on Systemic Arterial Hypertension In México].

    PubMed

    Rosas-Peralta, Martín; Palomo-Piñón, Silvia; Borrayo-Sánchez, Gabriela; Madrid-Miller, Alejandra; Almeida-Gutiérrez, Eduardo; Galván-Oseguera, Héctor; Magaña-Serrano, José Antonio; Saturno-Chiu, Guillermo; Ramírez-Arias, Erick; Santos-Martínez, Efrén; Díaz-Díaz, Enrique; Salgado-Pastor, Selene Janette; Morales-Mora, Gerardo; Medina-Concebida, Luz Elena; Mejía-Rodríguez, Oliva; Pérez-Ruiz, Claudia Elsa; Chapa-Mejía, Luis Raúl; Álvarez-Aguilar, Cleto; Pérez-Rodríguez, Gilberto; Castro-Martínez, María Guadalupe; López-Bárcena, Joaquín; Paniagua-Sierra, José Ramón

    2016-01-01

    This Consenso Nacional de Hipertensión Arterial Sistémica (National Consensus on Systemic Arterial Hypertension) brings together experiences and joint work of 79 specialists who have been in contact with the patient affected by systemic arterial hypertension. All concepts here presented were outlined on the basis of the real world practice of Mexican hypertensive population. The consensus was developed under strict methodological guidelines. The Delphi technique was applied in two rounds for the development of an appropriate statistical analysis of the concepts exposed by all the specialists, who posed key questions, later developed by the panel of experts of the Hospital de Cardiología, and specialists from the Centro Médico Nacional. Several angles of this illness are shown: detection, diagnosis, pathophysiology, classification, treatment and prevention. The evidence analysis was carried out using PRISMA method. More than 600 articles were reviewed, leaving only the most representative in the references. This document concludes with practical and useful recommendations for the three levels of health care of our country. PMID:27284844

  18. A Consensus on Fungal Polymerase Chain Reaction Diagnosis?

    PubMed Central

    White, P. Lewis; Barton, Richard; Guiver, Malcolm; Linton, Christopher J.; Wilson, Steve; Smith, Melvyn; Gomez, Beatriz L.; Carr, Michael J.; Kimmitt, Patrick T.; Seaton, Shila; Rajakumar, Kumar; Holyoake, Tessa; Kibbler, Chris C.; Johnson, Elizabeth; Hobson, Richard P.; Jones, Brian; Barnes, Rosemary A.

    2006-01-01

    The limitations of classical diagnostic methods for invasive fungal infections (IFIs) have led to the development of molecular techniques to aid in the detection of IFIs. Despite good published performance, interlaboratory reproduction of these assays is variable, and no consensus has been reached for an optimal method. This publication describes the first multicenter study of polymerase chain reaction methods, for the detection of Aspergillus and Candida species, currently used in the UK and Ireland by distribution and analysis of multiple specimen control panels. All three Candida methods were comparable, achieving a satisfactory level of detection (10 cfu), and the method of preference was dependent on the requirements of the particular laboratory. The results for the five Aspergillus assays were more variable, but two methods (2Asp and 4Asp) were superior (101 conidia). Formally, the overall performances of the two Aspergillus assays were comparable (κ statistic = 0.77). However, on the Roche LightCycler, there was a clear sample-type effect that greatly reduced the detection limit of the 4Asp method when testing whole blood samples. Therefore, the preferred Aspergillus method relied on the amplification platform available to the user. This study represents the initial process to achieve a consensus method for the diagnosis of IFIs. PMID:16825512

  19. International consensus diagnostic criteria for neuromyelitis optica spectrum disorders

    PubMed Central

    Banwell, Brenda; Bennett, Jeffrey L.; Cabre, Philippe; Carroll, William; Chitnis, Tanuja; de Seze, Jérôme; Fujihara, Kazuo; Greenberg, Benjamin; Jacob, Anu; Jarius, Sven; Lana-Peixoto, Marco; Levy, Michael; Simon, Jack H.; Tenembaum, Silvia; Traboulsee, Anthony L.; Waters, Patrick; Wellik, Kay E.

    2015-01-01

    Neuromyelitis optica (NMO) is an inflammatory CNS syndrome distinct from multiple sclerosis (MS) that is associated with serum aquaporin-4 immunoglobulin G antibodies (AQP4-IgG). Prior NMO diagnostic criteria required optic nerve and spinal cord involvement but more restricted or more extensive CNS involvement may occur. The International Panel for NMO Diagnosis (IPND) was convened to develop revised diagnostic criteria using systematic literature reviews and electronic surveys to facilitate consensus. The new nomenclature defines the unifying term NMO spectrum disorders (NMOSD), which is stratified further by serologic testing (NMOSD with or without AQP4-IgG). The core clinical characteristics required for patients with NMOSD with AQP4-IgG include clinical syndromes or MRI findings related to optic nerve, spinal cord, area postrema, other brainstem, diencephalic, or cerebral presentations. More stringent clinical criteria, with additional neuroimaging findings, are required for diagnosis of NMOSD without AQP4-IgG or when serologic testing is unavailable. The IPND also proposed validation strategies and achieved consensus on pediatric NMOSD diagnosis and the concepts of monophasic NMOSD and opticospinal MS. PMID:26092914

  20. International consensus diagnostic criteria for neuromyelitis optica spectrum disorders.

    PubMed

    Wingerchuk, Dean M; Banwell, Brenda; Bennett, Jeffrey L; Cabre, Philippe; Carroll, William; Chitnis, Tanuja; de Seze, Jérôme; Fujihara, Kazuo; Greenberg, Benjamin; Jacob, Anu; Jarius, Sven; Lana-Peixoto, Marco; Levy, Michael; Simon, Jack H; Tenembaum, Silvia; Traboulsee, Anthony L; Waters, Patrick; Wellik, Kay E; Weinshenker, Brian G

    2015-07-14

    Neuromyelitis optica (NMO) is an inflammatory CNS syndrome distinct from multiple sclerosis (MS) that is associated with serum aquaporin-4 immunoglobulin G antibodies (AQP4-IgG). Prior NMO diagnostic criteria required optic nerve and spinal cord involvement but more restricted or more extensive CNS involvement may occur. The International Panel for NMO Diagnosis (IPND) was convened to develop revised diagnostic criteria using systematic literature reviews and electronic surveys to facilitate consensus. The new nomenclature defines the unifying term NMO spectrum disorders (NMOSD), which is stratified further by serologic testing (NMOSD with or without AQP4-IgG). The core clinical characteristics required for patients with NMOSD with AQP4-IgG include clinical syndromes or MRI findings related to optic nerve, spinal cord, area postrema, other brainstem, diencephalic, or cerebral presentations. More stringent clinical criteria, with additional neuroimaging findings, are required for diagnosis of NMOSD without AQP4-IgG or when serologic testing is unavailable. The IPND also proposed validation strategies and achieved consensus on pediatric NMOSD diagnosis and the concepts of monophasic NMOSD and opticospinal MS. PMID:26092914

  1. Modelling Adaptive Learning Behaviours for Consensus Formation in Human Societies

    NASA Astrophysics Data System (ADS)

    Yu, Chao; Tan, Guozhen; Lv, Hongtao; Wang, Zhen; Meng, Jun; Hao, Jianye; Ren, Fenghui

    2016-06-01

    Learning is an important capability of humans and plays a vital role in human society for forming beliefs and opinions. In this paper, we investigate how learning affects the dynamics of opinion formation in social networks. A novel learning model is proposed, in which agents can dynamically adapt their learning behaviours in order to facilitate the formation of consensus among them, and thus establish a consistent social norm in the whole population more efficiently. In the model, agents adapt their opinions through trail-and-error interactions with others. By exploiting historical interaction experience, a guiding opinion, which is considered to be the most successful opinion in the neighbourhood, can be generated based on the principle of evolutionary game theory. Then, depending on the consistency between its own opinion and the guiding opinion, a focal agent can realize whether its opinion complies with the social norm (i.e., the majority opinion that has been adopted) in the population, and adapt its behaviours accordingly. The highlight of the model lies in that it captures the essential features of people’s adaptive learning behaviours during the evolution and formation of opinions. Experimental results show that the proposed model can facilitate the formation of consensus among agents, and some critical factors such as size of opinion space and network topology can have significant influences on opinion dynamics.

  2. Consensus conference on combination oral contraceptives and cardiovascular disease.

    PubMed

    1999-06-01

    At the June 1998 conference of the International Federation of Fertility Societies (IFFS), a consensus was reached that there is no reason to advise selective prescribing of oral contraceptives (OCs) containing different progestins on the basis of their effects on cardiovascular disease. All currently available low-dose OCs, regardless of their progestin component, are more beneficial for a woman's short- or long-term health than the alternative of use of no contraception or use of a less effective method. The usual precautions in selecting appropriate candidates for OC use should be applied. This consensus was reached after several investigators presented the results of their studies on OC use and cardiovascular risk to an IFFS panel. Consolidation of the available research evidence produced annual cardiovascular mortality rates per 100,000 among women 15-24 years old of 1.2 in OC non-users, 2.1 in users of second-generation OCs, and 1.8-2.3 in users of third-generation OCs; among women 35-44 years old, these rates were 9.2, 20.4, and 15.5-17.8, respectively. PMID:10360623

  3. Generic modes of consensus formation in stochastic language dynamics

    NASA Astrophysics Data System (ADS)

    Blythe, R A

    2009-02-01

    We introduce a class of stochastic models for the dynamics of two linguistic variants that are competing to become the single, shared convention within an unstructured community of speakers. Different instances of the model are distinguished by the way agents handle variability in the language (i.e., multiple forms for the same meaning). The class of models includes as special cases two previously studied models of language dynamics, the Naming Game, in which agents tend to standardize on variants that they have encountered most frequently, and the Utterance Selection Model, in which agents tend to preserve variability by uniform sampling of a pool of utterances. We reduce the full complexities of the dynamics to a single-coordinate stochastic model which allows the probability and time taken for speakers to reach consensus on a single variant to be calculated for large communities. This analysis suggests that in the broad class of models considered, consensus is formed in one of three generic ways, according to whether agents tend to eliminate, accentuate or sample neutrally the variability in the language. These different regimes are observed in simulations of the full dynamics, and for which the simplified model in some cases makes good quantitative predictions. We use these results, along with comparisons with related models, to conjecture the likely behaviour of more general models, and further make use of empirical data to argue that in reality, biases away from neutral sampling behaviour are likely to be small.

  4. Orthotic management of cerebral palsy: recommendations from a consensus conference.

    PubMed

    Morris, Christopher; Bowers, Roy; Ross, Karyn; Stevens, Phil; Phillips, David

    2011-01-01

    An international multidisciplinary group of healthcare professionals and researchers participated in a consensus conference on the management of cerebral palsy, convened by the International Society for Prosthetics and Orthotics. Participants reviewed the evidence and considered contemporary thinking on a range of treatment options including physical and occupational therapy, and medical, surgical and orthotic interventions. The quality of many of the reviewed papers was compromised by inadequate reporting and lack of transparency, in particular regarding the types of patients and the design of the interventions being evaluated. Substantial evidence suggests that ankle-foot orthoses (AFOs) that control the foot and ankle in stance and swing phases can improve gait efficiency in ambulant children (GMFCS levels I-III). By contrast, little high quality evidence exists to support the use of orthoses for the hip, spine or upper limb. Where the evidence for orthosis use was not compelling consensus was reached on recommendations for orthotic intervention. Subsequent group discussions identified recommendations for future research. The evidence to support using orthoses is generally limited by the brevity of follow-up periods in research studies; hence the extent to which orthoses may prevent deformities developing over time remains unclear. The full report of the conference can be accessed free of charge at www.ispoint.org. PMID:21335676

  5. Phenomenology and classification of dystonia: a consensus update

    PubMed Central

    Albanese, Alberto; Bhatia, Kailash; Bressman, Susan B.; DeLong, Mahlon R.; Fahn, Stanley; Fung, Victor S.C.; Hallett, Mark; Jankovic, Joseph; Jinnah, H.A.; Klein, Christine; Lang, Anthony E.; Mink, Jonathan W.; Teller, Jan K.

    2013-01-01

    This report describes the consensus outcome of an international panel consisting of investigators with years of experience in this field that reviewed the definition and classification of dystonia. Agreement was obtained based on a consensus development methodology during three in-person meetings and manuscript review by mail. Dystonia is defined as a movement disorder characterized by sustained or intermittent muscle contractions causing abnormal, often repetitive, movements, postures, or both. Dystonic movements are typically patterned and twisting, and may be tremulous. Dystonia is often initiated or worsened by voluntary action and associated with overflow muscle activation. Dystonia is classified along two axes: clinical characteristics, including age at onset, body distribution, temporal pattern and associated features (additional movement disorders or neurological features), and etiology, which includes nervous system pathology and inheritance. The clinical characteristics fall into several specific dystonia syndromes that help to guide diagnosis and treatment. We provide here a new general definition of dystonia and propose a new classification. We encourage clinicians and researchers to use these innovative definition and classification and test them in the clinical setting on a variety of patients with dystonia. PMID:23649720

  6. Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars.

    PubMed

    Shahin, Arwa; Smulders, Marinus J M; van Tuyl, Jaap M; Arens, Paul; Bakker, Freek T

    2014-01-01

    Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium. PMID:25368628

  7. Esophageal cancer screening in achalasia: is there a consensus?

    PubMed

    Ravi, K; Geno, D M; Katzka, D A

    2015-04-01

    Achalasia is an important but relatively uncommon disorder. While highly effective therapeutic options exist, esophageal cancer remains a long-term potential complication. The risk of esophageal cancer in achalasia remains unclear, with current guidelines recommending against routine endoscopic screening. However, given limited data and conflicting opinion, it is unknown whether consensus regarding screening practices in achalasia among experts exists. A 10-question survey to assess screening practices in achalasia was created and distributed to 28 experts in the area of achalasia. Experts were identified based on publications and meeting presentations in the field. Survey responses were received from 17 of 28 (61%) experts. Wide geographic distribution was seen among respondents, with eight (47%) from Europe or Australia, seven (41%) from the United States, and two (12%) from Asia. Screening for esophageal cancer was inconsistent, with nine (53%) experts endorsing the practice and eight (47%) not. Screening practices did not differ among geographic regions. No consensus regarding the risk for esophageal cancer in achalasia was seen, with three experts reporting no increased risk compared with the general population, eight experts a lifetime risk of 0.1-0.5%, three experts a 0.5-1% risk, two experts a 1-2% risk, and one expert a 3-5% risk. However, these differences in perception of risk did not influence screening practices. Upper endoscopy was utilized among all experts who endorsed screening. However, practices still varied with screening commencing at or within 1 year of diagnosis in two practices compared with 5 and 10 years in three respective practices each. Surveillance intervals also varied, performed every 2 years in four practices, every 3 years in four practices, and every 5 years in one practice. Practice variation in the management of achalasia itself was also seen, with initial treatment with Heller myotomy endorsed by eight experts, pneumatic

  8. Insertion Sequences

    PubMed Central

    Mahillon, Jacques; Chandler, Michael

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

  9. Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence.

    PubMed

    Bernardes, Juliana; Zaverucha, Gerson; Vaquero, Catherine; Carbone, Alessandra

    2016-07-01

    Traditional protein annotation methods describe known domains with probabilistic models representing consensus among homologous domain sequences. However, when relevant signals become too weak to be identified by a global consensus, attempts for annotation fail. Here we address the fundamental question of domain identification for highly divergent proteins. By using high performance computing, we demonstrate that the limits of state-of-the-art annotation methods can be bypassed. We design a new strategy based on the observation that many structural and functional protein constraints are not globally conserved through all species but might be locally conserved in separate clades. We propose a novel exploitation of the large amount of data available: 1. for each known protein domain, several probabilistic clade-centered models are constructed from a large and differentiated panel of homologous sequences, 2. a decision-making protocol combines outcomes obtained from multiple models, 3. a multi-criteria optimization algorithm finds the most likely protein architecture. The method is evaluated for domain and architecture prediction over several datasets and statistical testing hypotheses. Its performance is compared against HMMScan and HHblits, two widely used search methods based on sequence-profile and profile-profile comparison. Due to their closeness to actual protein sequences, clade-centered models are shown to be more specific and functionally predictive than the broadly used consensus models. Based on them, we improved annotation of Plasmodium falciparum protein sequences on a scale not previously possible. We successfully predict at least one domain for 72% of P. falciparum proteins against 63% achieved previously, corresponding to 30% of improvement over the total number of Pfam domain predictions on the whole genome. The method is applicable to any genome and opens new avenues to tackle evolutionary questions such as the reconstruction of ancient domain

  10. Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence

    PubMed Central

    Bernardes, Juliana; Zaverucha, Gerson; Vaquero, Catherine; Carbone, Alessandra

    2016-01-01

    Traditional protein annotation methods describe known domains with probabilistic models representing consensus among homologous domain sequences. However, when relevant signals become too weak to be identified by a global consensus, attempts for annotation fail. Here we address the fundamental question of domain identification for highly divergent proteins. By using high performance computing, we demonstrate that the limits of state-of-the-art annotation methods can be bypassed. We design a new strategy based on the observation that many structural and functional protein constraints are not globally conserved through all species but might be locally conserved in separate clades. We propose a novel exploitation of the large amount of data available: 1. for each known protein domain, several probabilistic clade-centered models are constructed from a large and differentiated panel of homologous sequences, 2. a decision-making protocol combines outcomes obtained from multiple models, 3. a multi-criteria optimization algorithm finds the most likely protein architecture. The method is evaluated for domain and architecture prediction over several datasets and statistical testing hypotheses. Its performance is compared against HMMScan and HHblits, two widely used search methods based on sequence-profile and profile-profile comparison. Due to their closeness to actual protein sequences, clade-centered models are shown to be more specific and functionally predictive than the broadly used consensus models. Based on them, we improved annotation of Plasmodium falciparum protein sequences on a scale not previously possible. We successfully predict at least one domain for 72% of P. falciparum proteins against 63% achieved previously, corresponding to 30% of improvement over the total number of Pfam domain predictions on the whole genome. The method is applicable to any genome and opens new avenues to tackle evolutionary questions such as the reconstruction of ancient domain

  11. Consensus-Degenerate Hybrid Oligonucleotide Primers for Amplification of Priming Glycosyltransferase Genes of the Exopolysaccharide Locus in Strains of the Lactobacillus casei Group

    PubMed Central

    Provencher, Cathy; LaPointe, Gisèle; Sirois, Stéphane; Van Calsteren, Marie-Rose; Roy, Denis

    2003-01-01

    A primer design strategy named CODEHOP (consensus-degenerate hybrid oligonucleotide primer) for amplification of distantly related sequences was used to detect the priming glycosyltransferase (GT) gene in strains of the Lactobacillus casei group. Each hybrid primer consisted of a short 3′ degenerate core based on four highly conserved amino acids and a longer 5′ consensus clamp region based on six sequences of the priming GT gene products from exopolysaccharide (EPS)-producing bacteria. The hybrid primers were used to detect the priming GT gene of 44 commercial isolates and reference strains of Lactobacillus rhamnosus, L. casei, Lactobacillus zeae, and Streptococcus thermophilus. The priming GT gene was detected in the genome of both non-EPS-producing (EPS−) and EPS-producing (EPS+) strains of L. rhamnosus. The sequences of the cloned PCR products were similar to those of the priming GT gene of various gram-negative and gram-positive EPS+ bacteria. Specific primers designed from the L. rhamnosus RW-9595M GT gene were used to sequence the end of the priming GT gene in selected EPS+ strains of L. rhamnosus. Phylogenetic analysis revealed that Lactobacillus spp. form a distinctive group apart from other lactic acid bacteria for which GT genes have been characterized to date. Moreover, the sequences show a divergence existing among strains of L. rhamnosus with respect to the terminal region of the priming GT gene. Thus, the PCR approach with consensus-degenerate hybrid primers designed with CODEHOP is a practical approach for the detection of similar genes containing conserved motifs in different bacterial genomes. PMID:12788729

  12. An Application of Supertree Methods to Mammalian Mitogenomic Sequences

    PubMed Central

    Campbell, Véronique; Lapointe, François-Joseph

    2010-01-01

    Two different approaches can be used in phylogenomics: combined or separate analysis. In the first approach, different datasets are combined in a concatenated supermatrix. In the second, datasets are analyzed separately and the phylogenetic trees are then combined in a supertree. The supertree method is an interesting alternative to avoid missing data, since datasets that are analyzed separately do not need to represent identical taxa. However, the supertree approach and the corresponding consensus methods have been highly criticized for not providing valid phylogenetic hypotheses. In this study, congruence of trees estimated by consensus and supertree approaches were compared to model trees obtained from a combined analysis of complete mitochondrial sequences of 102 species representing 93 mammal families. The consensus methods produced poorly resolved consensus trees and did not perform well, except for the majority rule consensus with compatible groupings. The weighted supertree and matrix representation with parsimony methods performed equally well and were highly congruent with the model trees. The most similar supertree method was the least congruent with the model trees. We conclude that some of the methods tested are worth considering in a phylogenomic context. PMID:20535231

  13. Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: a survey of alphoid sequences from different human chromosomes.

    PubMed Central

    Waye, J S; Willard, H F

    1987-01-01

    The human alpha satellite DNA family is composed of diverse, tandemly reiterated monomer units of approximately 171 basepairs localized to the centromeric region of each chromosome. These sequences are organized in a highly chromosome-specific manner with many, if not all human chromosomes being characterized by individually distinct alphoid subsets. Here, we compare the nucleotide sequences of 153 monomer units, representing alphoid components of at least 12 different human chromosomes. Based on the analysis of sequence variation at each position within the 171 basepair monomer, we have derived a consensus sequence for the monomer unit of human alpha satellite DNA which we suggest may reflect the monomer sequence from which different chromosomal subsets have evolved. Sequence heterogeneity is evident at each position within the consensus monomer unit and there are no positions of strict nucleotide sequence conservation, although some regions are more variable than others. A substantial proportion of the overall sequence variation may be accounted for by nucleotide changes which are characteristic of monomer components of individual chromosomal subsets or groups of subsets which have a common evolutionary history. PMID:3658703

  14. A STUDY ON THE STRUCTURE OF CONSENSUS BUILDING PROCESSES IN SOCIAL INFRASTRUCTURE DEVELOPMENT

    NASA Astrophysics Data System (ADS)

    Takada, Tomoki; Toyoda, Mitsuyo; Sago, Junzo; Seki, Motoi; Akiyama, Kazuya; Kuwako, Toshio

    The assessment of stakeholders' interests is a critical step in consensus building processes in social infrastructure development. The coordinator of these processes needs to pay attention to both concrete interests and deeper concerns behind them for successful consensus building. The authors have engaged in the management of the consensus building process for the Ten-noh river restoration project carried out on Sado Island, Niigata, and have successfully developed a restoration plan by combining voices from different perspectives. One of the key conditions for the successful consensus building is to incorporate stepby-step problem solving processes responding to the issues identified by stakeholders. Such a steady approach leads to the consensus of the project as a whole. The authors have developed a framework to analyze the structure of consensus building processes in details by establishing a chart that layouts stakeholder's opinions, interests, deeper concerns, and concrete issues that arise when promoting a project of social infrastructure development.

  15. Performance Consensus Problem of Multi-Agent Systems with Multiple State Variables

    NASA Astrophysics Data System (ADS)

    Hayashi, Naoki; Ushio, Toshimitsu

    A consensus problem has been studied in many fundamental and application fields to analyze coordinated behavior in multiagent systems. In a consensus problem, it is usually assumed that a state of each agent is scalar and all agents have an identical linear consensus protocol. We present a consensus problem of multi-agent systems where each agent has multiple state variables and a performance value evaluated by a nonlinear performance function according to its current state. We derive sufficient conditions for agents to achieve consensus on the performance value using an algebraic graph theory and the mean value theorem. We also consider an application of a performance consensus problem to resource allocation in soft real-time systems so as to achieve a fair QoS (Quality of Service) level.

  16. Populism vs. elitism: social consensus and social status as bases of attitude certainty.

    PubMed

    Prislin, Radmila; Shaffer, Emily; Crowder, Marisa

    2012-01-01

    This study examined the effects of social consensus and social status on attitude certainty that is conceptualized multi-dimensionally as perceived clarity and correctness of one's attitude. In a mock opinion exchange about a social issue, participants were either supported (high consensus) or opposed (low consensus) by most of the confederates. They were informed that their opinion (high status) or their opponents' opinion (low status) had the alleged psychological significance indicative of future success. Post-experimental attitude clarity was significantly greater when attitudinal position was associated with high rather than low status. Attitude correctness was interactively affected by social status and social consensus. Supporting the compensatory effect hypothesis, attitude correctness was comparable across the levels of social consensus as long as they were associated with high status, and across the levels of social status as long as they were associated with high social consensus. PMID:22558827

  17. Mapping and sequencing the human genome

    SciTech Connect

    1988-01-01

    Numerous meetings have been held and a debate has developed in the biological community over the merits of mapping and sequencing the human genome. In response a committee to examine the desirability and feasibility of mapping and sequencing the human genome was formed to suggest options for implementing the project. The committee asked many questions. Should the analysis of the human genome be left entirely to the traditionally uncoordinated, but highly successful, support systems that fund the vast majority of biomedical research. Or should a more focused and coordinated additional support system be developed that is limited to encouraging and facilitating the mapping and eventual sequencing of the human genome. If so, how can this be done without distorting the broader goals of biological research that are crucial for any understanding of the data generated in such a human genome project. As the committee became better informed on the many relevant issues, the opinions of its members coalesced, producing a shared consensus of what should be done. This report reflects that consensus.

  18. Mapping and Sequencing the Human Genome

    DOE R&D Accomplishments Database

    1988-01-01

    Numerous meetings have been held and a debate has developed in the biological community over the merits of mapping and sequencing the human genome. In response a committee to examine the desirability and feasibility of mapping and sequencing the human genome was formed to suggest options for implementing the project. The committee asked many questions. Should the analysis of the human genome be left entirely to the traditionally uncoordinated, but highly successful, support systems that fund the vast majority of biomedical research. Or should a more focused and coordinated additional support system be developed that is limited to encouraging and facilitating the mapping and eventual sequencing of the human genome. If so, how can this be done without distorting the broader goals of biological research that are crucial for any understanding of the data generated in such a human genome project. As the committee became better informed on the many relevant issues, the opinions of its members coalesced, producing a shared consensus of what should be done. This report reflects that consensus.

  19. Analysis of human immunodeficiency virus type 1 nef gene sequences present in vivo.

    PubMed Central

    Shugars, D C; Smith, M S; Glueck, D H; Nantermet, P V; Seillier-Moiseiwitsch, F; Swanstrom, R

    1993-01-01

    The nef genes of the human immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2) and the related simian immunodeficiency viruses (SIVs) encode a protein (Nef) whose role in virus replication and cytopathicity remains uncertain. As an attempt to elucidate the function of nef, we characterized the nucleotide and corresponding protein sequences of naturally occurring nef genes obtained from several HIV-1-infected individuals. A consensus Nef sequence was derived and used to identify several features that were highly conserved among the Nef sequences. These features included a nearly invariant myristylation signal, regions of sequence polymorphism and variable duplication, a region with an acidic charge, a (Pxx)4 repeat sequence, and a potential protein kinase C phosphorylation site. Clustering of premature stop codons at position 124 was noted in 6 of the 54 Nef sequences. Further analysis revealed four stretches of residues that were highly conserved not only among the patient-derived HIV-1 Nef sequences, but also among the Nef sequences of HIV-2 and the SIVs, suggesting that Nef proteins expressed by these retroviruses are functionally equivalent. The "Nef-defining" sequences were used to evaluate the sequence alignments of known proteins reported to share sequence similarity with Nef sequences and to conduct additional computer-based searches for similar protein sequences. A gene encoding the consensus Nef sequence was also generated. This gene encodes a full-length Nef protein that should be a valuable tool in further studies of Nef function. Images PMID:8043040

  20. Assessing excellence in translational cancer research: a consensus based framework

    PubMed Central

    2013-01-01

    Background It takes several years on average to translate basic research findings into clinical research and eventually deliver patient benefits. An expert-based excellence assessment can help improve this process by: identifying high performing Comprehensive Cancer Centres; best practices in translational cancer research; improving the quality and efficiency of the translational cancer research process. This can help build networks of excellent Centres by aiding focused partnerships. In this paper we report on a consensus building exercise that was undertaken to construct an excellence assessment framework for translational cancer research in Europe. Methods We used mixed methods to reach consensus: a systematic review of existing translational research models critically appraised for suitability in performance assessment of Cancer Centres; a survey among European stakeholders (researchers, clinicians, patient representatives and managers) to score a list of potential excellence criteria, a focus group with selected representatives of survey participants to review and rescore the excellence criteria; an expert group meeting to refine the list; an open validation round with stakeholders and a critical review of the emerging framework by an independent body: a committee formed by the European Academy of Cancer Sciences. Results The resulting excellence assessment framework has 18 criteria categorized in 6 themes. Each criterion has a number of questions/sub-criteria. Stakeholders favoured using qualitative excellence criteria to evaluate the translational research “process” rather than quantitative criteria or judging only the outputs. Examples of criteria include checking if the Centre has mechanisms that can be rated as excellent for: involvement of basic researchers and clinicians in translational research (quality of supervision and incentives provided to clinicians to do a PhD in translational research) and well designed clinical trials based on ground

  1. Minimizing recombinations in consensus networks for phylogeographic studies

    PubMed Central

    Parida, Laxmi; Javed, Asif; Melé, Marta; Calafell, Francesc; Bertranpetit, Jaume

    2009-01-01

    Background We address the problem of studying recombinational variations in (human) populations. In this paper, our focus is on one computational aspect of the general task: Given two networks G1 and G2, with both mutation and recombination events, defined on overlapping sets of extant units the objective is to compute a consensus network G3 with minimum number of additional recombinations. We describe a polynomial time algorithm with a guarantee that the number of computed new recombination events is within ϵ = sz(G1, G2) (function sz is a well-behaved function of the sizes and topologies of G1 and G2) of the optimal number of recombinations. To date, this is the best known result for a network consensus problem. Results Although the network consensus problem can be applied to a variety of domains, here we focus on structure of human populations. With our preliminary analysis on a segment of the human Chromosome X data we are able to infer ancient recombinations, population-specific recombinations and more, which also support the widely accepted 'Out of Africa' model. These results have been verified independently using traditional manual procedures. To the best of our knowledge, this is the first recombinations-based characterization of human populations. Conclusion We show that our mathematical model identifies recombination spots in the individual haplotypes; the aggregate of these spots over a set of haplotypes defines a recombinational landscape that has enough signal to detect continental as well as population divide based on a short segment of Chromosome X. In particular, we are able to infer ancient recombinations, population-specific recombinations and more, which also support the widely accepted 'Out of Africa' model. The agreement with mutation-based analysis can be viewed as an indirect validation of our results and the model. Since the model in principle gives us more information embedded in the networks, in our future work, we plan to investigate

  2. A logical sequence search for S100B target proteins.

    PubMed Central

    McClintock, K. A.; Shaw, G. S.

    2000-01-01

    The EF-hand calcium-binding protein S100B has been shown to interact in vitro in a calcium-sensitive manner with many substrates. These potential S100B target proteins have been screened for the preservation of a previously identified consensus sequence across species. The results were compared to known structural and in vitro properties of the proteins to rationalize choices for potential binding partners. Our approach uncovered four oligomeric proteins tubulin (alpha and beta), glial fibrillary acidic protein (GFAP), desmin, and vimentin that have conserved regions matching the consensus sequence. In the type III intermediate filament proteins (GFAP, vimentin, and desmin), this region corresponds to a portion of a coiled-coil (helix 2A), the structural element responsible for their assembly. In tubulin, the sequence matches correspond to regions of alpha and beta tubulin found at the alpha beta tubulin interface. In both cases, these consensus sequence matches provide a logical explanation for in vitro observations that S100B is able to inhibit oligomerization of these proteins. PMID:11106180

  3. Impulsive consensus seeking in directed networks of multi-agent systems with communication time delays

    NASA Astrophysics Data System (ADS)

    Wu, Quanjun; Zhou, Jin; Xiang, Lan

    2012-08-01

    In this article, we consider average consensus problem in directed delayed networked multi-agent systems having impulsive effects with fixed topology and stochastic switching topology. A simple impulsive consensus protocol for such networks is proposed, and some generic criteria for solving the average consensus problem are analytically derived. It is shown that a directed delayed networked multi-agent system can achieve average consensus globally exponentially with suitable impulsive gain and impulsive interval. Subsequently, two typical illustrative examples, along with computer simulation results, are provided to visualise the effectiveness and feasibility of our theoretical results.

  4. Cluster consensus of high-order multi-agent systems with switching topologies

    NASA Astrophysics Data System (ADS)

    Hou, Bo; Sun, Fuchun; Li, Hongbo; Chen, Yao; Xi, Jianxiang

    2016-09-01

    This paper investigates the cluster consensus problems of generic linear multi-agent systems with switching topologies. Sufficient criteria for cluster consensus, which generalise the results in existing literatures, are derived for both state feedback and observer-based control schemes. By using an averaging method, it is shown that cluster consensus can be achieved when the union of the acyclic topologies contains a directed spanning tree within each cluster frequently enough. We also provide a principle to construct digraphs with inter-cluster cyclic couplings that promote cluster consensus regardless of the magnitude of inter-agent coupling weights. Finally, numerical examples are given to demonstrate the effectiveness of the proposed approaches.

  5. Group consensus control for heterogeneous multi-agent systems with fixed and switching topologies

    NASA Astrophysics Data System (ADS)

    Wen, Guoguang; Huang, Jun; Wang, Chunyan; Chen, Zhi; Peng, Zhaoxia

    2016-02-01

    In this paper, the group consensus problems of heterogeneous multi-agent systems with fixed and switching topologies are investigated. First, a class of distributed group consensus protocol is proposed for achieving the group consensus of heterogeneous multi-agent systems by using the neighbours' information. Then, some corresponding sufficient conditions are obtained to guarantee the achievement of group consensus. Rigorous proofs are given by using graph theory, matrix theory and Lyapunov theory. Finally, numerical simulations are also given to verify the theoretical analysis.

  6. Group consensus of multi-agent systems in directed networks with noises and time delays

    NASA Astrophysics Data System (ADS)

    Shang, Yilun

    2015-10-01

    In this paper, group consensus problems in fixed directed networks of dynamic agents are investigated. Group consensus means that the agents in each group share a consistent value while there is no agreement between any two groups. Based on algebraic graph theory, sufficient conditions guaranteeing group consensus under the proposed control protocol in the presence of random noises and communication delays are derived. The analysis uses a stability result of Mao for stochastic differential delay equations, which ensures the consensus can be achieved almost surely and exponentially fast. Numerical examples are provided to demonstrate the availability of the obtained results as well as the effect of time delay/noise intensity.

  7. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding.

    PubMed

    Maccaferri, Marco; Ricci, Andrea; Salvi, Silvio; Milner, Sara Giulia; Noli, Enrico; Martelli, Pier Luigi; Casadio, Rita; Akhunov, Eduard; Scalabrin, Simone; Vendramin, Vera; Ammar, Karim; Blanco, Antonio; Desiderio, Francesca; Distelfeld, Assaf; Dubcovsky, Jorge; Fahima, Tzion; Faris, Justin; Korol, Abraham; Massi, Andrea; Mastrangelo, Anna Maria; Morgante, Michele; Pozniak, Curtis; N'Diaye, Amidou; Xu, Steven; Tuberosa, Roberto

    2015-06-01

    Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes. PMID:25424506

  8. Spreading the message. Building a general consensus on the environment.

    PubMed

    Burke, A

    1991-01-01

    In communicating an environmental message to society at large, it is useful to distinguish between decision-makers and the general public. The influence of decision-makers on public debates is as significant as their ability to implement decisions; in democratic societies, the two functions are inseparable. Proceeding from an environmental consensus, physicians can provide a source of impartial medical/ecological wisdom, and serve as mediators of public debates. For those purposes, a network of physicians and/or scientists can be useful; three examples are provided. Communicating to the general public can only be achieved economically through the mass news media, which operate under conditions very different from those of physicians and scientists. There is considerable room for improvement in environmental journalism, and physicians can make a useful contribution to any such process. It is an important issue, since the mass media constitute the 'ecology textbook' of the general public. PMID:1910871

  9. Proton and electron mean free paths: The Palmer consensus revisited

    NASA Technical Reports Server (NTRS)

    Bieber, John W.; Matthaeus, William H.; Smith, Charles W.; Wanner, Wolfgang; Kallenrode, May-Britt; Wibberenz, Gerd

    1994-01-01

    We present experimental and theoretical evidence suggesting that the mean free path of cosmic-ray electrons and protons may be fundamentally different at low to intermediate (less than 50 MV) rigidities. The experimental evidence is from Helios observations of solar energetic particles, which show that the mean free path of 1.4 MV electrons is often similar to that of 187 MV protons, even though proton mean free paths continue to decrease comparatively rapidly with decreasing rigidty down to the lowest channels (about 100 MV) observed. The theoretical evidence is from computations of particle scattering in dynamical magnetic turbulence, which predict that electrons will have a larger mean free path than protons of the same rigidity. In the light of these new results, 'consensus' ideas about cosmic-ray mean free paths may require drastic revision.

  10. A model of consensus formation for reconciling nursing's disciplinary matrix.

    PubMed

    Dobratz, Marjorie C

    2010-01-01

    With questions raised as to whether or not nursing knowledge should be developed from extant conceptual/theoretical models or from practice-based environments, this paper utilizes Kuhn's disciplinary matrix and Laudan's model of consensus formation to explore the changing nature of the discipline's structural matrix. Kuhn's notion that a discipline's structural matrix includes symbolic generalizations, models and exemplars, and Laudan's view that a maturing discipline embraces factual, methodological, and axiological (goals and aims) knowledge, and that context and discourse are also involved in advancing a discipline is described as a means for reconciling the source of nursing knowledge. This paper posits that shared axiological goals connect both theorists and practitioners, and resolve potential conflicts as to viable sources of nursing knowledge. Through shared goals that include humanization, meaning, quality of life, caring, consciousness, transcendence, and presence, which bridge both theoretical and practice approaches, nursing's charge to contribute to the good of society is fulfilled. PMID:20017883

  11. [Kawasaki disease: interdisciplinary and intersocieties consensus (clinical guidelines). Brief version].

    PubMed

    2016-08-01

    Kawasaki disease is an acute self-limiting systemic vasculitis. It is the most common cause of acquired heart disease, with the risk of developing coronary artery aneurysms, myocardial infarction and sudden death. Diagnosis is based on the presence of fever in addition to other clinical criteria. The quarter of the Kawasaki disease patients have "incomplete" presentation. Treatment with intravenous immunoglobulin within ten days of fever onset improves clinical outcomes and reduces the incidence of coronary artery dilation to less than 5%. Non-responders to standard therapy have shown a successful response with the use of corticosteroids and/or biological agents. The long-term management must be delineated according to the degree of coronary involvement in a multidisciplinary manner. To facilitate the pediatrician's diagnosis, treatment and monitoring of Kawasaki disease, a group of experts from the Argentine Society of Pediatrics and the Argentine Society of Cardiology carried out a consensus to develop practical clinical guidelines. PMID:27399018

  12. Facilitating faculty conversations: Development of consensus learning goals

    NASA Astrophysics Data System (ADS)

    Pepper, Rachel E.; Chasteen, Stephanie V.; Pollock, Steven J.; Perkins, Katherine K.

    2012-02-01

    Our upper-division course reform efforts at the University of Colorado start with expert input from non-PER faculty, and these conversations with faculty enrich and guide our course reforms. We have discovered additional benefits of these conversations, such as the fact that they serve as a forum for discussions of pedagogy and PER. However, it is not always obvious - to the faculty or to the PER researchers - what approach will lead to successful meetings. During the process of several course transformations we have met with diverse faculty to generate consensus learning goals and course assessments. We describe the general approach used to structure and facilitate these meetings, and include details on what these meetings entailed, how we achieved broad participation and productive conversations, as well as potential pitfalls to avoid.

  13. Four functions for four relationships: consensus definitions of university students.

    PubMed

    Jonason, Peter K

    2013-11-01

    In this study (N = 192; 124 women, 68 men), consensus definitions of one-night stands, booty-call relationships, friends-with-benefits, and serious romantic relationships were fashioned using a sample of university students. Participants provided a Likert and forced-choice assessment of how each relationship was characterized by the functions of sexual gratification, trial run, placeholder, and socioemotional support. Serious romantic relationships were primarily used to gain socioemotional support. Friends-with-benefits relationships were motivated by seeking a placeholder until someone better came along and as a trial run for a more serious relationship. Booty-call relationships and one-night stands were motivated primarily by a desire for sexual gratification. Men ascribed a greater range of reasons to engage in sexual relationships than women did and the more short-term the relationship was in nature, the greater the emergence of sex differences in ascribed functions. PMID:24217952

  14. International Consensus Document (ICON): Common Variable Immunodeficiency Disorders

    PubMed Central

    Bonilla, Francisco A.; Barlan, Isil; Chapel, Helen; Costa-Carvalho, Beatriz T.; Cunningham-Rundles, Charlotte; de la Morena, M. Teresa; Espinosa-Rosales, Francisco J.; Hammarström, Lennart; Nonoyama, Shigeaki; Quinti, Isabella; Routes, John M.; Tang, Mimi L.K.; Warnatz, Klaus

    2016-01-01

    The International Collaboration in Asthma, Allergy and Immunology initiated an international coalition among the American Academy of Allergy, Asthma & Immunology; the European Academy of Allergy and Clinical Immunology; the World Allergy Organization; and the American College of Allergy, Asthma & Immunology on common variable immunodeficiency. An author group was formed and then divided into individual committees. Within the committee, teams of authors were subgrouped to generate content for specific sections of the document. Content was derived from literature searches, relevant published guidelines, and clinical experience. After a draft of the document was assembled, it was collectively reviewed and revised by the authors. Where evidence was lacking or conflicting, the information presented represents the consensus expert opinion of the group. The full document was then independently reviewed by 5 international experts in the field, none of whom was among the authors of the original. The comments of these reviewers were incorporated before submission for publication. PMID:26563668

  15. Proceedings of the International Consensus on Periprosthetic Joint Infection.

    PubMed

    Parvizi, J; Gehrke, T; Chen, A F

    2013-11-01

    Louis Pasteur once said that: "Fortune favours the prepared mind." As one of the great scientists who contributed to the fight against infection, he emphasised the importance of being prepared at all times to recognise infection and deal with it. Despite the many scientific discoveries and technological advances, such as the advent of antibiotics and the use of sterile techniques, infection continues to be a problem that haunts orthopaedic surgeons and inflicts suffering on patients. The medical community has implemented many practices with the intention of preventing infection and treating it effectively when it occurs. Although high-level evidence may support some of these practices, many are based on little to no scientific foundation. Thus, around the world, there is great variation in practices for the prevention and management of periprosthetic joint infection. This paper summaries the instigation, conduct and findings of a recent International Consensus Meeting on Surgical Site and Periprosthetic Joint Infection. PMID:24151261

  16. The Kinesin-1 Chemomechanical Cycle: Stepping Toward a Consensus.

    PubMed

    Hancock, William O

    2016-03-29

    Kinesin-1 serves as a model for understanding fundamentals of motor protein mechanochemistry and for interpreting functional diversity across the kinesin superfamily. Despite sustained work over the last three decades, disagreements remain regarding the events that trigger the two key transitions in the stepping cycle: detachment of the trailing head from the microtubule and binding of the tethered head to the next tubulin binding site. This review describes the conflicting views of these events and highlights recent work that sheds light on these long-standing controversies. It concludes by presenting a consensus kinesin-1 chemomechanical that incorporates recent work, resolves discrepancies, and highlights key questions for future experimental work. It is hoped that this model provides a framework for understanding how diverse kinesins are tuned for their specific cellular roles. PMID:27028632

  17. CONSENSUS TREATMENT RECOMMENDATIONS FOR LATE-ONSET POMPE DISEASE

    PubMed Central

    Cupler, Edward J.; Berger, Kenneth I.; Leshner, Robert T.; Wolfe, Gil I.; Han, Jay J.; Barohn, Richard J.; Kissel, John T.

    2012-01-01

    Introduction Pompe disease is a rare, autosomal recessive disorder caused by deficiency of the glycogen-degrading lysosomal enzyme acid alpha-glucosidase. Late-onset Pompe disease is a multisystem condition, with a heterogeneous clinical presentation that mimics other neuromuscular disorders. Methods Objective is to propose consensus-based treatment and management recommendations for late-onset Pompe disease. Methods A systematic review of the literature by a panel of specialists with expertise in Pompe disease was undertaken. Conclusions A multidisciplinary team should be involved to properly treat the pulmonary, neuromuscular, orthopedic, and gastrointestinal elements of late-onset Pompe disease. Presymptomatic patients with subtle objective signs of Pompe disease (and patients symptomatic at diagnosis) should begin treatment with enzyme replacement therapy (ERT) immediately; presymptomatic patients without symptoms or signs should be observed without use of ERT. After 1 year of ERT, patients’ condition should be reevaluated to determine whether ERT should be continued. PMID:22173792

  18. The Spanish human papillomavirus vaccine consensus group: a working model.

    PubMed

    Cortés-Bordoy, Javier; Martinón-Torres, Federico

    2010-08-01

    Successful implementation of Human Papillomavirus (HPV) vaccine in each country can only be achieved from a complementary and synergistic perspective, integrating all the different points of view of the diverse related professionals. It is this context where the Spanish HPV Vaccine Consensus Group (Grupo Español de Consenso sobre la Vacuna VPH, GEC-VPH) was created. GEC-VPH philosophy, objectives and experience are reported in this article, with particular attention to the management of negative publicity and anti-vaccine groups. Initiatives as GEC-VPH--adapted to each country's particular idiosyncrasies--might help to overcome the existing barriers and to achieve wide and early implementation of HPV vaccination. PMID:20484987

  19. IMWG consensus on risk stratification in multiple myeloma.

    PubMed

    Chng, W J; Dispenzieri, A; Chim, C-S; Fonseca, R; Goldschmidt, H; Lentzsch, S; Munshi, N; Palumbo, A; Miguel, J S; Sonneveld, P; Cavo, M; Usmani, S; Durie, B G M; Avet-Loiseau, H

    2014-02-01

    Multiple myeloma is characterized by underlying clinical and biological heterogeneity, which translates to variable response to treatment and outcome. With the recent increase in treatment armamentarium and the projected further increase in approved therapeutic agents in the coming years, the issue of having some mechanism to dissect this heterogeneity and rationally apply treatment is coming to the fore. A number of robustly validated prognostic markers have been identified and the use of these markers in stratifying patients into different risk groups has been proposed. In this consensus statement, the International Myeloma Working Group propose well-defined and easily applicable risk categories based on current available information and suggests the use of this set of prognostic factors as gold standards in all clinical trials and form the basis of subsequent development of more complex prognostic system or better prognostic factors. At the same time, these risk categories serve as a framework to rationalize the use of therapies. PMID:23974982

  20. Continuous Glucose Monitoring: Evidence and Consensus Statement for Clinical Use

    PubMed Central

    Liebl, Andreas; Henrichs, Helmut R.; Heinemann, Lutz; Freckmann, Guido; Biermann, Eberhard; Thomas, Andreas

    2013-01-01

    Continuous glucose monitoring (CGM) is an essential tool for modern diabetes therapy. Randomized controlled studies have provided evidence that hemoglobin A1c (HbA1c) results can be improved in patients with type 1 diabetes with elevated baseline HbA1c when using CGM frequently enough and that the frequency and duration of hypoglycemic events can be reduced in patients with satisfactory baseline HbA1c. The CGM group within the Working Group Diabetes Technology (AGDT) of the German Diabetes Association (DDG) has defined evidence-based indications for the practical use of CGM in this consensus statement related to hypoglycemia (frequent, severe, or nocturnal) or hypoglycemia unawareness, insufficient metabolic control despite use of all possible therapeutic options and patient compliance, pregnancy associated with inadequate blood glucose results, and the need for more than 10 blood glucose measurements per day. Contraindications and defined preconditions for the successful use of CGM should be considered. PMID:23567009

  1. Multidisciplinary Management of Mastocytosis: Nordic Expert Group Consensus.

    PubMed

    Broesby-Olsen, Sigurd; Dybedal, Ingunn; Gülen, Theo; Kristensen, Thomas K; Møller, Michael B; Ackermann, Leena; Sääf, Maria; Karlsson, Maria A; Agertoft, Lone; Brixen, Kim; Hermann, Pernille; Stylianou, Eva; Mortz, Charlotte G; Torfing, Trine; Havelund, Troels; Sander, Birgitta; Bergström, Anna; Bendix, Marie; Garvey, Lene H; Bjerrum, Ole Weis; Valent, Peter; Bindslev-Jensen, Carsten; Nilsson, Gunnar; Vestergaard, Hanne; Hägglund, Hans

    2016-06-15

    Mastocytosis is a heterogeneous group of diseases defined by an increased number and accumulation of mast cells, and often also by signs and symptoms of mast cell activation. Disease subtypes range from indolent to rare aggressive forms. Mastocytosis affects people of all ages and has been considered rare; however, it is probably underdiagnosed with potential severe implications. Diagnosis can be challenging and symptoms may be complex and involve multiple organ-systems. In general it is advised that patients should be referred to centres with experience in the disease offering an individualized, multidisciplinary approach. We present here consensus recommendations from a Nordic expert group for the diagnosis and general management of patients with mastocytosis. PMID:26694951

  2. Outcome Measures for Artificial Pancreas Clinical Trials: A Consensus Report.

    PubMed

    Maahs, David M; Buckingham, Bruce A; Castle, Jessica R; Cinar, Ali; Damiano, Edward R; Dassau, Eyal; DeVries, J Hans; Doyle, Francis J; Griffen, Steven C; Haidar, Ahmad; Heinemann, Lutz; Hovorka, Roman; Jones, Timothy W; Kollman, Craig; Kovatchev, Boris; Levy, Brian L; Nimri, Revital; O'Neal, David N; Philip, Moshe; Renard, Eric; Russell, Steven J; Weinzimer, Stuart A; Zisser, Howard; Lum, John W

    2016-07-01

    Research on and commercial development of the artificial pancreas (AP) continue to progress rapidly, and the AP promises to become a part of clinical care. In this report, members of the JDRF Artificial Pancreas Project Consortium in collaboration with the wider AP community 1) advocate for the use of continuous glucose monitoring glucose metrics as outcome measures in AP trials, in addition to HbA1c, and 2) identify a short set of basic, easily interpreted outcome measures to be reported in AP studies whenever feasible. Consensus on a broader range of measures remains challenging; therefore, reporting of additional metrics is encouraged as appropriate for individual AP studies or study groups. Greater consistency in reporting of basic outcome measures may facilitate the interpretation of study results by investigators, regulatory bodies, health care providers, payers, and patients themselves, thereby accelerating the widespread adoption of AP technology to improve the lives of people with type 1 diabetes. PMID:27330126

  3. Italian consensus conference for colonic diverticulosis and diverticular disease

    PubMed Central

    Barbara, Giovanni; Pace, Fabio; Annese, Vito; Bassotti, Gabrio; Binda, Gian Andrea; Casetti, Tino; Colecchia, Antonio; Festi, Davide; Fiocca, Roberto; Laghi, Andrea; Maconi, Giovanni; Nascimbeni, Riccardo; Scarpignato, Carmelo; Villanacci, Vincenzo; Annibale, Bruno

    2014-01-01

    The statements produced by the Consensus Conference on Diverticular Disease promoted by GRIMAD (Gruppo Italiano Malattia Diverticolare, Italian Group on Diverticular Diseases) are reported. Topics such as epidemiology, risk factors, diagnosis, medical and surgical treatment of diverticular disease (DD) in patients with uncomplicated and complicated DD were reviewed by a scientific board of experts who proposed 55 statements graded according to level of evidence and strength of recommendation, and approved by an independent jury. Each topic was explored focusing on the more relevant clinical questions. Comparison and discussion of expert opinions, pertinent statements and replies to specific questions, were presented and approved based on a systematic literature search of the available evidence. Comments were added explaining the basis for grading the evidence, particularly for controversial areas. PMID:25360320

  4. A consensus statement on critical thinking in nursing.

    PubMed

    Scheffer, B K; Rubenfeld, M G

    2000-11-01

    The purpose of this study was to define critical thinking in nursing. A Delphi technique with 5 rounds of input was used to achieve this purpose. An international panel of expert nurses from nine countries: Brazil, Canada, England, Iceland, Japan, Korea, Netherlands, Thailand, and 23 states in the U.S. participated in this study between 1995 and 1998. A consensus definition (statement) of critical thinking in nursing was achieved. The panel also identified and defined 10 habits of the mind (affective components) and 7 skills (cognitive components) of critical thinking in nursing. The habits of the mind of critical thinking in nursing included: confidence, contextual perspective, creativity, flexibility, inquisitiveness, intellectual integrity, intuition, open-mindedness, perseverance, and reflection. Skills of critical thinking in nursing included: analyzing, applying standards, discriminating, information seeking, logical reasoning, predicting and transforming knowledge. These findings can be used by practitioners, educators and researchers to advance understanding of the essential role of critical thinking in nursing. PMID:11103973

  5. [Consensus report on the management of immune thrombocytopenia in pregnancy].

    PubMed

    Miyakawa, Yoshitaka

    2015-10-01

    Primary immune thrombocytopenia (ITP) is a benign hematological disorder characterized by platelet counts under 100×10(9)/l. We updated the consensus report for the management of ITP in pregnancy after a 20-year lag. For this update, not only hematologists, but also obstetricians, pediatricians, and anesthesiologists joined our committee. We recommend that physicians maintain platelet counts above 20×10(6)/l in the first and second trimesters. We also agree that counts should be at least 50×10(9)/l and 80×10(9)/l for vaginal and C-section deliveries, respectively. There might be no obvious reasons to forbid lactation in ITP patients receiving treatment with corticosteroids. In this educational session, I will discuss the differential diagnosis of thrombocytopenia and the management of ITP in pregnant women and their neonates based on international and updated domestic guidelines. PMID:26458448

  6. The Hartford Consensus IV: A Call for Increased National Resilience.

    PubMed

    Jacobs, Lenworth M

    2016-04-01

    Despite advances in the response to active shooter and intentional mass casualty events, a gap remains in our national preparedness and resilience. Drawing from experiences at myriad mass casualty events, the immediate responder (volunteer responder) represents an underutilized resource, yet one capable of dramatically increasing our all-hazards (injuries from all natural and man-made causes) national resilience. The overarching principle of the Hartford Consensus, outlined in previous reports, is that no one should die from uncontrolled bleeding. We have championed the following acronym to summarize what we have determined are appropriate steps to ensure that the maximum number of victims of these tragic events can be saved: THREAT: Threat suppression. Hemorrhage control. Rapid Extrication to safety. Assessment by medical providers. Transport to definitive care. PMID:27265929

  7. An Interactive Multi-Model for Consensus on Climate Change

    SciTech Connect

    Kocarev, Ljupco

    2014-07-02

    This project purports to develop a new scheme for forming consensus among alternative climate models, that give widely divergent projections as to the details of climate change, that is more intelligent than simply averaging the model outputs, or averaging with ex post facto weighting factors. The method under development effectively allows models to assimilate data from one another in run time with weights that are chosen in an adaptive training phase using 20th century data, so that the models synchronize with one another as well as with reality. An alternate approach that is being explored in parallel is the automated combination of equations from different models in an expert-system-like framework.

  8. Relational mate value: consensus and uniqueness in romantic evaluations.

    PubMed

    Eastwick, Paul W; Hunt, Lucy L

    2014-05-01

    Classic evolutionary and social exchange perspectives suggest that some people have more mate value than others because they possess desirable traits (e.g., attractiveness, status) that are intrinsic to the individual. This article broadens mate value in 2 ways to incorporate relational perspectives. First, close relationships research suggests an alternative measure of mate value: whether someone can provide a high quality relationship. Second, person perception research suggests that both trait-based and relationship quality measures of mate value should contain a mixture of target variance (i.e., consensus about targets, the classic conceptualization) and relationship variance (i.e., unique ratings of targets). In Study 1, participants described their personal conceptions of mate value and revealed themes consistent with classic and relational approaches. Study 2 used a social relations model blocked design to assess target and relationship variances in participants' romantic evaluations of opposite-sex classmates at the beginning and end of the semester. In Study 3, a one-with-many design documented target and relationship variances among long-term opposite-sex acquaintances. Results generally revealed more relationship variance than target variance; participants' romantic evaluations were more likely to be unique to a particular person rather than consensual. Furthermore, the relative dominance of relationship to target variance was stronger for relational measures of mate value (i.e., relationship quality projections) than classic trait-based measures (i.e., attractiveness, resources). Finally, consensus decreased as participants got to know one another better, and long-term acquaintances in Study 3 revealed enormous amounts of relationship variance. Implications for the evolutionary, close relationships, and person-perception literatures are discussed. PMID:24611897

  9. Consensus on guidelines for stereotactic neurosurgery for psychiatric disorders

    PubMed Central

    Nuttin, Bart; Wu, Hemmings; Mayberg, Helen; Hariz, Marwan; Gabriëls, Loes; Galert, Thorsten; Merkel, Reinhard; Kubu, Cynthia; Vilela-Filho, Osvaldo; Matthews, Keith; Taira, Takaomi; Lozano, Andres M; Schechtmann, Gastón; Doshi, Paresh; Broggi, Giovanni; Régis, Jean; Alkhani, Ahmed; Sun, Bomin; Eljamel, Sam; Schulder, Michael; Kaplitt, Michael; Eskandar, Emad; Rezai, Ali; Krauss, Joachim K; Hilven, Paulien; Schuurman, Rick; Ruiz, Pedro; Chang, Jin Woo; Cosyns, Paul; Lipsman, Nir; Voges, Juergen; Cosgrove, Rees; Li, Yongjie; Schlaepfer, Thomas

    2014-01-01

    Background For patients with psychiatric illnesses remaining refractory to ‘standard’ therapies, neurosurgical procedures may be considered. Guidelines for safe and ethical conduct of such procedures have previously and independently been proposed by various local and regional expert groups. Methods To expand on these earlier documents, representative members of continental and international psychiatric and neurosurgical societies, joined efforts to further elaborate and adopt a pragmatic worldwide set of guidelines. These are intended to address a broad range of neuropsychiatric disorders, brain targets and neurosurgical techniques, taking into account cultural and social heterogeneities of healthcare environments. Findings The proposed consensus document highlights that, while stereotactic ablative procedures such as cingulotomy and capsulotomy for depression and obsessive-compulsive disorder are considered ‘established’ in some countries, they still lack level I evidence. Further, it is noted that deep brain stimulation in any brain target hitherto tried, and for any psychiatric or behavioural disorder, still remains at an investigational stage. Researchers are encouraged to design randomised controlled trials, based on scientific and data-driven rationales for disease and brain target selection. Experienced multidisciplinary teams are a mandatory requirement for the safe and ethical conduct of any psychiatric neurosurgery, ensuring documented refractoriness of patients, proper consent procedures that respect patient's capacity and autonomy, multifaceted preoperative as well as postoperative long-term follow-up evaluation, and reporting of effects and side effects for all patients. Interpretation This consensus document on ethical and scientific conduct of psychiatric surgery worldwide is designed to enhance patient safety. PMID:24444853

  10. Seeking consensus for cyberinfrastructure governance in the USA

    NASA Astrophysics Data System (ADS)

    Allison, M. Lee; Zanzkerkia, Eva

    2014-05-01

    Governance of geosciences cyberinfrastructure is a complex and essential undertaking, critical in enabling distributed knowledge communities to collaborate and communicate across disciplines, distances, and cultures. Advancing science with respect to "grand challenges," such as global change, Earth system observation, modeling, and prediction, and core fundamental science, depends not just on technical cyber systems, but also on social systems for strategic planning, decision-making, project management, learning, teaching, and building a community of practice. Simply put, a robust, agile technical system depends on an equally robust and adaptable social system. Cyberinfrastructure development is wrapped in social, organizational and governance challenges which may significantly impede technical progress and result in inefficiencies, duplication of effort, incompatibilities, wasted resources or user frustration. These issues are also the most time consuming to resolve due to significant institutional and social inertia: hence the urgency for developing a governance blueprint. An agile development process is underway for governance of transformative investments in geosciences cyberinfrastructure through the US National Science Foundation's EarthCube Program. Agile development is iterative and incremental, and promotes adaptive planning and rapid and flexible response. Such iterative deployment across a variety of EarthCube stakeholders encourages transparency, consensus, accountability, and inclusiveness. A broad coalition of stakeholder groups comprises an Assembly to serve as a preliminary venue for identifying, evaluating, and testing potential governance models. To offer opportunity for ensure broader end-user input and buy-in, a crowd-source approach engages stakeholders not involved otherwise in the Assembly. Developmental evaluators from the social sciences embedded in the project will provide real-time review and adjustments. In order to ensure an open and

  11. Managing Carious Lesions: Consensus Recommendations on Carious Tissue Removal.

    PubMed

    Schwendicke, F; Frencken, J E; Bjørndal, L; Maltz, M; Manton, D J; Ricketts, D; Van Landuyt, K; Banerjee, A; Campus, G; Doméjean, S; Fontana, M; Leal, S; Lo, E; Machiulskiene, V; Schulte, A; Splieth, C; Zandona, A F; Innes, N P T

    2016-05-01

    The International Caries Consensus Collaboration undertook a consensus process and here presents clinical recommendations for carious tissue removal and managing cavitated carious lesions, including restoration, based on texture of demineralized dentine. Dentists should manage the disease dental caries and control activity of existing cavitated lesions to preserve hard tissues and retain teeth long-term. Entering the restorative cycle should be avoided as far as possible. Controlling the disease in cavitated carious lesions should be attempted using methods which are aimed at biofilm removal or control first. Only when cavitated carious lesions either are noncleansable or can no longer be sealed are restorative interventions indicated. When a restoration is indicated, the priorities are as follows: preserving healthy and remineralizable tissue, achieving a restorative seal, maintaining pulpal health, and maximizing restoration success. Carious tissue is removed purely to create conditions for long-lasting restorations. Bacterially contaminated or demineralized tissues close to the pulp do not need to be removed. In deeper lesions in teeth with sensible (vital) pulps, preserving pulpal health should be prioritized, while in shallow or moderately deep lesions, restoration longevity becomes more important. For teeth with shallow or moderately deep cavitated lesions, carious tissue removal is performed according toselective removal to firm dentine.In deep cavitated lesions in primary or permanent teeth,selective removal to soft dentineshould be performed, although in permanent teeth,stepwise removalis an option. The evidence and, therefore, these recommendations support less invasive carious lesion management, delaying entry to, and slowing down, the restorative cycle by preserving tooth tissue and retaining teeth long-term. PMID:27099358

  12. The second Geneva Consensus: Recommendations for novel live TB vaccines.

    PubMed

    Walker, K B; Brennan, M J; Ho, M M; Eskola, J; Thiry, G; Sadoff, J; Dobbelaer, R; Grode, L; Liu, M A; Fruth, U; Lambert, P H

    2010-03-01

    Infection with Mycobacterium tuberculosis continues to be a major public health burden in most developing parts of the world and efforts to develop effective strategies for containing the disease remain a priority. It has long been evident that effective mass vaccination programmes are a cost effective and efficient approach to controlling communicable diseases in a public health setting and tuberculosis (TB) continues to be a major target. One approach with increasing acceptance is based upon on live mycobacterial vaccines, either as recombinant BCG or rationally attenuated M. tuberculosis, thus generating a new live TB vaccine. The Geneva Consensus published in March 2005 set out the opinion on priorities and requirements for developing live mycobacterial vaccines for Phase I trials. In the intervening period much progress has been made in both preclinical and clinical development of new TB vaccines and has provided the impetus for organising the second Geneva Consensus (held at WHO headquarters, April 2009) to discuss issues, including: i. Explore the regulatory requirements for live TB vaccines to enter Phase I trials, in particular those based on attenuated M. tuberculosis. Particular attention was paid to the characterisation and safety package likely to be required, including issues of attenuation, the presence of antibiotic resistance markers in live vaccines and the nature of any attenuated vaccine phenotype. ii. To identify the general criteria for further clinical development from Phase I through to Phase III. iii. Obtain a perspective of the regulatory landscape of developing countries where Phase II and III trials are to be held. iv. Review manufacturing considerations for live TB vaccines and relevance of the WHO and European Pharmacopeia guidelines and requirements for BCG vaccine. v. Consider requirements and associated issues related to the use of these new vaccines within an existing BCG vaccination programme. PMID:20074686

  13. Consensus conference on the management of tumor lysis syndrome.

    PubMed

    Tosi, Patrizia; Barosi, Giovanni; Lazzaro, Carlo; Liso, Vincenzo; Marchetti, Monia; Morra, Enrica; Pession, Andrea; Rosti, Giovanni; Santoro, Antonio; Zinzani, Pier Luigi; Tura, Sante

    2008-12-01

    Tumor lysis syndrome is a potentially life threatening complication of massive cellular lysis in cancers. Identification of high-risk patients and early recognition of the syndrome is crucial in the institution of appropriate treatments. Drugs that act on the metabolic pathway of uric acid to allantoin, like allopurinol or rasburicase, are effective for prophylaxis and treatment of tumor lysis syndrome. Sound recommendations should regulate diagnosis and drug application in the clinical setting. The current article reports the recommendations on the management of tumor lysis syndrome that were issued during a Consensus Conference project, and which were endorsed by the Italian Society of Hematology (SIE), the Italian Association of Pediatric Oncologists (AIEOP) and the Italian Society of Medical Oncology (AIOM). Current concepts on the pathophysiology, clinical features, and therapy of tumor lysis syndrome were evaluated by a Panel of 8 experts. A consensus was then developed for statements regarding key questions on tumor lysis syndrome management selected according to the criterion of relevance by group discussion. Hydration and rasburicase should be administered to adult cancer patients who are candidates for tumor-specific therapy and who carry a high risk of tumor lysis syndrome. Cancer patients with a low-risk of tumor lysis syndrome should instead receive hydration along with oral allopurinol. Hydration and rasburicase should also be administered to patients with clinical tumor lysis syndrome and to adults and high-risk children who develop laboratory tumor lysis syndrome. In conclusion, the Panel recommended rasburicase for tumor lysis syndrome prophylaxis in selected patients based on the drug efficacy profile. Methodologically rigorous studies are needed to clarify its cost-effectiveness profile. PMID:18838473

  14. Priorities for endometriosis research: recommendations from an international consensus workshop.

    PubMed

    Rogers, Peter A W; D'Hooghe, Thomas M; Fazleabas, Asgerally; Gargett, Caroline E; Giudice, Linda C; Montgomery, Grant W; Rombauts, Luk; Salamonsen, Lois A; Zondervan, Krina T

    2009-04-01

    Endometriosis is an estrogen-dependent disorder where endometrial tissue forms lesions outside the uterus. Endometriosis affects an estimated 10% of women in the reproductive-age group, rising to 30% to 50% in patients with infertility and/or pain, with significant impact on their physical, mental, and social well-being. There is no known cure, and most current medical treatments are not suitable long term due to their side-effect profiles. Endometriosis has an estimated annual cost in the United States of $18.8 to $22 billion (2002 figures). Although endometriosis was first described more than 100 years ago, current knowledge of its pathogenesis, spontaneous evolution, and the pathophysiology of the related infertility and pelvic pain, remain unclear. A consensus workshop was convened following the 10th World Congress on Endometriosis to establish recommendations for priorities in endometriosis research. One major issue identified as impacting on the capacity to undertake endometriosis research is the need for multidisciplinary expertise. A total of 25 recommendations for research have been developed, grouped under 5 subheadings: (1) diagnosis, (2) classification and prognosis, (3) treatment and outcome, (4) epidemiology, and (5) pathophysiology. Endometriosis research is underfunded relative to other diseases with high health care burdens. This may be due to the practical difficulties of developing competitive research proposals on a complex and poorly understood disease, which affects only women. By producing this consensus international research priorities statement it is the hope of the workshop participants that researchers will be encouraged to develop new interdisciplinary research proposals that will attract increased funding support for work on endometriosis. PMID:19196878

  15. Consensus Paper: Language and the Cerebellum: an Ongoing Enigma

    PubMed Central

    Mariën, Peter; Ackermann, Herman; Adamaszek, Michael; Barwood, Caroline H. S.; Beaton, Alan; Desmond, John; De Witte, Elke; Fawcett, Angela J.; Hertrich, Ingo; Küper, Michael; Leggio, Maria; Marvel, Cherie; Molinari, Marco; Murdoch, Bruce E.; Nicolson, Roderick I.; Schmahmann, Jeremy D.; Stoodley, Catherine J.; Thürling, Markus; Timmann, Dagmar; Wouters, Ellen; Ziegler, Wolfram

    2014-01-01

    In less than three decades, the concept “cerebellar neurocognition” has evolved from a mere afterthought to an entirely new and multifaceted area of neuroscientific research. A close interplay between three main strands of contemporary neuroscience induced a substantial modification of the traditional view of the cerebellum as a mere coordinator of autonomic and somatic motor functions. Indeed, the wealth of current evidence derived from detailed neuroanatomical investigations, functional neuroimaging studies with healthy subjects and patients and in-depth neuropsychological assessment of patients with cerebellar disorders shows that the cerebellum has a cardinal role to play in affective regulation, cognitive processing, and linguistic function. Although considerable progress has been made in models of cerebellar function, controversy remains regarding the exact role of the “linguistic cerebellum” in a broad variety of nonmotor language processes. This consensus paper brings together a range of different viewpoints and opinions regarding the contribution of the cerebellum to language function. Recent developments and insights in the nonmotor modulatory role of the cerebellum in language and some related disorders will be discussed. The role of the cerebellum in speech and language perception, in motor speech planning including apraxia of speech, in verbal working memory, in phonological and semantic verbal fluency, in syntax processing, in the dynamics of language production, in reading and in writing will be addressed. In addition, the functional topography of the linguistic cerebellum and the contribution of the deep nuclei to linguistic function will be briefly discussed. As such, a framework for debate and discussion will be offered in this consensus paper. PMID:24318484

  16. [Consensus document on overactive bladder in older patients].

    PubMed

    Verdejo-Bravo, Carlos; Brenes-Bermúdez, Francisco; Valverde-Moyar, Maria Victoria; Alcántara-Montero, Antonio; Pérez-León, Noemí

    2015-01-01

    Overactive nladder (OAB) is a clinical entity with a high prevalence in the population, having a high impact on quality of life, especially when it occurs with urge urinary incontinence. It is very important to highlight the low rate of consultation of this condition by the older population. This appears to depend on several factors (educational, cultural, professional), and thus leads to the low percentage of older patients who receive appropriate treatment and, on the other hand, a large percentage of older patients with a significant deterioration in their quality of life. Therefore, Scientific societies and Working Groups propose the early detection of OAB in their documents and clinical guidelines. Its etiology is not well known, but is influenced by cerebrovascular processes and other neurological problems, abnormalities of the detrusor muscle of bladder receptors, and obstructive and inflammatory processes of the lower urinary tract. Its diagnosis is clinical, and in the great majority of the cases it can be possible to establish its diagnosis and etiopathogenic orientation, without the need for complex diagnostic procedures. Currently, there are effective treatments for OAB, and we should decide the most appropriate for each elderly patient, based on their individual characteristics. Based on the main clinical practice guidelines, a progressive treatment is proposed, with the antimuscarinics being the most recommended drug treatment. Therefore, a group of very involved professionals in clinical practice for the elderly, and representing two scientific Societies (Spanish Society of Geriatrics and Gerontology [SEGG], and the Spanish Society of Primary Care Physicians [SEMERGEN]) developed this consensus document with the main objective of establishing practices and valid strategies, focused to simplify the management of this clinical entity in the elderly population, and especially to improve their quality of life. The recommendations presented in this

  17. Nucleotide sequence of a cluster of early and late genes in a conserved segment of the vaccinia virus genome.

    PubMed Central

    Plucienniczak, A; Schroeder, E; Zettlmeissl, G; Streeck, R E

    1985-01-01

    The nucleotide sequence of a 7.6 kb vaccinia DNA segment from a genomic region conserved among different orthopox virus has been determined. This segment contains a tight cluster of 12 partly overlapping open reading frames most of which can be correlated with previously identified early and late proteins and mRNAs. Regulatory signals used by vaccinia virus have been studied. Presumptive promoter regions are rich in A, T and carry the consensus sequences TATA and AATAA spaced at 20-24 base pairs. Tandem repeats of a CTATTC consensus sequence are proposed to be involved in the termination of early transcription. PMID:2987815

  18. An evidence-based approach to prescribing NSAIDs in musculoskeletal disease: a Canadian consensus. Canadian NSAID Consensus Participants.

    PubMed Central

    Tannenbaum, H; Davis, P; Russell, A S; Atkinson, M H; Maksymowych, W; Huang, S H; Bell, M; Hawker, G A; Juby, A; Vanner, S; Sibley, J

    1996-01-01

    OBJECTIVE. To make recommendations for the long-term use of nonsteroidal anti-inflammatory drugs (NSAIDs) in primary care practice, particularly for patients at high risk for NSAID-induced complications. OPTIONS. The use of misoprostol to prevent gastrointestinal ulceration and other unwanted NSAIDs effects was considered. The role of cyclooxygenase-2 (COX-2) versus COX-1 inhibiting agents was also examined. OUTCOMES. Reduction of complications associated with long-term use of NSAIDs. EVIDENCE. Evidence was gathered in late 1995 from published research studies and reviews. Position papers were prepared by faculty and advisory board members and discussed at the Canadian NSAID Consensus Symposium in Cambridge, Ont., Jan. 26 and 27, 1996. VALUES. Recommendations were based on randomized, placebo-controlled clinical trials (level I evidence) and case-control studies (level II evidence) involving NSAID use when such evidence was available. When the scientific literature was incomplete or inconsistent in a particular area, recommendations reflect the consensus of the participants at the symposium (level III evidence). Physicians were recruited from across Canada for their expertise in rheumatology, gastroenterology, epidemiology, gerontology, family practice, and clinical and basic scientific research. BENEFITS, HARMS AND COSTS. Although a reduction in complications due to inappropriate NSAID use should reduce costs of additional investigations, admissions to hospital and time lost from work, definitive cost analysis studies are not yet available. RECOMMENDATIONS. Currently, no NSAID is available that lacks potential for serious toxicity; therefore, long-term use of NSAIDs should be avoided whenever possible, particularly in high-risk patients (e.g., those who are elderly, suffer from hypertension, congestive heart failure, renal or hepatic impairment or volume depletion, take certain concomitant medications or have a history of peptic ulcer disease) (level I evidence

  19. Charged single alpha-helices in proteomes revealed by a consensus prediction approach.

    PubMed

    Gáspári, Zoltán; Süveges, Dániel; Perczel, András; Nyitray, László; Tóth, Gábor

    2012-04-01

    Charged single α-helices (CSAHs) constitute a recently recognized protein structural motif. Its presence and role is characterized in only a few proteins. To explore its general features, a comprehensive study is necessary. We have set up a consensus prediction method available as a web service (at http://csahserver.chem.elte.hu) and downloadable scripts capable of predicting CSAHs from protein sequences. Using our method, we have performed a comprehensive search on the UniProt database. We found that the motif is very rare but seems abundant in proteins involved in symbiosis and RNA binding/processing. Although there are related proteins with CSAH segments, the motif shows no deep conservation in protein families. We conclude that CSAH-containing proteins, although rare, are involved in many key biological processes. Their conservation pattern and prevalence in symbiosis-associated proteins suggest that they might be subjects of relatively rapid molecular evolution and thus can contribute to the emergence of novel functions. PMID:22310480

  20. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel.

    PubMed

    González-Pérez, Abel; López-Bigas, Nuria

    2011-04-01

    Several large ongoing initiatives that profit from next-generation sequencing technologies have driven--and in coming years will continue to drive--the emergence of long catalogs of missense single-nucleotide variants (SNVs) in the human genome. As a consequence, researchers have developed various methods and their related computational tools to classify these missense SNVs as probably deleterious or probably neutral polymorphisms. The outputs produced by each of these computational tools are of different natures and thus difficult to compare and integrate. Taking advantage of the possible complementarity between different tools might allow more accurate classifications. Here we propose an effective approach to integrating the output of some of these tools into a unified classification; this approach is based on a weighted average of the normalized scores of the individual methods (WAS). (In this paper, the approach is illustrated for the integration of five tools.) We show that this WAS outperforms each individual method in the task of classifying missense SNVs as deleterious or neutral. Furthermore, we demonstrate that this WAS can be used not only for classification purposes (deleterious versus neutral mutation) but also as an indicator of the impact of the mutation on the functionality of the mutant protein. In other words, it may be used as a deleteriousness score of missense SNVs. Therefore, we recommend the use of this WAS as a consensus deleteriousness score of missense mutations (Condel). PMID:21457909

  1. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

    PubMed Central

    Tsirigos, Konstantinos D.; Peters, Christoph; Shu, Nanjiang; Käll, Lukas; Elofsson, Arne

    2015-01-01

    TOPCONS (http://topcons.net/) is a widely used web server for consensus prediction of membrane protein topology. We hereby present a major update to the server, with some substantial improvements, including the following: (i) TOPCONS can now efficiently separate signal peptides from transmembrane regions. (ii) The server can now differentiate more successfully between globular and membrane proteins. (iii) The server now is even slightly faster, although a much larger database is used to generate the multiple sequence alignments. For most proteins, the final prediction is produced in a matter of seconds. (iv) The user-friendly interface is retained, with the additional feature of submitting batch files and accessing the server programmatically using standard interfaces, making it thus ideal for proteome-wide analyses. Indicatively, the user can now scan the entire human proteome in a few days. (v) For proteins with homology to a known 3D structure, the homology-inferred topology is also displayed. (vi) Finally, the combination of methods currently implemented achieves an overall increase in performance by 4% as compared to the currently available best-scoring methods and TOPCONS is the only method that can identify signal peptides and still maintain a state-of-the-art performance in topology predictions. PMID:25969446

  2. Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells

    PubMed Central

    Dias, João D; Rito, Tiago; Torlai Triglia, Elena; Kukalev, Alexander; Ferrai, Carmelo; Chotalia, Mita; Brookes, Emily; Kimura, Hiroshi; Pombo, Ana

    2015-01-01

    Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and processing of nascent RNA. Extensive phosphorylation of serine residues at the largest RNAPII subunit occurs at its structurally-disordered C-terminal domain (CTD), which is composed of multiple heptapeptide repeats with consensus sequence Y1-S2-P3-T4-S5-P6-S7. Serine-5 and Serine-7 phosphorylation mark transcription initiation, whereas Serine-2 phosphorylation coincides with productive elongation. In vertebrates, the CTD has eight non-canonical substitutions of Serine-7 into Lysine-7, which can be acetylated (K7ac). Here, we describe mono- and di-methylation of CTD Lysine-7 residues (K7me1 and K7me2). K7me1 and K7me2 are observed during the earliest transcription stages and precede or accompany Serine-5 and Serine-7 phosphorylation. In contrast, K7ac is associated with RNAPII elongation, Serine-2 phosphorylation and mRNA expression. We identify an unexpected balance between RNAPII K7 methylation and acetylation at gene promoters, which fine-tunes gene expression levels. DOI: http://dx.doi.org/10.7554/eLife.11215.001 PMID:26687004

  3. Introduction to the Australian consensus guidelines for the management of neutropenic fever in adult cancer patients, 2010/2011. Australian Consensus Guidelines 2011 Steering Committee.

    PubMed

    Lingaratnam, S; Slavin, M A; Koczwara, B; Seymour, J F; Szer, J; Underhill, C; Prince, M; Mileshkin, L; O'Reilly, M; Kirsa, S W; Bennett, C A; Davis, I D; Morrissey, O; Thursky, K A

    2011-01-01

    The current consensus guidelines were developed to standardize the clinical approach to the management of neutropenic fever in adult cancer patients throughout Australian treating centres. The three areas of clinical practice covered by the guidelines, the process for developing consensus opinion, and the system used to grade the evidence and relative strength of recommendations are described. The health economics implications of establishing clinical guidance are also discussed. PMID:21272171

  4. Reconstructing of a Sequence Using Similar Sequences

    1995-11-28

    SIMSEQ reconstructs sequences from oligos. Similar known sequences are used as a reference. At present, simulated data are being used to develop the algorithm. SIMSEQ generates an initial random sequence, then generates a second sequence that is 60 to 90 percent similar to the first. Next, the second sequence is chopped into its appropriate oligos. All possible sequences are reconstructed to determine the most similar. Those with the highest similarity are printed as output.

  5. Towards a consensus on diagnostic criteria, measurement and trial design of the premenstrual disorders: the ISPMD Montreal consensus

    PubMed Central

    Bäckström, Torbjorn; Brown, Candace; Dennerstein, Lorraine; Endicott, Jean; Epperson, C. Neill; Eriksson, Elias; Freeman, Ellen; Halbreich, Uriel; Ismail, Khaled M. K.; Panay, Nicholas; Pearlstein, Teri; Rapkin, Andrea; Reid, Robert; Schmidt, Peter; Steiner, Meir; Studd, John; Yonkers, Kimberley

    2014-01-01

    Premenstrual disorders (PMD) are characterised by a cluster of somatic and psychological symptoms of varying severity that occur during the luteal phase of the menstrual cycle and resolve during menses (Freeman and Sondheimer, Prim Care Companion J Clin Psychiatry 5:30–39, 2003; Halbreich, Gynecol Endocrinol 19:320–334, 2004). Although PMD have been widely recognised for many decades, their precise cause is still unknown and there are no definitive, universally accepted diagnostic criteria. To consider this issue, an international multidisciplinary group of experts met at a face-to-face consensus meeting to review current definitions and diagnostic criteria for PMD. This was followed by extensive correspondence. The consensus group formally became established as the International Society for Premenstrual Disorders (ISPMD). The inaugural meeting of the ISPMD was held in Montreal in September 2008. The primary aim was to provide a unified approach for the diagnostic criteria of PMD, their quantification and guidelines on clinical trial design. This report summarises their recommendations. It is hoped that the criteria proposed here will inform discussions of the next edition of the World Health Organisation's International Classification of Diseases (ICD-11), and the American Psychiatric Association's Diagnostic and Statistical Manual of Mental Disorders, fifth edition (DSM-V) criteria that are currently under consideration. It is also hoped that the proposed definitions and guidelines could be used by all clinicians and investigators to provide a consistent approach to the diagnosis and treatment of PMD and to aid scientific and clinical research in this field. PMID:21225438

  6. Sequence diversity of wheat mosaic virus isolates.

    PubMed

    Stewart, Lucy R

    2016-02-01

    Wheat mosaic virus (WMoV), transmitted by eriophyid wheat curl mites (Aceria tosichella) is the causal agent of High Plains disease in wheat and maize. WMoV and other members of the genus Emaravirus evaded thorough molecular characterization for many years due to the experimental challenges of mite transmission and manipulating multisegmented negative sense RNA genomes. Recently, the complete genome sequence of a Nebraska isolate of WMoV revealed eight segments, plus a variant sequence of the nucleocapsid protein-encoding segment. Here, near-complete and partial consensus sequences of five more WMoV isolates are reported and compared to the Nebraska isolate: an Ohio maize isolate (GG1), a Kansas barley isolate (KS7), and three Ohio wheat isolates (H1, K1, W1). Results show two distinct groups of WMoV isolates: Ohio wheat isolate RNA segments had 84% or lower nucleotide sequence identity to the NE isolate, whereas GG1 and KS7 had 98% or higher nucleotide sequence identity to the NE isolate. Knowledge of the sequence variability of WMoV isolates is a step toward understanding virus biology, and potentially explaining observed biological variation. PMID:26590326

  7. Modular sequence elements associated with origin regions in eukaryotic chromosomal DNA.

    PubMed Central

    Dobbs, D L; Shaiu, W L; Benbow, R M

    1994-01-01

    We have postulated that chromosomal replication origin regions in eukaryotes have in common clusters of certain modular sequence elements (Benbow, Zhao, and Larson, BioEssays 14, 661-670, 1992). In this study, computer analyses of DNA sequences from six origin regions showed that each contained one or more potential initiation regions consisting of a putative DUE (DNA unwinding element) aligned with clusters of SAR (scaffold associated region), and ARS (autonomously replicating sequence) consensus sequences, and pyrimidine tracts. The replication origins analyzed were from the following loci: Tetrahymena thermophila macronuclear rDNA gene, Chinese hamster ovary dihydrofolate reductase amplicon, human c-myc proto-oncogene, chicken histone H5 gene, Drosophila melanogaster chorion gene cluster on the third chromosome, and Chinese hamster ovary rhodopsin gene. The locations of putative initiation regions identified by the computer analyses were compared with published data obtained using diverse methods to map initiation sites. For at least four loci, the potential initiation regions identified by sequence analysis aligned with previously mapped initiation events. A consensus DNA sequence, WAWTTDDWWWDHWGWHMAWTT, was found within the potential initiation regions in every case. An additional 35 kb of combined flanking sequences from the six loci were also analyzed, but no additional copies of this consensus sequence were found. Images PMID:8041609

  8. Ultra-fast consensus of discrete-time multi-agent systems under a unified framework

    NASA Astrophysics Data System (ADS)

    Zhang, Wenle; Liu, Jianchang

    2015-06-01

    This paper deals with the ultra-fast consensus problem of high-order discrete-time multi-agent systems under a unified framework. A multi-step neighbour-error predictive mechanism is established based on the future evolution of the network dynamic without predictive information. By predicting the dynamics of a network several steps ahead and adding this information into the consensus protocol, a novel ultra-fast consensus protocol with the self-feedback term is proposed. The asymptotic convergence factor is improved by a power of q + 1 compared to the routine consensus protocol. The ultra-fast consensus algorithm can overcome the influence of communication topology to the convergence speed toward consensus, and solve the difficult problem of selecting the optimal control gain which minimises the asymptotic convergence factor. Moveover, some sufficient conditions for ultra-fast consensus design are given herein. The ones decouple the design of the synchronising gains from the detailed graph properties, and explicitly reveal how the agent dynamic and the communication graph jointly affect ultra-fast consensus of discrete-time multi-agent systems. A simulation is performed to illustrate the effectiveness of the theoretical results.

  9. 75 FR 58016 - Consensus Standards, Standard Practice for Design, Alteration, and Certification of Airplane...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-23

    ... availability of consensus standards. The FAA expects a suitable consensus standard to be reviewed at least every two years. The two-year review cycle will result in a standard revision or reapproval. A standard is issued under a fixed designation (i.e., F2639-07); the number immediately following...

  10. 75 FR 2551 - NIH Consensus Development Conference: Lactose Intolerance and Health; Notice

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-15

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health NIH Consensus Development Conference: Lactose Intolerance and Health; Notice Notice is hereby given by the National Institutes of Health (NIH) of the ``NIH Consensus Development Conference:...

  11. Review of Consensus Standard Spectra for Flat Plate and Concentrating Photovoltaic Performance

    SciTech Connect

    Myers, D.

    2011-09-01

    Consensus standard reference terrestrial solar spectra are used to establish nameplate ratings for photovoltaic device performance at standard reporting conditions. This report describes reference solar spectra developed in the United States and international consensus standards community which are widely accepted as of this writing (June 2011).

  12. Consensus Auditory-Perceptual Evaluation of Voice: Development of a Standardized Clinical Protocol

    ERIC Educational Resources Information Center

    Kempster, Gail B.; Gerratt, Bruce R.; Abbott, Katherine Verdolini; Barkmeier-Kraemer, Julie; Hillman, Robert E.

    2009-01-01

    Purpose: This article presents the development of the Consensus Auditory-Perceptual Evaluation of Voice (CAPE-V) following a consensus conference on perceptual voice quality measurement sponsored by the American Speech-Language-Hearing Association's Special Interest Division 3, Voice and Voice Disorders. The CAPE-V protocol and recording form were…

  13. Subject Matter Relevance in Interpersonal Communication, Skills, and Instructional Accountability: A Consensus Model.

    ERIC Educational Resources Information Center

    Schuelke, L. David

    The author supports the position that change in the basic speech course is needed and proposes a consensus model to achieve this change. A consensus model approach to the basic course provides for a reduction in entropy regarding objectives, activities, and progress in the classroom. Applying the theories of interpersonal communication taught in…

  14. 78 FR 66642 - Updating OSHA Standards Based on National Consensus Standards; Signage

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-06

    ...On June 13, 2013, OSHA published in the Federal Register (78 FR 35559) a direct final rule that revised its signage standards for general industry and construction by updating the references to national consensus standards approved by the American National Standards Institute, a clearinghouse that verifies that the criteria for approval of consensus standards have been met. OSHA stated in that......

  15. The Status of Learning Disabilities in the States: Consensus or Controversy?

    ERIC Educational Resources Information Center

    McNutt, Gaye

    1986-01-01

    To determine the degree of controversy or consensus regarding definitions at the state level, questionnaires focusing on six learning disability topics were sent to each state education agency (SEA) and the District of Columbia. In general, more consensus than controversy exists when broad areas are considered. Changes in some SEA definitions…

  16. 29 CFR Appendix B to Subpart L of... - National Consensus Standards

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 5 2011-07-01 2011-07-01 false National Consensus Standards B Appendix B to Subpart L of..., DEPARTMENT OF LABOR OCCUPATIONAL SAFETY AND HEALTH STANDARDS Fire Protection Pt. 1910, Subpt. L, App. B Appendix B to Subpart L of Part 1910—National Consensus Standards The following table contains a...

  17. 29 CFR Appendix B to Subpart L of... - National Consensus Standards

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 5 2013-07-01 2013-07-01 false National Consensus Standards B Appendix B to Subpart L of..., DEPARTMENT OF LABOR OCCUPATIONAL SAFETY AND HEALTH STANDARDS Fire Protection Pt. 1910, Subpt. L, App. B Appendix B to Subpart L of Part 1910—National Consensus Standards The following table contains a...

  18. 29 CFR Appendix B to Subpart L of... - National Consensus Standards

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 5 2012-07-01 2012-07-01 false National Consensus Standards B Appendix B to Subpart L of..., DEPARTMENT OF LABOR OCCUPATIONAL SAFETY AND HEALTH STANDARDS Fire Protection Pt. 1910, Subpt. L, App. B Appendix B to Subpart L of Part 1910—National Consensus Standards The following table contains a...

  19. 29 CFR Appendix B to Subpart L of... - National Consensus Standards

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 5 2010-07-01 2010-07-01 false National Consensus Standards B Appendix B to Subpart L of..., DEPARTMENT OF LABOR OCCUPATIONAL SAFETY AND HEALTH STANDARDS Fire Protection Pt. 1910, Subpt. L, App. B Appendix B to Subpart L of Part 1910—National Consensus Standards The following table contains a...

  20. 29 CFR Appendix B to Subpart L of... - National Consensus Standards

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 5 2014-07-01 2014-07-01 false National Consensus Standards B Appendix B to Subpart L of..., DEPARTMENT OF LABOR OCCUPATIONAL SAFETY AND HEALTH STANDARDS Fire Protection Pt. 1910, Subpt. L, App. B Appendix B to Subpart L of Part 1910—National Consensus Standards The following table contains a...